Metrics details Environmental factors shape subsurface microbial ecosystems and well-characterized sites are ideal for determining how environmental parameters shape sediment communities Sediments from eight geologically and thermally distinct sites were drilled during International Ocean Discovery Program Expedition 385 in Guaymas Basin an expedition focused on the hydrothermal deep biosphere Using high-throughput 16S ribosomal nucleic acid sequencing and mineralogical/elemental X-ray spectroscopy we examine linkages and feedbacks between mineral composition We show subsurface life is dominated by heterotrophic cosmopolitan prokaryotes that thrive within a range of sediments and temperature conditions across Guaymas Basin Hydrothermally-affiliated lineages are detected in low numbers at sites with steepest temperature gradients within communities of mesophilic taxa that occur throughout Guaymas Basin and in other marine subsurface habitats hydrothermal lineages do not replace the cosmopolitan but remain specific to sites where volcanic intrusions drive hydrothermal circulation Overview of the International Ocean Discovery Program Expedition 385 (IODP385) drill sites a Bathymetry of Guaymas Basin with the locations of the IODP385 drill sites The inner figure shows the sampling location in Guaymas Basin; red lines depict the transformation faults and green lines show the oceanic spreading centers along the transformation faults in Guaymas Basin b the Ringvent area with Sites U1547 and U1548 Orange lines represent the traces of seismic profiles; A-E the different Holes drilled at each site c Interpolated in situ temperatures for sediment samples Bathymetric map of Guaymas Basin courtesy of D We relate these diversity profiles with cell abundances recovered from the same sites and depths and mineralogical characteristics of the sediments and we connect observed distributions of particular taxa to evidence for their metabolic activities in available metatranscriptome data from IODP 385 Targeted phylogenetic analyses for selected archaeal taxa identify ASVs affiliating with a few thermophilic and hyperthermophilic archaeal lineages that occur at specific sites albeit in smaller amplicon numbers relative to non-thermophilic subsurface bacteria and archaea that dominate the amplicon libraries at all sites Most sediment cores collected from each site extend into the sulfate-reducing zone the sulfate-methane transition (SMTZ) zone We note that the examined sediments at Ringvent sites U1547B and U1548B did not reach the deep methanogenic zone and that at Sites U1550B and U1552B sediments above the shallow SMTZs (~17 and 20 mbsf respectively) are only represented by one sample each Cell abundances are shown for the eight IODP385 drilling sites a Cell counts are plotted against the depth regime only for those samples discussed in this study (0.8 to ~ 180 meters below sea floor; mbsf) b Cell counts are plotted against temperature (2.8 oC to 68 oC) for samples discussed in this study Taxonomy bar chart for PacBio archaeal 16S rRNA gene sequencing results for subsurface sediment samples from all eight drilling sites The y-axis shows normalized ASV abundance of the identified archaeal taxa and x-axis indicates sediment depth in meters below sea floor (mbsf) while the secondary x-axis indicates temperature (oC) Sites with active hydrothermalism (U1547 and U1548) are shown in red Temperatures at Sites U1547 and U1548 are up to a 3-fold higher when compared to the temperatures observed at the other examined sites at similar depths suggesting a low effective population size and thus a high proportion of dormant cells It appears these Planctomycetota survive within shallow Guaymas Basin sediments but quickly become stressed by higher temperatures and lower nutrient availability with increasing depth this requires further examination including microscopy surveys Non-metric multidimensional scaling (nMDS) ordination plots of prokaryotic (MiSeq ASVs) and archaeal (PacBio ASVs) communities with mineralogical and geochemical parameters On the basis of Fisher’s method for combining p-values we show the geochemical/mineralogical variables with p-values < 0.05 resulting from a two-sided permutation test performed using envfit a Distribution of prokaryotic (bacterial and archaeal) communities are influenced by depth (mbsf) b Archaeal communities are affected by depth (mbsf) The directions of the arrows indicate a positive or negative correlation among the environmental parameters with the ordination axes Arrow length reflects correlation strength between environmental parameter and ASV occurrence and their depth temperature regimes are indicated by shape (circles for 2–20 °C; triangles for 20–45 °C and squares for 45–68 °C) the metatranscriptomes of this study and the recovered MAGs associated with Lokiarchaeia from the Guaymas subsurface do not show presence or expression of the hgc genes responsible for Hg methylation even below the SMTZ where sulfate is depleted A few known thermophilic and hyperthermophilic lineages were detected in samples from hydrothermally-active sites, albeit sporadically distributed, and found only at certain depths where their biomass was sufficient for detection of their marker genes (Fig. 4) Given their patchy representation across our datasets nMDS analyses considering only these individual lineages proved uninformative Phylogenetic analyses of specific taxonomic groups were used to explore connections between these lineages and known (hyper)thermophilic lineages (see section below) their distributions within the Guaymas dataset and their potential for different temperature preferences prompted us to make a closer examination of these phylum-level lineages we searched our metatranscriptomes and retrieved transcripts affiliated specifically with these lineages and we used long read (PacBio) 16S rRNA phylogenetic analyses to search for potentially thermotolerant or thermophilic groups within these phyla Distance phylogeny (Minimum Evolution) of Hadarchaeia based on PacBio 16S rRNA gene amplicons of ~800 base pairs ASVs are labeled with their IODP sediment sample of origin Bootstrap numbers are based on 1000 iterations Cultured hyperthermophilic Crenarchaeota serve as outgroup which further supports that this taxon prefers for cool and shallow Guaymas subsurface sediments and becomes stressed by more elevated downcore temperatures Distance phylogeny (Minimum Evolution) of Bathyarchaeia based on PacBio 16S rRNA gene amplicons of ~ 800 base pairs Distance phylogeny of Methanogens and anaerobic methane-oxidizing archaea based on PacBio 16S rRNA gene amplicons of ~ 800 base pairs Hydrothermal clones and hyperthermophilic species are highlighted in red The hyperthermophilic Methanococcales serve as outgroup Analyses of MiSeq and PacBio sequencing data of partial 16S rRNA genes in this study indicates that the composition of the heretofore largely unknown deep biosphere of Guaymas Basin resembles cosmopolitan microbial communities found in organic-rich marine subsurface sediments mesophilic microbial phyla already known from cold deep subsurface sediments in other locations Amplicon-based detection of this community falls off at relatively shallow depths and moderately high temperatures (near 45 °C at most sites) Sequence signatures of some hydrothermal microbial populations are detected within the archaeal 16S rRNA gene dataset using phylogenetic analyses of archaeal ASVs to tease out lineage-specific hydrothermal associations among the Bathyarchaeia Methanophagales/ANME-1 and Methanococcales against the dominant background of widespread mesophilic these thermophilic lineages are detected in relatively low ASV numbers and are largely limited to the hydrothermally impacted Ringvent sites falling below detection at other drilling sites We interpret the apparent preference of thermophiles for Ringvent sites as evidence that active hydrothermal circulation within the Ringvent system provides the energy supply required to sustain these thermophiles at a sufficient level so that their DNA can still be detected in nearby drilled sediments At subsurface sites further removed from hydrothermal circulation even if temperatures alone would appear sufficient to allow their growth while we do find evidence for some thermophilic hydrothermal vent archaea at Ringvent sites with active subsurface hydrothermal circulation subsurface life in Guaymas Basin sediments is not simply dominated by transplanted hydrothermal vent communities cosmopolitan subsurface bacteria and archaea show some thermal adaptability and mRNA data indicate that they manage to thrive within a wide range of sediments across all of Guaymas Basin Yet moderately high temperatures appear to select against this cosmopolitan subsurface sediment community indicating that elevated temperature exacerbates the challenges that subsurface microorganisms already face regarding energy limitation and substrates required for cell maintenance we ran the tracer perfluoromethyldecalin (PFMD) during drilling of holes at each site intended for microbiology PFMD was introduced into the drilling fluids with a high-pressure liquid chromatography pump (rate of injection: 9.77 × 10−3 × [stroke of mud-pump 0.55 ml min−1 at 50 mud-pump strokes min−1) to provide a final concentration of ~ 0.5 mg L−1 Since microbial cells are larger than these molecules they may not penetrate a sediment sample in proportion to the drilling fluid and therefore the tracer is regarded as providing a qualitative estimate of contamination potential To assess the possible degree of contamination within sediment core material 3cc syringe samples of sediment were collected at several depths along each hole throughout the expedition to measure the concentration of detected tracer along the radius of sediment cores using gas chromatography (GC) in the vessel laboratory Samples for GC analyses were collected on the core-receiving platform from the ends of freshly cut core sections immediately after core recovery Samples were collected at the top of the core – where the highest contamination is expected one ~ 3cc syringe sample was collected at the interface of the sediment core and the core liner a second sample was collected at the center of the sediment core and a third was collected in between these two All three samples were placed in 20 ml GC headspace vials Headspace samples were heated to volatilize any tracer present and the gas was injected into an Agilent 6890 N gas chromatograph with ECD after preparing and running calibration standards using 10−4 Any tracer detected on the interior of a whole round sample is interpreted to mean drilling fluid was possibly able to penetrate into the sample Cores were not processed for microbiology where detectable tracer was measured in the core interior Contamination was also assessed by analyzing the microbial composition of the drilling fluid (primarily composed of surface ocean water) post-cruise via DNA sequencing approaches A sample of the drilling fluid was collected at the beginning of drilling for every hole drilled for microbiology directly from the injection pipe on the rig floor into sterile bottles with screw caps Replicate 250 mL aliquots were filtered onto 45 mm 0.20 μm pore-size Millipore Durapore filters and frozen at −80 °C and marker gene libraries were prepared as for sediment samples Mineralogic analyses were performed with a Rigaku SmartLab XRD instrument equipped with a CuKα radiation source (λ = 1.54060 Å) using a 10 mm slit and at a tube voltage of 40 kV and a current of 40 mA Samples were first dried and crushed in a mortar and then randomly oriented powders were obtained after sieving at 63 µm Each measurement was done after vertical alignment between the X-ray source the surface of the sample and the detector For all XRD runs 2θ ranged between 3°–5° and 90° with a step size of 0.004° 2θ while the sample was rotating 60 times per minute mineral ID and quantification were carried out using the Rietveld method with Rigaku’s SmartLab Studio II and ICDD PDF-5 + 2024 database Amorphous silica % was estimated using Rigaku’s SmartLab Studio II amorphous phase detection tool Elemental analysis (elements from Mg to U) were obtained with a Hitachi X-MET8000 Geo analyzer on dried and crushed powders after sieving at 63 µm Measurements were run in triplicate for 60 s each and then averaged The mixture was thoroughly shaken for 60 min (Shake Master and subsequently sonicated at 160 W for 30 s for 10 cycles (Bioruptor UCD-250HSA; Cosmo Bio The detached cells were recovered by centrifugation based on the density difference of microbial cells and sediment particles which allows collection of microbial cells in a low-density layer the sample was transferred onto a set of four density layers composed of 30% Nycodenz (1.15 g cm−3) and 67% sodium polytungstate (2.08 g cm−3) Cells and sediment particles were separated by centrifugation at 10,000 × g for 1 h at 25 °C The light density layer was collected using a 20 G needle syringe and centrifuged at 5000 × g for 15 min at 25 °C The supernatant was combined with the previously recovered light density fraction The sediment was resuspended using 2.1 mL of 2.5% NaCl and 300 μL of detergent mix and shaken at 500 rpm for 60 min at 25 °C before the slurry sample was transferred into a fresh centrifugation tube where it was layered onto another density gradient and separated by centrifugation just as before and combined with the previously collected light density fraction and supernatant to form a single suspension for cell counting and 1545B-6H2 were prepared from DNA extracts by the Georgia Genomics and Bioinformatics Core (GGBC) at the University of Georgia Libraries for all other samples and control fluid filters were prepared internally through the amplification steps described below before sent to GGBC (for Illumina MiSeq) or the University of Delaware DNA Sequencing & Genotyping Center for final library preparation and sequencing Illumina MiSeq overhang adapter sequences were added to locus-specific primers for use in first round Polymerase Chain Reaction (PCR) amplifications 16S rRNA PCR amplifications were performed for each sample (1:10 dilution) in triplicate using SpeedStar™ HS DNA Polymerase (TaKaRa) and 10X Fast Buffer I as described by the manufacturer Thermocycling conditions were: 95 °C for 5 min; x30 (95 °C for 30 s 72 °C for 60 s); 72 °C for 5 min and a 4 °C hold PCR amplification replicates were combined and purified with AMPure® XP beads (Beckman Coulter) Extraction kit control amplifications were attempted at both Laboratories where extractions were physically performed with only one yielding an amplicon sufficient for library construction All libraries produced with 515F-Y/926 R amplified fragments were sequenced on an Illumina MiSeq platform with PE300 read lengths PCR reactions were performed using the SpeedSTARTM HS DNA Polymerase (TaKaRa) kit with the following modifications: each 25 μΜ PCR reaction contained up to 1 ng of template DNA 10 mM of each primer and DEPC water (Fisher BioReagents™) up to 25 μΜ The PCR reactions were performed in an Eppendorf Mastercycler Pro S Vapoprotect (Model 6321) thermocycler with the following conditions: 95 °C for 5 min The total volume of PCR reactions was run in 2% agarose gel (Low-EEO/Multi-Purpose/Molecular Biology Grade Fisher BioReagents™) and the correct size PCR products (~800 bp) were isolated and recovered from the gel using the Zymoclean Gel DNA Recovery Kit as instructed by the manufacturer Libraries for PacBio sequencing were prepared from the recovered and gel purified DNA extracts at the University of Delaware DNA Sequencing & Genotyping Center Illumina MiSeq 16S rRNA gene reads are deposited into the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) under access numbers SRR23641000-SRR23641053 The PacBio reads are deposited under SRA access numbers SRR23604162-SRR23604206 targeting the small ribosomal subunit (SSU) of 16S rRNA gene Each 25 μl PCR reaction was prepared using GoTaq G2 Flexi DNA Polymerase (Promega) and contained 0.5 U μl–1 GoTaq G2 Flexi DNA Polymerase 10 mM of each primer (final concentrations) These PCR amplifications were performed in an Eppendorf Mastercycler Pro S Vapoprotect (Model 6321) thermocycler with following conditions: 94 °C for 5 min The PCR reaction products were run in 2% agarose gels (Low-EEO/Multi-Purpose/Molecular Biology Grade Fisher BioReagents) to confirm absence of DNA products RNA quantification (ng μl−1) was performed using Qubit RNA High Sensitivity (HS) Amplified cDNAs from the DNA-free RNA extracts were prepared using the Ovation RNA-Seq System V2 (Tecan) following manufacturer’s suggestions cDNAs were submitted to the Georgia Genomics and Bioinformatics Core for library preparation and sequencing using NextSeq 500 PE 150 High Output (Illumina) The sequencing of the cDNA library from the control sample was unsuccessful as it failed to generate any sequences that met the length criterion of 300–400 base pairs -e 1e-5 --more-sensitive) was used to search against NCBI-NR database (release date: 2022-12-04) The TPM values of all transcripts annotated to same gene were summed and were added to a value of 1 (to avoid zeros) and normalized using log2-transformation Metatranscriptome reads were deposited to the National Center for Biotechnology Information Sequence Read Archive under accession numbers SRR22580929-SRR22580947 Defining boundaries for the distribution of microbial communities beneath the sediment-buried Temperature limits to deep subseafloor life in the Nankai Trough subduction zone Microbial communities associated with geological horizons in coastal subseafloor sediments from the Sea of Okhotsk Recent studies on bacterial populations 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Zenodo; https://doi.org/10.5281/zenodo.7710615 (2023) Download references We would like to acknowledge the crew and entire science party for IODP Expedition 385 for their assistance with sample collection Without their assistance this study would have been impossible We also thank Takeshi Terada and Megumi Becchaku for assisting with cell counting Ying-Li Zhou for assistance with the PacBio and metatranscriptome analyses Andy Solow (WHOI) for assistance with the statistical analyses This study was supported by the National Science Foundation Grant OCE-2046799 to V.E. by JSPS KAKENHI JP19H00730 and JP23H00154 to Y.M Current research in the Teske lab is supported by NASA Exobiology grant 21-5477 and by NSF Biological Oceanography grant 2048489 These authors contributed equally: Paraskevi Mara David Beaudoin & David Geller-McGrath Institute for Extra-cutting-edge Science and Technology Avantgarde Research (X-STAR) Japan Agency for Marine-Earth Science and Technology (JAMSTEC) University of North Carolina at Chapel Hill wrote the first draft of the paper and all authors contributed to its final form The authors declare no competing interests Communications Earth & Environment thanks William Brazelton and the other reviewer(s) for their contribution to the peer review of this work Primary Handling Editors: D’Arcy Meyer-Dombard Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations Download citation DOI: https://doi.org/10.1038/s43247-024-01662-7 Anyone you share the following link with will be able to read this content: Sorry, a shareable link is not currently available for this article. Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily. Volume 13 - 2025 | doi: 10.3389/feart.2025.1568130 formatted version of the article will be published soon You have multiple emails registered with Frontiers: If you already have an account, please login You don't have a Frontiers account ? You can register here The Guaymas Basin (GB) is a highly productive region in the Gulf of California Subseafloor sedimentary amorphous bio-opal and Ba/Ti records obtained from its northwestern and central areas reveal significant changes in exported productivity over the past 31,200 years Millennial-scale variability reflects the influence of wind-driven upwelling and shifts in climate variability operating at orbital Spatial heterogeneity in productivity recorded in International Ocean Discovery Program boreholes highlights regional differences in process dominance We identify seven distinct productivity phases: From ~31,200 to ~26,500 cal yr BP laminated sediments indicate strong seasonal variability and high productivity due to intense upwelling activity caused by northwesterly winds linked to a southward-shifted Intertropical Convergence Zone displayed pronounced fluctuations and a slight decline in productivity compared to the previous interval owing to the reduced influence of the North Pacific High on the GB during this period there were shifts of high and low productivity with opal minima coinciding with Heinrich events 2 and 1 Productivity declined slightly between ~11,700 and ~7,000 cal yr BP featuring a short highproductivity period within that timespan (~10,500 to ~10,300 cal yr BP) productivity decreased in the NW and increased in the central basin This contrast reflects enhanced winter-spring coastal wind-driven upwellings and reduced eddy activity in the west productivity increased in both studied areas The sedimentary Ba/Ti values in both holes generally indicate lower levels during the cold glacial period and higher levels during the warm interglacial period suggesting reduced biological barite accumulation and less organic matter export from the surface under cold climate conditions These changes correspond to documented climate transitions highlighting GB's sensitivity to global forcings (e.g. ice sheet retreat) and regional ocean-atmosphere interactions Our findings underscore the key role of dynamic physical processes in shaping long-term productivity patterns in marginal seas at high resolution Received: 28 Jan 2025; Accepted: 21 Apr 2025 * Correspondence: Ligia Perez-Cruz, Institute of Geophysics National Autonomous University of Mexico, Mexico City, Mexico Disclaimer: All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. 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All rights reserved Guaymas Basin is a young marginal rift basin in the Gulf of California characterized by active seafloor spreading rapid deposition of organic-rich sediments and steep geothermal gradients where sedimentary organic material of photosynthetic origin turns into hydrocarbons – potential microbial substrates After introducing the sources of hydrocarbons in the subsurface this short overview discusses the phylogenetic diversity temperature range and occurrence patterns of novel alkane-oxidizing bacteria and archaea in the hydrothermal sediments of Guaymas Basin Many of these alkane-degrading specialists function as syntrophic consortia where sulfate-reducing bacteria accept electron from methane- or alkane-oxidizing archaea and cultures of these methodologically and conceptually challenging microorganisms Guaymas Basin stands out as an indispensable field site that has consistently catalyzed new insights into the microbiology of anaerobic hydrocarbon oxidation and assimilation with the northern and southern axial troughs reaching 2000 m depth B) Bathymetry of the hydrothermal sampling area in the southern axial trough C) Hydrothermal hot spot at Cathedral Hill where cores 4991–14 and 15 were collected and thermophilic methane-oxidizing ANME-1c archaea (Benito Merino et al. 2022) and thermophilic alkane-degrading Alkanophagales archaea (Zehnle et al. The small mound in the center is hydrocarbon-saturated “Ace Chimney” a reliable source of alkane- and aromatics-degrading sulfate-reducing enrichments (Edgcomb et al. D) Hydrothermal hot spot with orange microbial mats at Mat Mound Massif; Candidatus Ethanivorans thermophilum was isolated from core 4869–26 collected at this location (Hahn et al. δ13C isotopic profiles for this site are shown in Fig E) Hydrothermal hot spot with white sulfur-oxidizing mats at Marker 14 where sediment cores 4570-LC1 and LC2 were collected the sources for thermophilic ANME-1 enrichments (Holler et al. The Guaymas Basin – A hot spot for hydrothermal generation and anaerobic microbial degradation of hydrocarbons ex-NASA Space Station Payload manager/space biologist Devon Island and Everest Base Camp veteran 2024 /PRNewswire/ -- Amigo LNG SA de CV (Amigo LNG) announced today that it has entered into a long-term LNG supply agreement with E&H ENERGY SDN BHD ("E&H") of Malaysia Amigo LNG will supply 3.6 MTPA (million tonnes per annum) of LNG to E&H for the Malaysian market over 20 years This agreement marks a significant milestone for E&H in the evolution of Malaysia's Gas Market Liberalisation regulated by the Energy Commission of Malaysia The future outlook of the Malaysian gas market is positive particularly in the Malaysian power sector Amigo LNG is a large-scale 7.8 MTPA liquefaction and export facility and the only project in the region with both FTA and non-FTA permits from the US Department of Energy The project is being developed in close cooperation with the State of Sonora and is located adjacent to the Port of Guaymas in Sonora Amigo LNG is a cornerstone of Sonora's strategy to position itself as a hub for near-shoring and connectivity to Asian markets via Pacific shipping routes At the signing event in Kuala Lumpur, Dato' Wan Adlil "This agreement is timely and aligns with the country's direction towards gas market parity by 2027 E&H Energy aims to be a significant contributor in providing energy solutions to the country particularly in the LNG and gas sectors in Peninsular Malaysia." "We are pleased to enter into this long-term agreement with E&H Energy This partnership supports our strategy to focus on supplying the growing Southeast Asian LNG market and capitalizes on the unique logistics solutions that Amigo provides optimizing shipping routes to the region," said Muthu Chezhian The implementation of Amigo LNG underscores Mexico's national commitment to a sustainable future One of the initiatives includes using biomethane produced locally from organic waste-based feedstock in Sonora which will be processed and blended with imported US natural gas This approach reduces the project's carbon footprint through waste reduction and promotes a closed-loop circular economy Amigo LNG effectively leverages the country's commitment to ESG principles and asset platform focused on LNG export and import terminal infrastructure LNG Alliance leverages partnerships with key energy sector players and investment partners to structure and deliver reliable and secure energy solutions to core operational markets in Mexico About E&H Energy E&H Energy Group has been active in the gas business since 2010 E&H Energy Group currently operates CNG and LNG facilities in Johor with an expanding footprint in Peninsular Malaysia E&H Energy Group became one of the first private companies in Malaysia to be awarded an LNG Import License under the Third-Party Access initiative of Malaysia's Energy Commission announced today that it entered into a binding Heads of.. Utilities Oil & Energy Gas Environmental Products & Services Do not sell or share my personal information: Located in Bozeman, MT For questions or comments contact the Ask Us Desk      D2L/Canvas      Mexico’s northern region hosts some of the most thriving according to the 2024 Urban Competitiveness Index published by the Mexican Institute for Competitiveness (IMCO) The Mexican NGO publishes the rankings annually. Sonora – all located in the north of Mexico – won the overall top spot for competitiveness in 2024 in one of IMCO’s four city-size categories The size categories range from cities with 1 million residents to cities with populations of under 250,000 The four top cities excelled in a long list of competitiveness indicators that included Sonora was the only state with two cities in top spots Every year, IMCO conducts the Urban Competitiveness Index (ICU) to assess the performance of and challenges faced by cities in Mexico which in total are home to over 62% of Mexico’s population IMCO uses 35 indicators grouped into six sub-indices Here’s a look at which cities won and why: Saltillo beat out 20 cities in its size category Saltillo’s number one ranking is attributed to its low incidence of homicides and vehicle theft its booming labor market and its having one of the highest rates of perceived security among residents Key areas for improvement that IMCO cited for Saltillo included its low number of health personnel (it ranked No 56 in this criteria out of all 66 cities competing) Runners-up just behind Saltillo were Mexico City Hermosillo ranked at the top of its category thanks to its solid labor market and its number of research centers relative to the size of the city’s economically active population IMCO also found Hermosillo to have the lowest percentage of households relying on water from external sources Key areas of opportunity for Hermosillo IMCO cited included increasing the construction of vertical housing and more sustainable water consumption La Paz won its size category in part due to having one of the highest monthly salaries for full-time employees and the highest number of research centers relative to the size of its economically active population It also ranked high on rates of perceived security among residents and rates of hotel occupancy namely electricity generation costs and infant mortality: in both these categories The other Sonora municipality that topped its category the port city of Guaymas won the top spot thanks to its number of research centers and its superior educational coverage for residents under 15 It also featured the smallest gender income gap included lowering its homicide rate and reducing the number of transport-related accidents in the city ADVERTISE WITH MND COMMUNITY GUIDELINES Subscription FAQ's Privacy Policy Mexico News Daily - Property of Tavana LLC Connecting decision makers to a dynamic network of information, people and ideas, Bloomberg quickly and accurately delivers business and financial information, news and insight around the world 2024 at 7:00 AM EDTBookmarkSaveThe Guaymas Port in Mexico is looking to reposition itself as a transport hub that officials say will accelerate nearshoring in the region Sonora Governor Alfonso Durazo announced this week that the port in the northwest region of Mexico would be revamped under a deal signed with the Port of Antwerp-Bruges International in Belgium and backed by a $220 million investment from the federal government Sign up for our daily Newsletter and stay up to date with all the latest news You are receiving this pop-up because this is the first time you are visiting our site You are using software which is blocking our advertisements (adblocker) we are relying on revenues from our banners So please disable your adblocker and reload the page to continue using this site.Thanks slowing down the growth of many produce commodities growers have reported morning time temperatures between 38°F and 43°F to us," says Frank Camera with Delta Fresh Produce While the low temperatures didn't kill the plants "We're now at the end of the Hermosillo squash production," he added The crop is transitioning to Guaymas and Sinaloa Yellow squash normally finishes around November 12 - 15 and that also happened this year "It usually finishes about five to six days after yellow squash but this year saw an earlier finish as it would have been too late for the last fruit to mature." Cantaloupes are also feeling the impact of the cold weather as it takes longer for sugar levels to develop we anticipated finishing around December 6 it may take up to an additional ten days for the fruit to have the right Brix." As a result harvest is expected to prolong until December 15 resulting in increased competition with offshore melons Production of green bell peppers started in the past 10 days at a time when California was still going Stockton and Coachella in California are all finishing up With fruit trending to be smaller at the beginning and end of the seasons the two regions are competing with prices in the upper teens to low $20s The pricing of jumbo size green bells on the other hand is the mid to upper $30s range Active markets leading up to ThanksgivingIt has taken a while for markets to react to the lower availability of product The squash market has improved and is now in the upper teens to low $20s prices were in the $8 - $10 range and towards the end of last week the markets were very active," commented Camera "We saw a really good pull leading up to Thanksgiving." Nevertheless Camera is already bracing for the week after Thanksgiving and the remainder of December "The week after Thanksgiving is always really quiet and while movement leading up to the Christmas and New Year's holidays should be decent resulting in lost business during two weeks of the December month It will make for an interesting month," Camera said production is moving to the winter growing regions Sinaloa is a key growing region for round tomatoes as well as cucumbers for Delta Fresh and they are also in the middle of the transition to Guaymas more Roma tomatoes are grown as well as grape tomatoes we cleaned the first grape tomatoes out of Guaymas and more volume will become available this week." For more information:Frank CameraDelta Fresh ProduceTel: (+1) 520-375-5581[email protected]www.deltafreshproduce.com FreshPublishers © 2005-2025 FreshPlaza.com Ducommun Incorporated (NYSE: DCO) (“Ducommun” or the “Company”) a global supplier of innovative electronic and structural solutions for the aerospace & defense industry is proud to announce the receipt of a major award totaling over $12M in revenue for Raytheon’s TOW missile system This award represents the first order for this legacy program that will now be produced at the Company’s world-class engineering and manufacturing performance center in Guaymas Mexico with the previous production location being at Ducommun’s Monrovia “We are thrilled to continue to earn the trust and confidence of Raytheon and welcome the opportunity to support the needs of our nation and the warfighter the TOW program demand for Ducommun had a pause over the past year due to the timing of orders but our value proposition for this program is world class and we had high confidence the customer would come back for additional orders and support This is also another important milestone for us as we continue to execute on our Vision 2027 strategy which includes transferring meaningful work to our low-cost “Raytheon continues to treat us as a true partner which we very much appreciate and as always remain relentless in our pursuit of building value for our customers and shareholders." Ducommun currently provides Raytheon with electronics harness cable assemblies and structural products on both legacy and emerging programs Ducommun Announces Award of Major Defense Orders For raytheon Radar Systems Ducommun Incorporated Recognized as Airbus Detail Parts Partner (D2P) $200 M Contract for Engine Nacelle Components Ducommun Lands New Work for 737-800 Boeing Converted Freighter Program Ducommun Wins Additional Work from Airbus for A320neo AFRL Awards Ursa Major $28.6M Contract for Responsive Space SAIC Awarded New $55M Mission Integration Contract From Space Development Agency SEA Secures Contract to Support UK Royal Navy Ship Availability and Resilience GDEB Awarded $12Bn Contract Modification for Virginia-Class Submarines Kuwait - PATRIOT Post-Deployment Build 8.1 Strategic Cooperation: LM and Rheinmetall to Join Forces on Centre of Excellence for European Security Ahead of Ready: Estonia Receives 1st HIMARS Poland - AIM-120D Advanced Medium Range Air-to-Air Missiles The Netherlands - Tomahawk Land Attack Missiles Elevate Your Business with Our Market Studies and LEGO® Magic –Editor's note: This post looks back to 2012 when the accompanying image was captured on a Mexican beach at a time when it was not widely known that adult great white sharks inhabited the Sea of Cortez an enormous great white shark sprawled on a beach near Guaymas Commercial fishermen Guadalupe and Baltazar (no last names provided) hauled the giant shark up in a net and towed it two miles to shore behind their 22-foot boat The graphic image tells the story of a town captivated by the rare sight of an apex predator said to measure 20 feet ALSO: Researchers encounter dozens of rare, shark-eating orcas; video “We were amazed and immediately realized that we had a huge The catch saddened conservationists and surprised many who were not aware that upper regions of the Sea of Cortez were utilized by such large white sharks It’s now known that adult great white sharks seasonally migrate into the Sea of Cortez to give birth This project was supported by the Pulitzer Center on Crisis Reporting This special reporting project from KJZZ's Fronteras Desk and the Arizona Daily Star explores an ongoing sewage crisis in Guaymas The port city’s deteriorating system frequently sends raw sewage running through the streets the governor declared the situation a sanitary and environmental emergency Sewage trickles down an arroyo just outside Teresa Cortez’s house in Guaymas — a southern Sonoran port city home to the tourist-beloved beach destination San Carlos residents in Guaymas have been living with a collapsing drainage system riddled with leaks and clogs Teresa Cortez stands near a huge pond of water created by sewage that is leaking from a pipe near her house in Guaymas life-long resident of the city who is raising four young grandchildren wastewater has bubbled up from a clogged pipe nearby flooding the arroyo and stagnating in huge More from Kendal Blust on The Show with host Mark Brodie The nauseating stench burns your eyes and throat Their eyes and noses sting because of the smell that gets inside." Teresa Cortez sits in her living room with four of her grandchildren They have all suffered this summer from the stench of sewage that runs in an arroyo near the house The kids can’t even go outside to play anymore eye and skin irritation or infections — even cholera a doctor who works for the city’s public health department “A lot of people are getting sick because of the sewage.” And it’s not just liquid sewage people need to worry about it becomes bacteria-laden dust that can blow into people’s eyes No matter how many precautions people take Contact with sand and sea water that has been contaminated can also pose a risk director for the Northwest Center for Biological Research in Guaymas Little work has been done to study the health impacts of the sewage spills in Guaymas and it would be hard to separate illness caused by wastewater from other factors like poor trash collection that leaves garbage often rotting in the streets it’s clear it’s impacting people’s well-being “There’s no doubt this is having adverse effects on public health.” And for residents like Cortez and her family Pedestrians make their way across Avenida Serdán in Guaymas where wastewater is running through the street on Sept Passing cars send waves of wastewater sloshing onto the sidewalk as pedestrians carefully pick their way across streets glistening with the rank runoff — much of which eventually flows straight into the sea “You get very sad when you see the sewage that’s going toward the ocean,” said Tomás Thomas co-owner of Marvida brewery in San Carlos — the tourist haven just northwest of Guaymas known for its beautiful beaches spectacular sunsets and striking mountains that roll right down to the sea “And San Carlos has all these activities like scuba diving they call it ‘sleepy San Carlos.’ It’s calm “And there’s no other place on the coast of Sonora that’s like this,” he said But he worries that the town’s tourism potential is at risk with frequent sewage leaks like one that plagued a popular beach known as Cotton Cove all summer sending sewage flowing from a manhole down a cobbled pathway and onto the sand where beachgoers splash in the surf Like many of the leaks in San Carlos and Guaymas and quickly coming back because underlying issues like broken pumps are rarely resolved wastewater regularly pools outside of homes and restaurants who is also concerned about the public health impacts and the image of our brewery on the marina.” Alfonso Durazo declared a sanitary emergency setting aside nearly half a million dollars to address the immediate crisis and promising to invest in a long-term solution head of the state infrastructure department which is taking a leading role in the state’s planned interventions Sewage trickles down a cobbled pathway onto Cotton Cove beach in San Carlos It never should have happened because there should have been a program earlier to attend to the issue so we didn’t get to this situation The problem is that there was no maintenance of the system The current administration understands that Guaymas is on the verge of a health and environmental crisis until he was replaced in September when new state leaders took office “We’ve always seen Guaymas as a very complicated very complex system with a lot of challenges “All the challenges that there are in every other water operating system in Sonora Those include obsolete and poorly maintained infrastructure; shallow pipes due to the city’s rocky soil; and a hilly landscape that makes it difficult and costly to pump sewage to oxidation lagoons which themselves provide insufficient wastewater treatment it’s really difficult to provide good service why should I pay you for providing such poor service,’” he said payments rates in Guaymas were as low as 19% — down from about 60% pre-pandemic That means the water commission in Guaymas barely has funds to pay its workers CEA officials estimate they put about $4 million into the insolvent Guaymas operation which has also accumulated about $15 million of debt according to a statement from current officials even when the department brings in 100% of what it charges even then it’s not enough to cover operating costs,” Cruz said “That’s one of the biggest challenges for Guaymas to update its water rates so that it reflects the real costs and can break this vicious cycle and start investing in the system.” A salon owner in downtown Guaymas set up a ramp across a stream of sewage on the streets outside his business on Sept Former state CEA director Sergio Avila agreed insisting the only way to fix the current crisis in Guaymas is to bring payments in line with costs Guaymas is one of just three municipalities in Sonora where water and sewage systems are operated at the state rather than local level But the municipal government still controls the water rates and has little motivation to make the unpopular decision to increase the cost when CEA bears the responsibility for providing services But Guaymas is far from alone in facing serious sewage issues and even locally operated systems face many of the same challenges: a high-ranking official with Hermosillo’s water utility told KJZZ in 2019 that maintenance of the capital city’s aging sewer system is minimal and breaks and collapses cost the city millions of dollars in repairs annually a man was killed in a sinkhole caused by the city’s deteriorating infrastructure Current officials promise to tackle the problem in Guaymas But some locals find it hard to trust leaders after decades of inaction we don’t even know who to believe anymore.” She has little confidence this administration will be different from previous ones and it’s easy to see why: a broken pipe just outside her front door runs with green liquid Day and night her home reeks with the stench of sewage “I’ve lived in this house my entire life,” she said She and several neighbors are staging a protest after making multiple complaints to the water commission without a response They’ve barricaded the road with bags of trash and debris and hold up signs demanding to be heard and attended to a few drivers complain about being rerouted by the demonstration But Fourcade said they should put themselves in her shoes — waking up every day in this stench “No one can feel what it’s like to live here,” she said Brenda Lopez works at her outdoor tortillas stand in Guaymas near where sewage is flooding the street on Sept Brenda Lopez is working at an open-air tortilla stand “Because people don’t want to buy things in this filth.” who’s playing nearby with some other children has spent 12 days with diarrhea and vomiting which she believes is caused by exposure to the sewage in the street here “I don’t even know what to do anymore,” she said and a trio of researchers are heaving a gray rubber rowboat off the back of a truck onto the edge of a huge lagoon in Guaymas They pick up yellow oars and row out into murky waters lined with bright green cattails and castor plants swaying in the breeze on this sticky and a noisy coot makes its presence known along the shore if it weren’t for the smell — an acrid stomach-turning stench And its four ponds are filled with countless gallons of Guaymas’ sewage and the water goes to the ocean there,” said Jaqueline García Hernández pointing to three large outflow pipes discharging into the nearby bay Floating wetlands on the La Salada oxidation lagoon in Guaymas are designed to help treat sewage that flows into the ponds Garcia runs the Environmental Sciences Lab at CIAD a federally funded research center in Guaymas sewage from Guaymas’ nearly 120,000 residents is pumped across the city’s hilly terrain to La Salada’s four oxidation ponds The lagoon relies on time-dependent natural processes to reduce organic matter and pathogens increasing by more than a third in the last 30 years and these pools are no longer doing their job That leaves insufficiently treated water pouring straight into a small bay of the Sea of Cortez still carrying levels of fecal coliforms up to 350 times the legal limit in Mexico Federal environmental regulations require wastewater being dumped into the ocean to contain less than 2,000 fecal coliform parts per 100 milliliters The four ponds of the La Salada oxidation lagoon are now insufficient to treat all of the wastewater pumped in a bacteria found in the intestines of warm-blooded animals are often used as a proxy for fecal contamination and other pathogenic bacteria in water The flow of wastewater in the ocean can have serious negative effects both to humans and the environment “In addition to all of the fecal bacteria and other pathogens that are a public health risk urban wastewater also carries other contaminants as well as nutrients that can create serious problems in the sea,” he said Those problems include harmful algal blooms and depleted oxygen levels that can kill aquatic life But Garcia and her team hope they’re on to a method that can significantly improve the lagoon’s performance and reduce the pathogens and nutrients in the water by creating a system of floating wetlands on the final oxidation pond “I think we can help reduce nutrients and fecal coliforms So those are the most important contaminants to harm the ocean,” she said use mesh platforms held afloat by plastic bottles to grow cattails on the surface of the pond The plants help remove dangerous pollutants and nutrients A 2019 pilot project showed wetlands placed near one of three drains into the sea significantly reduced levels of fecal coliforms compared to the other two outflows — though they were still well above environmental standards But Garcia said she feels confident that with funding to expand the wetland project to cover the entire final pond with floating cattails they could eventually bring the water into compliance And for much less cost than a conventional wastewater treatment plant but this is just a research project,” she said It would cost a tenth of a water treatment plant and I think it would be a good solution for Guaymas.” She thinks it would only cost about $100,000 to redesign the lagoons to maximize water contact with the wetlands and dramatically reduce nutrients and pathogens in the water “The common knowledge is that you need a water treatment plant to treat all of the sewage but these new treatments are equally efficient or even better,” she said And because so many cities in Mexico and around the world rely solely on oxidation lagoons she hopes their wetlands research will provide an inexpensive upgrade A gray heron rests on a floating wetland installed in the final pond of the La Salada oxidation lagoon in Guaymas “It is very optimistic to say that you could ever achieve any water quality standard for fecal coliforms at the end of a pipe no matter how many floating wetlands you have out there,” said David Walker a research scientist at the University of Arizona’s Department of Environmental Sciences oxidation lagoons are never used as the only form of sewage treatment Instead they are usually “polishers” for water that’s already passed through a conventional plant Even when lagoons have a high removal rate for pathogens like fecal coliform bacteria Insufficiently treated wastewater pours out of the La Salada oxidation lagoon in Guaymas “If you’re starting at a huge level (of pathogens) it’s really not difficult to show a high rate of removal efficiency,” he said “This doesn’t mean the effluent is by any means safe because that 10% residual could still be many fold higher than what would be considered safe to release into the environment.” Experts have been saying for decades that Guaymas needs multiple modern treatment plants — two for the city and another for nearby tourist town San Carlos which also relies solely on its own three-pond oxidation lagoon Water treated there is used to irrigate a nearby golf course but water-quality testing has turned up inconsistent results at the lagoon levels of fecal coliform bacteria were 40 times higher than Mexico’s national standards But just six weeks later results had dramatically improved and were in compliance with environmental norms suggesting that the effectiveness of the ponds depends on the volume of wastewater being pumped into the lagoon the lagoons will likely become less and less effective The water from the final pond is used to irrigate a golf course And government officials now say they are taking steps toward constructing at least one water treatment plant to address the overburdened lagoons “What we’re doing is reconfiguring the whole system so that part of the wastewater will be treated in conventional plants and the other part in the lagoons which will allow the oxidation lagoons to operate at the volume of input it was designed for and produce acceptable results,” said Aguilar “The other part is building a treatment plant for the rest of that water which then can be used to irrigate public gardens and parks,” he added The state water commission has said it’s working to acquire a 24-acre parcel of land in the northern part of the city for the facility This plan is part of the state government’s efforts to address what it declared in November as a health and environmental emergency in Guaymas caused by a neglected and deteriorating sewage system and having sewage flowing through the center of the city is unworthy of the people,” Aguilar said Sewage water flows down an arroyo in Guaymas said much of the problem is caused by years of poor maintenance including repairing broken pumps and replacing outdated pipes They will also try to address the water commission’s dismal financial situation in part by raising water rates that leaders say are far too low to cover costs local officials — who set the rates — have only approved an incremental increase that water commission leaders say won’t be enough to fill the gap between actual costs and user fees Aguilar said the state government has a strong motivation to find the funds necessary to address the current crisis “If we don’t resolve the basic sewage issues we can’t aspire to greater tourism potential or to develop our port,” he said referring to two major priorities of the current administration And that pushes us to resolve this with the resources that it takes.” Jaqueline Garcia and Germán Leyva paddle out into the La Salada oxidation lagoon to fix some floating wetlands that were blown off course during a recent storm But the Guaymas researchers aren’t giving up on their floating wetlands at La Salada They’re still optimistic about the potential to dramatically improve water quality here for a fraction of the cost of a conventional treatment plant “I have faith in this wetland system,” Garcia said While officials are promising the new treatment plant she said the reality is conventional plants are not only expensive to build “They are very expensive in energy and maintenance and they usually stop working in a few years “And water treatment plants also leave some contaminants out The wetlands are very efficient in treating those And a realistic one that can be implemented now Garcia and her fellow researchers aren’t opposed to a conventional treatment plant for Guaymas and they admit it would bring real benefits But they’re not going to wait around for one reporting for the Arizona Daily Star in Tucson The project site covers an estimated area of 150 acres The Amigo LNG terminal is a liquefied natural gas (LNG) facility that is currently under development on the west coast of Mexico in Guaymas This project will be owned and operated by LNG Alliance a Singapore-based company operating in the oil and gas sector and an affiliate of oil and gas company Epcilon LNG The LNG terminal will have a capacity of 7.8 million tonnes per annum (mtpa) It is designed as a land-based LNG liquefaction facility with compact environmental footprint and best-in-class technology The LNG produced will be loaded onto ocean-going LNG carriers destined for domestic markets within Mexico and reexport to other countries The LNG production is anticipated to commence in the second quarter (Q2) of 2026 The Amigo LNG facility will be located in  Guaymas at a coastal site situated on the Gulf of California The Amigo LNG terminal will include two liquefaction trains Train 1 will have a capacity of approximately 4.2mtpa while Train 2’s capacity will be 3.6mtpa The facilities at the terminal will include two full containment LNG storage tanks with the first tank having a storage capacity of 230,000m³ and the second having a capacity of 170,000m³ Additional infrastructure will encompass an LNG impoundment basin and one LNG recirculation pump for each storage tank The feed gas for the facility will be sourced from the cost-effective Permian shale basins in the US The terminal will operate on a tolling model, where offtakers will be responsible for sourcing their feed gas from the US Permian basin to ensure the delivery of LNG 5,000ft of aboveground cryogenic pipeline will be developed to connect the tanks LNG pumps and two LNG loading docks equipped with truck loading facilities A lateral gas pipeline will link the onshore gas spur line to two nearshore floating liquefied natural gas (FLNG) liquefaction barges Each FLNG barge will have a capacity of around 3.9mtpa and will be installed in two phases The nearshore facilities will feature a marine wharf capable of berthing Q-Flex vessels It will feature a 15m deep navigation channel with a turning circle diameter of 900m A small-scale jetty will also be constructed for smaller LNG vessels with capacities ranging between 5,000m³ and 15,000m³ The LNG for the Mexican market will be transported either by truck or by smaller vessels Epcilon intends to initially receive natural gas primarily from the US, which will be exported to Mexico via an established gas transmission pipeline network spanning both countries The primary transportation route includes the Trans-Pecos pipeline which carries gas from the Waha Hub near Fort Stockton Texas will first flow through the interconnected El Encino pipeline operated by Infraestructura Energetica Nova and then through the Topolobampo Pipeline managed by TC Energy The gas will continue on the Topolobampo pipeline into the interconnected Guaymas pipeline operated by Ienova at the El Oro interconnection A short lateral section at the Guaymas pipeline near the Port of Guaymas will serve the Amigo LNG facility The Amigo LNG terminal will provide substantial benefits to both the US and Mexico by giving US natural gas producers access to new markets leveraging the abundant and low-cost gas from regions such as the Permian Basin and Eagle Ford Formation Strategically located on the Gulf of California the terminal will serve as a cost-effective LNG source for Asia the facility will also benefit Mexican LNG markets especially those remote from the national gas pipeline grid through waterborne or truck-based deliveries The construction phase is also expected to support design Give your business an edge with our leading industry insights View all newsletters from across the GlobalData Media network As Mexico News Daily readers, you know all about the Maya Train. Maybe you’ve read about the Interoceanic Train But when was the last time you heard about the Sonora “ghost train?” The name doesn’t refer to a haunted locomotive: the “tren fantasma” earned its moniker when Sonora residents saw the tracks being built but couldn’t figure out why they were being built — or who was building them Their only clue was a leaked map of the local rail network which run from the port of Guaymas north through Hermosillo Ímuris and the border town of Nogales before finally crossing into the United States Instead of following International Highway 15 north like the current route the depicted tracks branched off east in Ímuris Some local residents worried about the railroad dividing their community building across their irrigation canals and damaging natural protected areas Others were alarmed when state officials offered to buy their land for as little as 1.8 pesos (less than US 10 cents) per meter Biologist Mirna Manteca of the Wildlands Network an NGO which works to conserve and rewild natural areas in North America tried to learn about the project after locals from the town of Ímuris approached her with their concerns Ímuris officials told her it was a state project Manteca contacted one federal office after another but none had information about a train being built in Ímuris “There’s no real information. There’s no official project,” Manteca told The Associated Press in November 2023 “They’ve kind of been ping ponging responsibilities back and forth … It’s like fighting a ghost.” Sonora Governor Alfonso Durazo said at a press conference that the new construction was part of a project to change the route of the existing Guaymas-Nogales railroad The state planned to modernize the port of Guaymas That meant the tracks needed to be moved out of Nogales to a less populated area “The modernization of the Guaymas port wouldn’t make sense without the relocation of the railroad tracks” in Nogales the Army was in charge of building the new tracks construction continues and the Ghost Train is more real every day information about the project remains mostly classified What we do know is that the port of Guaymas “With the modernization of the port of Guaymas… it will be possible to receive deep-draft tourism and commercial ships,” Sonora Governor Alfonso Durazo said at his third annual report on Sept adding that the port will serve both Chihuahua and the southwest United States Moving the new cargo will depend on the Ferromex train that runs from Guaymas to Nogales just meters from where cars and pedestrians cross the international border Three to four trains move through the city every day worsening the city’s snarled international border traffic and passing dangerously close to homes and public infrastructure With train traffic expected to increase to 15-20 trains a day, there is widespread agreement on the need to move the tracks “It is necessary to get the tracks out of Nogales,” agrees Sergio Müller strategy coordinator of the Sonora environmental collective Caminantes del Desierto “However the issue is how it’s done and where it’s done.” The project “doesn’t make sense,” Müller said “The construction ends up in the same point where it currently ends on the U.S Union Pacific Railroad has not expressed any intention to move their part of the tracks the railroad will approach the city of Nogales from the east then dive more than 30 meters under the city into a 2.5-kilometer tunnel to the border But the tunnel’s construction has faced problems an Hermosillo investigative reporter who covers corruption and accountability “Neighbors tell us almost every day via phone calls or WhatsApp messages that they feel tremors below their houses They even send photos with cracks on their walls,” Ibarra said explaining that the company is using explosives to carve out the tunnel much of the route has been cleared for construction About a third of the actual track has been built and none of the route’s six new bridges were complete as of early September Ibarra also said that tunnel workers told him they are a year behind schedule having only advanced 500 meters since they began blasting “It is impossible for the construction company to finish the tunnel on time according to contract,” which ends Sept sponsored by the National Institute for Transparency Access to Information and the Protection of Personal Data (INAI) found that the Army gave contracts worth nearly 650 million pesos (US $33.9 million) to companies whose lead stakeholders had participated in “facturera,” or invoice fraud and embezzlement of public funds during previous projects In response to the investigation, President López Obrador called for the investigation of the Hermosillo company 3PM the primary beneficiary of the dubious contracts most residents have now stopped speaking out publicly against the project “There are still communities today in resistance in Ímuris but they are continuing via the legal path a government-certified voluntary conservation area in the train’s path “were heavily pressured by the Army to sell the former owners stopped making public statements on the issue the new owners submitted a request to cancel Aribabi’s designation as a voluntary conservation area paving the way for the project’s environmental approval in August It appears extremely unlikely the infrastructure project will be finished by the end of September, as originally planned. Instead, it will likely continue into the administration of President-elect Claudia Sheinbaum, who will take office on Oct. 1. Rose Egelhoff is a freelance writer based in Mazatlán, Sinaloa. Follow her work at RoseEgelhoff.com Metrics details Methanogenic and methanotrophic archaea produce and consume the greenhouse gas methane using the reversible enzyme methyl-coenzyme M reductase (Mcr) Mcr variants that can activate multicarbon alkanes have been recovered from archaeal enrichment cultures are widespread in the environment but remain poorly understood Here we produced anoxic cultures degrading mid-chain petroleum n-alkanes between pentane (C5) and tetradecane (C14) at 70 °C using oil-rich Guaymas Basin sediments archaea of the genus Candidatus Alkanophaga activate the alkanes with Acrs and completely oxidize the alkyl groups to CO2 Alkanophaga form a deep-branching sister clade to the methanotrophs ANME-1 and are closely related to the short-chain alkane oxidizers Ca Alkanophaga shuttle electrons released from alkane oxidation to the sulfate-reducing Ca These syntrophic consortia are potential key players in petroleum degradation in heated oil reservoirs We obtained eight enrichment cultures thriving at 70 °C in which alkanes from C5-C14 were oxidized in combination with sulfate reduction Analyses of these cultures via omics approaches and physiological tests revealed that a sister clade of ANME-1 was oxidizing the alkanes after activation via Acrs coupled to sulfate reduction by a partner Thermodesulfobacterium Such consortia potentially contribute to souring in deeply buried Formation of sulfide over time in n-hexane (C6) (a) and n-tetradecane (C14) (b) cultures Gaps in concentration profiles indicate dilution events Arrows mark sampling for metagenomic and transcriptomic analyses Concentrations of dissolved inorganic carbon (DIC) sulfate and sulfide in the C6 (c) and C14 (d) cultures with arithmetic mean shown as a dotted line Source data Relative abundances of MAGs obtained from manual binning Alkanophaga volatiphilum (MAG 4) is abundant in cultures oxidizing shorter Alkanophaga liquidiphilum (MAG 1) is abundant in cultures oxidizing liquid alkanes between C8 and C14 A Thermodesulfobacterium with the genomic capacities for dissimilatory sulfate reduction Taxonomies of background MAGs are displayed at order level Background archaea are shaded grey; background bacteria are shaded brown Alkanophaga MAGs based on the concatenated alignment of 76 archaeal single-copy core genes Alkanophaga diverge at the root of ANME-1 (Ca The class Syntrophoarchaeia is highlighted with a shaded rectangle The outgroup consists of members of the Thermoproteota Double hybridization of C6 (c,d) and C14 (e,f) culture samples with a specific probe targeting the Ca red) and a general bacterial probe (EUBI-III Alkanophaga cells are abundant in the aggregates where they co-occur with bacterial cells Source data suggesting that archaea oxidize the alkanes and partner SRB perform sulfate reduction Phylogenetic placement of translated mcrA sequences of Ca Alkanophaga species contain three mcrA sequences all of which fall into the divergent branch of mcrAs The six acrA sequences form three clusters of two sequences each cluster containing one sequence of each Ca Expression of acrA genes during growth on various alkanes for both Ca Cultures in which the respective species was prevalent in the metagenomes are highlighted with shaded boxes The mean expression of all genes of the respective species is shown as a horizontal bar The acrA of the third cluster was strongly expressed The expression of the other acrA genes was low Extracted ion chromatograms (EICs) based on exact mass and a window of ±10 mDa of deprotonated ions of variants of C6-CoM (c) and C14-CoM (d) detected via liquid chromatography–mass spectrometry the upper shaded panels show the culture extract the shaded bottom panel shows the EIC produced with the exact mass of the C14-thiolate a fragmentation product derived in MS/MS experiments from the precursor C14-CoM Dashed vertical lines were added at retention times of peak maxima of standards (c) or standards and fragmentation products (d) for easier identification of peaks in the culture extracts While C6 is activated on the first and second carbon atom to a similar degree C14 is activated predominantly to ≥3-C14-CoM Source data Genomic capacities for alkane oxidation in Ca Colour-filled rectangles indicate presence of a gene; white rectangles indicate absence at least one gene coding for each subunit was found in case of a filled rectangle Metabolic model for syntrophic alkane oxidation Alkanophaga activates alkanes via the alkyl-coenzyme M reductase (Acr) A yet unknown pathway transforms alkyl-CoM to acyl-CoA including (1) acyl-CoA dehydrogenase (ACAD) (3) hydroxyacyl-CoA dehydrogenase (HADH) and (4) acyl-CoA acetyltransferase (ACAT) cleave acyl-CoA into multiple acetyl-CoA units The acetyl-CoA decarbonylase/synthase (ACDS) complex breaks the acetyl units into CO2 and a tetrahydromethanopterin (H4MPT)-bound methyl unit The methyl branch of the Wood-Ljungdahl pathway including (1) 5,10-methylene tetrahydrofolate reductase (MetF) and/or 5,10-methylene H4MPT reductase (Mer) (4) formylmethanofuran-H4MPT formyltransferase (Ftr) and (5) tungsten-containing formylmethanofuran dehydrogenase (Fwd) an electron transfer flavoprotein (Etf) serves as electron acceptor in the first step of the β-oxidation pathway Cofactor recycling is taken over by cytoplasmic heterodisulfide reductase (Hdr) NADH dehydrogenase (Ndh) and F420H2:quinone oxidoreductase (Fqo) Electrons from alkane oxidation are transferred to Ca DIET seems to rely on conductive filaments formed by type IV pilin (PilA) and/or flagellin B (FlaB) that are expressed by both partners and multihaem c-type cytochromes (MHCs) expressed solely by the bacterium syntrophicum follows the canonical dissimilatory sulfate pathway using the enzymes ATP-sulfurylase (Sat) APS-reductase (Apr) and dissimilatory sulfite reductase (Dsr) gene encoding propionyl-CoA decarboxylase; mce Source data Alkanophaga: alkano (new Latin): alkane and phaga (Greek): eating; volatiphilum: volatilis (Latin): volatile and philum (Greek): preferring; liquidiphilum: liquidus (Latin): liquid and philum (Greek): preferring; syntrophicum: syn (Greek): together with; trephein (Greek): nourish and icum (Latin): pertaining to Hydrothermally heated oil-rich deep-sea sediment in the Guaymas Basin petroleum (C5-C14) n-alkane-oxidizing archaea forming syntrophic consortia with the sulfate-reducing Ca neither molecular hydrogen nor formate are probably primary electron carriers This implies a minor role of MHCs in the interaction of both organisms but further analyses are necessary to confirm the identity of these structures This temperature optimum is reflected by the high relative abundance of Ca heated sediment layers of the Guaymas Basin inferring a crucial role of these archaea in thermophilic hydrocarbon transformation Crystallization efforts may resolve molecular and structural modifications of these Acrs that make use of such a wide substrate spectrum One could imagine that MHCs in the Syntrophoarchaeia ancestor were encoded on such a Borg This could explain why all MHCs are absent in Ca the presence of Borgs in other members of the Syntrophoarchaeia still needs to be examined Thermodesulfobacteria represent a new group of partner organisms for alkane-oxidizing archaea at high temperatures syntrophicum encodes and expressed several MHCs which could support DIET for both partners sampling technologies have greatly improved in recent years and the focus has shifted from amplification-based 16S rRNA gene to shotgun metagenome studies which should facilitate a more accurate molecular characterization of reservoir microorganisms future studies may disclose the coexistence and activity of Ca All chemicals were of analytical grade and obtained from Sigma Aldrich All incubations were done under gentle shaking (40 r.p.m.) in the dark A substrate-free culture served as a negative control Headspaces were filled with N2:CO2 (90:10; 1 atm overpressure) and incubated at 70 °C Sulfide production was measured every 2–4 weeks using a copper sulfate assay67 Once sulfide concentrations reached 12–15 mM cultures were diluted 1:3 with SRM and supplied with fresh substrate Activity doubling times were determined from the development of sulfide concentrations during the first two dilutions Sulfide concentrations over time were displayed using a logarithmic (base 2) y axis An exponential trend line with the formula \(y=n\times{e}^{{mx}}\) was generated the doubling time equals\(\,\frac{\mathrm{ln}(2)}{m}\) Triplicate 100 ml dilutions with 20 ml headspace were prepared from C6- and C14-oxidizing cultures supplied with substrate and incubated at 70 °C complemented by a substrate-free negative control Sulfate and DIC concentrations were measured from weekly subsamples until the cultures had reached sulfide concentrations of ≥15 mM Samples were sterile filtered using a GTTP polycarbonate filter (0.2 μM pore size; Millipore) 1 ml filtrate was transferred into synthetic-air-purged 12 ml Exetainer vials (Labco) filled with 100 µl phosphoric acid (45%) headspace DIC was measured by isotope ratio infrared spectroscopy (Thermo Fisher; Delta Ray IRIS with URI connect and Cetac ASX-7100 autosampler) with standards of known concentration 1 ml of the filtrate was fixed in 0.5 ml 100 mM zinc acetate The sample was centrifuged and the clear supernatant was diluted 1:50 in deionized water Sulfate was measured by ion chromatography (930 compact IC Metrohm) against standards with known concentrations determined by fluorometric DNA concentration measurement Samples were sequenced at the Max Planck-Genome-Centre (Cologne C6-C14 culture samples were sequenced as 2 × 250 paired-end reads on an Illumina HiSeq2500 sequencing platform The C5 culture sample was sequenced later because of slower growth together with a sample of the sediment slurry before incubation by which time the sequencing facility had changed their settings to 2 × 150 bp paired-end reads on an Illumina HiSeq3000 platform Between 4,140,953 and 4,234,808 raw reads were obtained per culture sample Thermodesulfobacterium syntrophicum MAGs from the C5 sample to the previously reconstructed ones was confirmed via FastANI the trimmed reads of the original slurry were mapped to the MAGs with CoverM where the colour of Alexa488 was changed to cyan to improve accessibility 10 ml of culture material collected after the third dilution at the exponential growth stage were filtered through an RNAse-free cellulose nitrate filter (pore size 0.45 μm; Sartorius) filters were incubated with 5 ml RNAlater for 30 min RNA was extracted from filters using the Quick-RNA miniprep kit (Zymo Research) Between 0.3 and 1.3 μg of total RNA were obtained per sample as determined by fluorometric RNA concentration measurement Samples were sequenced as 2 × 250 (C5: 2 × 150) paired-end reads at the Max Planck-Genome-Centre on the Illumina HiSeq2500 (C5: Illumina HiSeq3000) sequencing platform Between 4,043,349 and 4,785,231 raw reads were obtained per sample Fragments were first normalized to gene length The centred-log ratio (CLR) was calculated as the base-10 logarithm of read count Ci of gene i normalized by gene length Li in kilobases and divided by the geometric mean of all read counts C1 − Cn normalized by their respective gene length L1 − Ln Duplicates of C6- and C14-oxidizing culture were supplied with substrate and 5 mM (final concentration) BES A control culture was supplied with substrate but not with BES Cultures were incubated at 70 °C and sulfide concentrations were measured until the control cultures had reached >15 mM sulfide Metabolite samples were collected at sulfide levels of 10–14 mM An 80 ml culture sample of each substrate was pelleted via centrifugation (15 min pellets were resuspended in 1 ml of acetonitrile:methanol:water (2:2:1 v/v/v) and transferred to bead-beating tubes Samples were agitated for 15 min on a rotor with vortex adapter at maximum speed Samples were centrifuged for 20 min at 10,000 × g at 4 °C Coenzyme M (sodium 2-mercaptoethanesulfonate) (0.1 g) was dissolved in 2 ml 25% (v:v) ammonium hydroxide solution and twice the molar amount of bromoalkane was added We acquired 2- and 3-bromohexane from Tokyo Chemical under gentle shaking on a rotor with vortex adapter The clear upper phase (1 ml) was collected and stored at 4 °C Culture extracts and standards were analysed using high-resolution accurate-mass mass spectrometry on a Bruker maXis plus quadrupole time-of-flight (QTOF) mass spectrometer (Bruker) connected to a Thermo Dionex Ultimate 3000RS UHPLC system (Thermo Fisher) via an electrospray ionization (ESI) ion source Sample aliquots were evaporated under a nitrogen stream and re-dissolved in a methanol:water (1:1 v/v) mixture before injection A 10 μl aliquot of the metabolites was injected and separated on an Acclaim C30 reversed phase column (Thermo Fisher; 3.0 × 250 mm 3 µm particle size) set to 40 °C using a flow rate of 0.3 ml min−1 and the following gradient of eluent A (acetonitrile:water:formic acid 5:95:0.1 v/v/v) and eluent B (2-propanol:acetonitrile:formic acid followed by re-equilibration at 0% B from 51 min to the end of the analysis at 60 min to prepare the column for the next analysis The ESI source was set to the following parameters: capillary voltage 4,500 V The QTOF was set to acquire full scan spectra in a mass range of m/z 50–600 in negative ionization mode The C14 culture extract was additionally analysed in tandem mass spectrometry mode and mass spectra of the fragmentation products of m/z 337.1877 isolated in a window of 3 Da and fragmented with 35 eV were acquired Every analysis was mass-calibrated to reach mass accuracy of 1–3 ppm by loop injection of a calibration solution containing sodium formate cluster ions at the end of the analysis during the equilibration phase and using the high-precision calibration algorithm Data were processed using the Compass DataAnalysis software package v.5.0 (Bruker) Cultures originally grown with C6 and C14 were diluted 1:10 in fresh SRM. Dilutions were supplemented with alkanes between C5 and C14 for which growth had not been confirmed yet, and with shorter (C3 and C4) and longer (C16-C20) alkanes (Table 1) A negative (inoculated culture without substrate) and a positive (inoculated culture supplied with substrate with which the culture was originally grown) control were also set up Cultures were incubated at 70 °C and activity was tracked via sulfide measurements Once sulfide concentrations reached >10 mM The procedure was repeated and incubations that showed sustained activity over two dilutions were considered successful C6 and C14 cultures were divided into two 20 ml aliquots in 156 ml serum bottles the other one was treated with 10 mM (final concentration) sodium molybdate Hydrogen was measured by injecting 1 ml of headspace sample into a Peak Performer 1 gas chromatograph (Peak Laboratories) Measurements were taken in 1 h intervals up to 8 h after the start of the experiment A final measurement round was conducted from 24 h to 30 h in 2 h intervals Two replicates of C6- and C14-oxidizing cultures were supplied with substrate and with 10% H2 in the headspace or 10 mM (final concentration) sodium formate in the medium A control culture was supplied only with substrate Cultures were incubated at 70 °C and sulfide concentrations were measured until the control cultures had reached ≥15 mM sulfide Platelets were frozen using a Leica EM HPM100 high-pressure freezer (Leica) Frozen samples were transferred to a Leica EM AFS2 automatic freeze substitution unit and substituted at −90 °C in a solution containing anhydrous acetone and 0.1% tannic acid for 24 h 2% OsO4 and 0.5% anhydrous glutaraldehyde (Electron Microscopical Science) for a further 8 h After further incubation over 20 h at −20 °C samples were warmed to +4 °C and subsequently washed with anhydrous acetone Samples were embedded at room temperature in Agar 100 (Epon 812 equivalent) at 60 °C for 24 h Thin sections (80 nm) were counterstained using Reynolds lead citrate solution for 7 s and examined using a Talos L120C microscope (Thermo Fisher) Aliquots of C6- and C14-oxidizing cultures were diluted 1:6 supplied with substrate and incubated at 60–90 °C in 5 °C increments Sulfide production was tracked until the 70 °C cultures had reached >10 mM sulfide Official culture collections do not accept syntrophic enrichment cultures Non-profit organizations can obtain samples upon request Further information on research design is available in the Nature Portfolio Reporting Summary linked to this article The workflow for metagenome and transcriptome analysis, and the scripts for targeted reassembly and for the search of CxxCH motifs are available under https://github.com/zehanna/MCA70_analysis Further inquiries about bioinformatic analyses may be directed to the corresponding authors Methane and other hydrocarbon gases in marine sediment an easy and widespread process in hydrothermal systems: an overview Catagenesis 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Microbiol. 13 https://doi.org/10.3389/fmicb.2022.988871 (2022) Survey of hydrothermally-generated petroleums from the Guaymas Basin spreading center Evaluation of 16S rRNA gene primer pairs for monitoring microbial community structures showed high reproducibility within and low comparability between datasets generated with multiple archaeal and bacterial primer pairs Sulfate reducing microorganisms in high temperature oil reservoirs in Advances in Applied Microbiology (eds Gadd Establishing anaerobic hydrocarbon-degrading enrichment cultures of microorganisms under strictly anoxic conditions Anaerobic degradation of ethylbenzene and other aromatic hydrocarbons by new denitrifying bacteria A quick method for the determination of dissolved and precipitated sulfides in cultures of sulfate-reducing bacteria A modified SDS-based DNA extraction method for high quality environmental DNA from seafloor environments SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing Anvi’o: an advanced analysis and visualization platform for 'omics data Centrifuge: rapid and sensitive classification of metagenomic sequences CheckM: assessing the quality of microbial genomes recovered from isolates GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database Prokka: rapid prokaryotic genome annotation Pfam: the protein families database in 2021 phyloFlash: rapid small-subunit rRNA profiling and targeted assembly from metagenomes High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries MUSCLE: multiple sequence alignment with high accuracy and high throughput RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy ARB: a software environment for sequence data The domain-specific probe EUB338 is insufficient for the detection of all bacteria: development and evaluation of a more comprehensive probe set Multiple alignment of DNA sequences with MAFFT in Bioinformatics for DNA Sequence Analysis (ed Posada Seaview version 5: a multiplatform software for multiple sequence alignment in Multiple Sequence Alignment: Methods and Protocols (ed Katoh FeatureCounts: an efficient general purpose program for assigning sequence reads to genomic features MetaboLights: a resource evolving in response to the needs of its scientific community Download references This study was funded by the DFG under Germany’s Excellence Initiative/Strategy through the Clusters of Excellence EXC 2077 ‘The Ocean Floor—Earth’s Uncharted Interface’ (project no the Andreas Rühl Foundation and the Max Planck Society was funded by a Juan de la Cierva grant (FJC2019-041362-I) from the Spanish Ministerio de Ciencia e Innovación The Guaymas Basin expedition was supported by the National Science Foundation (Collaborative Research: Microbial Carbon cycling and its interactions with Sulfur and Nitrogen transformations in Guaymas Basin hydrothermal sediments) We thank the captain and crew of RV Atlantis for their excellent work during the expedition AT42-05; H Menger for technical support in the laboratory; K Ellrott for sharing their experience with CARD-FISH and microscopy; and A Boetius for fruitful scientific discussions Open access funding provided by Max Planck Society Present address: Biogeochemistry and Microbial Ecology Department Museo Nacional de Ciencias Naturales (MNCN-CSIC) Max Planck Institute for Marine Microbiology Centro Nacional de Biotecnología (CNB-CSIC) Max Planck Institute for Multidisciplinary Sciences conducted mass spectrometry measurements and analyses carried out transmission electron microscopy did cultivation and laboratory experiments as well as omics analyses and wrote the manuscript with contributions from all co-authors agreed to all manuscript contents and to the author list and its order Nature Microbiology thanks Song-Can Chen, Michael McInerney and the other, anonymous, reviewer(s) for their contribution to the peer review of this work. Peer reviewer reports are available Location of the Guaymas Basin in the Gulf of California Bathymetry of the southern end of the Southern Trough of the Guaymas Basin with the location of the Cathedral Hill hydrothermal vent area Sampling of the push core (4991-15) that was used for anoxic cultivations in an area densely covered by orange sulfur-oxidizing Beggiatoa mats Depth-temperature profile in the sampling site The temperature was measured using Alvin’s heatflow probe Push cores reached about 30 cm into the sediment where the temperature approached about 60 °C (sampling site photograph and temperature data courtesy of the Woods Hole Oceanographic Institution f Microbial community in the anoxic sediment slurry prepared from core 4991-15 before starting anoxic incubations based on 16S rRNA gene fragments recruited from the metagenome archaea and bacteria each make up around 50% For groups with unknown order assignment marked with * the next known higher taxonomic levels are indicated An ANME-1 group is abundant within the archaeal fraction while the bacterial fraction is very diverse Source data Gaps in sulfide level indicate dilution steps Pink arrows indicate the sampling points for metagenome and -transcriptome sequencing Samples were collected after the third dilution from cultures degrading (a) n-pentane The negative control (light gray line) consisted of a sediment slurry without added substrate Source data Partial acrA genes are shown in light pink Some gene names were shortened to fit the arrows Genes code for: acrA: alkyl-coenzyme M reductase alpha subunit; acrB: alkyl-coenzyme M reductase beta subunit; acrG: alkyl-coenzyme M reductase gamma subunit; fixC: flavoprotein dehydrogenase; yjiL: activator of 2-hydroxyglutaryl-CoA dehydratase; nC: nuoC-NADH:ubiquinone oxidoreductase; hycE2: [NiFe]-hydrogenase III large subunit; hyfC: formate hydrogenlyase; ycaO: ribosomal protein S12 methylthiotransferase accessory factor; rpf: rpf1-rRNA maturation protein; n: nuoI-formate hydrogenlyase subunit 6; paaJ: acetyl-CoA acetyltransferase; insQ: transposase; gd: gdb1-glycogen debranching enzyme; hdrA: heterodisulfide reductase subunit A; cu: cutA1-divalent cation tolerance protein; disA: c-di-AMP synthetase; cinA: ADP-ribose pyrophosphatase domain of DNA damage- and competence-inducible protein CinA; fwdA: formylmethanofuran dehydrogenase subunit A Source data Treatment with 2-bromoethanosulfonate (BES) BES (5 mM final concentration) was added to duplicates of C6 (a) and C14 (b) degrading cultures ( + BES) A control culture (-BES) did not receive BES The inhibition of alkane oxidation by BES corroborates an Acr-based substrate activation Addition of hydrogen or formate to C6 (c) and C14 (d)-degrading cultures All cultures were supplied with the original substrate The addition of 10% H2 into the headspace or 10 mM sodium formate into the medium did not accelerate sulfide production compared to positive controls Incubation at temperatures between 60 °C and 90 °C The C6-degrading culture (e) grows optimally at 70 °C and 75 °C while it still shows some activity at slightly lower (65 °C) and slightly higher (80 °C) temperatures The activity of the C14-degrading culture (f) seems to be limited to 70 °C Source data Samples were separated by liquid chromatography and extracted ion chromatograms (EICs) based on the exact mass of deprotonated ions of the Cx-alkyl-CoMs with a window of ±10 mDa were created Panels show the EICs of culture extracts together with synthetic standards Dashed vertical lines were added at the retention times of peak maxima of the standards for easier identification of peaks in the culture extracts Peaks with mass-to-charge ratios (m/z) of the respective alkyl-CoM were detected in all cultures indicating an activation at different carbon atoms While shorter alkanes are activated to a similar degree at subterminal and terminal positions longer alkanes are predominantly activated at non-terminal carbon atoms Cultures were diluted into fresh sulfate-reducer medium and supplemented with other n-alkanes between C3 and C20 No activity was observed for cultures supplied with C3 Source data Transcriptome reads were mapped to the MAGs of the two Candidatus Alkanophaga species and to Ca Fragment counts normalized to gene length (FPK) using a logarithmic y axis The average gene expression of each organism is indicated as arithmetic mean (sum of all FPK values divided by number of genes) depicted as a horizontal line The x-axis shows the genes encoding: acr: alkyl-CoM reductase met: 5,10-methylene tetrahydrofolate reductase mer: 5,10-methylene tetrahydromethanopterin (H4MPT) reductase ftr: formylmethanofuran-H4MPT formyltransferase fwd: tungsten-containing formylmethanofuran dehydrogenase Source data Alkanophaga species are highly similar to each other Alkanophaga in the class Syntrophoarchaeia might originate from the ancestor of Methanocellales while metF sequences cluster near those of close relatives Ca Source data syntrophicum is closely related to the already cultured Thermodesulfobacterium geofontis (OPF15T) and to Ca which functions as partner bacterium in the thermophilic anaerobic oxidation of methane The outgroup consists of members of the candidate phylum Bipolauricaulota The tree scale bar indicates 10% sequence divergence Source data The experiment was run once with one biological replicate per sample Images are representative for > 5 recorded images per sample Additional information on culture physiology and results from metagenome analyses 2a) and alignment of single-copy core genes used for archaeal phylogenomic tree calculation (Fig Alignment of mcrA sequences used for phylogenetic tree calculation (Fig 8b metF) sequences used for phylogenetic tree calculation Alignment of single-copy core genes used for bacterial phylogenomic tree calculation Download citation DOI: https://doi.org/10.1038/s41564-023-01400-3 Sign up for the Nature Briefing: Microbiology newsletter — what matters in microbiology research, free to your inbox weekly. Volume 12 - 2024 | https://doi.org/10.3389/feart.2024.1301999 The high-resolution analysis of radiolarians and silicoflagellates in sediments from Holes U1545A and U1549A drilled during IODP Expedition 385 in the Guaymas Basin in the Gulf of California provides detailed insights into the evolution of ocean circulation and water masses and its relation to Eastern Tropical Pacific Ocean climate conditions over the past 31,000 cal years BP (based on AMS radiocarbon dates) the Guaymas Basin experienced alternating circulation patterns of California Current Water (CCW) and Gulf of California Water (GCW) with an extended presence of the Pacific Intermediate Water (PIW) owing to: amplified jet streams; southern movement of the California Current System (CCS) and the incursion of CCW into the gulf; and increased North Pacific Intermediate Water (NPIW) formation The Last Glacial Maximum witnessed the incursion of CCW due to the stronger CCS The dominance of the PIW indicates the expansion and formation of NPIW The Heinrich-I event as manifested in the core record one suggesting GCW-like dominance and the other The Bølling-Ållerød interstadial featured the entry of Tropical Surface Water (TSW) linked with the northward migration of the Intertropical Convergence Zone transitioning to GCW as colder climatic conditions and more intense CCS The Holocene displayed alternating periods of TSW and GCW with a modern monsoon regime from 7,600 to 1,000 cal years BP From 1,000 cal years BP to the present the ITCZ shifted to the south Although several paleoceanographic studies have been developed in this region understanding the hydrographic structure of the GoC and processes forcing changes still needs to be well resolved It is crucial to unravel how the Pacific Ocean dynamic and global climate have influenced the gulf to decipher the intricate relationship between the ETPO and the GoC which in turn will shed light on climatic evolution during the late Quaternary High-resolution proxy data are also required to allow constrained models and enhance their accuracy This study focuses on siliceous microfossils—polycystine radiolarians (hereafter referred to as radiolarians) and silicoflagellates—to reconstruct hydrographic structure and circulation patterns in the GB during the past 31,000 cal years BP Although proxies have distinct sensitivities and limitations silicoflagellates and shallow-dwelling radiolarians respond similarly to specific physical and chemical environmental changes these proxies may be jointly considered when interpreting climate variations over time we present high-resolution records of radiolarian assemblages and silicoflagellates to (1) investigate hydrographic and climatic changes on glacial-interglacial and sub-millennial timescales and (2) establish the links of the regional hydrographic settings to the ETPO Understanding the occurrence of water masses in the past will expand the knowledge about oceanographic dynamics and its relationship with regional and global climatic variability FIGURE 1. (A) Map showing the position of atmospheric centers and ITCZ position during summer and winter. Winds direction in the Gulf of California is shown in bold arrows. NPH, North Pacific High; SLPS, Sonora Low Pressure Center; CCW, California Current Water; WMC, West Mexican Current. Continuous bold lines represent the southern limit of the California Current System (CCS) during summer and winter (Kessler, 2006) (B) Location of sampled drilling sites U1545A and U1549A FIGURE 2. (A) Water masses in the Guaymas Basin: GCW, Gulf of California Water; TSW, Tropical Surface Water; StSsW, Subtropical Subsurface Water; PIW, Pacific Intermediate Water; PDW, Pacific Deep Water (Lavin et al., 2009). (B) Dissolved oxygen concentration in Guaymas Basin (García et al., 2006) and we studied the uppermost 28 m of sediments (Cores 385-U1549A-1H to 4H) Sediments cored in Hole U1545A are mostly laminated diatom ooze and clay-rich diatom ooze, with laminae alternating between biogenic-particle-dominated (mainly diatom ooze) and terrigenous-particle-dominated (mainly clay minerals with minor siliciclastic silt) end members; the presence of lamination suggests that the hemipelagic sediments were deposited in suboxic to anoxic seafloor conditions (Teske et al., 2021b) Considering that a climatic signal would not have been recorded in this relatively instantaneously deposited event bed samples were not taken for analysis from this interval Radiocarbon 14C dates and calibrated ages for holes U1545A and U1549A in Holes U1545A (Sections U1545A-1H-1 to 5H-7 41 m depth) and U1549A (Sections U1549A-1H-1 to 4H-2 Bacon age-depth model for holes (A) U1545A and (B) U1549A there are indicated Markov Chain MonteCarlo iterations (top left) the distribution of accumulation rates (top middle) and the probability distributions for memory (top right) The lower plot indicates the age-depth model Individual radiocarbon dates are shown in probability density functions of calibrated ages The grey area indicates the uncertainty of the age model with dashed lines indicating 95% confidence intervals sediment accumulation rates are plotted versus age The sedimentation rates from the Holocene in our cores ranged from ∼0.82 mm/yr and 0.41 mm/yr, which agree with Barron et al. (2005), who reported 0.88 mm/yr for the past 10,000 years, and with Teske et al. (2019) which estimated rates from 0.23 mm/yr to 1 mm/yr for the last ∼5,000 years the factors are termed: 1) Gulf of California Water Related to the specific effects of the oxygen concentrations in radiolarians we cannot provide evidence about them; more studies are required with living radiolarians comparing populations dwelling in anoxic and suboxic conditions Factors loadings were plotted through the time and the main changes are described as follows showing the importance of the four radiolarian assemblages (factors) Factor scores of the radiolarian taxa characterizing the four radiolarian assemblages in holes U1545A and U1549A Silicoflagellates (L) Dictyocha fibula var Environmental affinities of the radiolarians and silicoflagellates used in this study to reconstruct the oceanographic changes in the Guaymas Basin its dominant occurrence in this factor suggests the PIW flow strengthened in Hole U1545A during these intervals FIGURE 6. (A) Stratigraphic column of the Hole U1545A showing lithology (Teske et al., 2021b). (B) Factor loadings of the four factors identified from the Q-mode factor analysis and (C) relative abundances of silicoflagellates in Hole U1545A. (D) Stratigraphic column of the Hole U1549A showing lithology (Teske et al., 2021a) (E) Factor loadings of the four factors identified from the Q-mode factor analysis and (F) relative abundances of silicoflagellates in Hole U1549A may indicate the development of local upwelling processes on the western margin of the GoC mainly due to coastally-trapped waves in summer This setting amplified its influence southward modifying the position of the polar and subtropical atmospheric jets and displacing the CCS that enabled the entry of CCW into the gulf FIGURE 7. Polar jet stream position (black arrow) during (A) the Last Glacial Maximum and, (B) the Holocene (Hughes et al., 2013). Climate cell boundaries in the northern hemisphere during (C) the Last Glacial Maximum and (D) the Holocene (Cheshire and Thurow, 2013) Guaymas basin is positioned at 27°N (red square) thoracites have been previously described for Hole U1545A the assemblage suggests the occurrence of the GCW-like water mass in the basin These conditions could be similar to the current cold winter-spring phase in the gulf promoting the intensification of upwellings and mesoscale gyres Factor 1, termed Tropical Surface Water, explains 48% of the total variance (Table 3), and showed its highest values from ∼11,500 to 11,000 and from 8,700 to 133 cal years BP (Figures 6D, E). This factor is represented by the species L. thoracites, by the T. octacantha group, the P. pylonium group, and by L. setosa. Factor scores of these species are 2.87, 2.45, 2.32, and 1.20, respectively (Figure 4) this radiolarian assemblage indicates of TSW into the basin thoracites in this assemblage indicates the occurrence of the GCW in the location of drilling lineata) increased incursion of the PIW into the GB; besides the radiolarian assemblage suggests the occurrence of the GCW in similar conditions as those currently occurring during the winter-spring phase in the GoC davisiana in this factor suggests the incursion of CCW into the GB during extreme-cold conditions when the polar atmospheric cell expanded and amplified its influence southward Silicoflagellates are abundant and well-preserved in sediments from both holes, with 16 species identified in Hole U1545A and 15 species in Hole U1549A. Based on their environmental affinities three species can be used as SST and water masses proxies: Octactis octonaria var. pulchra, O. speculum, and Dictyocha fibula var. messanensis (See Table 4; Figure 5) the climatic scenario proposed for these intervals is inferred as the result of an incursion of the CCW into the GB due to the expansion under the influence of the polar cell and the southward migration of the CCS The presence of this species in the sediments suggested a greater incursion of the TSW into the gulf enhanced by the weakening of NW winds and the strengthening of SE winds as occurs during the current boreal summer The abundance of O. octonaria var. pulchra ranges from 0.3% to 55%, and the average was 27.1%. The highest values of this species were recorded from ∼9,300 to 5,910 cal years BP. Other minor intervals were recognized from ∼15,010 to 14,230, 11,820 to 11,460, 10,920 to 10,390, 5,420 to 4,930, 4,010 to 3,020, 2,630 to 1960, and from 900 to 130 cal years BP (Figure 6F) Its presence in the sediments suggests the above-mentioned environmental conditions in Hole U1545A D. fibula var. messanensis shows an abundance ranging from 0% to 48.8%. The average relative abundance is 23.4%. This species shows three intervals of higher abundance, from ∼11,610 to 11,000, 10,150 to 9,320, and from ∼5,740 to 130 cal years BP (Figure 6F) The increase in the abundance of this species is attributed to a more evident incursion of the TSW into the gulf O. speculum has an abundance ranging of 0%–10.5% and an average of 1.2%. Its presence is almost exclusively restricted to the Pleistocene, which showed its highest values from ∼16,450 to 13,810 cal years BP. Other minor intervals were recognized from ∼12,620 to 12,010, 10,670 to 9,620 cal years BP, and a peak located at ∼6,030 cal years BP (Figure 6F) The presence of this species is probably related to the incursion of the CCW into the gulf resulting from the polar atmospheric cell expansion and the strengthening of the CCS The PDW could not be identified because of the lack of knowledge of the radiolarian living species in deep water environments in GoC and other regions in the Pacific Ocean we consider that the signal of the water masses captured in our records represents the main trends in ocean circulation in the GoC and its relationship with the dynamics of the ETPO and global climate changes pulchra in holes U1545A (continuous line) and U1549A (dashed line) is considered a transition from glacial to interglacial conditions and includes remarkable climatic events such as the Heinrich-1 event the Bølling-Ållerød (B/A) provides insights into changes in hydrographic structure including water masses and circulation patterns during the last 31,000 cal years BP contributing to the understanding of climatic and oceanographic conditions in the GoC Major climatic periods are identified in GB cores: pre-Last Glacial Maximum time (∼31,260–26,500 cal years BP) the Last Glacial Maximum (∼26,500–19,000 cal years BP) the Heinrich-I event (∼19,000–14,900 cal years BP) the Bølling-Ållerød (∼14,900–12,800 cal years BP) the Younger Dryas (∼12,800–11,600 cal years BP) and the Holocene (∼11,600 to present) Short-term events linked to DO cycles are also observed The Pre-Last Glacial Maximum period was characterized by alternation of the CCW and GCW; and the occurrence of an extended PIW The radiolarian assemblage represented by C davisiana revealed the incursion of the CCW into the basin; the assemblage We suggest that these conditions could be related to the amplification of the polar and subtropical jet streams promoting the southern movement of the CCS and the incursion of CCW into the gulf lineata suggests a significant occurrence of the PIW due to more vigorous North Pacific Intermediate Water formation the radiolarian assemblage of surface dwellers such as C as well as the silicoflagellate Octactis speculum supports the incursion of the CCW into the basin particularly from ∼24,750 to 21,490 cal years BP Radiolarian assemblage fluctuations during this period suggested that PIW was less evident from 23,500 to 21,240 cal years BP possibly due to the weakening of NPIW formation At the beginning (∼26,000 cal years BP) and mainly at the end (∼19,000 cal year BP) of LGM which might be related to the formation and expansion of the NPIW indicated by the radiolarian assemblage at the beginning and end of this period could be related to the formation and expansion of the NPIW from 23,500 to 21,240 cal years BP the PIW was less evident in the basin compared to the pre-LGM time suggesting circulation changes influenced by the Pacific Ocean we identified two major climatic conditions beginning with the dominance of GCW-like waters owing to the weakened AMOC and the establishment of the PMOC transporting saline waters northward and enhancing the occurrence of GCW-like conditions in the GB is related to the expanded formation of the NPIW and the occurrence of the CCW These changes may be linked to the North Pacific oceanic circulation changes during the last glacial termination Our records suggest that the Bølling-Ållerød was a period with distinct hydrographic shifts related to the transition from glacial to interglacial conditions Radiolarian assemblages and silicoflagellates suggested the alternated occurrence of three surface waters masses in the GB referring to (1) the TSW as demonstrated by the assemblage of T (2) the GCW revealed by the radiolarian assemblages of L and (3) the episodic incursion of the CCW depicted by the radiolarian assemblage of C auritus australis and the silicoflagellate O These hydrographic conditions could be linked to the ITCZ’s gradual northward migration and the NPH and climatic conditions are likely to be similar to modern ones with a marked seasonality the radiolarian assemblage suggests the dominance of CCW the formation of the GCW in the central GB correlates to colder climatic conditions in the Northern Hemisphere and the strengthening of the CCS the increased ocean-land thermal contrast and the gradual migration to the south of the NPH resulted in the intensification of NW winds and the formation of the GCW The TSW and the GCW alternate in the GB during the Holocene and the modern climatic monsoon regime is identified from ∼7,600 to 1,000 cal years BP From ∼1,000 to 130 cal years BP the occurrence of the GCW suggests the southern latitudinal migration of the ITZC that suggest warm and cold climatic conditions that may be related to transitions between cold stadial (GS) and warmer interstadial (GI) conditions of the Dansgaard-Oeschger (D-O) events (GIs 6 The original contributions presented in the study are included in the article/Supplementary Material further inquiries can be directed to the corresponding author The author(s) declare financial support was received for the research This study was financially supported by the IICEAC Project 418908 UNAM Project Number IN116623 for the partial financial support for this research This research used samples and data from the International Ocean Discovery Program (IODP) and the R/V JOIDES Resolution crew for recovering the cores and for their invaluable assistance during the IODP Expedition 385 Mauricio Velázquez-Aguilar acknowledges the Posgrado en Ciencias del Mar y Limnología and the financial support provided by the Consejo Nacional de Humanidades Ciencias y Tecnologías (CONAHCYT) for the PhD grant no for the detailed review and comments on the manuscript We thank M.Sc Marysol Valdez-Hernández for her kind support of the creation and edition of the figures The authors declare that the research was conducted in the absence of 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This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use distribution or reproduction in other forums is permitted provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited in accordance with accepted academic practice distribution or reproduction is permitted which does not comply with these terms *Correspondence: L. Pérez-Cruz, cGVyZXpjcnV6QGlnZW9maXNpY2EudW5hbS5teA== Disclaimer: All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations Any product that may be evaluated in this article or claim that may be made by its manufacturer is not guaranteed or endorsed by the publisher 94% of researchers rate our articles as excellent or goodLearn more about the work of our research integrity team to safeguard the quality of each article we publish Metrics details Microbes in Guaymas Basin (Gulf of California) hydrothermal sediments thrive on hydrocarbons and sulfur and experience steep fluctuating temperature and chemical gradients The functional capacities of communities inhabiting this dynamic habitat are largely unknown we reconstructed 551 genomes from hydrothermally influenced and nearby cold sediments belonging to 56 phyla (40 uncultured) In contrast to findings from cold hydrocarbon seeps hydrothermal-associated communities are more diverse and archaea dominate over bacteria Genome-based metabolic inferences provide first insights into the ecological niches of these uncultured microbes including methane cycling in new Crenarchaeota and alkane utilization in ANME-1 These communities are shaped by a high biodiversity partitioning among nitrogen and sulfur pathways and redundancy in core carbon-processing pathways The dynamic sediments select for distinctive microbial communities that stand out by expansive biodiversity and open up new physiological perspectives into hydrothermal ecosystem function While single-gene surveys allow us to address the phylogenetic diversity of microbial communities metagenomic analyses provide a connection between diversity and the functional potential encoded within sedimentary communities we still have a limited understanding of the spatial biodiversity and full metabolic potential of microbes inhabiting the basin We selected samples from methane- and sulfate-rich hydrothermal sediments covering a wide thermal range We hypothesize that microbial assemblages from hydrothermal sediments are phylogenetically distinct from those in the surrounding region and host a greater metabolic diversity we sequenced a total of ~4 billion genomic reads from eleven samples (two of which were from cool these data add 22 branches to the tree of life and enabled to us determine the genetic repertoire and metabolic versatility of these extreme hydrothermal communities This enrichment appears to be largely driven by the rich substrate availability by hydrothermal circulation and by inmixing of the electron acceptor sulfate (Supplementary Methods) a greater sampling size would be needed to disentangle the relative contribution of individual factors on community assembly such as temperature we also detected genes from this pathway in candidate phyla including Hydrothermarchaeota and Latescibacteria which might either oxidize acetate or perform acetogenesis making this the first example of an ANME-1 archaeon potentially able to use short-chain alkanes The detection of these unique methyl coenzyme-M reductase genes and pathways suggests that ANME-1 archaea are not limited to methane utilization and potentially able to oxidize alkanes anaerobically suggesting that those might utilize different substrates The most common [NiFe]-hydrogenase was found in ~25% of genomes and belongs to Group 3b that is involved in NADPH oxidation coupled to hydrogen evolution Genes for the dissimilatory reduction of sulfate to sulfide (sat aprAB and dsrAB) were found in few archaea (i.e Archaeoglobales) and several bacteria including Deltaproteobacteria soxCD) showed a restricted phylogenetic distribution and was only located in Epsilonproteobacteria and Gammaproteobacteria While on average ~10% of all genomes contained genes for sulfur and nitrogen cycling complete pathways for these processes were present in only few genomes Number in circles: Number of phylogenetic clusters that encode for individual core metabolic genes at each site fermentation genes were abundant across all sites denitrification genes were more common in cold and shallow samples and mcrA was completely absent from the background samples these findings suggest that the GB genomes are representative of the community as a whole and that they reflect key metabolic differences between the microbial communities present in hydrothermal and background samples Another metabolic feature that could allow for greater ecosystem stability could be metabolic plasticity switching metabolic processes in response to changes in environmental conditions We found indications for such plasticity in several bacterial genomes especially within the Delta- and Gammaproteobacteria that might couple the reduction of sulfur with the oxidation of carbon While we cannot determine which processes are active enhanced genotypic diversity might provide an additional adaptation strategy to variable environmental conditions This theory is consistent with our findings in which we not only observe phylogenetically diverse but also functionally redundant communities metabolic partitioning as well as functional redundancy that we observe appear to be characteristics of microbial communities in these dynamic hydrothermal vent sediments A limitation of the current study that complicates a definite description of the diversity patterns and functional redundancy present in Guaymas sediments is the low sample number and limited number of bins recovered from a subset of samples (i.e 4567_28 and 4488_9); given the limitations of deep-sea sampling different habitat and sediment types are represented unevenly Activity-based analyses of large sample numbers would more rigorously link genetic patterns to their environmental determinants These differences are likely linked to the unique environment in GB sediments characterized by by convective mixing of fluids resulting in variable thermal regimes and admixture of hydrothermal carbon and energy sources Most functional properties were shared widely among different phylogenetic lineages across different sampling sites with a greater functional redundancy of metabolic processes found in hydrothermal sediments One unique functional trait of hydrothermal compared to background sediments was the presence of methane cycling genes among novel lineages including a new deep-branching Crenarchaeota group We propose that the combination of dynamic seep and hydrothermal conditions in Guaymas Basin enhances microbial diversity and sustains a distinctive microbial community whose functional complexity and redundancy reflects the intricate and dynamic geochemical and thermal landscape of this habitat for each of the binning tools a scaffold-to-bin list was prepared and DAS Tool run on each of the eleven scaffold files as follows: DAS_Tool.sh -i Anvio_contig_list.tsv,Metabat_contig_list.tsv,ESOM_contig_list.tsv -l Anvio,Metabat,ESOM -c scaffolds.fasta --write_bins 1 Genomes were only analyzed further if they were more than 50% complete and showed a contamination below 10% Contaminants that were identified based on their phylogenetic placement (wrong taxonomic assignment compared to the average taxonomic assignment of the genes assigned to each bin) GC content (>25% difference compared to the mean of all scaffolds assigned to each bin) or abundance (>25% differences compared to the mean abundance of all scaffolds assigned to each bin) were manually removed from individual genomes This yielded a total of 247 archaea and 304 bacterial genomes To determine the relative abundance of each genome across the elven sequenced sediment samples we mapped the contigs from all binned genomes (i.e. using the “whole MAG”) against the high-quality reads of each individual metagenome (generating eleven sam files) The sam output was sorted and converted to bam as described above and we then used the metabat output which describes the read counts recruited by each contig All analyses were performed in R (version 3.3.3) ~47% of the high-quality metagenomic sequences could be binned with the notable exception of the sample from 4567_28 from which the recovered MAGs only recruited ~18% of reads for an undetermined reason The unaligned nucleotide sequences were concatenated and used as an input to run bwa against all eleven metagenomes to determine their relative abundance across samples normalized by gene length and library size and plotted using the ggplot2 package in R A phylogenetic tree was generated using a maximum likelihood-based approach using RAxML (settings: raxmlHPC-PTHREADS-AVX -T 10 -f a -m GTRGAMMA -N autoMRE -p 12345 -x 12345) 16S rRNA gene sequences were manually checked for contamination in cases with an inconsistent phylogenetic assignment between 16S rRNA gene sequences or the 37 protein-coding marker genes when all assigned proteins on the contig with the 16S rRNA gene showed a different taxonomic assignment (using blastp) compared to the remaining scaffolds of the respective genome A similar phylogenetic approach was taken to phylogenetically characterize other key genes of interest (i.e Genes of interest were identified in GB genomes using KAAS blastp or the HydDB webserver (for details see below) Published reference genes were extracted using the NCBI and Uniprot webservers (McrA ACD) as well as the HydDB webserver (hydrogenases) NmsA in KEGG or a custom blast search were combined in a single analysis K06446 and K09479 were included to build a phylogenetic tree Protein sequences from GB and reference genomes were combined and aligned using muscle (v3.8.31 trimmed using TrimAL and a phylogenetic tree generated using RAxML as described above Protein-coding genes falling on long branches were manually checked using blastp on the NCBI webserver and discarded if the annotation was not hydrogenase acyl-CoA dehydrogenase or glycyl radical enzyme Metabolic reconstructions were done for each individual genome but in several cases the results were summarized for major taxonomic lineages These clusters do not represent a specific taxonomic rank but were chosen to account for both phylogenetic diversity (Crenarchaeota are usually represented at order rank) as well as available genomes (the different phyla of the CPR superphylum were ranked together because they were represented by only few genomes) Genes assigned to core metabolic pathways are summarized in Supplementary Data 10. Hits for key metabolic marker genes found in major taxonomic clusters (Fig. 3) were verified across different databases (KAAS PFAM and TIGRPFAMs) and cross-checked with results from close reference genomes that fell within the same phylogenetic group as the genome of interest to reduce the chance of contamination Genes not found in close reference genomes were further validated with blastp using the NCBI webserver tool If a hit could not be confirmed or if the top phylogenetic hit for whole contig was not consistent with the phylogenetic assignment of the genome Bacterial diversity stabilizes community productivity Explaining microbial genomic diversity in light of evolutionary ecology varved sediments from the Gulf of California Intrusion of basaltic sills into highly porous sediments Sedimentary geochemistry of hydrothermal vents in Guaymas Basin Hydrothermal petroleum in mineralized mounds at the seabed of Guaymas Basin Microbial communities in methane- and short chain alkane-rich hydrothermal sediments of Guaymas Basin Carbon release by off-axis magmatism in a young sedimented spreading centre Anaerobic oxidation of methane at different temperature regimes in Guaymas Basin hydrothermal sediments and microbial mats: Complex seafloor expressions of subsurface hydrothermal circulation Mats of giant sulphur bacteria on deep-sea sediments due to fluctuating hydrothermal flow Genomic insights into potential interdependencies in microbial hydrocarbon and nutrient cycling in hydrothermal sediments Anaerobic oxidation of methane: Progress with an unknown process Microbial diversity of hydrothermal sediments in the Guaymas Basin: Evidence for anaerobic methanotrophic communities Microbial habitat connectivity across spatial scales and hydrothermal temperature gradients at Guaymas Basin Comparative study of Guaymas Basin microbiomes: Cold seeps vs Spatial heterogeneity and underlying geochemistry of phylogenetically diverse orange and white Beggiatoa mats in Guaymas Basin hydrothermal sediments Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea The growing tree of Archaea: new perspectives on their diversity a new lens for viewing the microbial world RubisCO of a nucleoside pathway known from Archaea is found in diverse uncultivated phyla in bacteria Unusual respiratory capacity and nitrogen metabolism in a Parcubacterium (OD1) of the Candidate Phyla Radiation Decarboxylating and nondecarboxylating glutaryl-Coenzyme A dehydrogenases in the aromatic Metabolism of obligately anaerobic bacteria Glycyl radical activating enzymes: Structure Microbial conversion of choline to trimethylamine requires a glycyl radical enzyme Genomic and metagenomic surveys of hydrogenase distribution indicate H2 is a widely utilised energy source for microbial growth and survival Schutte, C. A. et al. Filamentous giant Beggiatoaceae from Guaymas Basin are capable of both denitrification and dissimilatory nitrate reduction to ammonium (DNRA). Appl. Environ. Microbiol. 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K., Al-Bassam, M. M. & Zengler, K. Networks of energetic and metabolic interactions define dynamics in microbial communities. Proc. Natl Acad. Sci. 2015, 06034, https://doi.org/10.1073/pnas.1506034112 (2015) Methane metabolism in the archaeal phylum Bathyarchaeota revealed by genome-centric metagenomics MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph Community-wide analysis of microbial genome sequence signatures Anvi’o: an advanced analysis and visualization platform for ‘omics data Li, H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. Preprint at https://arxiv.org/abs/1303.3997 (2013) The sequence alignment/map format and SAMtools an efficient tool for accurately reconstructing single genomes from complex microbial communities Recovery of genomes from metagenomes via a dereplication The split-apply-combine strategy for data analysis PhyloSift: phylogenetic analysis of genomes and metagenomes trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB KAAS: an automatic genome annotation and pathway reconstruction server Callaghan, A. V. & Wawrik, B. AnHyDeg: a curated database of anaerobic hydrocarbon degradation genes. https://doi.org/10.5281/zenodo.61278 (2016) Twenty years of the MEROPS database of proteolytic enzymes Gapped BLAST and PSI-BLAST: a new generation of protein database search programs HydDB: A web tool for hydrogenase classification and analysis dbCAN: a web resource for automated carbohydrate-active enzyme annotation Download references Seitz for detailed comments on the manuscript Department of Energy Joint Genome Institute is supported by the Office of Science of the U.S This work was funded by a Sloan Foundation Ocean Sciences fellowship (FG-2016-6301) and National Science Foundation DEB: Systematics and Biodiversity Sciences (grant number 1753661) provided to B.J.B and Guaymas Basin fieldwork was supported by U.S National Science Foundation grants OCE-0647633 and OCE-1357238 and were involved in writing the manuscript reconstructed the genomes and performed the analyses Publisher’s note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations Download citation DOI: https://doi.org/10.1038/s41467-018-07418-0 a shareable link is not currently available for this article Communications Earth & Environment (2024) Sign up for the Nature Briefing newsletter — what matters in science Metrics details with active methane venting and seep fauna exist in response to magma emplacement into sediments These sites evolve over thousands of years as magma freezes into doleritic sills and the system cools Although several cool sites resembling cold seeps have been characterized the hydrothermally active stage of an off-axis site was lacking good examples we present a multidisciplinary characterization of Ringvent an ~1 km wide circular mound where hydrothermal activity persists ~28 km northwest of the spreading center Ringvent provides a new type of intermediate-stage hydrothermal system where off-axis hydrothermal activity has attenuated since its formation hydrothermal biota coexisting with seep fauna and porewater biogeochemical signatures indicative of hydrothermal circulation such sites are hard to find and characterize but they provide critical missing links to understand the complex evolution of hydrothermal systems resolving and mapping the extent of hydrothermalism versus cold seepage in the greater Guaymas Basin system requires site-specific studies Seismic and bathymetric survey of Ringvent (A) The shallow subsurface seismic profile obtained by AUV Sentry shows that continuously visible sediment stratification is obliterated in dome-shaped whiteout zones that represent gas intrusions; flares of gas and fluid flow emerge from the tops of these gas intrusions The profile is crossing Ringvent from the Northwest [A -186.140640/27.5108089] to the Southeast [A’; -186.126694/27.5027676] (B) Contour-shaded Sentry bathymetry of Ringvent A donut-shaped topographical high characterized by abundant tubeworm colonies and carbonate outcrops and incised by gullies and pockmark-like depressions The seafloor is gradually rising westwards In-situ observations of seafloor minerals and fauna. (A) Tubeworm colonies resembling Lamellibrachia occurring on the Ringvent mound (ORP sampling site, Alvin dive 4864). (B) A single sulfur-oxidizing Riftia tubeworm growing on a small mat-covered mound that provides warm fluids of ca. 10–20 °C (Table 2) visible as shimmering optical distortions in the warm water plume (near ORP site (C) Lace-like authigenic minerals emerging from sediment cover at incised gully (near heatflow site 5 A and E are photomicrographs of thin sections; B-D and F are SEM microphotographs; analyses were performed by C G-I) Selected images of subsurface silicate Silicate nodule collected at 2.35 m sediment depth in core P11 SEM/EDX microphotographs of the nodule surface showing bead-like formations coated with silica at intermediate and (I) at high magnification with barite crystal rosettes on the silica matrix These similarities suggest that the silica-rich deposits of Ringvent form by diffuse flow and conductive cooling of silica-rich hydrothermal solutions These findings indicate that anaerobic methane oxidation occurs locally in the silica-dominated matrix of Ringvent and imply the presence of methane and methane-oxidizing microorganisms Seawater inmixing and ventilation resolve the apparent contradiction that decreasing methane concentrations towards the surface are not accompanied by carbon-isotopic signatures of porewater methane oxidation and is consistent with methane removal predominantly by seawater inmixing and dilution (A) Archaeal and (B) bacterial community summaries for all lineages with >2% sequence abundance based on 16S rRNA gene amplicons recovered from piston-cored sediments 2.02–2.07 mbsf; Core P06_3 and P06_4 at 2.25–2.3 and 3.75–3.80 mbsf; core P10_2 and P10_4 at 1.24–1.29 and 3.73–3.78 mbsf; Core P11_2 and P11_5 at 1.15–1.20 and 4.63–4.68 mbsf; Core P12_4 at 3.73–3.78 mbsf; Core P13_4 Taxonomic groups are generally shown at the class level sometimes at the order (ANME-1) or family level (Phycisphaerae Rarefaction curves for (C) archaeal and (D) bacterial 16S rRNA amplicons for the same samples and sequence datasets indicating methane-oxidizing microbial populations in the currently active Ringvent mound Subsurface hydrothermal flow is driven by a gradually cooling but still-active subsurface sill that generates patterns of hydrothermal venting and recharge Sediments rich in sulfate are indicated in red and sediments with coexisting methane and sulfate are marked in purple The inset photo shows the porous mineral deposits of the Ringvent mound hydrothermal conditions with potential for ongoing silica deposition are found on the ring mound in localized hotspots sometimes within small depressions and gullies that may have originated during episodes of increased hydrothermal activity methane-imprinted nodules persist in core P11 until ca and indicate that methane flux and methane-derived carbonate precipitation have slowed down gradually These timelines imply that carbonate nodules should have formed at former sediment surfaces where sulfate would have been available and deposition of methane-imprinted carbonates as seen in the sediment column of core P11 species richness in this core has not fully recovered and appears impoverished in particular by comparison to core P10 as depth and proximity to the heat source increase Deep drilling at Ringvent should constrain the patterns of hydrothermal circulation and recharge and allow the development of a well-constrained chronology for hydrothermal activity A deep-sea drilling cruise to Guaymas Basin (IODP Expedition 385) is targeting Ringvent to comprehensively investigate the subsurface foundations for off-axis hydrothermal venting in Guaymas Basin During the R/V Atlantis survey in December 2016, thermal profiles were measured in the surficial sediment using Alvin’s 1-meter heatflow probe (https://ndsf.whoi.edu/alvin/using-alvin/sampling-equipment/) that contains thermal sensors every 20 cm starting 10 cm under the attached plastic disk that limits probe penetration and rests on the seafloor once the probe was inserted 5 to 10 minutes until the temperature readings had stabilized Seafloor mineral samples and shallow sediment push cores were collected during Alvin dives 4864 and 4865 in December 2016 Ringvent observations by Sentry were made during dives 410 and 411 Small amounts of gas were cryo-concentrated before isotopic measurements Values are reported in the per mil (‰) notation relative to Vienna Pee Dee Belemnite (VPDB) The δ13C values of all the acidified samples used for radiocarbon analyses were approximately −20 to −22‰ as expected for marine primary producers-derived organic matter Samples selected for carbonate isotope analyses were freeze-dried and roasted under vacuum to eliminate organic matter Isotope analyses was performed on ~500 µg of sediment using a Kiel devise coupled with a Thermo MAT 253 gas ratio mass spectrometer at the University of California Reproducibility of in-house standards is 0.07‰ for δ18O and 0.03‰ for δ13C Phase identification was made with PDF-2 and ICSD databases Mineral phases from core P11 were analyzed separately with a Rigaku Smart Lab XRD using 0.003° resolution 5°/minute using a ICDD PDF4+ 2019 database (Ivano Aiello Branching patterns were checked with 1000 bootstrap reruns All partial 16S rRNA sequence data obtained at MBL are publically available on the NCBI SRA repository (BioProject: PRJNA420722; SRA experiment accession entrees SRX3440273-SRX3440290) the partial 16S rRNA sequences selected for phylogeny construction are included in Supplementary Materials The methyl coenzyme M reductase alpha subunit gene sequences are deposited at GenBank under accession numbers MH931022 to MH931084 Geochemical data are available at the BCO-DCO under these reference links: Porewater methane data: https://www.bco-dmo.org/dataset/661750/data Porewater sulfate data: https://www.bco-dmo.org/dataset/661775/data Porewater DIC data: https://www.bco-dmo.org/dataset/661658/data Porewater sulfide: https://www.bco-dmo.org/dataset/661808/data Transition from hydrothermal vents to cold seeps records timing of carbon release in the Guaymas Basin chimneys and microbial mats: complex seafloor expressions of subsurface hydrothermal circulation Evidence for two distinct hydrothermal systems in the Guaymas Basin Initial Reports of the Deep Sea Drilling Project Rifting under steam – How magmatism triggers methane venting from sedimentary basins Carbon release by off- axis magmatism in a young sedimented spreading centre Release of methane from a volcanic basin as a mechanism for initial Eocene global warming Hydrothermal venting of greenhouse gases triggering Early Jurassic global warming How contact metamorphism can trigger global climate changes: Modeling gas generation around igneous sills in sedimentary basins Modeling fluid flow in sedimentary basins with sill intrusions: Implications for hydrothermal venting and climate change Chemical speciation drives hydrothermal vent ecology Linking hydrothermal geochemistry to organismal physiology: Physiological versatility in Riftia from sedimented and basalt-hosted vents Silica-carbonate stromatolites related to coastal hydrothermal venting in Bahía Concepción and fluid-inclusion microthermometry of seafloor hydrothermal deposits in the southern trough of Guaymas Basin Authigenic carbon entombed in methane-soaked sediments from the northeastern transform margin of the Guaymas Basin Gas-seep related carbonate and barite authigenic mineralization in the northern Gulf of California Redox conditions and authigenic mineralization related to cold seeps in central Guaymas Basin Oxygen and carbon isotope fractionation in biogenic aragonite: Temperature effects Deglacial climatic oscillations in the Gulf of California Oceanographic variability in the southern Gulf of California over the past 400 years: Evidence from faunal and isotopic records from planktic foraminifera Palaeoceanographic history of the Guaymas Basin Late quaternary climatic and oceanographic changes in the Northeast Pacific as recorded by dinoflagellate cysts from Guaymas Basin Evidence of active methanogen communities in shallow sediments of the Sonora Margin cold seeps Variation in CH4 and CO2 carbon-isotope composition in the sedimentary section in the Guaymas Basin Stable isotopic analyses of interstitial gases in quaternary sediments from the Gulf of California In Initial Reports of the Deep Sea Drilling Project Sources and hydrothermal alteration of organic matter in quaternary sediments: a synthesis of studies from the central Gulf of California Light hydrocarbon gases in Guaymas Basin hydrothermal fluids: thermogenic versus abiogenic origin Genomic insights into potential interdependencies in microbial hydrocarbon and nutrient cycling in hydrothermal sediment communities Microbial communities in methane and short alkane-rich hydrothermal sediments of Guaymas Basin The Prokaryotes – Deltaproteobacteria and Epsilonproteobacteria Identification of the dominant sulfate-reducing bacterial partner of anaerobic methanotrophs of the ANME-2c clade Single-cell genomics reveals a diverse metabolic potential of uncultivated Desulfatiglans-related Deltaproteobacteria widely distributed in marine sediment isolated from a methanogenic paraffin-degrading enrichment culture and emended description of the family Methane-cycling archaeal diversity in hydrothermal sediment investigated by general and group-specific functional gene and 16S rRNA gene PCR primers and temporal relations of hydrothermal sulfide-sulfate-silica chimneys at the northern Cleft segment Hydrothermal silica chimney fields in the Galapagos spreading center at 86°W Sulfide-impregnated and pure silica precipitates of hydrothermal origin from the Center Indian Ocean Petrology of hydrothermal mineralization: a vertical section through the TAG mound A model for growth of steep-sided vent structures on the Endeavour Segment of the Juan de Fuca Ridge: Results of a petrologic and geochemical study Lloyd, K. G. et al. Spatial structure and activity of sedimentary microbial communities underlying a Beggiatoa spp. mat in a Gulf of Mexico hydrocarbon seep. PLoS ONE 5(1), e8738, https://doi.org/10.1371/journal.pone.0008738 (2010) Spectrophotometric determination of hydrogen sulfide in natural waters Sources of mud volcano fluids in the Gulf of Cadiz – indications for hydrothermal imprint Radiocarbon evidence that carbon from the Deepwater Horizon spill entered the planktonic food web of the Gulf of Mexico A simple headspace equilibration method for measuring dissolved methane Seasonal variation in methane oxidation in a landfill cover soil as determined by an in situ stable isotope technique On the isotopic chemistry of carbonates and a paleotemperature scale Comparison of brush and biopsy sampling methods of the ileal pouch for assessment of mucosa-associated microbiota of human subjects Hydrogen limitation and syntrophic growth among natural assemblages of thermophilic methanogens at deep-sea hydrothermal vents community-supported software for describing and comparing microbial communities Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform UCHIME improves sensitivity and speed of chimera detection R package version 2.2-1 (2015); [accessed 2018 June 25] Phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data QIIME allows analysis of high-throughput community sequencing data Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB Phylogenetic Analysis Using Parsimony (and Other Methods) MEGA4: Molecular evolutionary genetics analysis (MEGA) Software version 4.0 Download references This work was funded by NSF OCE grant 1449604 “Rapid Proposal: Guaymas Basin site survey cruise for IODP proposal 833” to Andreas Teske; NSF C-DEBI grant “Characterizing subseafloor life and environments in Guaymas Basin” to Andreas Teske Ivano Aiello and Ana Christina Ravelo; and collaborative NSF Biological Oceanography grants 1357238 and 1357360 “Collaborative Research: Microbial carbon cycling and its interaction with sulfur and nitrogen transformations in Guaymas Basin hydrothermal sediments” to Andreas Teske and Samantha B We thank the Alvin and Sentry teams for a stellar performance during Guaymas Basin cruise AT37-06 and the science crew of RV El Puma for their dedication and “can-do” collaborative spirit during the 2014 Guaymas coring campaign Sequencing of bacterial and archaeal communities was supported by the Deep Carbon Observatory and performed at the Marine Biological Laboratory in Woods Hole GEOMAR Helmholtz Centre for Ocean Research Adam Soule developed the concept for this manuscript Andreas Teske headed the R/V Atlantis cruise in December 2016 collected thermal profiles and mineral samples at Ringvent compiled the biological seafloor observations and performed the phylogenetic analyses of partial 16S rRNA gene sequences Daniel Lizarralde analyzed the Sentry subbottom chirp files Adam Soule compiled the detailed Sentry bathymetry Andreas Teske and Ryan Sibert measured the thermal sediment gradients during Alvin dives 4864 and 4865 Joye co-organized the 2016 Atlantis cruise Ivano Aiello and Carlos Mortera (Chief scientist) sailed with R/V El Puma in October 2014 and collected piston cores for geochemistry sedimentology and DNA sampling at Ringvent Porewater geochemical analyses were performed by Luke McKay and Tiffany Turner for sulfide Christian Hensen and Benjamin Brunner for sulfate Porewater sulfide from Alvin push cores was determined by Christopher R Solid phase carbonate analyses and 14C dating of sediments were performed by Ana Christina Ravelo Carles Canet and Fernando Núñez-Useche; silica minerals were analyzed by Carles Canet and initial community characterizations based on the VAMPS dataset were performed by Andrew Buckley Dylan White amplified the mcrA genes and constructed the mcrA gene phylogeny Ramirez performed sequence-based microbial community characterizations and comparisons Andreas Teske prepared the 16S rRNA gene sequence alignments and phylogenetic trees and wrote the manuscript with input from all authors Download citation DOI: https://doi.org/10.1038/s41598-019-50200-5 Sign up for the Nature Briefing: Microbiology newsletter — what matters in microbiology research Metrics details Hydrothermal sediments contain large numbers of uncultured heterotrophic microbial lineages we amended Guaymas Basin sediments with proteins nucleic acids or lipids under different redox conditions and cultivated heterotrophic thermophiles with the genomic potential for macromolecule degradation We reconstructed 20 metagenome-assembled genomes (MAGs) of uncultured lineages affiliating with known archaeal and bacterial phyla including endospore-forming Bacilli and candidate phylum Marinisomatota One Marinisomatota MAG had 35 different glycoside hydrolases often in multiple copies This population has the potential to degrade a broad spectrum of polysaccharides including chitin We also describe thermophiles affiliating with the genera Thermosyntropha and Kosmotoga with the capability to make a living on nucleic acids Several populations seemed to lack extracellular enzyme machinery and thus likely scavenged oligo- or monomers (e.g. MAGs affiliating with Archaeoglobus) or metabolic products like hydrogen (e.g. MAGs affiliating with Thermodesulfobacterium or Desulforudaceae) The growth of methanogens or the production of methane was not observed in any condition indicating that the tested macromolecules are not degraded into substrates for methanogenesis in hydrothermal sediments and genomes of microorganisms that actively degrade abundant necromass macromolecules under oxic These findings improve our understanding of the carbon flow across trophic levels and indicate how primary produced biomass sustains complex and productive ecosystems Identifying the microorganisms and enzymes involved in the degradation of macromolecules in hydrothermal sediments is thus relevant for our understanding of biogeochemical cycling and ecosystem functioning in deep-sea environments A Core 4862-8 was recovered from hot hydrothermal sediments covered by an orange Beggiatoa mat and characterized by a steep thermal gradient that reached up to 146 °C in 30 cm below seafloor (cmbsf) B Core 4871-20 was recovered from temperate sediments characterized by a light-gray patch of sulfur deposits and infaunal worms and a moderate thermal gradient that reached ca C Enrichment cultures from slurries of cores 4862-8 and 4871-20 were supplemented with four types of carbon sources and incubated under oxic sulfate-amended and fermentative conditions D Timeline of data collection during the period of incubation All enrichment cultures were incubated at 60 °C for 4 weeks Hydrogen and methane concentrations of the anoxic enrichments were measured weekly using an SRI 310C gas chromatograph with thermal conductivity detector and molecular sieve column (see also Supplementary Information) After each measurement the headspace was purged with Argon to exclude product inhibition by the produced hydrogen an increase in hydrogen from one week to another does not only represent an increase in the amount of hydrogen Cells were enumerated by direct microscopic counts from the cultures during the first and third week of incubation the paraformaldehyde fixed cells were sonicated filtered onto a polycarbonate filter (0.2 µm pore size) embedded in Citifluor:Vectashield (4:1) and counted using 20 grids (100 × 100 µm) per sample (see also Supplementary Information) Total nucleic acids were extracted from all 48 enrichments with a modified protocol based on Zhou et al. [33] we treated 5 ml of sample using chemical (extraction buffer without CTAB) physical (3× freeze thaw) and enzymatic steps (overnight at 37 °C in lysozyme solution) for extraction of the DNA Extraction blanks were included to assess potential laboratory contamination during extraction DNA concentrations were measured fluorometrically using a Qubit 2.0 fluorometer (Thermo Fisher Scientific We classified the metagenome-assembled genomes (MAGs) as potential degraders of the carbon substrates based on their presence in enrichment cultures amended with the particular macromolecule and the presence of enzymes involved in extracellular cleavage and intracellular degradation of the particular macromolecule in their genome (Supplementary Information) methane and hydrogen production was measured using gas chromatography and growth was estimated using cell counts Hydrogen was measured weekly in sulfate-reducing and fermentative anoxic cultures that were supplemented with proteins (PRO) or polysaccharides (POL) having a temperate or a hot sediment as inoculum hence a straight line represents constant production and increasing line means increasing production of hydrogen per time B non-metric multidimensional scaling (NMDS) analyses (95% confidence ellipse) and C relative sequence abundance of the most abundant bacterial clades in the temperate and hot sediment used as inocula and in enrichment cultures supplemented with proteins (PRO) lipids (LIP) or polysaccharides (POL) under oxic sulfate-reducing or fermentative (no added electron acceptor) conditions after four weeks of incubation The used inoculum is indicated at the top of the graph Relative sequence abundances are based on 16S rRNA V4/V5 gene amplicons Culture conditions enriching MAGs are shown. Frequently, different enrichment conditions (carbon sources and redox conditions) selected for the same MAG, as determined by mapping the sequences of each MAG to the metagenomes of each cultivation regime. (Left) Guaymas Basin enrichment cultures supplemented with proteins (blue) lipids (purple) or polysaccharides (orange) under oxic sulfate-reducing or fermentative conditions (Right) Environmental metagenomes from Guaymas Basin The abundance estimates are expressed as contigs per million reads (CPM) calculated with metaWRAP’s Quant bins module Quant bins uses Salmon to align reads from each sample to the bins producing coverage values for each contig in the same manner as transcripts per million (TPM) The abundance of each MAG in each sample is calculated by taking the length-weighted average of the MAG’s contig coverage Main culture conditions enriching MAGs are shown: proteins (blue), nucleic acids (pink), lipids (purple) or polysaccharides (orange) under oxic (triangle), sulfate-reducing (square) or fermentative (circle) conditions. A complete list of the annotations is reported in Supplementary Data 2 (peptidases) and 3 (CAZymes). Shown are each MAGs major extracellular enzymes and transporters necessary to make a living on protein (blue) Extracellular enzymes are depicted close to the MAG in which they occur Arrows represent processes that each MAG is capable of while dotted arrows show potential flow of monomers/oligomers provided by other MAGs Despite lacking the extracellular nucleases and CAZymes GB067 was also abundant in the nucleic acid and polysaccharide enrichments likely because it contained the necessary transporters and catabolic pathways to scavenge monomers Transporters that occur in only one of the population genomes are shown in colored font ABC-SP and Agl were only present in MAG GB067 The MAGs also encoded 6 (1) polysaccharide lyases and CAZymes belonging to 35 (21) different glycoside hydrolase families which comprise enzymes for the degradation of all seven provided polysaccharides including alginate The Marinisomatota MAGs lacked most of the common sugar transporters that were found in the other populations yet contained many genes annotated as TonB proteins (K03832) and TonB-dependent receptors A complete list of the annotations is reported in Supplementary Data 2 Spore-forming lineages were found in oxic (Bacilli) and anoxic conditions (Moorellia and Desulfotomaculia) or novel metabolisms could also explain this gap in knowledge and merit further investigation The finding that methane was not produced during thermophilic degradation of biomass constituents thus merits further investigation and if confirmed has implications for the deep-sea methane cycle Biomass carbon that was assimilated using subsurface-derived methane at hydrothermal sediments may not be converted back into methane The heterotrophic populations enriched in our study showed the potential to consume energy-rich complex carbon compounds including proteins These populations can mineralize the organic matter from primary production in overlying waters and from local chemosynthesis in hydrothermal sediments macromolecule-degrading thermophiles apparently occur more broadly in hydrothermal systems worldwide and are not limited to sediments but could thrive in hydrothermal chimneys or in surface-attached biofilms The degradation of primary produced biomass or of necromass by uncultured heterotrophs may be a widespread process relevant for our understanding of the diversity and carbon cycling in marine ecosystems Future studies are needed to characterize the abundance and activity of uncultured macromolecule degraders at cold seeps and hydrothermal vents to further improve our understanding of carbon exchanges between the lithosphere and biosphere All sequence data is available at NCBI under BioProject ID PRJNA635695. 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organic matter: a thermodynamic analysis Transient exposure to oxygen or nitrate reveals ecophysiology of fermentative and sulfate-reducing benthic microbial populations represents a novel group of hyperthermophilic methanogens Diversity of methane-cycling archaea in hydrothermal sediment investigated by general and group-specific PCR primers and temperature on methane production in surface sediments of the Gulf of Mexico Methanogen diversity evidenced by molecular characterization of methyl coenzyme M reductase A (mcrA) genes in hydrothermal sediments of the Guaymas Basin A large-scale evaluation of algorithms to calculate average nucleotide identity Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes International Journal of Systematic and Evolutionary Microbiology 2014;64(Pt_2):346–51 Bypassing Cultivation To Identify Bacterial Species Download references We are grateful to the captain and crew of the R/V Atlantis AT37-06 as well as the crew of the human occupied vehicle Alvin for their tireless support Sampling at Guaymas Basin was supported by NSF (OCE-1357238) We thank Gunter Wegener and Barbara McGregor for help with onboard research activities We thank Michael Nightingale and Bernhard Meyer for advice concerning geochemical measurements We also thank Aleksey Morozov and Nicole Robichaud at the W Keck Ecological and Evolutionary Genetics Facility of the Marine Biological Laboratory (MBL) for sequence processing We thank Richard Fox and Anna Shipunova for computing resources assistance provided by the MBL Bay Paul Center and Bhavya Papudeshi and Miguel Desmarais for bioinformatics analyses assistance We appreciate the laboratories that collected and analyzed the data that allow our MAG comparisons Present address: Barnstable County Department of Health and Environment Present address: Multiphase Chemistry Department Isabella Hrabe de Angelis & Marc Strous and wrote the manuscript with input from all co-authors MAB processed metagenomes metabolic annotations (DRAM) KCW processed metagenomes metabolic annotations (DRAM) MS provided chemicals and helped design the study performed headspace measurements and analyzed data Download citation DOI: https://doi.org/10.1038/s41396-021-01026-5 Metrics details Deep marine sediments (>1mbsf) harbor ~26% of microbial biomass and are the largest reservoir of methane on Earth the deep subsurface biosphere and controls on its contribution to methane production remain underexplored we use a multidisciplinary approach to examine methanogenesis in sediments (down to 295 mbsf) from sites with varying degrees of thermal alteration (none current) at Guaymas Basin (Gulf of California) for the first time Traditional (13C/12C and D/H) and multiply substituted (13CH3D and 12CH2D2) methane isotope measurements reveal significant proportions of microbial methane at all sites with the largest signal at the site with past alteration relative microbial methane decreases at differing rates between sites Gibbs energy calculations confirm methanogenesis is exergonic in Guaymas sediments with methylotrophic pathways consistently yielding more energy than the canonical hydrogenotrophic and acetoclastic pathways metagenomic sequencing and cultivation attempts indicate that methanogens are present in low abundance We find only one methyl-coenzyme M (mcrA) sequence within the entire sequencing dataset we identify a wide diversity of methyltransferases (mtaB but only a few sequences phylogenetically cluster with methylotrophic methanogens Our results suggest that the microbial methane in the Guaymas subsurface was produced over geologic time by relatively small methanogen populations which have been variably influenced by thermal sediment alteration Higher resolution metagenomic sampling may clarify the modern methanogen community This study highlights the importance of using a multidisciplinary approach to capture microbial influences in dynamic deep subsurface settings like Guaymas Basin methanogens and their contribution to methane production remain understudied This is in-part because these sediments are hard to access and often poorly characterized precluding both laboratory and theoretical studies of the in situ microbial communities A Bathymetry and geographical location of Guaymas Basin The three sites of interest are indicated by circles: blue (U1545 B Artistic interpretation of hydrothermal mobilization of buried organic carbon where magmatic sills intrude into the sediment C Downcore geochemical profiles and depths from which samples for metagenomic sulfate and sulfide porewater concentrations and the black lines depict temperature (Teske When triangles are: 1) upside down they indicate Sample set 1 of metagenomic samples (see methods for details) and 2) dark orange they indicate samples from hole C/D *Note that values of methane concentration at U1545 and U1546 are multiplied by 10 The shallowest methane peak at U1547 (~115 mbsf) is not easily seen because of the high concentration Gibbs energies (ΔGr) of the nine methanogenic catabolisms (reactions 1–9) listed below were calculated using  in situ physicochemical data (e.g. species activities) collected down the sediment column of each site: Since we assess several disproportionation reactions (e.g values of ∆Gr are reported in units of kJ/mol-carbon-transferred to allow for standardized energetic comparisons To fully distinguish ions of 13CH3D from 12CH2D2 from each other and their respective interferences the Panorama was operated at a mass resolving power ≥40,000 Sample and standard bellows were adjusted to match ion current intensities (ranging from ~2–3 × 10−10 amps) in two stages One centers on 13CH3D+ to simultaneously measure values of 13CH4+/12CH4+ and 13CH3D+/12CH4+ for up to 20 blocks of sample vs The second centers on 12CH2D2+ to simultaneously determine values of 12CH3D+/12CH4 and 12CH2D2+/12CH4 for up to 40 blocks of sample vs The solid lines represent average ΔGr values and the shaded envelopes around them refer to the possible range of ΔGr for that reaction based on a range of substrate concentrations (see Supplementary Table 2) The dashed lines above 50 mbsf indicate methane concentrations were below the detection limit and an activity of 10−7 was used in the calculations The vertical dashed black lines refer to ΔGr = 0 and the grey blocks represent the sulfate-methane transition zone *No ranges for the Gibbs energies of hydrogenotrophic methanogenesis are shown because in situ measurements of CO2 and H2 were used rather than a range of substrate concentrations (see methods) The phylogenies were constructed using IQ-TREE V6 LG+F+R10 and LG+F+I+I+R5s were selected for mcrA using the Bayesian Information Criterion (BIC) Bootstrap values were calculated using non-parametric bootstrapping with 1000 replicates represented by purple circles A Traditional (δ13C vs. δD), (B) multiply substituted (13CH3D vs. 12CH2D2) isotopic measurements and associated errors, C Bernard plot (δ13C vs. C1/(C2 + C3) of methane samples taken from the depths indicated in Fig. 2 purple and grey polygons in each panel refer to regions in isotopic and chemical space that are indicative of biotic thermogenic (LMT late maturity thermogenic or abiotic sources (SA serpentinization abiotic The solid grey line in (C) represents the equilibrium distribution of the indicated methane isotopologues from 0–1000 °C Measurement error is indicated by the error bars around each point See the legend for the meaning of samples shapes Neither cell presence/growth nor methane production were detected in any of the enrichments throughout the multi-year period we herein collectively refer to thermogenic and abiotic sources of methane as “non-microbial” we only discuss the partitioning of methane sources below the SMTZ of each site in what we will refer to as the methanogenic zone (MZ) as low methane concentrations did not permit isotopic measurements in shallower sediment a strong non-microbial signal is present at relatively shallow depths Although sill-induced sediment disturbance was not found at U1545 deep sill at 540 mbsf could be a source of the non-microbial methane non-microbial methane could have diffused laterally from the deeply emplaced sill of the neighboring U1546 The average PMM of each measured sample is represented by black dots with error bars indicating the full range of possible PMM The dashed black line is an extrapolation of the patterns seen from the measured samples The red line is the concentration of methane in mM as a function of depth much of the microbial methane at U1546 may have been produced by previous generations of methanogens We posit that while the number of methanogenic cells at U1547 may be low their per-cell activity may be quite elevated the microbial methane signal quickly depletes likely due to strong inputs of sill-produced methane from below the proximity of the MZ to the sill at this site appears detrimental to the methanogen community Equilibrated isotopologue values in the shallow part of the MZ corroborate this microbial methane seems to be a significant proportion of the overall methane at all three sites with evidence that the methanogen community at U1546 is (or was) the most active microbial methane at U1545 and U1547 has isotopologue values near-equilibrium while values out of equilibrium are observed at U1546 It would follow that microbial methane production at U1545 and U1547 would result from low-energy catabolisms (e.g. where Reactions 4 and 9 are methylotrophic pathways; while at U1546 methane is produced from the higher energy methylotrophic catabolic suite (Reactions 5–8) with a spotlight on methylotrophyic mathanogenesis through metagenomic sequencing and cultivation attempts Further investigation is needed to identify these lineages and to determine if they are actively competing with methanogens for methylated compounds where most microbial methane appears to have accumulated only two depths below the SMTZ were sampled Due to the steep thermal gradient at U1547 cell densities dropped off more quickly and sequencing was only possible above the SMTZ the SMTZ is located at depths where cell densities are low and little DNA can be extracted further limiting accessibility to DNA from the methanogenic zone or they can be understood as evidence that methanogens are part of the rare biosphere in the Guaymas Basin subsurface Multiply substituted methane isotope measurements indeed suggest the microbial methane at U1546 was produced in a more energy-rich environment and through pathways with higher Gibbs energy yields than at U1545 or U1547 While isotopic evidence of microbial methane remains hidden above the SMTZ Gibbs energy calculations reveal various methanogenic reactions are exergonic throughout the entire sediment columns of the three sites with methylotrophic methanogenesis pathways yielding the most energy The identification of mtaB and mttB sequences that are phylogenetically related to methanogens also supports the potential dominance of methylotrophic type methanogenesis particularly above the SMTZ; suggesting methanogens may be even more widespread in marine sediments than traditionally thought metagenomic analysis and cultivation attempts yield little evidence of methanogens suggesting they do not represent a major proportion of the overall microbial community at Guaymas Better DNA extraction techniques and higher sampling resolution may reveal more about this deep and rare biosphere genomic and cultivation-based evidence of methanogens in subsurface Guaymas may remain hidden because these approaches only capture the currently active microbial community while thermodynamics and isotopic measurements inform on methane accumulation throughout geologic time Through our multidisciplinary approach we conclude low abundance methanogenic communities have been active in deep sediments over geologic time with variable influences from thermal sediment alteration leading to the accumulation of the observed microbial methane in the deep subsurface sediments of Guaymas Basin Methanogens maintain their crucial ecological role even in dynamic sediment environments such as Guaymas Basin where they are presented with obstacles such as thermal stressors The metagenomes generated during and analysed during the current study are available in the National Center for Biotechnology Information (NCBI) Genbank database under BioProject PRJNA909197 with accession numbers SRR22580929-SRR22580947 and SRR25383461- SRR25383464 while metagenome assembled genomes (MAGs) were generated and searched for methanogens they are not discussed in this study and will instead be reported on in upcoming publications from IODP 385 The biomass and biodiversity of the continental subsurface population sizes and doubling/replacement times of microorganisms in natural settings Exploring deep microbial life in coal-bearing sediment down to ~2.5 km below the ocean floor The fate of organic carbon in marine sediments - New insights from recent data and analysis Global diffusive fluxes of methane in marine sediments Global estimates of hydrate-bound gas in marine sediments: how much is really out there Deep-biosphere methane production stimulated by geofluids in the Nankai accretionary complex Distinguishing and understanding thermogenic and biogenic sources of methane using multiply substituted isotopologues Distributions of microbial activities in deep subseafloor sediments Cultivation and biogeochemical analyses reveal insights into methanogenesis in deep subseafloor sediment at a biogenic gas hydrate site Emerging topics in marine methane biogeochemistry Heterotrophic Archaea dominate sedimentary subsurface ecosystems off Peru Asgard archaea capable of anaerobic hydrocarbon cycling Characteristics and Evolution of sill-driven off-axis hydrothermalism in Guaymas Basin – the Ringvent site Biogeochemical and microbial survey of gravity cores from the Guaymas Basin and Sonora Margin Martens C. Generation of short chain acid anions in hydrothermally altered sediments of the Guaymas Basin, Gulf of California-ScienceDirect. 1990. https://www.sciencedirect.com/science/article/pii/0883292790900376 Chemistry of submarine hydrothermal solutions at 21 °N Teske A, Callaghan AV, LaRowe DE. Biosphere frontiers of subsurface life in the sedimented hydrothermal system of Guaymas Basin. Front Microbiol. 2014. https://www.frontiersin.org/article/10.3389/fmicb.2014.00362 Formation temperatures of thermogenic and biogenic methane Controls on the isotopic composition of microbial methane Teske A, Lizarralde D, Höfig T Site U1546 [Internet]. International Ocean Discovery Program; 2021. (Proceedings of the International Ocean Discovery Program). Available from: http://publications.iodp.org/proceedings/385/104/385_104.html Teske A, Lizarralde D, Höfig T Methods [Internet]. International Ocean Discovery Program. 2021. (Proceedings of the International Ocean Discovery Program). Available from: http://publications.iodp.org/proceedings/385/102/385_102.html Sulfur disproportionation is exergonic in the vicinity of marine hydrothermal vents Generation and utilization of volatile fatty acids and alcohols in hydrothermally altered sediments in the Guaymas Basin Distribution and isotopic composition of trimethylamine dimethylsulfide and dimethylsulfoniopropionate in marine sediments exchangeable and bound aliphatic amines in marine sediments: initial results The determination of volatile amines in aquatic marine systems: A review Minireview: demystifying microbial reaction energetics Trimmomatic: a flexible trimmer for Illumina sequence data MEGAHIT v1.0: A fast and scalable metagenome assembler driven by advanced methodologies and community practices KofamKOALA: KEGG Ortholog assignment based on profile HMM and adaptive score threshold a software platform to evaluate large (meta)genomic collections according to their metabolic machinery: unraveling the sulfur cycle phylogenetically informed classification of genes within metagenomes MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets Metabolic marker gene mining provides insight in global mcrA diversity and coupled with targeted genome reconstruction sheds further light on metabolic potential of the Methanomassiliicoccales Deep-branching ANME-1c archaea grow at the upper temperature limit of anaerobic oxidation of methane Zehnle H, Laso-Pérez R, Lipp J, Teske A, Wegener G Candidatus Alkanophaga archaea from heated hydrothermal vent sediment oxidize petroleum alkane. 2022. https://doi.org/10.21203/rs.3.rs-2096998/v1 UniProt: the Universal Protein Knowledgebase in 2023 a novel archaeal phylum with unique and versatile carbon cycling pathways eggNOG 6.0: enabling comparative genomics across 12 535 organisms Fast and sensitive protein alignment using DIAMOND Methanogenesis pathways of methanogens and their responses to substrates and temperature in sediments from the South Yellow Sea The relative abundances of resolved l2CH2D2 and 13CH3D and mechanisms controlling isotopic bond ordering in abiotic and biotic methane gases Exchange catalysis during anaerobic methanotrophy revealed by 12CH2D2 and 13CH3D in methane Sulfur cycling and methanogenesis primarily drive microbial colonization of the highly sulfidic Urania deep hypersaline basin Light hydrocarbons in recent Texas continental shelf and slope sediments Revised genetic diagrams for natural gases based on a global dataset of >20,000 samples Methane sources and sinks in continental sedimentary systems: New insights from paired clumped isotopologues 13CH3D and 12CH2D2 Low Δ 12 CH 2 D 2 values in microbialgenic methane result from combinatorial isotope effects Clumped isotope effects of thermogenic methane formation: Insights from pyrolysis of hydrocarbons Theoretical estimates of equilibrium carbon and hydrogen isotope effects in microbial methane production and anaerobic oxidation of methane Methanogenic archaea: ecologically relevant differences in energy conservation Diversity and Evolution of Methane-Related Pathways in Archaea Doubly substituted isotopologues of methane hydrate (13CH3D and 12CH2D2): Implications for methane clumped isotope effects source apportionments and global hydrate reservoirs Experimental investigation on the controls of clumped isotopologue and hydrogen isotope ratios in microbial methane Clumped isotopes link older carbon substrates with slower rates of methanogenesis in northern lakes Clumped methane isotopologue-based temperature estimates for sources of methane in marine gas hydrates and associated vent gases Rate limits and isotopologue fractionations for microbial methanogenesis examined with combined pathway protein cost and isotopologue flow network models Rapid metabolism fosters microbial survival in the deep Diversity of prokaryotes and methanogenesis in deep subsurface sediments from the Nankai Trough Relative importance of methylotrophic methanogenesis in sediments of the Western Mediterranean Sea Methyl-compounds driven benthic carbon cycling in the sulfate-reducing sediments of South China Sea Microbial methanogenesis in the sulfate-reducing zone of sediments in the Eckernförde Bay Microbial substrate preference dictated by energy demand rather than supply Environmental evidence for net methane production and oxidation in putative ANaerobic MEthanotrophic (ANME) archaea ANME-1 archaea may drive methane accumulation and removal in estuarine sediments Teske A Molecular survey of methane-cycling archaea in methane-soaked subsurface sediments (Guaymas Basin Poster presented at: American Society for Microbiology Nasika S, Runthala A Current strategic limitations of phylogenetic tools badly impact the inference of an evolutionary tree. bioRxiv. 2021. https://www.biorxiv.org/content/10.1101/2021.01.21.427545v1 Lever M Acetogenesis in the Energy-Starved Deep Biosphere–A Paradox? Front Microbiol. 2012. https://www.frontiersin.org/article/10.3389/fmicb.2011.00284 Metagenomic signatures of the Peru Margin subseafloor biosphere show a genetically distinct environment Biogeographical distribution and diversity of microbes in methane hydrate-bearing deep marine sediments on the Pacific Ocean Margin a methanogen isolated from marine sediment near a cold seep at Four-Way Closure Ridge offshore southwestern Taiwan Methanogenic Activity in Sediment from Leg 64 Cultivation of methanogenic community from subseafloor sediments using a continuous-flow bioreactor Widespread energy limitation to life in global subseafloor sediments Microbial life under extreme energy limitation Download references supported by NIH Shared Instrumentation (grant number 1S10OD010786-01); and all IODP Expedition 385 scientists We thank the following for funding support: IODP for scheduling Expedition 385; USSSP (OCE1450528) for salary support for seagoing scientists that enables cruise participation and the Post Expedition Award to D.P Bojanova; NSF (grant number BIO-OCE 2048489) to A.P Teske; USC Deparment of Earth Sciences to D.P Bojanova; the NSF-sponsored Center for Dark Energy Biosphere Investigations (C-DEBI) (grant number OCE0939564) to D.P LaRowe; NASA Exobiology (80NSSC21K0477) to E.D Young; NASA Exobiology grant “Linking methane biogeochemistry to microbial biosignatures in the Guaymas Basin” (award number A22-0244-001) to J.L Teske; and Simons Foundation (award number 687165) to B.J Statewide California Electronic Library Consortium Download citation DOI: https://doi.org/10.1038/s41396-023-01485-y Metrics details Analyses of gene expression of subsurface bacteria and archaea provide insights into their physiological adaptations to in situ subsurface conditions We examined patterns of expressed genes in hydrothermally heated subseafloor sediments with distinct geochemical and thermal regimes in Guaymas Basin RNA recovery and cell counts declined with sediment depth we obtained metatranscriptomes from eight sites at depths spanning between 0.8 and 101.9 m below seafloor We describe the metabolic potential of sediment microorganisms and discuss expressed genes involved in tRNA and rRNA modifications that enable physiological flexibility of bacteria and archaea in the hydrothermal subsurface Microbial taxa in hydrothermally influenced settings like Guaymas Basin may particularly depend on these catalytic RNA functions since they modulate the activity of cells under elevated temperatures and steep geochemical gradients protein maintenance and circadian rhythm were also identified The concerted interaction of many of these genes may be crucial for microorganisms to survive and to thrive in the Guaymas Basin subsurface biosphere Here we examine the total RNA pool from deep subsurface sediments (≥0.8 and up to 101.9 meters below sea floor; mbsf) that were drilled during International Ocean Discovery Program (IODP) Expedition 385 in Guaymas Basin and we provide the first insights into gene expression in the deep biosphere of this hydrothermally active seafloor spreading center A Bathymetry of Guaymas Basin with IODP Expedition 385 drilling sites U1545 to U1552 Light green to deep blue contour lines indicate the increasing water depth in meters The inner figure shows the overall sampling location in Guaymas Basin; red lines depict the transformation faults Drilling sites included two adjacent sedimented sites in the northwestern flanking regions with (U1546) and without (U1545) a deep sill intrusion at ~350-430 mbsf; two sites at the hydrothermally active Ringvent formation recently emplaced hot sill creates steep temperature gradients and drives hydrothermal circulation (sites U1547 and U1548); one site 3.2 km offset from a cold seep on the northwestern flanking regions (U1549) and a cold seep site with a shallow hydrate area on the Sonora Margin (U1552) IODP 385 also drilled the northern axial valley (U1550) and the southwestern franking region known to receive terrestrial sediment input (U1551) B Temperature gradients in the Guaymas Basin subsurface (Source Data) Sites and depths are along the Y axis of the heatmap and depths are given in meters below sea floor (mbsf) Expression levels are normalized as log2 transformation of TPM + 1 (a value of 1 was added to TPM values to avoid zeros) Tun-AFO Tungsten-containing aldehyde ferredoxin oxidoreductases Key genes involved in nitrogen cycling showed generally low expression levels (Fig. 4) Co-expression of genes involved in putatively complete denitrification (narG/H/I nosZ) was detected at the cold seep site U1549B at 1.5 mbsf Hydroxylamine reductase (hcp) and hydroxylamine dehydrogenase (hao) genes involved in ammonia production were moderately expressed at shallow and intermediate depths of sites U1549B and U1547B We did not detect expressed genes for nitrification (e.g. consistent with pervasive anoxia of Guaymas subsurface sediments Relatively abundant expression levels of urea and ornithine cycling were detected in samples from almost all examined sites between 0.8 and 36.8 msbf RNA editing is an essential process detected in prokaryotes and eukaryotes that involves posttranscriptional modifications of tRNA In prokaryotes has been described using cultured bacterial and archaeal strains (see “Discussion”) Manual curation was performed on the decontaminated and non-redundant BLASTx results generated with DIAMOND against NCBI-NR database (Supplementary Table 2 and depths are given in meters below seafloor (mbsf) Expression levels are normalized as log2 transformation of TPM + 1 (a value of 1 added to TPM values to avoid zeros) These findings further support efficient protein repair and recycling in the hydrothermally influenced subsurface Evidence of putative archaeal circadian clocks in the Guaymas hydrothermal subsurface is intriguing; nonetheless and the detection of KaiC transcripts only in shallow sediments may reflect an evolutionary remnant whose possible effect on archaeal fitness gradually disappears in the deep biosphere the recycling of metabolic byproducts (e.g. CO2) in the Guaymas subsurface could be linked to DNA/RNA (nucleotide/ribonucleotide) synthesis dNDP recycling can be energetically less costly than de novo synthesis and the most promising strategy for heat-stressed cells that must conserve energy for other processes including repair of damaged DNA and proteins were recovered within our metatranscriptomes Prokaryotic activity and gene expression in the Guaymas Basin subsurface are not maintained by extremophiles that are fundamentally different from other microorganisms This study on expressed genes by Guaymas subsurface microorganisms from sites and depths with contrasting biogeochemistry and temperature profiles indicates that some fraction of the subsurface prokaryotic community is active and that many/most of these taxa must be efficient recyclers that struggle to survive and access sufficient resources for their maintenance and growth these populations at any given time are likely balancing the capacity for activity with inevitable periods of dormancy or even death Aside from the use of metabolic strategies for obtaining carbon and energy previously associated with deep biosphere (e.g. survival in the Guaymas subsurface is also facilitated by mechanisms that permit fine-tuning of cellular activities that include RNA editing These processes collectively help diverse bacterial and archaeal lineages to succeed/persist in this challenging habitat The thermal and geochemical gradients that emerge from this circulation shape the abundance and activity of the deep subsurface biosphere of the basin site 1550B is documented to have great hydrocarbon formation near the sill/sediment contact and site U1551B to receive terrigenous inputs Sediment cores were collected using the drilling vessel JOIDES Resolution Holes were first advanced using advanced piston coring (APC) and then extended core barrel (XCB) coring as necessary Temperature measurements were made using the advanced piston corer temperature (APCT-3) and Sediment Temperature 2 (SET2) tools downhole logging used the triple combination and Formation MicroScanner sonic logging tool strings After bringing core sections onto the core receiving platform of the D/V JOIDES Resolution sampling for RNA occurred immediately after core retrieval on the core receiving platform by sub-coring with a sterile cutoff 50cc syringe into the center of each freshly cut core section targeted These sub-cores were immediately frozen in liquid nitrogen and stored at –80 °C whole round sections were immediately transferred (within 30 min) to the laboratory after placing them in gas-tight sterile bags gloves and laboratory coats were worn during sample handling in the laboratory where core samples were transferred from their gas-tight bags onto sterilized foil on the bench surface inside a Table KOACH T 500-F system which creates an ISO Class I clean air environment (Koken Ltd. the bench surface was targeted with a fanless ionizer (Winstat BF2MA Japan) for neutralizing static charge on the surface of working materials especially plasticware to avoid contamination by electrostatic attraction the exterior 2 cm of each extruded section was removed using a sterilized ceramic knife The core interior was transferred to sterile 50-mL Falcon tubes and immediately frozen at –80 °C for post cruise analyses Each 25 μl PCR reaction was prepared using GoTaq G2 Flexi DNA Polymerase (Promega) and contained 0.5 U μl–1 GoTaq G2 Flexi DNA Polymerase 4 μM of each primer (final concentrations) RNA quantification (ng μl–1) was performed using Qubit RNA High Sensitivity (HS) The sequencing of the cDNA library from the control sample was unsuccessful as it failed to generate any sequences that met the length criterion of 300-400 base pairs -e 1e–5 --more-sensitive) was used to search against NCBI-NR database (release date: 2022-12-04) We recognize that any automated and manual pipeline that is used to assign gene function has the caveat that publicly available databases may contain some protein sequences that have not been functionally validated on the bench PCR amplifications were performed using the SpeedSTAR HS DNA Polymerase (TAKARA) kit with the following modifications: each 25 μl PCR reaction contained up to 1 ng of template DNA 10 mM of each primer and DEPC water (Fisher BioReagents) The PCR amplifications were performed in an Eppendorf Mastercycler Pro S Vapoprotect (Model 6321) thermocycler with the following conditions: 95 °C for 5 min The total volume of PCR reactions was run in 2% agarose gel (Low-EEO/Multi-Purpose/Molecular Biology Grade Fisher BioReagents) and the correct size PCR products (~800 bp) Libraries for DNA PacBio sequencing (long-read sequencing) were prepared from the recovered and gel purified DNA extracts at the University of Delaware DNA Sequencing & Genotyping Center PacBio reads were deposited to the National Center for Biotechnology Information Sequence Read Archive under access numbers SRR23604162-SRR23604206 The sediment sampling for cell counts occurred immediately after core retrieval on the core receiving platform by sub-coring with a sterile tip-cut 2.5 cc syringe from the center of each freshly cut core section Approximately 2 cm3 sub-cores were immediately put into tubes containing fixation solution consisting of 8 mL of 3xPBS (Gibco PBS Fischer) and 5% (v/v) neutralized formalin (Thermo Scientific Shandon Formal-Fixx Neutral Buffered Formalin) The sample was transferred onto a set of four density layers composed of 30% Nycodenz (1.15 g cm–3) and 67% sodium polytungstate (2.08 g cm–3) The sediment was resuspended using 2.1 ml of 2.5% NaCl and 300 μl of detergent mix and shaken at 500 rpm for 60 min at 25 °C the Count Nuclei function of the MetaMorph software (Molecular Devices) was used to detect and enumerate microbial cells The raw metatranscriptome sequencing data in this study have been deposited in the National Center for Biotechnology Information Sequence Read Archive under the accession numbers SRR22580929-SRR22580947 The microbiomes of deep-sea hydrothermal vents: distributed globally Exploring the composition and diversity of microbial communities at the Jan Mayen hydrothermal vent field using RNA and DNA The metatranscriptome of a deep-sea hydrothermal plume is dominated by water column methanotrophs and lithotrophs Microbial community structure and functioning in marine sediments associated with diffuse hydrothermal venting assessed by integrated meta-omics Functional interactions among filamentous Epsilonproteobacteria and bacteroidetes in a deep-sea hydrothermal vent biofilm Seafloor incubation experiment with deep-sea hydrothermal vent fluid reveals effect of pressure and lag time on autotrophic microbial communities Coupled RNA-SIP and metatranscriptomics of active chemolithoautotrophic communities at a deep-sea hydrothermal vent Carbon isotope systematics of individual hydrocarbons in hydrothermal petroleums from the Guaymas Basin archaeal and fungal community structure in hydrothermal sediments of Guaymas Basin Carbon release by sill intrusion into young sediments measured through scientific drilling Glycine cleavage system: reaction mechanism Four families of folate-independent methionine synthases Structural framework for the mechanism of archaeal exosomes in RNA processing Ski2-like RNA helicase structures: common themes and complex assemblies Universal RNA-degrading enzymes in Archaea: Prevalence activities and functions of β-CASP ribonucleases Retrohoming of a bacterial group II intron: mobility via complete reverse splicing independent of homologous DNA recombination Advances in Experimental Medicine and Biology (eds Jensen Polynucleotide phosphorylase: Not merely an RNase but a pivotal post-transcriptional regulator Ribonucleoside-5’-diphosphates (NDPs) support RNA polymerase transcription suggesting NDPs may have been substrates for primordial nucleic acid biosynthesis Ribonucleoside diphosphate reductase is a component of the replication hyperstructure in Escherichia coli DNA synthesis from diphosphate substrates by DNA polymerases A bacterial group II intron encoding reverse transcriptase Escherichia coli competence gene homologs are essential for competitive fitness and the use of DNA as a nutrient Archease from Pyrococcus abyssi improves substrate specificity and solubility of a tRNA m5C methyltransferase The thermosome: archetype of group II chaperonins Distribution and evolution of von Willebrand/integrin A domains: widely dispersed domains with roles in cell adhesion and elsewhere Structure and interactions of the archaeal motility repression module ArnA-ArnB that modulates archaellum gene expression in Sulfolobus acidocaldarius Minimal tool set for a prokaryotic circadian clock Proposed role for KaiC-like ATPases as major signal transduction hubs in Archaea Near-surface heating of young rift sediment causes mass production and discharge of reactive dissolved organic matter Carbamyl Phosphate: Many forms of life use this molecule to synthesize arginine Experimental evidence for the functional importance and adaptive advantage of A-to-I RNA editing in fungi Characterization of an extremely thermophilic tRNA-methylthiotransferase Understanding RNA modifications: the promises and technological bottlenecks of the ‘epitranscriptome’ Sulfur amino acids regulate translational capacity and metabolic homeostasis through modulation of tRNA thiolation The MiaA tRNA modification enzyme is necessary for robust RpoS expression in Escherichia coli Teske A, Lizarralde D, Höfig TW, and the Expedition 385 Scientists. Guaymas Basin Tectonics and Biosphere. Proceedings of the International Ocean Discovery Program, 385: College Station, TX (International Ocean Discovery Program) (2021). https://doi.org/10.14379/iodp.proc.385.2021 The ribosome as a switchboard for bacterial stress response Microbial selection and survival in subseafloor sediment Messenger RNA degradation in bacterial cells DNA as a nutrient: novel role for bacterial competence gene homologs Heterotrophic archaea dominate sedimentary subsurface ecosystems off Peru The Alba protein family: structure and function Comparative genomics and evolution of proteins involved in RNA metabolism The two faces of Alba: the evolutionary connection between proteins participating in chromatin structure and RNA metabolism tRNA wobble-uridine modifications as amino acid sensors and regulators of cellular metabolic state Cloning and characterization of tRNA (m1A58) methyltransferase (TrmI) from Thermus thermophilus HB27 a protein required for cell growth at extreme temperatures Iron-sulfur proteins responsible for RNA modifications A tRNA modification balances carbon and nitrogen metabolism by regulating phosphate homeostasis Transfer RNA processing in archaea: unusual pathways and enzymes Spatial distribution and activity of viruses in the deep-sea sediments of Sagami Bay Prokaryote diversity and virus abundance in shallow hydrothermal vents of the Mediterranean Sea (Panarea Island) and the Pacific Ocean (North Sulawesi-Indonesia) Ecogenomics reveals viral communities across the Challenger Deep oceanic trench A circadian clock in a nonphotosynthetic prokaryote Crystal structure of the electron transfer complex rubredoxin rubredoxin reductase of Pseudomonas aeruginosa Large protein organelles form a new iron sequestration system with high storage capacity Shelf-to-basin iron shuttle in the Guaymas Basin Repair or degrade: the thermodynamic dilemma of cellular protein quality-control The kinetic parameters and energy cost of the Hsp70 chaperone as a polypeptide unfoldase Quantitative analysis of small-subunit rRNA genes in mixed microbial populations via 5’-nuclease assays Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin New cell extraction procedure applied to deep subsurface sediments Zhou YL, Mara P. Analysis of the deep biosphere metatranscriptomes. Zenodo Accessed 2023. https://doi.org/10.5281/zenodo.7710615 Download references Daniel Lizarralde (WHOI) for the edited bathymetric map of Guaymas Basin This study was supported by the National Science Foundation Grant OCE-2046799 to VE JSPS KAKENHI JP19H00730 and JP23H00154 to YM and China Postdoctoral Science Foundation (2022M720039) and Guangdong Natural Resources Foundation (GDNRC[2023]30) to Y-LZ Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou) Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star) AT and PM conceived of the experiments and designed the sampling strategy for analyses discussed in this paper AT served as Co-Chief Scientist for IODP Expedition 385 with assistance from other IODP 385 shipboard microbiologists and provided cell count data and cell count figures PM extracted RNA from samples for metatranscriptome analyses and DNA for the 16S rRNA marker gene analyses Y-LZ and DB analyzed metatranscriptome data PM wrote the first draft of the paper and all authors contributed to its final form a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law Download citation DOI: https://doi.org/10.1038/s41396-023-01492-z World Journal of Microbiology and Biotechnology (2024) SF Chronicle critic Michael Bauer skewered Guaymas with a one-star review in 2016 Tiburon’s waterfront Mexican hangout, Guaymas, is closing its doors after over 30 years The last restaurant’s last service will take place on September 3 awarding it one star for serving “what tasted like a collection of cheap ingredients Tiburon isn’t exactly brimming with hot (or even very good) restaurants so the loss of Guaymas as a pre- or post-ferry destination will be likely be felt by those wishing for a waterside margarita There’s no word yet on who may take over the space which features excellent views of San Francisco and Angel Island In a statement on the website, the restaurant group’s CEO and President John Tallichet said “We would like to thank our loyal customers, as well as the City of Tiburon, the dedicated staff, and all of our longtime partners, including our landlord who has been supportive through this transition.” No further details on the reason for the closure were given. Until it closes after Labor Day, it will continue to serve lunch, dinner, and happy hour. Stay tuned for more on what could take over this very prime real estate in the near future. Oops. Something went wrong. Please enter a valid email and try again. Volume 5 - 2014 | https://doi.org/10.3389/fmicb.2014.00362 Temperature is one of the key constraints on the spatial extent and biogeochemical function of subsurface life A model system to explore these interrelationships should offer a suitable range of geochemical regimes carbon substrates and temperature gradients under which microbial life can generate energy and sustain itself we make the case for the hydrothermally heated sediments of Guaymas Basin in the Gulf of California as a suitable model system where extensive temperature and geochemical gradients create distinct niches for active microbial populations in the hydrothermally influenced sedimentary subsurface that in turn intercept and process hydrothermally generated carbon sources We synthesize the evidence for high-temperature microbial methane cycling and sulfate reduction at Guaymas Basin – with an eye on sulfate-dependent oxidation of abundant alkanes – and demonstrate the energetic feasibility of these latter types of deep subsurface life in previously drilled Guaymas Basin locations of Deep-Sea Drilling Project 64 Schematic representation of the Guaymas Basin subsurface with deep basement marine sedimentation and organic carbon input (brown drops) immobilized carbon in the sediment (dark-brown horizontal pellets) volatile pyrolysis products (orange drops) and hypothetical fluid flow pathways (arrows) The black dotted lines indicate potential flow paths along fracture lines in the sediments; actually existing flow paths vary in location and vertical extent the microbial mats of Guaymas Basin represent the last stage of the microbial gauntlet in the sediments as they intercept energy and carbon sources from hydrothermally active sediment and modulate microbial oxidation and carbon assimilation processes at the sediment/water interface FIGURE 2. The microbial gauntlet modifies the fluxes of deep carbon and gasses toward the sediment surface. The top row shows examples for sulfur-oxidizing microbial mats dominated by filamentous Beggiatoaceae at well-documented hydrothermal seepage hot spots on-axis (A, Biddle et al., 2012; B, McKay et al., 2012) and off-axis in Guaymas Basin (C, Lizarralde et al., 2011) The Beggiatoaceae mats intercept DIC for autotrophic assimilation and sulfide for oxidation with nitrate as the electron acceptor consume or modify the carbon and energy sources that are available at the sediment surface (for example sulfide DIC and methane) extend into the hydrothermal sediments of Guaymas Basin Given the strong hydrothermal gradients at Guaymas Basin it is likely that the depth range of microbial processes is to a large part determined by temperature By extrapolating from current evidence for microorganisms and microbial processes in surficial sediments (summarized in the following paragraphs) we hypothesize that the subsurface is permeated most deeply by microbial groups that tolerate maximal in situ temperatures and extremely reduced redox regimes This is the domain of microbial methane and sulfur cycling; the temperature limits on these processes are outlined here Guaymas Basin serves as an obvious platform to reconcile the gaps in our understanding of anaerobic hydrocarbon transformation with the elucidation of the metabolic versatility of Archaea this homolog of ethylbenzene dehydrogenase may serve as a new in situ biomarker of anaerobic alkane transformation Guaymas Basin sediments and enrichments offer the opportunity to “bioprospect” for these diagnostic enzymes and their genes no studies have definitely linked the detection of methylsuccinate with genetic biomarkers or other evidence indicative of a fumarate addition pathway the persistence of methanogenic activity even in deep sediments and the high temperature ranges of microbial methanogenesis and methane oxidation the Guaymas Basin sediments provide a model system to investigate these distinct methane oxidation pathways in the deep subsurface the potential for different hydrocarbon activation strategies can be investigated in situ via metagenomic and/or metatranscriptomic approaches Although Guaymas Basin has not been mined in situ for anaerobic hydrocarbon intermediates via metabolite analysis functional key genes provide targets for metabolite profiling efforts Given recent advances in our understanding of the biochemical pathways that govern anaerobic hydrocarbon oxidation we are well poised to exploit omic-based methodologies to address questions regarding the metabolic strategies of thermophiles and hyperthermophiles with respect to hydrocarbon oxidation Given the lower measured temperatures at hole 477 this hydrothermal regime must have cooled by the time of drilling the temperature measurements during DSDP leg 64 suggest that microbially compatible temperatures extend into much of the subsurface in Guaymas Basin since drilling and sampling designs avoid the hot spreading center Reactions considered to provide energy for microorganisms in Guaymas basin sediments the oxidation of all of the n-alkanes by sulfate have the potential to provide energy for microorganisms at all depths ranging from about –5 to –9 kJ (mol e-)-1 the longer-chain alkanes provide more energy per mole of electrons transferred there is little variation in energy availability as a function of depth Because the concentration of octane was only reported at two depths at Site 481A values of ΔGr are only reported for these depths (black dots) the lines represent calculations carried out at a number of depths along with interpolated values FIGURE 3. (A) Gibbs energy of sulfate reduction, ΔGr, coupled to methane and C2–C8 n-alkane oxidation in Guaymas Basin sediments (DSDP Leg 64, Hole 481A) in units of Joules per mole of electrons transferred, J (mol e-)-1. The reactions that these values of ΔGr refer to are listed in Table 1 (B) Energy availability in Guaymas Basin sediments (DSDP Leg 64 Hole 481A) in units of Joules per cubic centimeter of sediment calculated using the Gibbs energy of reaction and the number of moles of the limiting substrate (n-alkane) in a cm3 of sediment The temperature tolerances and energy yields of microbial processes in the Guaymas Basin subsurface strongly suggest that microbial life is capable of colonizing these hydrothermally impacted sediments to considerable depths While the hottest sediments in hydrothermal hot spots of the spreading center are likely to remain beyond the range of microbial life moderately heated sediments at a judiciously chosen distance from channelized hydrothermal flow (such as those targeted on DSDP Leg 64) provide a very reasonable chance to explore the depth extent genetic and functional diversity of subsurface life under hydrothermal controls This paper originated during a Theme Team II Subsurface Biogeography workshop on deep subseafloor drilling in Guaymas Basin held at Wrigley Marine Station on Catalina Island The workshop was supported by NSF Science and Technology Center for Dark Energy Biosphere Investigations (C-DEBI) and by the US Science Support Program of the International Ocean Discovery Program (IODP) LaRowe acknowledges the NASA Astrobiology Institute based at USC Callaghan acknowledges NSF (Molecular and Cellular Biosciences We thank all workshop attendants for stimulating discussions on Guaymas Basin research perspectives Identification of enzymes involved in anaerobic benzene degradation by a strictly anaerobic iron-reducing enrichment culture Pubmed Abstract | Pubmed Full Text | CrossRef Full Text Oil weathering after the Deepwater Horizon disaster led to the formation of oxygenated residues Pubmed Abstract | Pubmed Full Text | CrossRef Full Text Expanding frontiers in deep subsurface microbiology CrossRef Full Text Hydrocarbons in surface sediments from a Guaymas Basin hydrothermal vent site CrossRef Full Text Identification of new enzymes potentially involved in anaerobic naphthalene degradation by the sulfate-reducing enrichment culture N47 Pubmed Abstract | Pubmed Full Text | CrossRef Full Text Pubmed Abstract | Pubmed Full Text | CrossRef Full Text Denitrification and environmental factors influencing nitrate removal in Guaymas Basin hydro-thermally-altered sediments CrossRef Full Text represents a new species within the sulfate-reducing archaebacteria CrossRef Full Text Enzymes involved in the anaerobic oxidation of n alkanes: from methane to long-chain paraffins Pubmed Abstract | Pubmed Full Text | CrossRef Full Text Metabolomic investigations of anaerobic hydrocarbon-impacted environments Pubmed Abstract | Pubmed Full Text | CrossRef Full Text “The complete genome sequence of Desulfococcus oleovorans Hxd3 alkane-degrading bacterium,” in American Society for Microbiology 108th General Meeting (Boston Anaerobic alkane-degrading strain AK-01 contains two alkylsuccinate synthase genes Pubmed Abstract | Pubmed Full Text | CrossRef Full Text Diversity of benzyl- and alkylsuccinate synthase genes in hydrocarbon-impacted environments and enrichment cultures Pubmed Abstract | Pubmed Full Text | CrossRef Full Text The genome sequence of Desulfatibacillum alkenivorans AK-01: a blueprint for anaerobic alkane oxidation Pubmed Abstract | Pubmed Full Text | CrossRef Full Text Anaerobic biodegradation of n-hexadecane by a nitrate-reducing consortium Pubmed Abstract | Pubmed Full Text | CrossRef Full Text two novel thermophilic archaea isolated from the Guaymas Basin hydrothermal vent site Pubmed Abstract | Pubmed Full Text | CrossRef Full Text Leg 64 seeks evidence on development of basins CrossRef Full Text “Long-chain paraffin metabolism by a methanogenic bacterial consortium enriched from marine sediments,” in 8th International Symposium of Subsurface Microbiology (Germany: Garmisch-Partenkirchen) De la Lanza-Espino CrossRef Full Text Molecular characterization of sulfate-reducing bacteria in the Guaymas Basin Pubmed Abstract | Pubmed Full Text | CrossRef Full Text Hydrothermal oil of Guaymas Basin and implications for petroleum formation mechanisms CrossRef Full Text Biocorrosive thermophilic microbial communities in Alaskan North Slope oil facilities Pubmed Abstract | Pubmed Full Text | CrossRef Full Text Survival and growth of two heterotrophic hydrothermal vent archaea Pyrococcus strain GB-D and Thermococcus fumicolans under low pH and high sulfide concentrations in combination with high temperature and pressure regimes Pubmed Abstract | Pubmed Full Text | CrossRef Full Text Anaerobes Wachstum Neuartiger Sulfatreduziernder und Nitratreduzierender Bakterien auf n-Alkanen und Erdöl (1982) “Mass physical properties of Pliocene to Quaternary sediments in the Gulf of California Deep Sea Drilling Project Leg 64” in Initial Reports of the Deep Sea Drilling Project Intrusion of basaltic sills into highly porous sediments and resulting hydrothermal activity CrossRef Full Text Microbial sulfate reduction in deep-sea sediments at the Guaymas Basin hydrothermal vent area: influence of temperature and substrates CrossRef Full Text Nitrite-driven anaerobic methane oxidation by oxygenic bacteria Pubmed Abstract | Pubmed Full Text | CrossRef Full Text “Geochemistry of interstitial gases in sedimentary deposits of the Gulf of California Deep Sea Drilling Project Leg 64,” in Initial Reports of the Deep Sea Drilling Project sulfate reduction and crude oil biodegradation in hot Alaskan oilfields Pubmed Abstract | Pubmed Full Text | CrossRef Full Text “Geochemistry of interstitial waters and sediments,” in Initial Reports of the Deep Sea Drilling Project “Hydrothermal activity in the Guaymas Basin Gulf of California: a synthesis,” in Initial Reports of the Deep Sea Drilling Project Government Printing Office),1159–1167 Genes encoding the candidate enzyme for anaerobic activation of n-alkanes in the denitrifying bacterium Pubmed Abstract | Pubmed Full Text | CrossRef Full Text Mats of giant sulfur bacteria on deep-sea sediments due to fluctuation hydrothermal flow CrossRef Full Text a novel hyperthermophilic archaeum that oxidizes Fe2+ at neutral pH under anoxic conditions CrossRef Full Text Reverse methanogenesis: testing the hypothesis with environmental genomics Pubmed Abstract | Pubmed Full Text | CrossRef Full Text Metagenome reveals potential microbial degradation of hydrocarbon coupled with sulfate reduction in an oil-immersed chimney from Guaymas Basin Pubmed Abstract | Pubmed Full Text | CrossRef Full Text “Anaerobic biodegradation of hydrocarbons including methane,” in The Prokaryotes: Prokaryotic Physiology and Biochemistry Thermodynamics of hydrothermal systems at elevated temperatures and pressures CrossRef Full Text Theoretical prediction of thermodynamic behavior of aqueous electrolytes at high pressures and temperatures: 4 and apparent molal and standard and relative partial molal properties to 600°C and 5 kb CrossRef Full Text Field and laboratory studies of methane oxidation in an anoxic marine sediment–evidence for a methanogen-sulfate reducer consortium CrossRef Full Text Pubmed Abstract | Pubmed Full Text | CrossRef Full Text Anaerobic oxidation of benzene by the hyperthermophilic archaeon Ferroglobus placidus Pubmed Abstract | Pubmed Full Text | CrossRef Full Text hyperthermophilic archaeum from a deep-sea hydrothermal environment CrossRef Full Text Massive natural occurrence of unusually large bacteria (Beggiatoa spp.) at a hydrothermal deep-sea vent site CrossRef Full Text Comparative physiological studies on hyperthermophilic Archaea isolated from deep-sea hot vents with emphasis on Pyrococcus strain GB-D Pubmed Abstract | Pubmed Full Text Rapid identification of hyperthermophilic methanococci isolated from deep-sea hydrothermal vents Pubmed Abstract | Pubmed Full Text | CrossRef Full Text SUPCRT92–A software package for calculating the standard molal thermodynamic properties of minerals and reactions from 1 bar to 5000 bar and 0°C to 1000°C CrossRef Full Text CrossRef Full Text Comparison of thermophilic methanogens from submarine hydrothermal vents CrossRef Full Text Jørgensen Bacterial sulfate reduction above 100°C in deep-sea hydrothermal vent systems Pubmed Abstract | Pubmed Full Text | CrossRef Full Text Jørgensen Thermophilic bacterial sulfate reduction in deep-sea sediments at the Guaymas Basin hydrothermal vents (Gulf of California) CrossRef Full Text Effects of temperature and pressure on sulfate reduction and anaerobic oxidation of methane in hydrothermal sediments of Guaymas Basin Pubmed Abstract | Pubmed Full Text | CrossRef Full Text A high pressure thermal gradient block for investigating microbial activity in multiple deep-sea samples Pubmed Abstract | Pubmed Full Text | CrossRef Full Text a novel hyperthermophilic archaeon capable of oxidizing organic acids and growing autotrophically on hydrogen with Fe(III) serving as the sole electron acceptor Pubmed Abstract | Pubmed Full Text | CrossRef Full Text “Evidence for two distinct hydrothermal systems in the Guaymas Basin,” in Initial Reports of the Deep Sea Drilling Project Survey of hydrothermally generated petroleums from the Guaymas Basin spreading center CrossRef Full Text “Introduction and explanatory notes,” in Initial Reports of the Deep Sea Drilling Project Anaerobic oxidation of long-chain n-alkanes by the hyperthermophilic sulfate-reducing archaeon doi: 10.1038/ismej.2014.58 [Epub ahead of print] Pubmed Abstract | Pubmed Full Text | CrossRef Full Text Anaerobic oxidation of fatty acids and alkenes by the hyperthermophilic sulfate-reducing archaeon Archaeoglobus fulgidus Pubmed Abstract | Pubmed Full Text | CrossRef Full Text Metagenomic analysis and metabolite profiling of deep-sea sediments from the Gulf of Mexico following the Deepwater Horizon oil spill Pubmed Abstract | Pubmed Full Text | CrossRef Full Text Distribution and in situ abundance of sulfate-reducing bacteria in diverse marine hydrocarbon seep sediments Pubmed Abstract | Pubmed Full Text | CrossRef Full Text Anaerobic degradation of ethylbenzene by a new type of marine sulfate-reducing bacterium Pubmed Abstract | Pubmed Full Text | CrossRef Full Text Pubmed Abstract | Pubmed Full Text | CrossRef Full Text Anaerobic oxidation of n-dodecane by an addition reaction in a sulfate-reducing bacterial enrichment culture Pubmed Abstract | Pubmed Full Text | CrossRef Full Text A conspicuous nickel protein in microbial mats that oxidize methane anaerobically Pubmed Abstract | Pubmed Full Text | CrossRef Full Text CrossRef Full Text “Energetic constraints on life in marine deep sediments,” in Life in Extreme Environments: Microbial Life in the Deep Biosphere Biochemical and genetic characterization of benzylsuccinate synthase from Thauera aromatica: a new glycyl radical enzyme catalysing the first step in anaerobic toluene metabolism Pubmed Abstract | Pubmed Full Text | CrossRef Full Text L’Haridon Hot subterranean biosphere in a continental oil reservoir CrossRef Full Text CrossRef Full Text CrossRef Full Text carbon acquisition and electron transport pathways suggested by the draft genome of a single orange Guaymas Basin Beggiatoa (Cand Pubmed Abstract | Pubmed Full Text | CrossRef Full Text are orange: single-filament genome-enabled identification of an abundant octaheme cytochrome with hydroxylamine oxidase hydrazine oxidase and nitrite reductase activities Pubmed Abstract | Pubmed Full Text | CrossRef Full Text Mobile elements in a single-filament orange Guaymas Basin Beggiatoa (“Candidatus Maribeggiatoa”) sp draft genome: evidence for genetic exchange with cyanobacteria Pubmed Abstract | Pubmed Full Text | CrossRef Full Text Metabolic versatility and indigenous origin of the Archaeon Thermococcus sibiricus Pubmed Abstract | Pubmed Full Text | CrossRef Full Text Generation of short chain organic acid anions in hydrothermally altered sediments of the Guaymas Basin CrossRef Full Text Microbial Ecology of a Manmade Oil Spill in the Gulf of Mexico and a Natural Hydrothermal Oil Seep in the Gulf of California CrossRef Full Text Detection of putatively thermophilic anaerobic methanotrophs in diffuse hydrothermal vent fluids Pubmed Abstract | Pubmed Full Text | CrossRef Full Text Pubmed Abstract | Pubmed Full Text | CrossRef Full Text Zero-valent sulphur is a key intermediate in marine methane oxidation Pubmed Abstract | Pubmed Full Text | CrossRef Full Text Identification of naphthalene carboxylase as a prototype for the anaerobic activation of non-substituted aromatic hydrocarbons Pubmed Abstract | Pubmed Full Text | CrossRef Full Text Microbial nitrate-dependent cyclohexane degradation coupled with anaerobic ammonium oxidation Pubmed Abstract | Pubmed Full Text | CrossRef Full Text abundant at hydrothermal vents of the Guaymas Basin Pubmed Abstract | Pubmed Full Text Identification of critical members in a sulfidogenic benzene-degrading consortium by DNA stable isotope probing Pubmed Abstract | Pubmed Full Text | CrossRef Full Text “Methanogenic activity in sediment from leg 64 Gulf of California,” in Initial Reports of the Deep Sea Drilling Project 14C ages of hydrothermal petroleum and carbonate in Guaymas Basin Gulf of California: implications for oil generation doi: 10.1130/0091-7613 (1991)019<0253:CAOHPA>2.3.CO;2 CrossRef Full Text Anaerobic degradation of benzene in BTX mixtures dependent on sulfate reduction Pubmed Abstract | Pubmed Full Text | CrossRef Full Text Molecular characterization of a sulfate-reducing consortium which mineralizes benzene CrossRef Full Text Use of stable isotopes to identify benzoate as a metabolite of benzene degradation in a sulphidogenic consortium Pubmed Abstract | Pubmed Full Text | CrossRef Full Text Biodegradation of an alicyclic hydrocarbon by a sulfate-reducing enrichment from a gas condensate-contaminated aquifer Pubmed Abstract | Pubmed Full Text | CrossRef Full Text Pubmed Abstract | Pubmed Full Text | CrossRef Full Text Rullkötter “Organic petrography and extractable hydrocarbons of sediment from the Gulf of California Anaerobic oxidation of hydrocarbons in crude oil by new types of sulphate-reducing bacteria Pubmed Abstract | Pubmed Full Text | CrossRef Full Text Pubmed Abstract | Pubmed Full Text | CrossRef Full Text The temperature dependence of the standard-state thermodynamic properties of aqueous nonelectrolytes CrossRef Full Text Shipboard Scientific Party and 481,” in Initial Reports of the Deep Sea Drilling Project Calculation of the thermodynamic and transport properties of aqueous species at high pressures and temperatures–correlation algorithms for ionic species and equation of state predictions to 5 kb and 1000°C CrossRef Full Text Calculation of the thermodynamic and transport properties of aqueous species at high pressures and temperatures–standard partial molal properties of organic species CrossRef Full Text Calculation of the thermodynamic and transport properties of aqueous species at high pressures and temperatures–standard partial molal properties of inorganic neutral species CrossRef Full Text Calculation of the thermodynamic properties of aqueous species at high pressures and temperatures–effective electrostatic radii dissociation constants and standard partial molal properties to 1000°C and 5 kbar CrossRef Full Text “Appendix II: carbon/carbonate and nitrogen analysis CrossRef Full Text deeply branching deltaproteobacterium from a deep-sea hydrothermal vent of the Eastern Lau Spreading Center Pubmed Abstract | Pubmed Full Text | CrossRef Full Text Anaerobic transformation of alkanes to fatty acids by a sulfate-reducing bacterium Pubmed Abstract | Pubmed Full Text | CrossRef Full Text Sünwoldt “New reactions in anaerobic alkane and alkene metabolism,” in DFG-Priority Programme 1319 Third Meeting: Biological Transformations of Hydrocarbons Without Oxygen–From the Molecular to the Global Scale (Freiburg: Deutsche Forschungsgemeinschaft) Prediction of the thermodynamic properties of aqueous metal complexes to 1000°C and 5 kb CrossRef Full Text Cell proliferation at 122°C and isotopically heavy CH4 production by a hyper-thermophilic methanogen under high pressure cultivation Pubmed Abstract | Pubmed Full Text | CrossRef Full Text Calculation of the thermodynamic and transport properties of aqueous species at high pressures and temperatures–revised equations of state for the standard partial molal properties of ions and electrolytes CrossRef Full Text Pubmed Abstract | Pubmed Full Text | CrossRef Full Text Microbial diversity in hydrothermal sediments in the Guaymas Basin: evidence for anaerobic methanotrophic communities Pubmed Abstract | Pubmed Full Text | CrossRef Full Text Anaerobic degradation of aromatic compounds coupled to Fe(III) reduction by Ferroglobus placidus Pubmed Abstract | Pubmed Full Text | CrossRef Full Text CrossRef Full Text Enhanced gene detection assays for fumarate-adding enzymes allow uncovering of anaerobic hydrocarbon degraders in terrestrial and marine systems Pubmed Abstract | Pubmed Full Text | CrossRef Full Text Complete genome sequence of Thermococcus sp a hyperthermophilic archaeon isolated from a deep-sea hydrothermal vent area Pubmed Abstract | Pubmed Full Text | CrossRef Full Text Field and laboratory studies on the bioconversion of coal to methane in the San Juan Basin Pubmed Abstract | Pubmed Full Text | CrossRef Full Text Bacterial sulfate reduction in hydrothermal sediments of the Guaymas Basin CrossRef Full Text Origins of methane in hydrothermal systems Pubmed Abstract | Pubmed Full Text | CrossRef Full Text C1–C8 hydrocarbons in sediments from Guaymas Basin Gulf of California–comparison to Peru Margin CrossRef Full Text Methane formation and methane oxidation by methanogenic bacteria Citation: Teske A, Callaghan AV and LaRowe DE (2014) Biosphere frontiers of subsurface life in the sedimented hydrothermal system of Guaymas Basin. Front. Microbiol. 5:362. doi: 10.3389/fmicb.2014.00362 Copyright © 2014 Teske, Callaghan and LaRowe. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY) provided the original author(s) or licensor are credited and that the original publication in this journal is cited *Correspondence: Andreas Teske, Department of Marine Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA e-mail:dGVza2VAZW1haWwudW5jLmVkdQ== Metrics details Previous studies of microbial communities in subseafloor sediments reported that microbial abundance and diversity decrease with sediment depth and age and microbes dominating at depth tend to be a subset of the local seafloor community the existence of geographically widespread subsurface-adapted specialists is also possible we use metagenomic and metatranscriptomic analyses of the hydrothermally heated sediment layers of Guaymas Basin (Gulf of California Mexico) to examine the distribution and activity patterns of bacteria and archaea along thermal We find that the composition and distribution of metagenome-assembled genomes (MAGs) dominated by numerous lineages of Chloroflexota and Thermoproteota correlate with biogeochemical parameters as long as temperatures remain moderate but downcore increasing temperatures beyond ca MAG size and diversity decrease with increasing temperature indicating a downcore winnowing of the subsurface biosphere specific archaeal MAGs within the Thermoproteota and Hadarchaeota increase in relative abundance and in recruitment of transcriptome reads towards deeper marking the transition towards a specialized deep To learn more about bacterial and archaeal communities of the deep downcore trends of diversity and activity in increasingly hot sediments need to be examined and microbial communities and their genomes have to be tracked downcore as far as microbial biomass and DNA yield allow investigating downcore changes in microbial abundance community composition and activity in well-characterized geochemical and thermal gradients requires a suitable field site where extensive physical chemical and microbial gradients can be sampled in adequate resolution by sediment coring and drilling diversity and activity of the deep biosphere in Guaymas Basin have remained largely unknown A Guaymas Basin bathymetry with drill sites B Bathymetry of Ringvent with drill sites within and on the periphery of the Ringvent site and U1549) where metagenomic and metatranscriptomic samples were collected D Temperature profiles for drill sites where metagenomic and metatranscriptomic samples were collected The lines indicated linear functions that were fitted to in-situ temperature measurements Cell count and temperature data are provided in the Source Data file These contrasting sites provide an opportunity for a comprehensive analysis of subsurface microbiota at different temperatures and depths To assess the environmental distribution and genomic potential of microbes living in the deep biosphere of Guaymas Basin we analyzed reconstructed metagenome-assembled genomes (MAGs) from depths ranging from 0.8 to 219.5 mbsf at these thermally and geochemically contrasting sites We also provide evidence for the activity of specific bacterial and archaeal lineages by mRNA transcript mapping on bacterial and archaeal MAGs To describe temperature-related trends in MAG recovery and diversity we categorized our samples into three groups according to temperature; cool (2–20 °C) Each column shows the percentage of total pre-processed metagenomic reads (relative abundance) that mapped to all 89 MAGs for samples ordered by increasing temperature from left to right on the x-axis (annotated by site numbers and depths in mbsf) and Hot) are separated by vertical dashed lines Each row shows the abundance profile of an individual MAG across all samples MAGs are color-coded by phylum on the left and annotated by GMP (Guaymas MAG Prokaryote) numbers 001 to 089 and order-level affinity to the right Panel section A denotes bacterial MAGs and panel section B denotes archaeal MAGs Relative MAG abundances are provided in the Source Data file Each column shows the percentage of total pre-processed metatranscriptome reads (relative abundance) that mapped to all 89 MAGs Relative transcript abundances are provided in the Source Data file Transcriptional activity of these MAGs suggests their inherent physiological adaptations to warm and reducing habitats are advantageous in the Guaymas Basin subsurface as well The nMDS plot depicts the correlation of Guaymas Basin MAG occurrence with in-situ environmental parameters (plot stress: 0.106) we show environmental variables with p-values < 0.05 resulting from a two-sided permutation test The directions of the arrows indicate a positive or negative correlation among the environmental parameters with the ordination axes (temperature p = 0.0445; dissolved inorganic carbon (DIC) Arrow length reflects correlation strength between environmental parameter and MAG occurrence and their temperature regimes are indicated by shape (circles for 2–20 °C; triangles for 20–45 °C and squares for 45–62 °C) nMDS plot parameters for samples and their MAGs are provided in the Source Data file the environmental parameters that impact MAG composition change downcore pH and salinity that impact MAGs in cool sediments to biogeochemical parameters reflecting terminal organic matter degradation DIC- and methane-enriched deep subsurface environment may select for specific phyla or taxa with autotrophic capabilities (e.g. become secondary to the impact of temperature itself In addition to genes for core metabolic processes (e.g. biosynthesis of nucleotides and amino acids) Guaymas Basin MAGs contain widespread genomic features that extend across multiple bacterial and archaeal phyla Some of these widespread genomic features have obvious adaptive value and are thus retained for survival while others challenge assumptions on subsurface adaptations and evolutionary constraints under subsurface conditions The Guaymas Basin subsurface yields predominantly MAGs affiliated with specific phylum-and order-level lineages that show distinct mesophilic and thermophilic preferences This suggests lineages appearing at specific depths and temperature ranges respond to environmental factors which in turn shape their occurrence patterns Our central working hypothesis is that the Guaymas Basin subsurface community is not a random assemblage but reveals phylogenetic and functional structure that can be tracked downcore Our account of this structured community focuses on dominant bacterial and archaeal phyla (Chloroflexota Hadarchaeota); an extended overview on further bacterial and archaeal MAGs is provided in the Supplementary Note the Guaymas Basin subsurface Chloroflexota generally prefer cool or moderately warm habitats Although the archaea contributed only 26 MAGs compared to 63 bacterial MAGs to our total, and represent fewer phylum-level lineages, they exhibit greater thermal range (Fig. 2) MAGS of two dominant archaeal phyla—the Thermoproteota (11 MAGs) and the Hadarchaeota (4 MAGs)—prefer warm and hot subsurface sediments and are introduced here in greater detail; additional archaeal lineages are discussed in the Supplementary Note Boxplots show estimated genome size of MAGs that recruited at least 0.1% of metagenomic reads from samples collected in cool (2–20 °C) The Median is shown as the middle horizontal lines and interquartile ranges are shown as boxes (whiskers extend to 1.5 times the interquartile range) Each data point is overlaid on the boxplots and values at the top denote adjusted p-values from two-sided partially overlapping samples t-tests comparing estimated genome sizes by temperature (panel A) and depth (panel B) regimes Panels C and D display the relationship between average estimated genome size in each metagenomic sample plotted against temperature (C) and depth (D) using linear regression The blue lines in panels C and D denote the regression lines with the fitted values +/− 1.96 standard error indicated by the grey bands The values at the top of panels C and D denote the p-value and adjusted R-squared value of the fit The Source Data file provides genome size estimates for MAGs contributing at least 0.1% of metagenomic reads for cool samples (n = 74) and hot samples (n = 5); genome size estimates for MAGs contributing at least 0.1% of metagenomic reads for shallow samples (n = 62) intermediate samples (n = 59) and deep samples (n = 21); and averaged MAG genome size estimates for each sample Panels A and B show the MAGs that recruited metagenomic reads from samples t sites U1547B and U1548B (in red) and sites U1545B and U1549B (in green) plotted against temperature (A) and depth (B) using best-fit linear regression The solid lines in panels A and B denote the regression lines the p-values and adjusted R-squared values of the fits of each regression line are shown and their depths and temperatures are provided in the Source Data file Whole round samples for DNA-based studies were capped with ethanol-sterilized endcaps transferred to the microbiology laboratory and stored briefly at 4 °C in heat-sealed tri-foil gas-tight laminated bags flushed with nitrogen until processing the exterior 2 cm of the extruded core section were removed using a sterilized ceramic knife sampling occurred immediately after core retrieval on the core receiving platform by sub-coring with a sterile Thirteen libraries were sequenced with NovaSeq S4 PE150 (Illumina) at the University of California and thirteen libraries were sequenced with NextSeq550 (Illumina) at the University of Delaware DNA Sequencing & Genotyping Center Metagenome sequence reads were deposited to the National Center for Biotechnology Information Sequence Read Archive under access numbers SRR23614663-23614677 and SRR22580794-SRR22580807 (Bioproject PRJNA909197) The CoverM tool automatically concatenated all the MAGs into a single file and metagenomic reads were recruited to MAG contigs setting the parameter --min-read-percent-identity to 95 and --min-read-aligned-percent to 50 The “Relative Abundance” CoverM method on the “genome” setting was used to calculate the percent of total metagenomic reads per sample that mapped to each of the 89 MAGs A custom R script was utilized to concatenate all coverM output files into a single file in a matrix format (with each sample representing a column and each row representing total percent of DNA-Seq reads per sample that mapped to a MAG) and was used for heatmap plotting MetaPathPredict cannot yet be applied to archaeal MAGs Gene annotations were generated for predicted genes from bacterial MAGs which generated predictions for the presence or absence of KEGG modules based on the gene annotations of all bacterial MAGs and resulting p-values were adjusted for multiple comparisons via Benjamini-Hochberg correction The average estimated genome size of MAGs that recruited at least 0.1% of reads from metagenomic samples (n = 26) was fitted using linear regression against temperature and depth measurements affiliated with the samples The number of non-redundant MAGs that recruited at least 0.1% of reads from metagenomic samples (n = 26) was fitted using linear regression against temperature and depth measurements affiliated with the samples Temperature values were interpolated for each sample using linear regression of the local thermal gradient (°C/m) multiplied by depth (mbsf) All 89 MAGs were individually scanned for secondary metabolic biosynthetic gene clusters using antiSMASH 6.092 with default parameters Resulting gene cluster prediction results (in GenBank format) were parsed and their gene content was analyzed Clusters with a total length less than 5kb were discarded from downstream analysis to minimize the inclusion of fragmented biosynthetic clusters in the analysis RNA was extracted from 19 sediment samples from sites U1545B-U1552B and a blank sample (control) using the RNeasy PowerSoil Total RNA Kit (Qiagen) following the manufacturer’s protocol with modifications which are discussed below RNA samples were prepared from samples spanning the depths 0.8 to 101.9 mbsf were first washed twice with absolute ethanol (200 proof; purity ≥ 99.5%) and sterile DEPC water (once) to reduce hydrocarbons and other inhibitory elements that otherwise resulted in low RNA yield 13-15 grams of frozen sediments were transferred into UV-sterilized 50 ml Falcon tubes (RNAase/DNase free) using clean autoclaved and ethanol-washed metallic spatulas Each sample transferred into the 50 ml Falcon tube received an equal volume of absolute ethanol and was shaken manually for 2 min followed by 30 seconds of vortexing at full speed to create a slurry Samples were spun in an Eppendorf centrifuge (5810R) for 2 minutes at 2000 x g The supernatant was decanted and after the second wash with absolute ethanol an equal volume of DEPC water was added into each sample and samples were spun for 2 minutes at 2000 x g and each sediment sample was immediately divided into three 15 mL Falcon tubes containing beads provided in the PowerSoil Total RNA Isolation Kit (Qiagen) The RNA extraction protocol was followed as suggested by the manufacturer with the modification that the RNA extracted from the three aliquots was pooled into one RNA collection column All steps were performed in a UV-sterilized clean hood equipped with HEPA filters Surfaces inside the hood and pipettes were thoroughly cleaned with RNase AWAYTM (Thermo Scientific™) before every RNA extraction and in between extraction steps Each 25 μl PCR reaction was prepared using 0.5 U μl–1 GoTaq® G2 Flexi DNA Polymerase (Promega) 4 μM of each primer (final concentrations) PCR reactions used an Eppendorf Mastercycler Pro S Vapoprotect (Model 6321) thermocycler with following conditions: 94 °C for 5 min The PCR products were run in 2% agarose gels (Low-EEO/Multi-Purpose/Molecular Biology Grade Fisher BioReagents™) to confirm absence of DNA amplification All steps through cDNA preparation were completed the same day to avoid freeze/thaw cycles cDNAs were submitted to the Georgia Genomics and Bioinformatics Core for sequencing using NextSeq 500 PE 150 High Output (Illumina) The cDNA library generated from our control did not contain detectable DNA It was nonetheless submitted for sequencing but it failed to generate any sequences that met the minimum length criterion of 300-400 base pairs and metatranscriptome reads were recruited to MAG contigs A custom R script was utilized to concatenate all coverM output files into a single file in a matrix format with each sample representing a column and each row representing total percent of RNA-Seq reads per sample that mapped to a MAG The output was used in this study for heatmap plotting to examine evidence for activity of the taxa for which we recovered MAGs Metatranscriptome reads were deposited to the National Center for Biotechnology Information Sequence Read Archive under accession numbers SRR22580929-SRR22580947 (Bioproject PRJNA909197) Approximately 2 cm3 sub-cores were immediately put into tubes containing fixation solution consisting of 8 mL of 3xPBS (Gibco™ PBS Fischer) and 5% (v/v) neutralized formalin (Thermo Scientific™ Shandon™ Formal-Fixx™ Neutral Buffered Formalin) 100 mM ethylenediamine tetraacetic acid [EDTA] The mixture was thoroughly shaken for 60 min (Shake Master and subsequently sonicated at 160 W for 30 s for 10 cycles (Bioruptor UCD-250HSA; Cosmo Bio The sample was transferred onto a set of four density layers composed of 30% Nycodenz (1.15 g cm–3) and 67% sodium polytungstate (2.08 g cm–3) Cells and sediment particles were separated by centrifugation at 10,000 × g for 1 h at 25 °C The light density layer was collected using a 20G needle syringe and centrifuged at 5000 × g for 15 min at 25 °C The sediment was resuspended using 2.1 mL of 2.5% NaCl and 300 μL of detergent mix and shaken at 500 rpm for 60 min at 25 °C Further information on research design is available in the Nature Portfolio Reporting Summary linked to this article The limits of life and the biosphere in Earth’s interior Weathering and biodegradation of hydrothermal petroleum in the north rift of Guaymas Basin Initial Reports of the Deep-Sea Drilling Project Characteristics and evolution of sill-driven off-axis hydrothermalism in Guaymas Basin–the Ringvent site scalable and accurate tool for assessing microbial genome quality using machine learning Expanded diversity of microbial groups that shape the dissimilatory sulfur cycle FeGenie: a comprehensive tool for the identification of iron genes and iron gene neighborhoods in genome and metagenome assemblies Proteomic study of Desulfovibrio ferrophilus IS5 reveals overexpressed extracellular multi-heme cytochrome associated with severe microbiologically influenced corrosion Diversity of rare and abundant prokaryotic phylotypes in the Prony Hydrothermal Field and comparison with other serpentinite-hosted ecosystems Metabolic strategies shared by basement residents of the Lost City hydrothermal field Microbial diversity and sulfur cycling in an early Earth analogue: From novelty to modern commonality Genomic and transcriptomic evidence for carbohydrate consumption among microorganisms in a cold seep brine pool Regulation of bacterial virulence by two-component systems Two-component systems and their co-option for eukaryotic signal transduction In vivo effects of sporulation kinases on mutant Spo0A proteins in Bacillus subtilis a highly conserved redox-responding global two-component regulatory system Enhancing production of bio-isoprene using hybrid MVA pathway and isoprene synthase in E Fungal and prokaryotic activities in the marine subsurface biosphere at Peru Margin and Canterbury Basin inferred from RNA-based analyses and microscopy Recent studies on bacterial populations and processes in subseafloor sediments: A review Metabolic strategies of marine subseafloor Chloroflexi inferred from genome reconstructions Community genomic analyses constrain the distribution of metabolic traits across the Chloroflexi phylum and indicate roles in sediment carbon cycling Depth-discrete metagenomics reveals the roles of microbes in biogeochemical cycling in the tropical freshwater Lake Tanganyika Characterization of an Aldehyde Oxidoreductase from the mesophilic bacterium Aromatoleum aromaticum EbN1 a member of a new subfamily of tungsten-containing enzymes Valid publication of the names of forty-two phyla of prokaryotes Proteogenomic analyses indicate bacterial methylotrophy and archaeal heterotrophy are prevalent below the grass root zone Comparative genomics reveals thermal adaptation and a high metabolic diversity in Candidatus Bathyarchaeia Predominant archaea in marine sediments degrade detrital proteins Archaeal diversity in waters from deep South African gold mines Expression of divergent methyl/alkyl coenzyme M reductases from uncultured archaea Methyl/alkyl-coenzyme M reductase-based anaerobic alkane oxidation in archaea Evolutionary genomics of defense systems in Archaea and Bacteria Growth temperature and genome size in bacteria are negatively correlated suggesting genomic streamlining during thermal adaptation Environmental stress leads to genome streamlining in a widely distributed species of soil bacteria Microbiomes in the Challenger Deep slope and bottom-axis sediments Interactions between temperature and energy supply drive microbial communities in hydrothermal sediment Biogeography and ecology of the rare and abundant microbial lineages in deep-sea hydrothermal vents New microbial biodiversity in marine sediments including biosphere: geosphere interactions Pyrite formation from FeS and H2S is mediated through microbial redox activity Influence of commercial DNA extraction kit choice on prokaryotic community metrics in marine sediment Andrews, S., et al. (2012). FastQC: a quality control tool for high throughout sequence data. Babraham Institute, UK. http://www.bioinformatics.babraham.ac.uk/projects/fastqc 0: a fast and scalable metagenome assembler driven by advanced methodologies and community practices MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets Binning metagenomic contigs by coverage and composition Efficient architecture-aware acceleration of BWA-MEM for multicore systems 2019 IEEE International Parallel and Distributed Processing Symposium (IPDPS) METABOLIC: high-throughput profiling of microbial genomes for functional traits Geller-McGrath, D., et al. (2022). MetaPathPredict: A machine learning-based tool for predicting metabolic modules in incomplete bacterial genomes. BioRxiv, https://doi.org/10.1101/2022.12.21.521254 (2022) Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples R. Core Team (2018). R: A language and environment for statistical computing. R Core Team R Foundation for Statistical Computing, Vienna, Austria. Available online at https://www.R-project.org/ Package ‘ggplot2.’ create elegant data visualizations using the grammar of graphics How to compare the means of two samples that include paired observations and independent observations: A companion to Derrick antiSMASH 6.0: improving cluster detection and comparison capabilities Geller-McGrath, D. Metagenomic profiles of Archaea and Bacteria within thermal and geochemical gradients of the Guaymas Basin deep subsurface. Zenodo https://zenodo.org/record/8422630 (2023) Download references The authors would like to acknowledge the crew and entire science party for IODP Expedition 385 for their assistance with sample collection Without their assistance this study would be impossible The authors would also like to thank Gustavo Ramírez for his assistance with DNA extractions using his method We thank Mark Shaw and Bruce Kingham in the University of Delaware DNA Sequencing & Genotyping Center for assistance with sample preparation and Illumina sequencing This study was supported by NSF Grant OCE-2046799 to VE and YM took primary responsibility for collecting the samples during IODP Expedition 385 together with shipboard scientists served as Co-Chief Scientist of IODP Expedition 385 extracted DNA and RNA for metagenomes and metatranscriptomes prepared metagenome libraries for sequencing DGM took primary responsibility for bioinformatic processing of metagenome data and mapping of transcripts to MAGs analyzed the MAG data and VE and AT contributed to data interpretation co-wrote the first draft of the manuscript and all authors contributed to its final form Nature Communications thanks Rika Anderson reviewer for their contribution to the peer review of this work Download citation DOI: https://doi.org/10.1038/s41467-023-43296-x Something new will open in former Guaymas location by 2019 Representatives declined to comment on the cuisine or concept that could occupy Guaymas Given Mina’s extensive stable of restaurants though there’s always the possibility of dropping in an entirely new concept — perhaps even one that’s been tested in the group’s Mina Test Kitchen a Mexican collaboration with Houston chef Hugo Ortega the Italian coastal pop-up from chef Adam Sobel would certainly be comfortable additions to the sleepy dining scene in Tiburon Guaymas lingered there for over thirty years; it most recently served mediocre Mexican food at the hands of Specialty Restaurants Corporation, which purchased it in 2008. Former SF Chronicle critic Michael Bauer skewered it with a one-star review in 2016 that declared the complimentary tortilla chips to be the best part of the meal there Onward and upward; stay tuned for more details on exactly what Mina Group plans for the space Metrics details organic-rich hydrothermal sediments produce complex hydrocarbon mixtures including saturated We examined sediments from push cores from Guyamas sites with distinct temperature and geochemistry profiles to gain a better understanding on abiotic and biological hydrocarbon alteration Here we provide evidence for biodegradation of hopanoids producing saturated hydrocarbons like drimane and homodrimane as intermediate products These sesquiterpene by-products are present throughout cooler sediments but their relative abundance is drastically reduced within hotter hydrothermal sediments Within the sterane pool we detect a trend toward aromatization of steroidal compounds within hotter sediments The changes in hopane and sterane biomarker composition at different sites reflect temperature-related differences in geochemical and microbial hydrocarbon alterations In contrast to traditionally observed microbial biodegradation patterns that may extend over hundreds of meters in subsurface oil reservoirs Guaymas Basin shows highly compressed changes in surficial sediments the available evidence from surficial and deep subsurface sediments indicates that the transformation of sedimentary organic matter into hydrocarbons is a persistent and widespread process in Guaymas Basin that Such activities of microorganisms would contribute to the complex carbon pools available under the sulfidic and anoxic conditions of these hydrothermal sediments They also may provide sensitive bioindicators for the early stages of microbial diagenesis in organic-rich hydrothermal sediments The Cathedral Hill site (4991) and Marker 14 (4998) sites are covered with white, yellow and orange mats of sulfur-oxidizing bacterial mats (Beggiatoaceae). The two sites differ by temperature gradient. Scale bars are 10 cm based on Alvin’s laser beam scaler and the diameter of Alvin pushcores. Courtesy of Andreas Teske, U. North Carolina, Chapel Hill/NSF/AUV Sentry/2016 ©Woods Hole Oceanographic Institution. The large peaks in chromatograms a–f are = o-terphenyl and perdeuterated tetracosane internal standards added during the sample preparation is shown as a 3D GC×GC-HRT mountain plot (a) and as color contour plot of the same GC×GC-HRT chromatogram (b) Annotated peaks include polynuclear aromatic hydrocarbon (PAHs) compounds as well as sesquiterpanes These chromatograms compare the presence and relative abundance of hydrocarbons in the core top compared to about mid-level in the core The Cathedral Hill core 4991-7 (a) compares the 0–6 and 12–18 cm depth intervals The Marker 14 core 4998-15 (b) hydrocarbons in the 0–7 and 14–21 cmbsf depth intervals Compounds that remain at the same abundance throughout the core vanish in the subtraction chromatogram (cancelletion) Red peaks highlight compounds with positive values lower core depth (12–18 and 14–21 cmbsf) intervals were subtracted from the 0–7 cmbsf interval Red peaks represent hydrocarbons that are more abundant in the 0–7 cmbsf interval blue peaks represent negative values and indicate greater relative abundance in the deeper depth interval red peaks indicate compounds present in higher abundance in the surficial depth interval and blue peaks are those more abundant down core and cyanobacteria are therefore likely to only be minor contributors to the hopane pool The molecules 17α(H),21β(H)-hopane and cholestane were used as model compounds Blue arrows indicate microbial biodegradation transforming hopanoids to sesquiterpanes and red arrows indicate abiotic oxidation to form aromatized hopanoid and steroid compounds This strongly skewed distribution and abundance pattern in hot core 4998-15 and the much more gradual concentration changes of these degradation products in the temperate core 4991-7 suggest different degrees of hydrothermal mobilization and concentration towards surficial sediments a Shows aromatization of the ααα-steranes b shows resulting C-ring monoaromatic steroidal compounds and c shows resulting triaromatic steroidal compounds triaromatic steranes are unlikely to be retained long-term We speculate that due to the volcanic or hydrothermal heat at both sites (Uzon caldera and Guaymas Basin) the accumulating deposition-derived sterane signal is more widely detectable in the upper sediment than the bacterial hopanoid pool that represents indigenous bacterial communities inhabiting the relatively narrow habitable zone in hot sediment the sesquiterpanoids are derived from hopanoid precursor molecules therefore most reasonable that the adundant Guaymas sesquiterpanoids resulted from the transformation of hopanoids Guaymas Basin sediments thus show clear evidence of microbially catalyzed hopane degradation This microbial breakdown of hopane could contribute to the carbon pools available under the sulfidic and anoxic conditions occurring in the Guyamas Basin hydrothermally distinct sediments Peak assignments start at F to correlate with Supplementary Fig and K are the hopanoids 17α(H),22,29,30-trisnorhopane and Q are the hopenes identified as 17(21)-hopene and S are hopanoids that contain an oxygen hetero atom Fossil fungal hyphae samples from fractured bedrock contained a quite significant number of hopanoids ranging from C27 to C35 Since Guaymas sediments harbor diverse fungal phyla including zoosporic fungi (e.g Chytridiomycota) and Neocallimastigomycota (21) it remains to be investigated whether Neocallimastigomycota and/or other fungal phyla utilize hopanoids to substitute for sterols under anoxic and sulfidic conditions or whether novel hopanoids are part of their membrane mosaic moderate temperature gradients extend the zone of hydrocarbon and biomarker accumulation deeper into the sediments than at hotter Marker 14 where steep temperature gradients compress the zone of hydrocarbon and biomarker accumulation into the top ~7 cmbsf and they provide an attractive model system for exploring the microbial mechanisms pathways and agents of hydrocarbon degradation in compound- and microbe-specific detail Microbial mat-covered hydrothermal sediments were thermally profiled using Alvin’s 50 cm heat flow probe (https://ndsf.whoi.edu/alvin/using-alvin/sampling-equipment/) The 50 cm probe contains five thermal sensors every 10 cm starting 5 cm under the attached plastic disk (the “puck”) that limits probe penetration and rests on the seafloor once the probe is fully inserted first with the puck 5 cm above the seafloor temperature readings stabilized and were recorded within Alvin Sediment cores were divided into three depth horizons of 6–10 cm thickness ~40 ml subsamples of each depth horizon were aliquoted into two sterile 50 ml Falcon tubes and were immediately centrifuged at 3000 rpm for 15 min to separate porewater from sediment cakes the porewaters were carefully collected using a 60 ml sterile syringe and filtered through a 0.45 μm cellulose filter (Millipore Porewater samples of ~20 ml were collected into gas-tight serum vials sealed with black stoppers and crimp seal and stored at 4 °C The sediment cakes from each horizon were kept in 50 mL Falcon tubes and stored at 4 °C until hydrocarbon analysis Highly resolved GC×GC FID chromatographic analyses were performed as described previously (17) using a LECO system consisting of an Agilent 7890A GC configured with a split/splitless auto-injector (7683B series) and a dual-stage cryogenic modulator (LECO Samples were injected in the splitless mode The cold jet gas was dry N2 and chilled with liquid N2 The hot jet temperature offset was 5 °C above the temperature of the secondary GC oven and the inlet temperature was isothermal at 310 °C Two capillary GC columns were utilized in this GC×GC experiment First- and second-dimension separations were performed on a Restek Rxi-1ms column (60 m length 0.25 μm df) and a 50% phenyl polysilphenylene-siloxane column (SGE BPX50 The temperature program of the main oven was held isothermal at 65 °C (12.5 min) and was then ramped from 65 to 340 °C at 1.25 °C min−1 The second-dimension oven was isothermal at 70 °C (12.5 min) and then ramped from 70 to 345 °C at 1.25 °C min−1 while the modulation period between stages was 7.50 s with a 3.00 s cooling period between modulations FID data were sampled at an acquisition rate of 100 data points per second The GC×GC was configured for splitless auto-injection Hydrogen as carrier gas was at a constant flow of 1 mL/min GC×GC − HRT chromatographic analysis was performed on a LECO Pegasus GC×GC − HRT 4D system consisting of an Agilent 7890B GC configured with a LECO LPAL3 split/splitless auto-injector system and a dual-stage cryogenic modulator (LECO The cold jet gas was dry N2 chilled with liquid N2 The hot jet temperature offset was 10 °C above the temperature of the main GC oven and the inlet temperature was isothermal at 310 °C 0.25 μm df) and a SGE BPX-50 column (2 m length The temperature program of the main oven was held isothermal at 60 °C (5 min) and was then ramped from 60 to 335 °C at 1.5 °C min−1 The hot jet pulse width was 2 s with a modulation period of 10 s The second-dimension oven was held isothermal at 65 °C (5 min) and was then ramped from 65 to 340 °C at 1.5 °C min−1 The carrier gas was helium at a flow rate of 1 mL min−1 HR-TOF data were sampled at an acquisition rate of 100 spectra per second (actual data collection rate was 97.2222 spectra per second) in the mass range of 40−600 amu The ionization method was electron ionization (EI) with an electron energy of −70 V and the extraction frequency was 1.75 kHz GC×GC-FID and GC×GC-HRT data were acquired and analyzed using LECO ChromaTOF®software version 5.21 Hydrocarbons and their fate in Guaymas Basin sediments have been studied previously using laboratory experiments and analytical techniques Here we provide for the first time an extensive assessment of ~200 semivolatile hydrocarbon compounds in porewaters and sediment cakes from AUV Alvin push cores and discuss their overall distribution and fate at three distinct hydrothermal areas located the southern axial trough of Guaymas Basin These sites are known for their contrasting biogeochemistry and thermal profiles We couple these data with in-depth GCxGC investigation on the biomarker profile of the most contrasting sediment cores (from Cathedral Hill vs Marker 14) to provide information on the presence/distribution of predominant indicators of microbial hydrocarbon degradation (e.g. C-ring monoaromatic and triaromatic steranes) that could derive from early diagenesis and/or the existing oxidative conditions in Guaymas Basin We illustrate the changing composition of saturated and alkylated polyaromatic hydrocarbons in these deep hydrothermal seep sediment cores from contrasting sites providing a more detailed understanding of hydrothermal and biological hydrocarbon alteration in this setting Further information on research design is available in the Nature Research Reporting Summary linked to this article C1-C8 hydrocarbons in sediments from Guaymas Basin Gulf of California—comparison to Peru Margin 14.C ages of hydrothermal petroleum and carbonate in Guaymas Basin In Marine Hydrocarbon Seeps—Microbiology and Biogeochemistry of a Global Marine Habitat (eds Teske Organic petrography and extractable hydrocarbons of sediments from the Eastern North Pacific Ocean In Initial Reports of the Deep-Sea Drilling Project (eds Curray In InitialReports of the Deep Sea Drilling Project (eds Curray 385 (International Ocean Discovery Program Recent high-resolution mapping of Guaymas hydrothermal fields (Southern Trough) Hydrocarbon transformations in sediments from the Cathedral Hill hydrothermal vent complex at Guaymas Basin Gulf of California—a chemometric study of shallow seep architecture Microbial hydrocarbon degradation in Guaymas Basin—exploring the roles and potential interactions of fungi and sulfate-reducing bacteria Tracking the weathering of an oil spill with comprehensive two-dimensional 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(American Association of Petroleum Geologists Memoir and fluid-inclusion microthermo-metry of seafloor hydrothermal deposits in the southern trough of Guaymas Basin Prospects for commercial production of diatoms Chemical properties of biosilica and bio-oil derived from fast pyrolysis of Melosira varians Algal origin of sponge sterane biomarkers negates the oldest evidence for animals in the rock record Confined-pyrolysis as an experimental method for hydrothermal organic synthesis Characterization of hydrothermally generated oil from the Uzon caldera Petroleum biodegradation and oil spill bioremediation Aerobic biodegradation of hopanes and other biomarkers by crude oil-degrading enrichment cultures A novel microbial hydrocarbon degradation pathway revealed by hopane demethylation in a petroleum reservoir Biomarkers in crude oil revealed by comprehensive two-dimensional gas chromate-graphy time-of-flight mass spectrometry: depositional paleoenvironmental proxies Identification of some bicyclic alkanes in petroleum and tetraaromatic hopanes in Kukersite share and their stable carbon isotopic composition Identification and quantification of polyfunctionalized hopanoids by high temperature gas chromatography–mass spectrometry Biodegradation of aromatic hydrocarbons in crude oils from the Barrow Sub-basin of Western Australia Interpreting Molecular Fossils in Petroleum and Ancient Sediments (Prentice-Hall Close association of active nitrifyers with Beggiatoa mats covering deep-sea hydrothermal sediments Bacterial community structure from Guaymas Basin as determined by analysis of phospholipid ester-linked fatty acids Biogeochemical evidence that thermophilic archaea mediate the anaerobic oxidation of methane Microbial communities of hydrothermal Guaymas Basin surficial sediment profiled at 2 millimeter-scale resolution Asgard archaea are capable of anaerobic hydrocarbon cycling Download references We thank the Alvin and Sentry teams for their expertise and the science crew for collegial support during Guaymas Basin cruise AT42-05 Carol Arnosti (University of North Carolina-Chapel Hill) for their helpful comments and suggestions on the manuscript This work was supported by NSF OCE-1829903 to V.E Mexican sampling permits are noted in the cruise authorization CTC no Department of Marine Chemistry and Geochemistry conceived the project and acquired funding and all authors contributed to the final writing and editing Communications Earth & Environment thanks Meijun Li and the other, anonymous, reviewer(s) for their contribution to the peer review of this work. Primary Handling Editors: Olivier Sulpis, Joe Aslin, Heike Langenberg. Peer reviewer reports are available Download citation DOI: https://doi.org/10.1038/s43247-022-00582-8 Sonora is reeling from an armed attack late last week that left three people dead and two others seriously injured. One of those killed was a woman taking part in a protest against gender violence. This weekend, feminist groups in Sonora and across Mexico held marches and vigils in honor of Marisol Cuadras — an 18-year-old activist killed during an attack on the municipal palace in Guaymas, Sonora. Cuadras belonged to the local collective Feministas del Mar that was there demanding women’s safety as part of a peaceful demonstration on International Day for the Elimination of Violence Against Women. Authorities have said the attack was not directed at the protesters, but at the local security head — a military captain appointed in 2019 as part of a federal plan to address violence by putting military leaders at the helm of local police in Sonora. “We’re seeing, sadly, in the most painful way, that this strategy isn’t working,” said Krimilda Bernal, director of the citizen watchdog Sonora Security Observatory. “The military heads are really not improving security at the local level.” Instead, she said, the states increasing dependence on the military has coincided with increasing violence across the state, where murders are at an all-time high. Cuadras, who turned 18 in March, was studying renewable energy at a local college. She has been described by family and friends as a environmental activist and a proud feminist. A bodyguard for the mayor, Antelmo Eduardo, 40, was also killed during the attack, as was one of the attackers, who authorities identified Sunday as a 49-year-old window washer believed to have been recruited by criminal groups. Another young woman at the protest and a press person for the mayor were also severely injured. Mexico’s president recently detailed major infrastructure investments that will help the Sonoran port city of Guaymas. In the initial phase, President Andres Manuel Lopez Obrador said that some 5 billion pesos — or roughly $250 million — will be invested in the city’s port, as well as a new highway to the city. Half of that will go toward modernizing the port itself: reinforcing docks, expanding the port and adding cranes, according to AMLO, as the president is widely known. That will make it easier to use for shipping grains and cars produced in Sonora, which sometimes have to be moved as far south as Sinaloa to be loaded onto ship. Volume 4 - 2017 | https://doi.org/10.3389/fmars.2017.00417 the presence at a few tens of kilometers of cold seeps and hydrothermal vents coupled with comparable sedimentary settings and depths offer a unique opportunity to assess and compare the microbial community composition of these deep-sea ecosystems The microbial diversity in sediments from three cold seep and two hydrothermal vent assemblages were investigated using high-throughput 16S rRNA-sequencing Numerous bacterial and archaeal lineages were detected in both cold seep and hydrothermal vent sediments Various potential organic matter degraders (e.g. MBG-D) and methane and sulfur cycling related microorganisms (e.g. sulfate-reducing lineages) were detected in both ecosystems This suggests that analogous metabolic processes such as organic matter degradation and anaerobic methane oxidation coupled to sulfate reduction were probably occurring in these two contrasted ecosystems These highlighted “core microbiome” of the Guaymas Basin chemosynthetic ecosystems might therefore result from the combined presence of up-rising fluid emissions and high sedimentary rates of organic matter in the Basin coupled with the detailed ribotype analysis of major archaeal lineages (ANME-1 also suggest a potential connectivity among deep-sea ecosystems of the Guaymas Basin likely due to the sedimentary context and the absence of physical border thermophilic and hyperthermophilic lineages (e.g. etc.) were exclusively identified in hydrothermally impacted sediments highlighting the strong influence of temperature gradients and other hydrothermally-related factors such as thermogenic sulfate reduction and sulfide formation on microbial community composition these results remain hardly comparable since different methodologies were used the aim of this study is to compare Guaymas Basin cold seep and hydrothermal vent sedimentary ecosystems functioning through the analysis of the microbial community composition Diversity and spatial distribution of microbial communities were investigated to determine to what extent the microbial communities inhabiting seep and vent sediments are comparable in the unique context of the Guaymas Basin we focused our work on the identification of the main drivers explaining the highlighted singularities and/or similarities between these two nearby ecosystems To answer these questions, sediment cores from three cold seep sites (Vasconcelos BIG13, Ayala BIG14, and Vasconcelos BIG18 sites) and two hydrothermal vent sites (Morelos and MegaMat sites) in the Guaymas Basin, which exhibited comparable surface assemblages (vesicomyid clams or microbial mat, Figure 1) were investigated diversity and distribution of microbial communities from the seawater/sediment interface down to 12 cmbsf were explored using 454-pyrosequencing coupled with geochemical analyses all the samples were collected during the same oceanographic cruise and analyzed in identical conditions by the same experimenters and with the same methodological approach Bathymetric map of the Sonora Margin (cold seep area) and Southern Trough (hydrothermal vent area) in the Guaymas Basin Localization and pictures of the sampling sites Five contrasted sediment areas of the Guaymas Basin were explored in this study Three cold seep sites located at the Sonora Margin and two hydrothermal vent sites located at the Southern Trough were investigated Sediment samples were collected using 20-cm long push cores operated by the manned submersible Nautile during the “BIG” cruise (June 2010) Sampling sites were selected according to visual observations of the seafloor and methane plumes in the water column Two cold seep sites (Ayala and Vasconcelos BIG13) and one hydrothermal vent site (Morelos) were colonized by chemosynthetic vesicomyid bivalves (Figure 1 was covered by abundant and scattered vesicomyid aggregates distributed on an estimated area within a 10-m radius located 1 km away from the Ayala site and at 1,570 m water depth was characterized by vesicomyid populations surrounding a large and thin microbial mat located at 2,007 m water depth in the hydrothermal field was colonized by vesicomyid populations surrounding a large area of sediments covered by a thin white layer Two sites hosted thick microbial mats at the sediment surface: the Vasconcelos BIG18 cold seep site and the MegaMat hydrothermal vent site (Figure 1, Table S1). The Vasconcelos BIG18 site, located 30 m away from the vesicomyid Vasconcelos BIG13 site, was colonized by a thick white Beggiatoa-like mat (called WM14 in Vigneron et al., 2013) whereas sediment surface at the MegaMat site located about 240 m south from the Morelos vesicomyid site was covered with white and yellow microbial mats near a hydrothermal mound overgrown by Riftia bushes Temperature measurements were performed in situ using an independent thermal lance T-Rov (NKE Electronics France) for cold seep habitats or using the temperature sensor of the submersible for hydrothermal vent sediments sediment cores were immediately transferred in cold room (~8°C) for sub-sampling Sediment cores were cut into 2-cm thick layers and then frozen at −80°C for further nucleic acid extractions Replicate of crude DNA extracts were then pooled together whatever the extraction method used and purified using the Wizard DNA clean-up kit (Promega WI) according to the manufacturer instructions Purified DNA extracts were stored at −20°C The primers were fused to 5- to 10-nucleotide key tags and to the 454 GS-FLX sequencing adaptor using the Lib-A chemistry To allow multiplex sequencing of the 22 different samples (five sampling locations with the different sediment sections) fusion primers were designed to minimize secondary structures and following Roche recommendations (Table S3) The 16S rRNA genes amplifications were performed under the following conditions: 10 min at 95°C for denaturation then 30 cycles for Bacteria or 35 cycles for Archaea with 30 s at 95°C and 45 s at 72°C followed by a final elongation step of 6 min at 72°C PCR amplifications were performed in triplicate using Brilliant III Ultra-Fast SYBR® Green QPCR Master Mix (Agilent Technologies 0.5 μM of each primer (Eurofins MWG Operon The final volume was adjusted to 25 μL with sterile water Absence of contaminations was checked by negative controls PCR products were pooled and purified on TAE agarose gel (1.2%) using PCR clean-up Gel extraction Nucleospin® Gel and PCR clean-up kit (Macherey-Nagel Microfluidic digital PCR (Fluidigm Corporation CA) was used to quantify nucleic acids in purified amplicons Amplicon products obtained for each PCR replicate were mixed equimolarly (108 molecules per microliter of each amplicon) Emulsion PCR and sequencing were then performed on a 454 Life Sciences Genome Sequencer GS-FLX (PicoTiterPlate divided in four regions; Roche Diagnostics emulsion PCR and sequencing were performed by the Biogenouest platform (Rennes and (v) affiliated to Archaea when Bacteria was targeted and inversely were removed from the dataset Using the tag combinations, sequences were assigned to their respective sample. Sequences were pre-clustered using the Mothur pipeline, as recommended to reduce potential pyrosequencing errors (Schloss et al., 2009) Then samples were normalized and all the following analyzes were performed on the same number of sequences per sample for the bacterial (1,096 sequences) and the archaeal (1,413 sequences) regions Sequences have been assigned to a same taxonomical level (phylum or genus) within an analysis The sequences that could not be assigned to the taxonomical level used were affiliated to “Unclassified” followed by the lowest identified taxonomical level (e.g. The raw sequencing data have been submitted to the NCBI database under BioProject accession numbers PRJNA278499 and PRJNA394915 whereas up to 0.18 mM of methane were detected at 15 cmbsf in sediment core of Morelos vesicomyid vent site Geochemical profiles in sediments of the Guaymas Basin dissolved sulfate (full and empty diamond) and dissolved sulfide (full and empty circle) concentrations in porewater sediments White areas correspond to depth of sediment cores used for microbial community analysis Sediment cores were from vesicomyid habitats: (A) Ayala—cold seeps and from microbial mat habitats: (D) Vasconcelos BIG18—cold seeps and (E) MegaMat M27—hydrothermal vent In situ temperature measurements at the cold seep sites (Vasconcelos BIG18 Ayala and Vasconcelos BIG13) indicated a constant temperature around 3°C throughout the forty-first centimeters of sediments By contrast in the hydrothermal vent area the temperature increased with depth temperature increased from 3.2°C at 5 cmbsf to 15.6°C at 55 cmbsf whereas the temperature strongly increased in MegaMat microbial mat vent sediments and up to 120.5°C at 50 cmsbf below the white microbial mat and 113°C at 10 cmbsf and up to 123°C at 50 cmbsf in sediment underlying the yellow microbial mat (Figure S1) All sediment cores had a limited oxygen depth penetration ranging from 0.2 to 0.55 cmbsf After sequence quality filtering, a total of 37,261 partial 16S rRNA gene sequences were used for the bacterial community composition analysis. Taxonomic affiliation of the sequences highlighted different bacterial community structures according to sampling sites (Figure 4 and Table S6) Venn diagrams representing the proportion of shared bacterial and archaeal taxa at phylum and genus levels Numbers in brackets correspond to the number of different lineages Taxa indicated in black were selected as representative taxa of seep and vent sediment microbial communities Relative abundance of bacterial and archaeal taxa (16S rRNA gene sequences affiliated to taxonomical level 6) detected in vesicomyid and microbial mat habitats both for cold seep and hydrothermal vent areas Bacterial and archaeal groups represented <1% of the sequenced reads were clustered in “Other.” The environmental variables explained 57.4 and 62.9% of the variance in archaeal and bacterial community composition and the RDA models were significant (p = 0.001) After sequence quality filtering, a total of 48 042 partial 16S rRNA gene archaeal sequences were analyzed to explore the archaeal community composition (Figure 4 and Table S5) Statistical analysis of community composition highlighted distinct archaeal community compositions between the different habitats (Figures 4 and Figure S2). RDA analyses indicated that temperature and dissolved sulfide porewater concentration were the main environmental parameters shaping the archaeal community composition in the samples (p = 0.002, Figure 5) representing 70% of the MBG-D 16S rRNA gene sequences were detected in both cold seep and hydrothermally-influenced sediments Network representing ribotype (16SrRNA sequences being identical at 99.6% similarity) distribution among the ANME-1 (A) and MBG-D (C) lineages according to the sampling sites Each circle represents a ribotype and diameter of the circles represents the number of sequences included in each ribotype (keys to the node size represent the highest number the lowest number and an intermediate value Color of the circles illustrates the proportion of the sequences detected in each sampling site (blue and light blue: microbial mat and vesicomyid cold seep sites red and light red: microbial mat and vesicomyid hydrothermal vent sites) Singletons were removed for this analyses to make the graphs more readable The three lineages represented were selected as representative taxa of chemosynthetic ecosystems detected in hydrothermal vent sites as well as cold seep sites in our study The Guaymas Basin is a unique environment which harbors not only hydrothermal chimneys, mounds (Callac et al., 2015) and hydrothermally impacted sediments (i.e., sediments percolated by hydrothermal fluid) (Teske et al., 2002) but also cold seep sediments (Vigneron et al., 2013; Cruaud et al., 2015) area of hydrothermally impacted sediments and cold seep sediments were investigated to compare the microbial community compositions and potential functions present in these contrasted ecosystems in absence of physical borders and in a similar geochemical context characterized by the accumulation of organic-rich sediments comparable temperature conditions were also detected at the seawater/sediment interface (Figure S1) These common features are likely due to the unusual sedimentary context of the Basin This suggests that the presence of a comparable shallow microbial community in both cold seep and hydrothermal sediments was likely allowed by the seawater cooling of the hydrothermal sediments (<20°C at 5 cmbsf; Figure S1) Although predicting functional profiles from 16S rRNA data and related known lineages can be misleading some potential metabolic capacities can be hypothesized from the community composition identified in the sediments these potential organic matter degraders might represent an important proportion of the “core microbiome” of the Guaymas Basin chemosynthetic areas hydrocarbons of the seepages might sustain similar microbial functions in these two ecosystems resulting in visually similar landscape on the seafloor as well as the other potential sulfate reducing lineages identified in these sediments (e.g. potentially allowing transient crossing of vesicomyids the sampled sediments in the Morelos site might be not sufficiently influenced by the metabolism of the bivalves (exudates bioturbation) and the difference of microbial community composition between vesicomyid-colonized sediments might also be due to an influence of the hydrothermal fluid on vesicomyids behavior Nonetheless, the proportion of endemic microorganisms was correlated with temperature, confirming that this parameter might be one of the key constraints on the spatial extent, physiological and phylogenetic diversity, and biogeochemical function in marine sediment microbial communities (Teske et al., 2014) more than high temperature conditions specific to the hydrothermal vent area other hydrothermal activity-related features such as abiotic reactions and vesicomyids behavior toward hydrothermal fluid emission might shape the sedimentary microbial community composition and associated metabolisms and might also be likely responsible for the differences observed between these two environments Finally, the existence of similar microbial populations in the surface sediments of the two ecosystems and the potential continuity revealed by ribotype network analyses of archaeal lineages support the hypothesis of a potential connectivity among deep-sea ecosystems (Portail et al., 2016) microorganisms might be dispersed globally across the seafloor or the hydrosphere and environmental conditions (temperature specific compounds associated with hydrothermal fluids) might then select specific and highly adapted microorganisms and J-CC: performed laboratory work; PC and AV: analyzed the data; PC and M-AC-B: discussed and wrote the manuscript We are indebted to the crews of the research vessel l'Atalante and the submersible Nautile of the cruise “BIG” and the scientific team for their work on board This cruise was funded by IFREMER (France) and has benefited from a work permit in Mexican waters (DAPA/2/281009/3803 and Sophie Coudouel for helpful scientific discussions This study was supported by a Carnot Institute funding and by 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This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY) *Correspondence: Perrine Cruaud, cGVycmluZS5jcnVhdWRAZ21haWwuY29t Volume 6 - 2019 | https://doi.org/10.3389/fmars.2019.00815 This article is part of the Research TopicCurrent Topics in Marine Organic Biogeochemical ResearchView all 21 articles The Guaymas Basin spreading center situated in the Gulf of California is characterized by a thick layer of organic-rich sediments that are thermally altered by hydrothermal fluids thereby providing a bottom water source of dissolved organic carbon (DOC) to the water column The potential for heterotrophic microbial communities in the water column to metabolize this organic matter source has not yet been investigated In order to assess heterotrophic potential in the water column of the Guaymas Basin we measured the activities of carbohydrate-hydrolyzing extracellular enzymes at the chlorophyll maximum These measurements were carried out using water obtained from repeat CTD casts over the course of a week and from bottom water collected by HOV Alvin at hydrothermally active areas with extensive chemosynthetic microbial mats Repeat measurements at subsurface depths were very comparable across sampling dates and CTD casts Exo-acting (terminal-unit-cleaving) monosaccharide hydrolase activities were typically higher in deeper waters than in surface waters the spectrum of endo-acting (mid-chain-cleaving) polysaccharide hydrolase activities was broader than at shallower depths The high enzyme activities in Guaymas Basin bottom waters indicate an unusually active heterotrophic community that is responding to influx of DOC and nutrients into bottom waters from the hydrothermally affected sediments or to the availability of chemosynthetically produced biomass This DOC could potentially stimulate activities of heterotrophic microbes providing a source of organic substrates at depth that could supplement the sinking flux of particulate organic carbon from the surface ocean This possibility has not yet been investigated Sampling in the Guaymas Basin provides the opportunity to assess microbial heterotrophic activities in an environment that is potentially fueled with substrates from the bottom as well as from the surface ocean Repeat CTD casts and water samples collected from HOV Alvin over the course of the cruise provided the opportunity to assess the range and variability of heterotrophic enzyme activities in this hydrothermally affected location Sampling sites and water column parameters Incubations were conducted in replicate 4 mL acrylic cuvettes (n = 3) containing single substrates at enzyme-saturating levels (15 μM final concentration; determined at the beginning of the expedition) and 1.5 mL of seawater The cuvettes were incubated in the dark for up to 12 h Incubation temperatures were close to in situ temperatures (DCM: 20°C; OMZ: 5°C; Plume: 5°C; Bottom and near bottom: 3°C) Fluorescence was measured at the beginning and the end point using a Turner Biosystems TBS-380 fluorometer with excitation/emission channels set to “UV” (365 nm excitation Control cuvettes were prepared with artificial seawater (Sea salts 38 g L–1; Sigma) and MUF-substrates and incubated under the same conditions as the live cuvettes to control for abiotic substrate degradation Fluorescence changes over time were calibrated using MUF standard and used to calculate potential hydrolysis rates The maximum hydrolysis rate among all time points in a sample was used as a measure of the maximum potential rate at which the microbial community could access a specific polysaccharide Control incubations with artificial seawater did not reveal abiotic substrate degradation All rates reported here represent potential hydrolysis rates as added substrate competes with naturally occurring substrates for active enzyme sites hydrolysis rates are likely zero order with respect to substrate and represent maximum potential rates Bacterial cells were fixed with formalin (2% final conc.) and stained with 4′, 6-diamidino-2-phenylindole (DAPI; Porter and Feig, 1980) on a 0.2-μm polycarbonate filter Either 40 frames of view or 200 cells were counted per slide using epifluorescence microscopy (Olympus Differences in hydrolysis rates (averages of n = 3) were tested with one-way ANOVAs and Student’s t-test at the 5% significance level Results from ANOVAs were compared with Tukey’s post hoc test Statistical analysis was conducting using JMP Pro 14 software DOC concentrations were generally higher at depths below the DCM than at the DCM, except for CTD 2 (Table 1) Highest DOC levels at 2112 ± 13.6 μM were found in Alvin water near a massive structure of hydrothermal deposits (Dive 4565) Bacterial cell numbers at 50 m were somewhat higher (CTD 1 and CTD 4) or at the same level (CTD 3) than those at the bottom Activities of exo-acting enzymes (a-glu, b-glu, b-xyl, b-fu) were measurable at all depths for all CTD casts, with the exception of a-glu at OMZ for CTD4 where no activity was measurable (Figure 1) Figure 1. Activities of exo-acting enzymes in water taken from CTD casts 2 – 5 and in water taken with HOV Alvin. a-glu - 4-MUF α-D-glucopyranoside; b-glu - 4-MUF β-D-glucopyranoside; b-xyl - 4-MUF ß-D-xylopyranoside; b- fu - 4-MUF ß-D-fucoside. DCM, Deep chlorophyll maximum; OMZ, Oxygen minimum zone; Bottom, Bottom water; Plume, Turbidity plume near the bottom (see Table 1 for water depths and temperatures) Hydrolysis rates are average rates of n = 3 ± standard deviation Letters indicate results of the post hoc analysis of treatment-specific differences in rates (one-way ANOVAs p < 0.05); rates with the same letters are indistinguishable from one another means not available; ∗ means that a-glu activity was 0 patterns of enzyme activities varied more among casts and b-glu and b-fu activities varied by a factor of approximately 2 among casts; b-xyl activities were similar among casts with average activities ranging from ∼17 to 25 nmol L–1 h–1 The range of exo-acting activities (approximately 12–46 nmol L–1 h–1) in Alvin-collected water was similar to the range of activities measured in water collected at depths of 1800 and 1950 m; b-xyl activities were notably higher than the other activities in Dive 5470 water Results from post hoc comparison of depth-specific differences in exo-acting enzyme activities following a one-way ANOVA or a T-Test (CTD 2 only) with p < 0.05 Xylan hydrolysis was also measurable (in one of two replicates for Dive 4567; at trace levels in water from Dive 4565) and hydrolysis of laminarin and pullulan was comparable to rates measured in bottom water Activities of endo-acting enzymes in water taken from CTD cast 1 and in water taken with HOV Alvin Hydrolysis rates are average rates of n = 2 ± their range ∗ means that hydrolysis was detected in only one of the replicates in addition to input of sinking POC from the productive surface waters been previously reported for the marine water column; hydrolysis rates were generally comparable to those of the other substrates measured here The contrast in patterns of exo- and endo-acting activities may provide a clue as to the types of carbohydrates that are enzymatically hydrolyzed in the waters of the Guaymas Basin the high rates of exo-acting b-xyl activities and considerable rates of exo-acting b-fu activities at the DCM and OMZ contrast sharply with the lack of measurable endo-acting xylanase and fucoidanase activities at the same depths in the water column Exo-acting enzymes hydrolyze individual monosaccharides either from the terminal end of a chain We suggest that the exo-acting enzymes are therefore targeting specific branches of complex polysaccharides in the water column; deeper in the water column where both endo- and exo-acting enzymes are active fucoidan-like and xylan-like polysaccharides (potentially sourced from the sediments) are more likely being hydrolyzed Further characterization of microbial heterotrophic activities and the organisms carrying it out should be a next step in investigation of this unique environment The data from this study are available on figshare at https://figshare.com/articles/Hydrolytic_enzyme_activities_and_CTD_data/11120501 Both authors planned the research and wrote the manuscript KZ carried out all shipboard measurements and analyzed samples post-cruise Funding for this work came from NSF OCE-0848793 and OCE-1736772 to CA and UNC Office of Postdoctoral affairs to KZ Funding for the research expedition came from NSF OCE-0647633 to Andreas Teske (chief scientist) We thank Andreas Teske for the invitation to join the cruise and scientific party of R/V Atlantis (AT 15-56) for their assistance at sea We also thank the Martens lab at UNC for assistance with the DOC analysis Characterization of marine bacteria and the activity of their enzyme systems involved in degradation of the algal storage glucan laminarin Alonso-Sáez Factors controlling the year-round variability in carbon flux through bacteria in a coastal marine system Evidence for hydrogen oxidation and metabolic plasticity in widespread deep-sea sulfur-oxidizing bacteria A new method for measuring polysaccharide hydrolysis rates in marine environments CrossRef Full Text | Google Scholar Substrate specificity in polysaccharide hydrolysis: contrasts between bottom water and sediments CrossRef Full Text | Google Scholar Fluorescent derivatization of polysaccharides and carbohydrate-containing biopolymers for measurement of enzyme activities in complex media Functional differences between Arctic sedimentary and seawater microbial communities: contrasts in microbial hydrolysis of complex substrates Microbial extracellular enzymes and the marine carbon cycle Google Scholar Latitudinal gradients in degradation of marine dissolved organic carbon Community structural differences shape microbial responses to high molecular weight organic matter Structure and function of high Arctic pelagic High dissolved extracellular enzyme activity in the deep central Atlantic Ocean Prokaryotic extracellular enzymatic activity in relation to biomass production and respiration in the meso- and bathypelagic waters of the (sub)tropical Atlantic Water column anomalies associated with hydrothermal activity in the Guaymas Basin CrossRef Full Text | Google Scholar D’Ambrosio Composition and enzymatic function of particle-associated and free-living bacteria: a coastal/offshore comparison The microbiology of deep-sea hydrothermal vent plumes: ecological and biogeographic linkages to seafloor and water column habitats Microbial diversity and biogeochemistry of the Guaymas Basin deep-sea hydrothermal plume and resulting hydrothermal activity in the Guaymas Basin Heterotrophic extracellular enzymatic activities in the Atlantic Ocean follow patterns across spatial and depth regimes CrossRef Full Text | Google Scholar Significance of exoenzymatic activities in the ecology of brackish water: measurements by means of methylumbelliferyl-substrates CrossRef Full Text | Google Scholar Functional characterization of polysaccharide utilization loci in the marine Bacteroidetes ‘Gramella forsetti’ KT 0803 Ocean-color variability in the Gulf of California: scales from days to ENSO Bacterial activity along a trophic gradient Changes in bacterial activity and community structure in response to dissolved organic matter in the Hudson River Phosphorus composition of sinking particles in the Guaymas Basin CrossRef Full Text | Google Scholar “Algal polysaccharides,” in The Polysaccharides Google Scholar The use of DAPI for identifying and counting aquatic microflora CrossRef Full Text | Google Scholar Transparent exopolymer particles in a deep-sea hydrothermal system: Guaymas Basin CrossRef Full Text | Google Scholar Laminated diatomaceous sediments from the guaymas basin slope (central gulf of california): 250,000-year old climate record Organic geochemistry of recent sediments from Guaymas Basin Functional variation among polysaccharide-hydrolyzing microbial communities in the Gulf of Mexico Expression of sulfatases in Rhodopirellula baltica and the diversity of sulfatases in the genus Rhodopirellula Complete genome sequence of the complex carbohydrate-degrading marine bacterium Citation: Ziervogel K and Arnosti C (2020) Substantial Carbohydrate Hydrolase Activities in the Water Column of the Guaymas Basin (Gulf of California) Copyright © 2020 Ziervogel and Arnosti. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY) *Correspondence: Kai Ziervogel, a2FpLnppZXJ2b2dlbEB1bmguZWR1 Are you ready to explore the cutting-edge advancements shaping the electronics manufacturing industry? The May 2025 issue of SMT007 Magazine is packed with insights, innovations, and expert perspectives that you won’t want to miss. Has X-ray’s time finally come in electronics manufacturing? Join us in this issue of SMT007 Magazine, where we answer this question and others to bring more efficiency to your bottom line. It’s that time again. If you’re going to Anaheim for IPC APEX EXPO 2025, we’ll see you there. In the meantime, consider this issue of SMT007 Magazine to be your golden ticket to planning the show. Libra Industries, a privately-held systems integration and electronics manufacturing services (EMS) provider, is excited to announce the acquisition of Benchmark Electronics’ Guaymas, Mexico Facility, effective Jan. 17, 2020. Libra Industries will retain the 100+ Guaymas associates and all customer accounts. The acquisition gives Libra Industries room to grow and the company plans to leverage the expanded capabilities that the Guaymas operation offers. The acquisition is key for the long-term growth and success of Libra’s strategic accounts. The addition of the Guaymas facility includes redundancy in sheet metal, machining, assembly & systems integration. Rod Howell, CEO of Libra Industries, commented: “We are looking forward to completely integrating the Guaymas facility into our systems and processes. This will give them access to all of the benefits of our world-class IT and business analytics infrastructure. These tools are a major game changer for our customers – providing real-time data with custom analytics.” With the addition of Guaymas, Libra Industries now operates five world-class manufacturing facilities, including its operations in Ohio and Texas. The company serves a diverse base of industries such as medical, military/aerospace, semiconductor and industrial. Libra Industries serves customers who require customized solutions with technically sophisticated manufacturing and quality requirements. Libra Industries continues to invest to provide customized manufacturing solutions to help make its customers more competitive and improve their profitability. For more information about Libra Industries, visit www.libraindustries.com. A Singapore-based company plans to build a major natural gas facility in neighboring Sonora. LNG Alliance intends to invest $2.1 billion in a gas liquefaction facility in Sonoran port city Guaymas, state government officials say. The liquefied natural gas would then be shipped to Japan, Indonesia and other Asian countries, as well as other parts of Mexico itself. Sonoran Governor Alfonso Durazo said that Sonora played a key role in enabling the project. The project will be built on roughly 250 acres of state-owned land administered by the port authority, according to Durazo. In return, he said the state will receive “a small part of the benefits” generated by the company. The facility’s construction is expected to create some 3,000 jobs, and nearly 300 once operations begin. Volume 13 - 2022 | https://doi.org/10.3389/fmicb.2022.845250 This article is part of the Research TopicInsights in Extreme Microbiology: 2021View all 16 articles Sulfate reduction is the quantitatively most important process to degrade organic matter in anoxic marine sediment and has been studied intensively in a variety of settings offers the unique opportunity to study sulfate reduction in an environment characterized by organic-rich sediment and high geothermal gradients (100–958°C km−1) We measured sulfate reduction rates (SRR) in samples taken during the International Ocean Discovery Program (IODP) Expedition 385 using incubation experiments with radiolabeled 35SO42− carried out at in situ pressure and temperature The highest SRR (387 nmol cm−3 d−1) was recorded in near-surface sediments from Site U1548C which had the steepest geothermal gradient (958°C km−1) SRR were generally over an order of magnitude higher than at similar depths at other sites (e.g. 387–157 nmol cm−3 d−1 at 1.9 mbsf from Site U1548C vs 46–1.0 nmol cm−3 d−1 at 2.1 mbsf from Site U1552B) Site U1546D is characterized by a sill intrusion but it had already reached thermal equilibrium and SRR were in the same range as nearby Site U1545C The wide temperature range observed at each drill site suggests major shifts in microbial community composition with very different temperature optima but awaits confirmation by molecular biological analyses At the transition between the mesophilic and thermophilic range around 40°C–60°C sulfate-reducing activity appears to be decreased particularly in more oligotrophic settings but shows a slight recovery at higher temperatures the recalcitrant organic matter such as kerogen is thermally cracked leading to the production of short-chain organic molecules which can be utilized in situ by microorganisms Sulfate concentrations are high near the sediment–water interface due to downward diffusion of sulfate from the overlying water column With increasing depth sulfate concentration decreases as the rate of sulfate consumption exceeds the downward flux There are two pathways of microbial sulfate reduction: Organoclastic sulfate reduction: 2CH2O + SO42− = 2HCO3− + H2S Methanotrophic sulfate reduction: CH4 + SO42− = HCO3− + HS− + H2O Sites U1545C and U1546D have a similar stratigraphy since the distance between these two sites is only about 1.1 km while the sediment at Site U1545C reveals an undisturbed sedimentary profile the sediment in Site U1546D was intruded by a sill around 350–430 m below seafloor (mbsf) thus these two sites offer a chance to study the impact of sill intrusion on sedimentary biogeochemical cycling Figure 1. Sampling sites in Guaymas Basin. Image adapted from Teske et al. (2020). Colored boxed indicate sampling sites where SRR could be measured. The color scheme is used for data plotted in Figures 2–4. The red line in the insert map is the boundary between the North American and Pacific tectonic plates. The red star in the map indicates the sampling site of Elsgaard et al. (1994) Sites U1547B and U1548C are located inside and outside of a ringvent (circular hydrothermal mound) sills intruded into the sediment at relatively shallow depths; ca This hydrothermally active area was chosen to study the effects of extremely steep geothermal temperature gradients (958°C km−1 at Site U1548C) on biological processes Site U1551B is the only site from the southeast region of Guaymas Basin Sediment at this site is of predominantly terrestrial region Site U1552B is located close to cold methane seeps and gas hydrates were recovered Although SRR were measured previously in Guaymas Basin, the studies focused only on the top 40 cm sediment (Jørgensen et al., 1992; Elsgaard et al., 1994; Weber and Jørgensen, 2002) thus the rates and distribution of microbial sulfate reduction in the deep subseafloor and thermal effect on microbial sulfate reduction are still unclear We investigated microbial sulfate reduction down to 326 mbsf in subsurface sediment of Guaymas Basin using 35S radiotracer incubations in the laboratory at approximate in situ temperature and pressure whole round core (WRC) segments were cut off and capped The WRC was then brought into the ship’s lab put into gas-tight aluminum foil bags flushed with N2 gas due to a technical malfunction on board the drill ship some samples were stored in an oxic atmosphere for several weeks Samples from Site U1547B were compromised by the extended exposure to oxygen and no reliable SRR measurements could be conducted Samples from sites U1549B and U1550B also suffered from the exposure to oxygen albeit for much shorter duration SRR measurement of samples from sites U1549B and U1550B was partially successful but the quality of the data remained inconclusive we used only SRR measurements from uncompromised samples from sites U1545C The seawater media for the SRR measurement were prepared as follows, based on Morono et al. (2017): 0.2 g KH2PO4 0.5 g MgCl2 × 6H2O and 0.15 g CaCl2 × 2H2O were mixed with 1 L of ultrapure water (UPW) About 3 ml of 0.1% resazurin was added to the media and autoclaved About 5 ml of Na2S solution (0.12 g Na2S in 10 ml UPW) and 5 ml of NaHCO3 solution (0.84 g NaHCO3 in 10 ml UPW) were added to the media after autoclaving The media were bubbled with N2/CO2 gas for at least 2 h it was stored in pre-combusted crimp bottles with N2 gas until use within a few days For all samples from sites U1545C and U1546D 0.71 g Na2SO4 was also added to set the sulfate concentration to 5 mM we approximated the in situ porewater sulfate concentration by adding a separately prepared sterile 1 M Na2SO4 stock solution to those samples Killed controls (KC) and media controls (MC) were also prepared and incubated 20% of zinc acetate was added to the sample instead of medium to stop all microbial activity MC consisted of only the sterile medium and no sediment together with the downhole temperature gradient All samples were incubated within ±2°C of their respective in situ temperature Incubation was terminated by depressurization of the high-pressure cylinder followed by removal of the crimp vial from the pressure cylinder and quantitative transfer of its contents into a 50 ml centrifuge tube preloaded with 5 ml of 20% zinc acetate solution to terminate microbial activity Remaining sediment pieces were flushed out with 10 ml of 20% zinc acetate solution to transfer all of the incubated sediment into the centrifuge tube All samples were stored at −20°C until analysis Temperature gradients of the different sampling sites of IODP Exp (A) Downhole temperature gradients of sites U1545 (blue line) and U1546 (red line) measured in situ Blue circles and red triangles show sampling depth and incubation temperature of each sample from sites U1545C and U1546D (B) Downhole temperature gradients of sites U1548 (green line) and purple squares show sampling depth and incubation temperature of each sample from sites U1548C The black lines in both figures show the average global geothermal gradient of 25°C km−1 Note the different depth scales on the two graphs We used a slightly modified version of the cold chromium distillation of Kallmeyer et al. (2004) to liberate the reduced sulfur species from the sediment they were centrifuged for 10 min at 2,500 × g For quantification of total radioactivity (aTOT) we mixed 50 μl of the supernatant with 4 ml of scintillation cocktail (Rotiszint® eco plus LSC-Universalcocktail The rest of the supernatant was carefully decanted off The sediment pellet was then quantitatively transferred to the distillation flask and mixed with 15 ml N To ensure complete mixing of the sediment with the chemicals a magnetic stir bar was added to the reaction flask The flask was connected to a constant stream of nitrogen gas (approximately 5–10 bubbles per second) in order to maintain strictly anaerobic conditions during the distillation 8 ml of 6 M hydrochloric acid (HCl) and 15 ml of 1 M chromium (II) chloride solution were added to the flask via a reagent port The chemicals will convert all reduced sulfur species (TRIS) to H2S which is driven out of solution by the stream of nitrogen gas The produced gas is then led from the flask through a Poly-Ether-Ether-Ketone (PEEK) tube to the citrate trap filled with 7 ml of a buffered citric acid solution (19.3 g citric acid and pH 4) to trap any aerosols potentially containing unreacted 35SO42− radiotracer but let all H2S pass the gas is led to a trap containing 7 ml of 5% (w/v) zinc acetate To prevent overflowing of the zinc acetate trap a few drops of silicon-based antifoam are added containing the produced H235S are quantitatively transferred into a 20 ml plastic scintillation vial and mixed with 8 ml scintillation cocktail for quantification of radioactivity by scintillation counting Each round of distillations also included one distillation blank (DB) containing just a few drops of non-radioactive zinc sulfide carrier and the distillation chemicals mentioned above The DB was used to detect potential carry-over between distillation runs and therefore tracks the cleanliness of the distillation equipment Counter blanks (CB) containing just 5% zinc acetate and scintillation cocktail in the same ratios as the samples are added to each run of the scintillation counter Counter blanks are required to quantify the background activity all signals not associated with radioactivity We use a HIDEX 600 SL Liquid Scintillation Counter (HIDEX Oy and the surface of the vial is wiped with 70% ethanol in order to remove any potential contamination on the vial’s surface Since the samples recovered during the expedition were incubated as slurries with additional medium the total incubation conditions deviate considerably from in situ conditions The measured rates should therefore be considered “potential” SRR (pSRR) The formula of Jørgensen (1978) for calculation of SRR based on radioisotope incubations was designed for whole core incubations MQL = MDL + k × σb false positives will only occur above MDL and not below The only parameter where the MQL and MDL become relevant is aTRIS due to the extremely low microbial activity in our samples aTOT is always well above the detection limit Values of aTOT < MDL are discarded for values MDL < aTOT < MQL and aTOT > MQL SRR calculated from values aTOT > MQL represent actual turnover measurements and exclude false positives with a level of confidence of 95% whereas SRR calculated from values MDL < aTOT < MQL are rates that could be detected but cannot be distinguished from the inherent background of LSC with a sufficient level of confidence The calculated SRR depends on sulfate concentration and the aTRIS/aTOT ratio therefore the MQL is different for each sample (A,B) Sulfate reduction rates (SRR) for sites U1545C (blue circles) and U1546D (red triangles) plotted against sampled depth Closed symbols indicate measurements SRR > MQL and open symbols MDL < SRR < MQL See the definitions of MQL and MDL in the “Materials and Methods” section (C,D) SRR for same sites plotted against incubation temperature (E,F) Concentrations of sulfate and methane The data were obtained from the Laboratory Information Management System (LIMS) report Gray bar indicates Sulfate–Methane Transition Zone (SMTZ) All SRR measurements from Site U1548C were above the MQL (A–C) SRR for sites U1548C (green circles) and U1552B (purple squares) plotted against sampled depth (D–F) SRR for same sites plotted against incubation temperature (G–I) Concentrations of sulfate and methane Owing to technical problems with our scintillation counter we were not able to use the blank measurements (KC which is crucially important to assess the SRR data A list of all SRR measurements is provided in the Supplementary Table S1 A third potential factor appears to be local heating around sills to further elevate microbial activity Comparison of SRR in subsurface sediments from the tropical eastern Pacific Ocean (ODP Leg 201 25 MPa) instead of atmospheric pressure when applying even higher pressure (45 MPa) SRR increased even further but the increase in SRR when raising the pressure from 25 to 45 MPa was not as pronounced as for the pressure increase from 0.1 to 25 MPa Sulfate concentration in the media used for all samples from sites U1545C and U1546D was set to 5 mM which is lower than in situ porewater sulfate concentrations of near-surface samples and higher for the deep samples Although the sulfate concentration of the deep samples was increased SRR of most of the deep samples were below MQL which we interpret as either electron donor (organic substrate) limitation or a generally very small or metabolically slow SRM community that could not adapt to elevated sulfate levels within the 10 days incubation time Abiological sulfate reduction, also termed thermochemical sulfate reduction (TSR), is assumed to occur only at temperatures well over 100°C (Jørgensen et al., 1992; Machel, 2001) and turnover rates are much slower than biological sulfate reduction we thus assume that SRR measured in our study are exclusively caused by microbial activity these deviations cannot explain differences in rates over several orders of magnitude between the sites depth profiles that appear to be closely controlled by porewater sulfate concentration even when incubation conditions differ considerably from in situ conditions Site U1548C suggests that heating does have a positive effect on microbial activity the comparison between sites U1545C and U1546D shows that heating caused by sill intrusion at Site U1546D is only temporary For a more detailed understanding of the influence of sill intrusion and local heating on subsurface microbiology it would be necessary to recover a suite of sediment samples affected by the entire emplacement and cooling history of sills plus their non-intruded counterparts for comparison with a local minimum around 40°C–60°C followed by an increase and local maximum around 65°C A more detailed characterization of the organic matter is still lacking so we can only assume that the sedimentary organic material is already more recalcitrant at the time of deposition causing a more rapid decrease in substrate availability and hence thermal cracking starts at greater depth due to the comparatively lower geothermal gradient pushing the potential source of substrates for subsurface life even deeper but also less variation in SRR with temperature Given the low cell abundances in parts of the cores recovered by Exp. 385 (Morono et al., 2017 comm.) investigations of microbial community structure in these samples is challenging our interpretations of changes sulfate reducer community await confirmation by molecular biological analyses We measured SRR in deep subseafloor sediment from several sites in Guaymas Basin which were expected to have high microbial activity and abundance compared to other non-hydrothermal subsurface sediments due to their high content of bioavailable organic matter Sulfate-reducing activity in Guaymas Basin was detected down to nearly 300 mbsf but at most sites only with low turnover rates of approximately 0.5 pmol cm−3 d−1 reaching 10 to 100s of nmol cm−3 d−1 The highest SRR of 387 nm cm−3 d−1 was found at Site U1548C where the sediment is very organic-rich and the geothermal gradient is roughly 1,000°C km−1 supposedly leading to thermal cracking of organic matter already at shallow depth The wide range of the current temperatures in these drill cores requires microbial communities with different temperature optima ranging from psychrophiles over mesophiles to thermophiles There is some indication that heating of the sediment leads to elevated microbial activity but it appears that this effect is only temporarily and ceases once the temperature has decreased again The original contributions presented in the study are included in the article/Supplementary Material; further inquiries can be directed to the corresponding author TN wrote manuscript with input from all coauthors All authors contributed to the article and approved the submitted version TN and FS are funded through DFG grants to JK (grant # 670521 and 651694) The authors would like to thank the crew of IODP Exp 385 (Guaymas Basin Tectonics and Biosphere) for providing samples and data Teske provided comments on an earlier version of the manuscript The Supplementary Material for this article can be found online at: https://www.frontiersin.org/articles/10.3389/fmicb.2022.845250/full#supplementary-material 1. ^https://rosetta.iodp.tamu.edu/A/TechDoc/5682?encoding=UTF-8 2. ^https://rosetta.iodp.tamu.edu/A/TechDoc/7146?encoding=UTF-8 3. ^http://www-odp.tamu.edu/publications/pubs_tn.htm 4. ^https://web.iodp.tamu.edu/OVERVIEW/ a novel amino acid degrading and sulfate reducing bacterium from an anaerobic dairy wastewater lagoon The use of chromium reduction in the analysis of reduced inorganic sulfur in sediments and shales Microorganisms persist at record depths in the subseafloor of the Canterbury Basin Google Scholar Limits for qualitative detection and quantitative determination CrossRef Full Text | Google Scholar Die 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microorganisms in sediments from sites 618 and 622,” in Initial reports of the deep sea drilling project Google Scholar “Anaerober Abbau von Fettsäuren und Benzoesäure durch neu isolierte Arten sulfat-reduzierender Bakterien.” PhD Thesis Germany: Georg-August-Universität Göttingen Google Scholar Studies on dissimilatory sulfate-reducing bacteria that decompose fatty acids PubMed Abstract | CrossRef Full Text | Google Scholar Bacterial life at the bottom of the Philippine trench PubMed Abstract | CrossRef Full Text | Google Scholar Kallmeyer J (2022) Biological Sulfate Reduction in Deep Subseafloor Sediment of Guaymas Basin Received: 29 December 2021; Accepted: 01 February 2022; Published: 03 March 2022 Copyright © 2022 Nagakura, Schubert, Wagner and Kallmeyer. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY) *Correspondence: Jens Kallmeyer, a2FsbG1AZ2Z6LXBvdHNkYW0uZGU= †These authors have contributed equally to this work and that means that Yaqui residents of Guaymas are once again going to sea for their annual jellyfish catch in the Gulf of California men and women from Yaqui communities in the coastal municipality have been fishing every May for cannonball jellyfish a species eaten in Asian countries such as China Japan and Thailand and used in the manufacture of cosmetics and medicines One community where many women are involved in the annual jellyfish fishery is Guásimas de Belem located about 40 kilometers from the city of Guaymas Residents have had a license to catch cannonball jellyfish Locals rise early in the morning to go to sea on small fishing boats known as pangas an activity that allows many women to achieve economic independence a net and a packed lunch to keep hunger at bay Small pangas are filled with four to six tonnes of jellyfish and even more so because they’re not used to doing heavy work,” said fisherman Baldomero González One Yaqui woman who has continued to fish for aguamala year after year despite the risks is María Estela Guitimea there’s no money for frijoles [beans],” she said Guitimea goes fishing year-round with her husband they focus on catching cannonball jellyfish “It’s teamwork: he operates [the boat] and we both fish with nets; I’m at the front … You never know if you’ll make it back [to land] That’s why I ask God to save me from any problems I might have,” she said I like the sea but sometimes the pangas flip over,” she added saying that she’s more concerned about drowning than being attacked by a marine animal such as a shark Once the jellyfish are brought back to Guásimas they are inspected to make sure that they measure the minimum required length of 11 centimeters The Yaquis then sell their catch to the Chinese owners of processing plants set up annually in the town (Three processing plants usually operate in Guásimas but only one was set up this year because strong winds had a negative impact on the cannonball jellyfish season.) A kilo of aguamala sells for between 1.8 and 4 pesos (about US $0.10 to $0.20) which doesn’t sound like much but adds up given that each panga brings in daily catches of four to six tonnes Yaqui women also earn money preparing the jellyfish for export in the processing plants “Our earnings come from the tonnes [of aguamala] we process,” said Jessica Canales told Milenio that the work she is currently doing at the plant helps her support herself and her two-year-old daughter “[The work] helps us because we don’t have to depend on anyone We are able to give food to our children without needing a man,” she said According to the National Aquaculture and Fisheries Commission more than 12,300 tonnes of cannonball jellyfish were exported from Mexico last year generating an economic spillover of 30.5 million pesos (US $1.5 million) Source: Milenio (sp)  an Auburn LLC that closed the purchase just last week for $1,650.000 The purchase involved just the 3,100-square-foot building that houses the restaurant – and various cross-references led us to the discovery that the new owner appears to be the company that owns the Maharaja Cuisine of India restaurant less than a block away (which is a tenant there so we’ll be following up both with them and with the Tacos Guaymas regional mini-chain that the West Seattle restaurant is part of ADDED: A further check of nearby records shows the same company bought another building on the block – the one holding Pharmaca and Flying Apron – in August of this year for $2.7 million SUNDAY UPDATE: A text reply from a Guaymas rep: “We do hope to be able to find a new lease nearby But it is correct (we) were Informed a few days ago we would need to vacate by the 12th We hope to set up a Go Fund Me account for our employees who we informed the same day of the need to close.” TUESDAY NIGHT: Here’s the GoFundMe link that sucks to find out that your business has to close in 2 weeks and all your staff is out of work in the middle of the holiday season I’m so sorry that’s happening to them Owner being paid good amount of $$$$ deal was made between Taquira owner and new building Owener from long time.  This was the first Taqueria Guaymas  of the regional mini chain I believe back in the early 90s is when it opened the murals were painted by The Rivera Family’s Dad they lived in a house beside the 7 11 in the junction I will miss this restaurant once it is closed they have been a local anchor in the junction for decades Their other location closed due to vandalism along Broadway in Capitol Hill over the last year or so Many of the current employees have worked there many many many years especially Teresa in the day time.  employee received good compensation everyone is happy they aren’t required to give more notice at the very least The fact it’s someone who owns another business in the area too makes it worse… You’d think they’d have more respect for other businesses that have been here since forever Granted with Maharaja the people I’ve seen working there have not even been respectful to those of us living right across the alley yelling at us to F off for politely asking them to quiet down at 1-3am and so on They have also thrown things at our cars and the building and smoke in large groups right under our windows it makes me wonder if the owner is inconsiderate too If someone was smart they would open up either a 13 Coins or similar restaurant open 24 HRs or a restaurant with coffee salad and magazines that’s open 24 HRs and don’t tell me it wouldnt succeed there is a place just like that in Albuquerque thats lasted 20 years called Flying Star Cafe Just someone who’s daddy has deep pockets So frustrating to watch when you know they’re not gonna make it I’ve never been to this particular Mexican food place but I’m sure the workers can get unemployment really quickly  there’s tons of jobs everywhere I don’t know why they would need to set up a GoFundMe for them when there’s restaurants begging for employees right now its bad enought about the paid parking in the back Isn’t there supposed to be some West Seattle podcast now The owner of the Great American diner on the corner opposite to the 7-11 is a guy called Glen An exceedingly nice guy and extremely hard working Definately not someone who tapped into parents money to open that place as you seem to be accusing.Perhaps you should go eat there and talk to him before throwing your generalized it says right in the article that the purchaser owns the building maharaja is in….not the business but good on you to take a minute to complain about a local business while complaining that they aren’t supporting local businesses it says “the company that owns the Maharaja”  – not the owner of the building which I assume is either Capaluto or Menashe since they seem to own the whole junction.   Yes company owned Maharaja and now they are opening new resturant concept.  Yes owner received good amount of money and employee being paid 2 weeks compensation Maybe Taqueria can fill the vacancy up the street that Maharaja is creating when Maharaja moves down the street to this new location and we will still get the best of both worlds The best of both worlds only if you’re male.  The last 2 times I went to maharaja with my partner they stared at her like she was part of the menu.  Not the most comfortable of places for a woman I’ve had that experience there – I do takeout from them a lot now I’ve had them argue with me about the spice level ask me if I’m “sure” I want goat Unfortunately I don’t know of any other Indian nearby who makes most of the fried things with chickpea flour – I can’t have wheat Price seems really low for something that will be a cash cow for the lot alone Sucks that it’ll lead to another demo and big ugly apartment when there’s other areas to build density like parking lots I believe the one in White Center is also closed Obviously no one ever taught you if you don’t have something nice to say don’t say anything at all You obviously aren’t much of a local/your one of the shoobies that moved here because of the tech industry But this location means a lot to the locals We’ve been going here for decades and the staff has been incredible and food has never once and literally never once been bad This place just isn’t West Seattle anymore but claiming that West Seattle doesn’t exist anymore is quite the stretch.  Really the biggest problem with WS right now is people who keep freaking out and writing things like ‘I’m team F** West Seattle” now.  No true WSeattlite would ever type that all the employee being well taking care by the owner  I used to go there quite regularly though I’ve noticed they’ve had to raise prices quite a bit in the last couple years This is just sad news .  I’m not happy,  I loved this restaurant.  Owner received good amount of money and employee being taking care very well by taqueria owner their super prawn quesadilla is the meal of dreams Why isn’t the Council protecting businesses from eviction as well as those who refuse to pay apartment rent?  Owner received good amount of money and employee received good compensation everyone is happy Noooooo!!!!!!!  Such a staple and such yummy food!  I’m so pissed off that local businesses can just get evicted like this and livlihoods in tatters it’s in their lease agreement that they signed Pretty common stipulation in any business lease They may have been able to purchase the property if they wanted like the coffee shop did a couple years ago.  It’s wrong information they are not being evicted owner being paid good amount of money and employee being paid very well.  Huge loss – really nice people who ran that business and food we enjoyed getting often   Very sorry to see this business closed Never understand why you kick a tenant out with no plan to replace them One reason is to clear the way for major renovations or for re-developing the property Commercial tenants don’t have the same degree of legal protection as do residential tenants here in Seattle  I will miss them Our family is super disappointed by this news I hope that the staff can find new work soon hibiscus juice) & Manuel Rivera’s murals (Diego Rivera was his uncle).   & Th is right about the Maharaja No way!  We’ve just returned from a vacation in Mexico City and saw his uncle’s incredible murals at the Palacio del Belles Artes.  I’d better get up there for a meal and check out Diego’s nephews murals with a new eye!  Sorry to see them go and feel badly for the staff being so close to the holidays.  Merry friggin’ Christmas.  :-(   Owner received good amount of money and employee received good compensation everyone is happy  How many times do you want to post the same comment Maybe you shouldn’t have given the business the boot on two weeks’ notice right before the holidays 😣 I’m perplexed that the new building owners would give two weeks notice to a long-standing business…with employees who have families to feed…during the holidays Were they notified during he sale process this would come or was this a shock?! Wow but why don’t they develop responsibly and respectfully The city really drops the ball by letting developers rape neighborhoods for a buck.  This news is very sad for our family and pray they continue business in seattle somewhere anywhere we will come Our family has been coming to eat here for 20 plus years since I was in elementary :( my babies had their first frijoles here The memories of our family gatherings and all the great people who worked there I will never forget! We will be popping in multiple times before they close.  I think the ghost of Marley should make a midnight visit to the buyers definitely won’t support whatever business takes their place The Vargas familia grew up here getting the corn quesadilla and rice kids meal and taking our plates to the kitchen when we were done Even as adults we have done the same thing Really going to miss our Guaymas dinner followed by Husky’s after!  I guess the good thing is that we know not to support the jerks that own Maharaja They’ve shown us what kind of terrible and inhumane people they are I’m so sorry for the folks losing their livelihoods right before the holidays–it’s never good any time I’m trying to remember other restuarants that have come and gone.  Who remembers “Shakeys” where Taco Time now resides Or the cute little Vietnamese joint where Lulu coffee is I mean Yasuko’s.  Charlestown Cafe.  What was the restaurant before Maharaja’s Safeway/Rite Aid?  Remember Tradewell?  Guaymas was my kid’s first restuarant That’s the way it goes.  It’ll be a multistory building with a Starbucks Subway,  and a Chipotle or something on ground level.   It’s what you voted for This has been our go-to place for delicious Mexican food for many years Fingers crossed they can find another spot in WS soon Their staff has always been friendly and efficient Thank you for 20+ years of great meals.   Another WS institution bites the dust We also used to have a Sambo’s which became Dennys and we had Skippers fish and chips We had dinner there every Monday night while my kids were in school And it was the first restaurant my kids every went to I hope they find a new home in the Junction! Because it may be legal doesn’t make it ethical to throw employees out on the street I’ve certainly been on the recieving end of the letter of the law over the intent of the law you’ll start to see a number of stalled properties or projects (attracting vandalism/tagging): the old Swedish Clinic owner gave me 30 days to shut down a 6,000 sq ft store and 30 employees They gave my lease to Chase Bank while we were negotiating a new lease extension Chase recently closed that very same location (Classic) Was across from you many years ago Have had to relocate several times (last two locations are still vacant) My next to last spot was purchased and new owner agreed to 90 day notice.  Gave me 20 Rick Cook-owner Rick’s (Pshychic) Barber Shop I accidentally called the cops on you breaking into your own shop good havin u on the strip after all these years Got a ton of friends that been going to u for years I hope someone steps up to take hi res pics of those murals so they can replicate them as wall paper at a new location!   I lived for the super burrito both times I was pregnant!  What about the “hydrant” location?  Or naked crepe As disappointing as it is not to have this restaurant one silver lining is: restaurant workers these days can get another job in a second usually with higher wages and better benefits All they will have to do is walk down the street  I am more disappointed about the likely redevelopment which will presumably look like what’s right across the street Shiny and gleaming but with no soul.  which would be awfully small to redevelop alone; the other parcel now owned by the same company/person is two buildings away Dear God when is the madness going to end and please don’t build any more condos!!  We need a functioning junction with something other than bars!!! first Lee’s Asian then Kamei and now Tacos Guaymas The West Seattle I know and love is disappearing I ate here often and always appreciated the friendly staff It’s truly appalling to give 2-weeks notice 2-weeks before the holidays I hope the GoFundMe site gets up and published.   More importantly I hope they find another WS home.   Should’ve been the other other Mexican place instead That ‘other’ Mexican place supports multiple families as well…and the owner has always been generous to the community and his staff.  They nearly all live within walking distance of the restaurant…can’t get much more local than that They stayed open during the worst of the pandemic providing take-out and delivery food and it’s sad to see so many empty tables now days.  They used to be packed on weekends…I think there’s just too much competition any more.  Yeah the food is your typical Jalisco style…not trendy…but the portions are big and the drinks are strong.  It won’t be that long before their building is bulldozed for new condos but they have a few years left.  Show them some support while you still can I am convinced this must’ve been some sort of disinformation bot posting because who could ever dig on Puerto Vallarta? and prices that reflect what Mexican food should be I am mostly amused by these comments from people that can’t abide by change the neighborhood was different before you were born or moved here too :) I’m sad for Guaymas to go too but come on I am pretty sure that West Seattle (junction well at least the bridge will be fixed in a few months (hahahahahahahahahahahahahah)What is going to happen to the other things on the same block considered the same block/building?I am really sad I moved to White Center (got priced out of the good side of Roxbury condos and high end bars/restaurants opening where it was just….local Pharmaca/Bin 41/Flying Apron is another building It’s bad enough when a good restaurant goes under because business was bad successful favorite just gets unceremoniously kicked out Food = 6/10 — Staff = 8/10 — Not having to go to Taco Time Chipotle or straight-garbage Puerto Vallarta for “Mexican food” = 10/10   The shutdown of Taqueria Guayma’s  is indeed a true loss for The Junction Maybe the new building owners other businesses are doing so well that they had extra cash to be able to buy the two non-adjacent Junction properties I think next year would be their 30th year in the Junction I just hope that it doesn’t turn into another Eastern Bloc architecture multi story building.  The Junction has such a nice historical and neighborhood feel.  Greed over community  Produce on one side and fish or meat on the other side some locals set up a Costco style chicken rotisserie joint Please enter your username or e-mail address You will receive a new password via e-mail 6750 W. Peoria Ave, Suite 121, Peoria, 623-248-1734, heroicoguaymasrestaurant.com and designers have captured all sides of the Valley with award-winning and insightful writing and investigative features keep our 385,000 readers in touch with the Valley's latest trends Nine people were shot dead including one youth in four separate attacks in the space of 72 hours during a bloody weekend in Guaymas The Sonora Attorney General’s Office said that four people were found dead on Friday at the pier of the Manga 1 fish farm in San Carlos Nuevo Guaymas Two of the men were later identified through their fingerprints in Fátima neighborhood and his body was dumped on a dirt road in an attack in the community of Las Guásimas Another three people were injured in the attack A pickup truck with bullet holes and bullet shells from various weapons was found by police a man’s body was found with gunshot wounds in the Santa Clara sports field in San José de Guaymas There were 55 murders in the city in the first four months of the year The newspaper also said that the spate of killings represented a rise on the four month average: in 2020 there were 144 murders in Guaymas and 149 in 2021 Violence in Guaymas hasn’t been restricted to remote areas or specific neighborhoods: an attack outside the Guaymas municipal palace killed three people in November The city had a per capita murder rate above 100 per 100,000 people last year according to a study by a Mexican non-governmental organization the Citizens Council for Public Security and Criminal Justice (CCSPJP) Guaymas remained off the CCSPJP’s list of the 50 most violent cities in the world because it didn’t meet the requirement for inclusion of a population over 300,000 With reports from El Imparcial This project was produced in partnership with KJZZ's Fronteras Desk Listen to the two-part radio series at sewagecrisis.kjzz.org This project was supported by the Pulitzer Center on Crisis Reporting Leer en español Sonora — A few feet from the front porch of Claudia Fourcade’s childhood home an exposed sewer pipe filled with green liquid exudes a putrid odor Waste drips into a growing puddle in the middle of the road holds a handwritten sign on orange posterboard We can’t take it anymore.” She and her neighbors have staged a small protest this late summer afternoon constructing a roadblock of trash and debris to get the attention of water company workers An arroyo flooded with sewage in downtown Guaymas empties into a bay Fourcade said the stench infiltrates her home She can’t even do laundry at home because the smell permeates her clothes “It’s really uncomfortable living like this.” Once she tried to cover the broken pipe with concrete But when the pressure of the waste became too great Fourcade’s exposed sewer pipe exemplifies a common problem in Guaymas: poorly installed infrastructure so many sewer pipes were installed too near the surface former regional director for the Comisión Estatal del Agua Empalme and the small Yaqui community of Vicam who has a degree in hydraulics and a master’s in business administration He worked in various local directorial roles for the CEA between 1993 and 2015 plus five years as regional director between 2009 and 2014 The pipes should be buried at a depth of 50 centimeters over at least a 20-centimeter bed of sand to cushion them many pipes were installed on top of uneven rocks and the pressure of overhead traffic quickly results in broken or collapsed pipes was one of four former directors of the CEA who spoke with the Star about the root causes of Guaymas and San Carlos’ sewer crisis the former CEA directors described the major challenges facing the under-resourced utility company: rocky soil and mountainous topography While sewage problems are common throughout Sonora Guaymas faces all those challenges at once said former CEA regional director Ivan Cruz a catastrophic summer of sewage crises culminated in the Sonoran state government declaring a health emergency in early November “There are other sewage issues in the state secretary for infrastructure and urban development in Sonora “Nothing should arrive at being an emergency A couple doors down from Fourcade’s protest Brenda Lopez is making flour tortillas by hand as her 6-year-old son He was recently sick for 12 days with diarrhea and vomiting Brenda Lopez makes flour tortillas by hand as her 6-year-old son Jesus plays with neighbors an exposed sewer pipe has been leaking into the street for weeks Lopez said her son was sick for 12 days with diarrhea and vomiting The odor from the open sewer pipe isn't helping her business “Who would come buy tortillas in this stink?” she said New state CEA director José Luis Jardines Moreno and regional director David Pintor — who oversees Guaymas Empalme and Vicam — were appointed in September In response to the Star and KJZZ’s questions a governor’s office spokesman provided written responses that he said were compiled by various departments in the agency The agency said infrastructure failures necessitated the emergency declaration to protect the health of citizens Clogged pipes and broken sewage pumps “represent a risk to the health of the people who pass through the area and requires expedited attention to solve the problem,” the CEA statement said in Spanish it is planned to carry out major investments in drinking water sewerage and sanitation in order to finally resolve this situation.” Water shortages have exacerbated the sewer problems in Guaymas and San Carlos former CEA regional directors Roberto Romano and Ahumada said PVC sewer pipes are designed to carry a steady flow of pressurized water But Guaymas and San Carlos residents have had a rationed water system in which households receive the city’s potable water only a few days a week water shortages or line breaks have resulted in much longer stretches without water most homes have water storage tanks on their roofs holding excess water for use on days when there’s no flow from the city The inconsistent water flow strains sewer pipes which have to withstand intermittent dry spells between periods of high-pressure water flow who was CEA regional director for 4½ years before leaving the position in 2019 “They are not designed for that type of pressure,” he said “They are designed for stable water conduction.” Another issue is the aging aqueduct that brings Guaymas’ water from Obregon At 31 years old it is reaching the end of its useful life was flooded with sewage for much of the summer because of collapsed sewer pipes and broken sewage pumps street vendors sold food and drinks as pedestrians picked their way across the wet pavement on Sept CEA workers attempt to break up a clogged pipe using a thin rod called a varillo The city’s sewage pumps are poorly maintained “If you go and look at one of the pumping stations only three of the city’s network of 11 sewage pumps were functioning “We reached a point where many areas of Guaymas were flooded with sewage,” he said in a text message in Spanish “People have had to learn to live with this problem due to the indifference of past governments.” Sewage problems exist throughout all of Sonora “Guaymas has a problem,” he said in Spanish “Anything that leaks can be seen by everyone because it all flows to a focal point in the city.” 13 found that the wastewater flowing on Avenida Serdán had fecal coliform levels of 7.8 million parts per 100 milliliters Fecal coliforms are the type of bacteria found in the intestines of warmblooded animals and they’re often used as a proxy for fecal contamination in water Open-air food vendors operate downtown even as the streets are flooded with sewage said Jaqueline García Hernández of Guaymas’ Center for Investigation in Nutrition and Development Even when the pools of sewage evaporate or drain away contaminated dirt coats the streets and wafts through the air Guaymas doesn’t have a separate stormwater system; all water flows into the sewer system That means rainwater collects everything in its path — including sand and the bountiful piles of trash in the streets — and washes it into the already overloaded sewer system perhaps well-intentioned residents sometimes open the manhole covers to allow more rainwater to drain from the streets This summer the level of trash in the streets was worse than usual Local media reported contract disputes and a COVID-19 outbreak at PASA as the culprits leaving Guaymas residents not only flooded with sewage but surrounded by mountains of garbage — which comes with its own health risks Any study on the health impacts of sewage in Guaymas would be confounded by the simultaneous health risk of rotting trash in the streets “Garbage collection in the city is very deficient and represents a serious problem due to its adverse effects on public health also including risks of gastrointestinal and respiratory diseases,” he said the Star took water samples from Guaymas bays as well as samples from the natural wastewater treatment system in San Carlos The lagoons are the sole wastewater treatment available in either San Carlos or Guaymas Testing results revealed sewage contamination in a Guaymas bay in violation of federal environmental standards and confirmed that the wastewater flowing through downtown Guaymas was raw sewage The Star’s testing also revealed that the oxidation lagoon in San Carlos is not consistently effective in purifying the human waste that is pumped there San Carlos doesn’t have a modern wastewater treatment plant It relies on a three-pond oxidation lagoon which is supposed to clean wastewater through the natural interaction of sunlight the water is supposed to meet the federal environmental standard for agricultural use: a daily average of less than 2,000 fecal coliform parts per 100 milliliters But water-quality testing by the Star shows the lagoon’s effectiveness varies dramatically depending on the volume of waste flowing into it without corresponding support for the aging sewer system or any concrete plans for a modern wastewater treatment facility San Carlos’ wastewater treatment system is also solely dependent on an oxidation lagoon with the exception of the homes that are on septic systems and some private businesses that have built their own oxidation lagoons on the outskirts of town The Country Club also has its own single-pond oxidation lagoon The natural wastewater treatment method is supposed to use a combination of sunlight it’s used only as a secondary or tertiary treatment after wastewater has already gone through a conventional water treatment plant research scientist in the University of Arizona’s Department of Environmental Sciences “oxidation ponds were never meant to be a sole source of treatment anywhere An oxidation pond is literally the least anybody can do,” Walker said “there’s not much teeth in the regulations to stop them from doing that.” Many under-resourced Mexican towns and cities rely solely on oxidation lagoons making do with inadequate wastewater treatment senior scientist and Mexico representative for the Tucson-based Center for Biological Diversity “It’s usual — but it’s not good,” said Olivera Even the oxidation lagoons that succeed at reducing levels of fecal contamination aren’t addressing other contaminants like heavy metals and chemicals like nitrogen and phosphorous And even if a lagoon has a 90% or more rate of removal for fecal coliform bacteria that figure sounds more impressive than it is “If you’re starting at a huge (fecal-coliform) level because that 10% residual (fecal-coliform level) could still be many fold higher than what would be considered safe to release into the environment.” the solids and sediment sink to the bottom of the pond oxygen and bacteria eats away at the dangerous pathogens in the waste the water is supposed to meet the federal environmental standard for agricultural use: a daily average of 2,000 fecal coliform parts per 100 milliliters But water-quality testing conducted by the Star shows that San Carlos’ oxidation lagoon is inconsistent with its effectiveness varying dramatically depending on the volume of waste flowing into the lagoons the oxidation lagoon was overflowing into an adjacent meadow with wastewater from the lagoon filling the grasses 16 from the final “clean” pond had fecal coliforms numbering 78,000 parts per 100 milliliters according to the analysis done by CIAD Guaymas That’s nearly 40 times the daily threshold under Mexico’s federal environmental standards fecal coliform levels must average under 1,000 parts per 100 milliliters to comply with the standards.) But water-quality testing improved dramatically six weeks later when the lagoon wasn’t overflowing into the meadow: taken from the oxidation lagoon’s “clean” pond on Sept tested well within federal standards: 450 fecal coliform parts per 100 milliliters San Carlos relies on an oxidation lagoon to treat its wastewater but the oxidation lagoon hasn’t been maintained in years a former water company director for Guaymas and San Carlos said regular maintenance of the lagoon should happen annually to ensure the water discharged from the ponds meets federal environmental standards when the lagoon’s water level was noticeably lower than previous tests showed fecal coliform levels of just 15 parts per 100 milliliters The results suggest wastewater volume generated in late September and November was lower than in the busy summer months allowing the oxidation lagoon to do its job effectively But it also suggests the oxidation lagoon will become increasingly ineffective as San Carlos’ population grows Despite the inconsistency of San Carlos’ oxidation lagoon the “treated” wastewater is still used to irrigate the golf course at the San Carlos Country Club Former CEA regional director and Guaymas native Roberto Romano said that during his tenure he was living in the Country Club when residents started complaining about sewage smells “Many people left the San Carlos golf course because of the smell,” he said Romano secured state funding for the San Carlos oxidation lagoon to be cleaned out: the bottom dredged to deepen the lagoon That modest effort greatly improved the lagoon’s performance and eliminated the smell on the golf course If that type of maintenance were done annually the lagoon could stay in good working condition the beach town’s wastewater treatment system — an oxidation lagoon with three ponds — overflows into an adjacent meadow Horses often visit to drink the overflowing water there which tested at 78,000 fecal coliform parts per 100 milliliters based on samples taken by the Arizona Daily Star on Aug That’s nearly 40 times the federal daily standard for safe agricultural use of wastewater “It would take less than 1 million pesos (about $46,000) every year to maintain the oxidation lagoon,” Romano said but it can be perfect water for irrigation San Carlos Golf Club owner Lenny Manzon declined a request to be interviewed about the current quality of the irrigation water on the golf course not black water,” he said when approached at the golf course He directed any further questions to the CEA While the CEA at the state level operates the water and sewer systems in Guaymas those local CEA companies are each audited separately — and their financial performances are miles apart with higher water rates and a high percentage of users who pay their water bills But the CEA in Guaymas is financially broken CEA Guaymas recorded a loss of $29 million pesos according to a 2020 CEA Guaymas financial audit Empalme and Vicam have accumulated a total debt of nearly $325.2 million pesos The financial problems at CEA Guaymas have a few main causes • Forty percent of the CEA’s primary product — the potable water that is transported from Obregon Some level of loss is expected; in the U.S. about 15% of potable water is lost to evaporation and natural processes But a 40% loss is an unsustainable waste of a scarce resource • Too many users in Guaymas fail to pay their water bills and water rates are far too low compared to the cost of producing and transporting the water said former state CEA director Sergio Avila in an interview only 19% of Guaymas users paid their water bill Payment rates in San Carlos are closer to 90% • The CEA must negotiate with two powerful worker unions who have made aggressive demands leading to an inefficient and oversized workforce Empalme and Vicam could operate efficiently with half as many workers An arroyo intended for stormwater drainage is filled with raw sewage from overflowing manholes across El Rastro neighborhood This arroyo empties into a stream that flows directly into a Guaymas bay the Star took water samples from the stream to be tested for fecal coliforms Results showed 14 million fecal coliform parts per 100 milliliters in the stream The federal environmental standard for safe discharge of wastewater into national bodies of water is 2,000 fecal coliform parts per 100 milliliters Three CEA regional directors point to the two unions that represent CEA workers as partially responsible for CEA Guaymas’ financial woes CEA Guaymas has two unions: one representing front-line workers and another for higher-level engineers and technicians Seventy percent of CEA Guaymas’ spending goes to worker payroll and bonuses Romano described situations in which an electrical problem shuts off a sewage pump over the weekend only a worker from a particular union can flip the switch to turn the pump back on leading to unnecessary delays in stopping sewage flows Romano said in his 4½ years as CEA regional director the time that demands on the administrator,” he said But CEA workers say that without the unions they wouldn’t even have uniforms or protective footwear Guaymas resident Antonio Chavoya left the CEA after 29 years in 2020 frustrated by never having the tools to do the job including working vehicles with good tires and fuel in them A salon owner in downtown Guaymas has set up a ramp across a raw sewage stream to keep customers’ feet dry Sewage floods in downtown Guaymas were constant over the summer leaving residents sickened with gastrointestinal distress combined with badly neglected sewer infrastructure led the state of Sonora to declare a health emergency in Guaymas The lack of payment from users is another complex issue “The water company is supposed to be autonomous But it’s not,” former CEA regional director Romano said Many in Guaymas don’t pay because the potable water and sewer service is poor there’s little chance of the CEA having the resources to improve service CEA Guaymas gets a state subsidy to help cover its expenses according to a statement from the current CEA administration in Hermosillo that subsidy will be about $83 million pesos But it’s not enough to cover needed maintenance and other expenses Users also have doubts about whether their money is going toward improving service or whether it’s being mishandled by corrupt public officials “The main action should be to regain the trust of citizens to convince them that there will be no more corruption that their payment will be used to improve the water and sewer service,” he said there will be a flow of capital with which to maintain the pumping equipment in good condition.” broken sewage pumps meant raw sewage poured from worker-access points like this manhole in El Rastro neighborhood on Aug The state of Sonora declared a state of emergency in Guaymas because of the collapsing and neglected sewer infrastructure requiring a costly network of sewage pumps to bring residents’ wastewater over steep hills to the city’s only wastewater treatment system which even CEA leaders now admit is inadequate is the only treatment the wastewater receives before it’s discharged into the sea Former CEA regional director Ahumada pointed to massive energy costs needed to operate the sewage pumps or roughly $252,000 — almost half its monthly income from user payments he said — on energy expenditures to serve its 60,000 contracted users Compare that to the $6 million pesos spent in the city of Obregon which has 230,000 domestic users but much flatter terrain “We’re talking about one-quarter of the users but almost the same energy costs,” he said Guaymas’ network of sewage pumps must work hard to move sewage over steep hills; much of that sewage from the densely populated north end of Guaymas travels six hilly miles to reach the oxidation lagoon at the southern side the city A wastewater treatment plant on the north side — and ideally two additional plants in other areas of the city — would significantly reduce the city’s energy expenditures It would also reduce the volume of wastewater flowing to the overtaxed oxidation lagoon in south Guaymas the CEA shared a database of sewage-leak reports received in Guaymas over the last four years The database shows a steady increase from 1,024 reports in 2017 to 1,474 reports in the first eight months of 2021 aside from a dip to 829 during the unusually dry year of 2020 Those numbers surely understate the extent of the problem Many no longer make official complaints to the CEA Some call friends who work at the CEA or approach CEA workers on the street for help Leaning out of his front door in the El Rastro neighborhood in downtown Guaymas Hector Montoya describes an “unbearable” sewage situation outside his doorstep While the sewage flooding has been worse this summer which got a healthy level of monsoon rain compared to the 2020’s dry summer he says the sewage has been a problem for the 15 years he’s lived there “All of it is flowing to the sea,” he said The stream of sewage next to Montoya’s house originates from a manhole cover in the alley next to his home Someone has arranged a series of concrete blocks as steppingstones for pedestrians to use when crossing the stream the sewage flow eventually joins a concrete arroyo wet with sewage from other overflowing manholes in the neighborhood The stream continues down the arroyo toward the sea passing a lonely basketball hoop and flowing parallel to a large cemetery before crossing under a busy overpass where Monica Castro works long hours amid the sickening smell Castro wasn’t only dealing with the sewage in the arroyo another stream had been spilling from a manhole cover for two months drenching the road in front of her workplace Her store is now filled with flies and sometimes she doesn’t eat all day because of the smell Monica Castro works long hours at the Six convenience store where she had to deal with overpowering odors from two major sewage flows near her store in August the stink permeates inside the store and turns our stomachs,” Castro said in Spanish The boy who helps me in the afternoon was vomiting because he couldn’t bear the smell.” the stink permeates inside the store and turns our stomachs,” she said in Spanish The boy who helps me in the afternoon was vomiting but whatever they did made no difference: The sewage trail in front of her store is still flowing She also blames residents who throw their trash into the street The Star tested samples from the waste-filled arroyo that was flowing toward the bay and confirmed it to be raw sewage with 14 million fecal coliform parts per 100 milliliters The Star also sampled water from along the shore of the bay into which the sewage flowed The results showed more than 240,000 fecal coliform parts per 100 milliliters That’s more than 100 times the federal standard for wastewater discharges into national waters a veterinarian who runs the Wildlife Rescue Coria lives in the San Bernardo neighborhood More research is needed about the impact of sewage on marine life fecal contaminants have been shown to damage coral reefs have been shown to cause tumors in sea turtles like those CRRIFS rescues and releases into the sea each year Coria wishes more people would remember how interconnected human health is with that of the animals in their environment We are not separated from the environment,” she said “Everything we do to the environment is reaching us.” Recent monsoon rainfall has revived a natural spring on a residential street near Starr Pass Contact reporter Emily Bregel at emily.bregel@gmail.com or on Twitter: @EmilyBregel reporter for KJZZ’s Fronteras Desk in Hermosillo Subscribe to stay connected to Tucson. A subscription helps you access more of the local stories that keep you connected to the community As sewage spills continue to plague the port city of Guaymas and its tourist sector of San Carlos Sonoran state officials are throwing cold water on a fast-moving $5.5 billion proposal to build a massive desalination plant in Puerto Peñasco… Get up-to-the-minute news sent straight to your device is a date that the Yaqui community in the town of Loma de Bácum will never forget riven into two factions over the imminent construction of a gas pipeline planned to cross straight through their territory One part of the community saw the pipeline as a threat to the 20,000 members of the Yaqui indigenous group and the environment they depend on The other part welcomed the pipeline as a source of development and also because seven other Yaqui communities had already voiced their approval of it Hundreds of people took part in the conflict a group of armed people had attacked the Guardia Tradicional station where Loma de Bácum’s Yaqui authorities usually meet and dozens of children had been caught in the middle of a violent exchange upon leaving school One person was dead and 11 vehicles were torched The events have left deep scars in the community the Guaymas-El Oro gas pipeline will run 330 kilometers (205 miles) 18 kilometers (11 miles) of it through Yaqui land in Loma de Bácum together with the 505-kilometer (314-mile) Guaymas-El Sásabe pipeline are intended to form a larger project known as the Sonora pipeline The entire project is being developed by Gasoducto de Aguaprieta a branch of the Mexico City-based company IEnova itself a subsidiary of San Diego-based Sempra Energy Loma de Bácum is one of eight communities that form the Yaqui nation in the state of Sonora in northwestern Mexico The majority of the families in Loma de Bácum oppose the pipeline crossing their territory according to the town’s Yaqui authorities consulted by Mongabay Latam The authorities claim Gasoducto de Aguaprieta persuaded the majority of the Yaqui communities with payments of sums of money and the use of force by Sonoran authorities we saw our territory being colonized by that industry colonized by people outside of the Yaqui tribe,” said Yaqui lawyer Anabela Carlón a leader in the movement to stop the pipeline the anti-pipeline faction made a legal request to stop the pipeline’s construction The district judge in the city of Obregón sided with them ordering that construction of the pipeline could not continue without the consent of all eight Yaqui communities Loma de Bácum became a stone in the shoe of the other seven Yaqui communities Mexico’s secretary of energy carried out a prior consultation with all eight Yaqui communities on Sept but the result was the same: seven communities accepted the construction of the pipeline The town expressed its “decisive and categorical rejection of the construction and operation of the Guaymas-El Oro section of the Sonora pipeline within the segment located in the territory corresponding to this town,” according to a statement published by the secretary’s office the lack of a unanimous favorable vote did not stop the government from giving the project a green light community members in favor of the pipeline supported by people from the pro-pipeline Yaqui town of Loma de Guamúchil as well as outsiders (called Yoris) sent by the company and the government tried to oust Loma de Bácum’s traditional Yaqui authorities in order to appoint others who favored the pipeline the anti-pipeline contingent rose up and denounced what they called an “attempted coup d’état.” A conflict ensued that spun out around a local school Several children and adults fainted in shock The violence lasted about two hours before the Sonora police and the Mexican navy broke it up told local media outlets that the Sonoran government was waiting for the Yaqui nation to resolve its conflicts so that the project could continue without setbacks all the necessary permissions were in order Some of the traces of the violent episode involving the Yaquis and Yoris can still be seen in the center of Loma de Bácum more than a year and a half later Eleven burned vehicles remind residents and visitors of the carnage that took place The twisted remains of the vehicles will stay where they are because residents opposed to the pipeline consider them a symbol of an achievement “This is going to stay here because it serves as a warning for those who want to invade: think twice,” said resident Higinio Ochoa Vega Less visible remnants of the incident are the memories of the children and their teachers caught up in the violence “They had never seen anything like it,” said Martín Valencia Cruz because nothing like it had ever happened in the community before One person died from a .22-caliber gunshot wound to the chest: Cruz Buitimea Piñas who was part of the group defending the construction of the pipeline a Yaqui volunteer fireman who was assisting the Guardia Tradicional that day was sentenced to 15 years in prison for the murder even though he was armed with a .45-caliber weapon according to Loma de Bácum’s traditional authorities but says the worst part of the ordeal is that children were placed in the middle of a conflict between hundreds of adults He and many other pipeline opponents claim the pro-pipeline faction did so deliberately “It was very serious for us to have used children from the community as human shields; that was very terrible and that is something that isn’t forgiven here,” Valencia said The spokesperson for the seven Yaqui communities in favor of the pipeline told media outlets the day after the conflict that they hoped for a resolution from the government the groups he represents were not armed during the conflict the Mexican Office of the United Nations High Commissioner for Human Rights visited Sonora first in February 2017 and then in March 2017 to “discuss” the right to prior consultation that the Yaqui communities have “The delegation from the UN emphasized the right of the indigenous communities to express their prior consent to the infrastructure projects that concern them,” the office said in a statement a federal tribunal directed the secretary of energy to comply with the judge’s order halting construction of the pipeline that the Yaquis of Loma de Bácum had won in 2016 The companies constructing the pipeline responded by continuing the project And the Yaqui community responded by digging out a section of the pipeline The incident was reported by local media outlets as an act of vandalism on the part of the Yaqui people Less than a kilometer from the center of Loma de Bácum a path runs toward the desert that reaches some signage for the pipeline work one has to pass in front of a Sonoran police station that maintains constant surveillance there is a hole in the ground that used to hold a 10-meter section of the pipeline the same man who was proud of the 11 vehicles that were burned He agreed to go with Mongabay Latam back to the location where the pipeline was removed because that is what our Yaqui oath says; it’s why we’re here,” said Ochoa He spoke with the energy of a boxer in the corner of a ring in the middle of a fight The hole remains the same as when the Yaqui dug it and there is no evidence of any personnel from the pipeline company in the area As for the green section of pipe dug out of the ground it is kept behind the Guardia Tradicional police station in plain sight of anyone who passes through the town a piece of land belonging to the community was set on fire went to ask for an explanation from the suspects and once again shots were fired and houses and vehicles burned The worst part is that there was a second fatality: Víctor Adolfo Molina Vázquez was questioned about the confrontations in Loma de Bácum a few days after Vázquez’s death He said the confrontations were unrelated to the pipeline One of the most upsetting things about the whole situation for many Yaqui in Loma de Bácum is that the bonds between the communities have been weakened so much that it resulted in violence and death it’s crucial that there be a consensus between the eight communities said a community member named Guadalupe Flores Gasoducto de Aguaprieta did not respond to requests for information by Mongabay Latam statements to the press given by Juan Rodríguez Castañeda state that “the construction has been following strict quality procedures and is under the supervision of specialists [The company] remains in continuous contact with the entire community and authorities from the Civil Protection Agency.” The project’s executive summary maintains that the pipeline is necessary because energy demands in Mexico have grown more than the country’s gross domestic product (GDP) and that in 2020 the country will have an energy “deficit.” The summary says the pipeline is intended to connect northeastern Mexico to the National Pipeline System — a goal outlined in the country’s National Energy Strategy 2013-2027 and one reason the Mexican government supports the project the pipeline remains incomplete and work on the Yaqui section has stopped “We defend our territory because without land there is no life; we would disappear and as Yaquis we would just be one more poor population in Mexico,” she said She also explained the relationship between her community and the environment “We live to understand the language of nature to be able to go to other dimensions inside of our beliefs Nature takes us to other worlds,” Carlón said an investigator from the National Institute of Anthropology and History in Sonora “indigenous people from Sonora created not only a relationship with nature and they learned to use all their resources no Indian died of thirst while crossing the desert.” Where a Yori person might not see anything the Yaqui people take a simple mesquite and turn it into flour as well as more than 100 medicinal plants in the area The relationship between the Yaqui tribe and the environment was one of the arguments used by the legal team against the construction of the pipeline and was what allowed them to obtain the order suspending the project in 2016 The attorney representing the anti-pipeline group from Loma de Bácum argued that those deciding whether or not to allow the pipeline’s construction must consider “the direct harms generated towards their material and immaterial assets.” the representative of the seven pro-pipeline Yaqui communities the Yaqui tribe has a plan to return to pre-colonial times when The traditional authorities from Loma de Bácum plan to plant 4,000 hectares (almost 9,890 acres) of diverse organic crops “We want our children to be well-developed It is the vision we have,” said Guadalupe Flores that vision is better than the one of their children in the middle of an armed conflict Banner image courtesy of Canal Sonora Mexico The “fortress conservation” model is under pressure in East Africa as protected areas become battlegrounds over history and global efforts to halt biodiversity loss Mongabay’s Special Issue goes beyond the region’s world-renowned safaris to examine how rural communities and governments are reckoning with conservation’s colonial origins and trying to forge a path forward […] the leading provider of shelter services for foreign manufacturers in Mexico is pleased to welcome CMI Group Aerospace and Defense to the Roca Fuerte Manufacturing Community in Guaymas Ariz.-based CMI Group has delivered quality machined and assembled components to the aerospace and commercial industries The company serves global aerospace brands with the production of thousands of part types and an emphasis on solid customer relationships “Our mission is to meet today's complex challenges head-on by providing the highest quality products and services to our customers while maintaining a competitive We believe that expanding into Guaymas perfectly positions CMI to do just this," says Mark McFeely This expansion brings CMI’s capabilities to the center of one of Mexico’s most robust aerospace manufacturing clusters CMI expects to hire 70 employees in Guaymas and technicians – with plans to grow to 200 employees by 2024.  “We chose to expand into Mexico because our aggressive growth plans require us to access a young we ultimately chose Guaymas because it has the most stable workforce,” says Marco Hernandez “We partnered with Tetakawi on this project due to their responsiveness and a strong history of helping aerospace companies expand into Mexico." The new 43,500-square-foot facility features wide-ranging CNC machining capabilities The company is also expanding its super-precision grinding CMI plans to launch a technical center dedicated to developing innovative new methods for serving its aerospace customers "I am pleased that CMI partnered with Tetakawi to expand into Guaymas I am confident that they will become one of Mexico's next aerospace success stories," says Luis Felipe Seldner "We look forward to building a strong relationship with CMI and delivering services that allow them to grow and reach their potential in Mexico." CMI Group provides machined component parts and small assembled components to the aerospace CMI partners with both customers and vendors through long-term contracts that prioritize working together as a team as CMI believes in building a safe and friendly team-first work environment for its members For more information, visit https://cassmac.com/ We’re in the business of providing relevant information through print and electronic media, organizing events to bring industrial value chain actors together and services to create new business relationships. Our goal is to improve our clients’ competitiveness. Libra Industries, a valued portfolio company of CW Industrial Partners (CWI), is thrilled to announce the launch of its cutting-edge Powder Coat paint line in their Guaymas, Mexico factory­­, adding surface finishing capabilities and services. The powder coating process, a sustainable alternative to traditional wet painting, leverages top-of-the-line powders and cutting-edge equipment to achieve finishes that are both durable and aesthetically pleasing. Libra Industries is dedicated to providing quick turnarounds for small orders, high-volume production, high-temperature coatings, and multi-coat applications. Material preparation at the facility includes an array of essential steps such as degreasing, di-water treatments, and Zirconium (Zr) coating. With this facility, Libra Industries aims to set new standards for quality, versatility, and efficiency in the field of surface finishing. The addition of this advanced paint line in Guaymas, Mexico, is a testament to Libra Industries' commitment to offering comprehensive manufacturing solutions to meet the diverse needs of its valued customers. This facility aligns perfectly with their mission to provide outstanding manufacturing capabilities across multiple sectors.​​​​ Volume 13 - 2022 | https://doi.org/10.3389/fmicb.2022.831828 Hydrocarbons are degraded by specialized types of bacteria Their occurrence in marine hydrocarbon seeps and sediments prompted a study of their role and their potential interactions using the hydrocarbon-rich hydrothermal sediments of Guaymas Basin in the Gulf of California as a model system This sedimented vent site is characterized by localized hydrothermal circulation that introduces seawater sulfate into methane- and hydrocarbon-rich sediments and thus selects for diverse hydrocarbon-degrading communities of which methane alkane- and aromatics-oxidizing sulfate-reducing bacteria and archaea have been especially well-studied Current molecular and cultivation surveys are detecting diverse fungi in Guaymas Basin hydrothermal sediments and draw attention to possible fungal-bacterial interactions and underlying hypotheses that guide current experiments on this topic in the Edgcomb and Teske labs in 2021 and that we will revisit during our ongoing investigations of bacterial and fungal communities in the deep sedimentary subsurface of Guaymas Basin These hydrocarbon-rich hydrothermal sediments provide excellent opportunities for investigating sedimentary microbial hydrocarbon biodegradation because seep sediment microbiota have been exposed to long-term selection pressure by hydrocarbon exposure The cascading health impacts of hydrocarbon contamination lend particular urgency to microbial hydrocarbon degradation and bioremediation research It has been recovered frequently from deep-drilling surveys offshore Taiwan A second lineage of independently branching deep subsurface clones is also annotated as a member of the Desulfoarculaceae and occurs in the hot sediments (ASVs 219 and 251) The physiological capabilities of these misidentified “Desulfoarculaceae” remain unknown hydrothermal seep sediments of Guaymas Basin harbor a high diversity of hydrocarbon-degrading Deltaproteobacteria which participate in hydrocarbon degradation either individually or in syntrophic association with specialized archaea whereas cold sediments from the same region contain a considerably more restricted range of Deltaproteobacteria pure culture isolations and sequencing surveys cannot reveal whether these sulfate reducers might benefit from mutualistic interactions and whether they show enhanced activity in the presence of the second major group of hydrocarbon-degrading organisms that share the same sedimentary habitat Table 1. Sample site key for published fungal isolates from Guaymas Basin (Keeler et al., 2021; sampling key not reported therein) syntrophic growth of fungi with bacteria or archaea that can utilize the products of fungal hydrocarbon metabolism or co-cultures that allow for sequential utilization of hydrocarbon compounds and degradation products within the same habitat may be a win-win strategy for all microbiota involved in hydrocarbon degradation and the existence of unique fungal biosurfactants it is possible some Fungi play a critical role in facilitating the bio-availability of hydrocarbons to other microbial populations (i.e. to other Fungi or Bacteria) and by synthesizing biosurfactants maintained culture cell densities over 3 weeks in liquid medium with naphthalene substituted as the sole C source under reducing anoxic conditions (100x in situ naphthalene concentration provided) To evaluate the role of fungi in hydrocarbon degradation a deeper culturing effort was needed in order to obtain the broadest possible diversity of in situ fungi from different sites and depths The Edgcomb lab is collaborating with Gaetan Burgaud at the University of Brest to carry out high-throughput fungal culturing efforts This collaboration has yielded ∼200 unique fungal isolates from subsurface Guaymas sediments and all isolates in the collection are currently being tested for production of biosurfactants Figure 4. Microphotographs of Guaymas Basin fungal strains imaged under fluorescence after calcofluor staining, which highlights the chitin cell walls of fungi. Strains were isolated from Guaymas Basin sediments (Table 1) and images were taken after 40 days of incubation with the polyaromatic substrate naphthalene (5 μg/ml) in co-culture with Desulfobacterales-dominated sulfate-reducing bacteria Panel (A) shows growth of the filamentous ascomycete fungus Cadophora malorum and panel (B) shows filamentous arrangement of cells of the yeast-like ascomycete fungus Aureobasidium pullulans The active microbiota might involve aerobic as well as anaerobic fungi that share the surficial sediment habitat with similarly diverse bacteria These deep subsurface sediments vary significantly in their thermal Comparing sites where temperatures increase steeply above shallow and sites with more gradual temperature gradients offer a chance to systematically examine the influences of temperature and pressure and cell abundances along cores from these eight sites will inform on the distribution of deep biosphere microbiota (bacteria and microbial fungi) in this hydrothermal setting along temperature analyses of genomic potential in metagenomes and MAGs and studies of cultured fungal isolates will reveal the likely nutritional sources (e.g. buried organic material) that allow bacteria we may discover diverse fungal-bacterial syntrophic interactions that allow the syntrophic partners to survive by adapting to different sources of carbon and/or energy and by cooperating in accessing substrates that individual taxa cannot access alone Using new molecular assays and long-term enrichments diverse fungal-bacterial syntrophic interactions might be discovered that allow these partners to survive in the anoxic deep biosphere by adapting to different carbon and energy sources it will be possible to go beyond studies of individual fungal and sulfate-reducing species and their capabilities to oxidize hydrocarbon and low-molecular weight organic compounds and to explore the possibility that selected fungal-bacteria co-cultures and syntrophic cultures enhance the accessibility of particular hydrocarbons through successive or simultaneous reactions The original contributions presented in the study are included in the article/Supplementary Material VE led the fungal-bacterial interactions project and designed the experiments AT wrote the first draft of the manuscript All authors commented and edited the manuscript in turn This project was supported by collaborative NSF Biological Oceanography grants OCE-1829903 and OCE-1829680 “Hydrothermal fungi in the Guaymas Basin Hydrocarbon Ecosystem” to VE and AT and collaborative NSF Biological Oceanography grants OCE-2046799 and OCE-2048489 “IODP-enabled Insights into Fungi and Their Metabolic Interactions with Other Microorganisms in Deep Subsurface Hydrothermal Sediments” to VE and AT PM was supported by OCE-2046799 and OCE-1829903 Sampling in Guaymas Basin was supported by collaborative NSF Biological Oceanography grant 1357238 “Collaborative Research: Microbial carbon cycling and its 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This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY) *Correspondence: Virginia P. Edgcomb, dmVkZ2NvbWJAd2hvaS5lZHU= Volume 14 - 2023 | https://doi.org/10.3389/fmicb.2023.1279865 Unsubstituted aromatic hydrocarbons (UAHs) are recalcitrant molecules abundant in crude oil which is accumulated in subsurface reservoirs and occasionally enters the marine environment through natural seepage or human-caused spillage The challenging anaerobic degradation of UAHs by microorganisms in particular under thermophilic conditions we established benzene- and naphthalene-degrading cultures under sulfate-reducing conditions at 50°C and 70°C from Guaymas Basin sediments We investigated the microorganisms in the enrichment cultures and their potential for UAH oxidation through short-read metagenome sequencing and analysis Dependent on the combination of UAH and temperature A Thermoplasmatota archaeon was abundant in the benzene-degrading culture at 50°C because the archaeon lacked most known genes for benzene degradation Two novel species of Desulfatiglandales bacteria were strongly enriched in the benzene-degrading culture at 70°C and in the naphthalene-degrading culture at 50°C Both bacteria encode almost complete pathways for UAH degradation and for downstream degradation They likely activate benzene via methylation The two species constitute the first thermophilic UAH degraders of the Desulfatiglandales In the naphthalene-degrading culture incubated at 70°C a Dehalococcoidia bacterium became enriched which encoded a partial pathway for UAH degradation Comparison of enriched bacteria with related genomes from environmental samples indicated that pathways for benzene degradation are widely distributed while thermophily and capacity for naphthalene activation are rare Our study highlights the capacities of uncultured thermophilic microbes for UAH degradation in petroleum reservoirs and in contaminated environments the GB can be considered a surface analogue for petroleum reservoirs which is well suited to study microbial processes like anaerobic AH degradation at high temperatures we incubated hydrothermally heated GB sediment with different UAHs as electron donor and sulfate as electron acceptor at 50°C and 70°C 5 mL of the silicone oil-UAH mixture were added to the slurries supplying a final UAH concentration of 10 mM A negative control contained 5 mL silicone oil without substrate The headspaces were filled with 2 atm N2:CO2 (90:10) and bottles were incubated at gentle shaking (40 rpm) in the dark DNA was also extracted in the same way from a 1 g pellet of dried sediment slurry (dry weight 202 mg mL−1) that was produced from the combined cores 4991-13 and 4991-14 The final DNA concentrations were determined in a fluorometric assay DNA yields were 0.2 μg (B50) and 0.7 μg (original sediment) Libraries were sequenced as 2 × 150 bp paired-end reads on an Illumina HiSeq3000 platform at the Max-Planck-Genome-Centre (Cologne Between 4,142,459 (B70) and 4,247,237 (N70) raw reads were obtained The optimal growth temperature (OGT) was predicted for the publicly available MAGs with the OGT_prediction tool (version 1.0.3) Key genes for anaerobic UAH/AH oxidation and downstream degradation were identified in Desulfatiglandales and SZUA-161 MAGs by running the previously built protein databases on the amino acid sequences of the MAGs in the same way and with the same selection criteria as described in the section “Genome annotation.” The raw reads of short-read metagenome sequencing of the original sediment slurry and the four enrichment cultures have been deposited in the NCBI Sequence Read Archive (SRA) under BioProject PRJNA1013425 (accessions SRR25925499-SRR25925503) The bash script used for the identification of CxxCH motifs in protein sequences of the MAGs is available under https://github.com/zehanna/UAH_oxidation Thermophilic microorganisms from Guaymas Basin sediment oxidize aromatic hydrocarbons (A) Sampling site of petroleum hydrocarbon-rich push cores in the Guaymas Basin Push cores used for anoxic incubations are indicated by white arrow heads (B) Sequential dilution of sulfide-producing anoxic slurries strongly reduced sediment content (from left to right: original slurry (C–F) Sulfide production in anoxic cultures supplied with benzene (C,E) and naphthalene (D,F) incubated at 50°C (yellow filling) and 70°C (red filling) Gaps in sulfide profiles indicate dilution events After more than 1.5 years of cultivation we retrieved short-read metagenomes from the original sediment used for incubations and from the four active cultures B50 Microbial community compositions differ in anaerobic UAH-degrading cultures depending on substrate and incubation temperature (A) Mean coverages of the 47 MAGs reconstructed from the co-assembly of metagenomes of benzene- and naphthalene-supplied cultures at 50°C and 70°C (B) Relative abundances of MAGs assigned to the domains archaea or bacteria in the four metagenomes (C) Relative abundances of the MAGs on order-level The Caldisericota in our culture may have a similar function While the H4F WL pathway for CO2 fixation is only 50% complete in MAG 48 it encodes both phosphate butyryltransferase and butyrate kinase for butyrate synthesis The produced butyrate and/or acetate may then fuel other microbial groups which could oxidize butyrate through the β-oxidation pathway and/or convert acetate to acetyl-CoA for various purposes which also affiliates with Thermoplasmatota lacks acetate kinase for conversion of acetate to acetyl-CoA but encodes a β-oxidation pathway for utilization of butyrate multiple symbiotic interactions might co-exist in this culture More studies are required to elucidate the mechanisms in this complex but highly active culture Figure 3. Benzene degradation pathways in MAGs recovered from benzene-oxidizing cultures at 50°C (A) and 70°C (B). Genes were identified via BLASTp search against local databases of proteins of interest. For proteins and pathways encoded by several genes, completeness was calculated as percentage of present genes of total genes of the pathway/protein. For pathway genes and abbreviations see Supplementary Table S7 The estimated OGT of 65°C for this MAG supports the thermophilic character of this organism like MAG 16 (Bipolaricaulales) and MAG 17 (Archaeoglobales) also encode proteins for anaerobic benzene degradation and in case of MAG 17 a complete DSR pathway MAG 17 encodes one of two subunits of anaerobic benzene carboxylase (AbcA) which could enable it to degrade benzene via carboxylation It is thus possible that the two organisms contribute to a small degree to benzene oxidation and/or sulfate reduction we expect the organism represented by MAG 9 to be the main active organism in the culture it is capable of the three-step RD of naphthalene encoding homologues of 2-naphtoyl-CoA reductase (NCR) 5,6-dihydro-2-naphthoyl-CoA reductase (DHNCR) and both N47 and NaphS2 type of 5,6,7,8-tetrahydro-2-naphthoyl-CoA reductase (THNCR) An almost complete thn operon and lower BCoA pathway facilitates RH and oxidation to acetyl-CoA followed by complete oxidation to CO2 via the CODH/ACS complex and the remaining H4F WL pathway enabling the organism to shuttle electrons from naphthalene oxidation directly into sulfate reduction The incubation temperature is very close to the estimated OGT of the organism of 55°C Its high relative abundance and its extensive genomic capacity for naphthalene degradation suggest that the bacterium represented by MAG 34 is the dominant maybe even the only naphthalene oxidizer in the culture Figure 4. Naphthalene degradation pathways in MAGs recovered from naphthalene-oxidizing cultures at 50°C (A) and 70°C (B). Genes were identified via BLASTp search against local databases of proteins of interest. For proteins and pathways encoded by several genes, completeness was calculated as percentage of present genes of total genes of the pathway/protein. For pathway genes and abbreviations see Supplementary Table S7 In the N70 culture (Figure 4B), MAG 33 (Dehalococcoidia) encodes only one protein of the methylation pathway, and lacks naphthalene carboxylase, thus limiting its options for naphthalene activation. Yet, MAG 33 encodes NCL, two of the three reductases required for RD, and about two thirds of the thn operon for RH, among others the putative ring-cleaving hydrolase ThnL (Meckenstock et al., 2016) it encodes an almost complete lower BCoA pathway plus a complete CODH/ACS and H4F WL pathway which would enable it to oxidize naphthalene to CO2 thus it is possible that the missing 15% encode naphthalene-activating UbiD-like carboxylases and DHNCR which would enable it to degrade naphthalene Because none of the other MAGs with relative abundances ≥5% in this culture encode numerous genes for activation MAG 33 is the most likely candidate for naphthalene oxidation MAG 33 encodes only one of three proteins of the DSR pathway and is therefore probably incapable of sulfate reduction it is possible that naphthalene oxidation in this culture occurs via syntrophic interactions While membrane-bound hydrogenases are absent in MAG 33 both MAGs 33 and 31 encode formate dehydrogenases which could facilitate electron transfer from MAG 33 to MAG 31 via formate Direct transfer via DIET is also conceivable and both MAG 33 and MAG 31 encode several multi-heme cytochromes We aimed to bring the results from our enrichment cultures into a wider ecological context and examined the distribution of AH degradation genes and pathways in the larger taxonomic groups of the microorganisms that we enriched in our study. We refrained from examining the phylogeny of the Thermoplasmatota MAG 53 (M8_bin1702), because the Thermoplasmatota phylogeny was well-resolved in the recent study by Liu et al. (2020) we focused on two bacterial groups with which abundant MAGs from our cultures were affiliated: the order Desulfatiglandales (class DSM-4660) and the order SZUA-161 (class Dehalococcoidia) Both group distributions likely reflect sampling efforts rather than actual occurrence and/or abundance Environmental origin of bacterial MAGs of the Desulfobacterota order Desulfatiglandales (A) and of the Dehalococcoidia order SZUA-161 (B) Coordinates were acquired from metadata accompanying the MAGs deposited at NCBI Considering the current data on both bacterial groups it seems plausible that both are widely distributed and capable of inhabiting diverse environments with a potential preference for hydrothermal vent areas we examined the phylogenomic placement of Desulfatiglandales MAGs and the SZUA-161 MAG from our study in their larger taxonomic groups and investigated the genomic potential of environmental Desulfatiglandales and SZUA-161 MAGs for anaerobic UAH degradation we were able to reconstruct the MAGs of the likely most thermophilic genus of the class and enrich the currently most thermophilic organism and anaerobic AH degrader of the clade at temperatures slightly above its predicted OGT likely grow at mesophilic temperatures about 20°C lower (OGT 44°C) the second group consists of four species of one genus: species (1) GCA_019306325.1; species (2) GCA_003646995.1 and MAG 47; species (3) MAG 34; and species (4) MAG 36 and GCA_019309225.1 Members of group two are predicted moderate thermophiles with OGTs around 50–55°C which coincides with the enrichment of the MAG 34 bacterium at 50°C Figure 6. Genomic capacities for anaerobic aromatic hydrocarbon degradation in genomes of the bacterial order Desulfatiglandales. MAGs recovered in this study are highlighted in bold, MAG 9 dominant in the benzene 70°C (B70) culture and MAG 34 dominant in the naphthalene 50°C (N50) culture are additionally highlighted in red and yellow, respectively. For pathway genes and abbreviations see Supplementary Table S7 Genes coding for central enzymes for the anaerobic AH metabolism are widely distributed within the order Desulfatiglandales and do not appear to be connected to specific clades CODH/ACS and bacterial-type H4F WL pathway are also ubiquitously present and should allow a downstream oxidation of aromatic compounds The DSR pathway is strongly represented for coupling to sulfate reduction even though the pathway is incomplete in about a third of the included MAGs In some cases this may be a result of low completion in MAGs GCA_015223015.1 and GCA_016776415.1 The BamB subunit of ATP-independent class II BCR is similarly as represented as BzdQ thus both ATP-dependent and -independent BCRs seem to be used by Desulfatiglandales NCL-encoding genes are present in only eight MAGs and the complete operon encoding THNCR in 12 MAGs The combined presence of all genes required for naphthalene degradation via carboxylation is rare next to the known naphthalene-degrader NaphS2 MAG 34 from the N50 culture is the only MAG encoding the complete naphthalene degradation pathway MAG 34 also contains key genes for the anaerobic activation of benzene Thus this bacterium might also be capable of benzene and/or benzene derivate degradation The study further showed that most Dehalococcoidia MAGs recovered from marine sediment encoded bcr-type BCRs which were absent in Dehalococcoidia MAGs from groundwater or seawater Figure 7. Genomic capacities for anaerobic aromatic hydrocarbon degradation in MAGs of the Dehalococcoidia order SZUA-161. The MAG recovered in this study from the naphthalene 70°C (N70) culture is highlighted in red. For pathway genes and abbreviations see Supplementary Table S7 The SZUA-161 family encodes several key pathway genes for benzene degradation SZUA-161 seem to rely on ATP-dependent BCRs both for the methylation and carboxylation pathway are not encoded by members of the SZUA-161 family and all MAGs encode one or more subunits of the four-subunit THNCR while SZUA-161 likely cannot activate naphthalene directly they might be able to dearomatize naphthyl-derivatives All SZUA-161 family MAGs encode complete CODH/ACS complexes and partial or complete H4F WL pathways which they could use for oxidation of dearomatized naphthyl-residues to CO2 two MAGs of the SZUA-161 family encode complete DSR pathways and the other six MAGs encode partial DSR pathways insinuating that these organisms are capable of sulfate reduction a metabolic trait that was previously not associated with members of the Dehalococcoidia More high-quality MAGs are needed for more reliable predictions about UAH/AH degradation capacity in this family Cultures of anaerobic thermophilic UAH-degraders have not previously been established from GB sediment but lacked most other genes of this pathway and BCR and the enzymes of the lower BCoA pathway are required for further oxidation the high relative abundance of this MAG suggests an important role in the culture Whether and by which mechanism this archaeon degrades benzene requires further investigation In the N70 culture, we identified MAG 33 of the Dehalococcoidia order SZUA-161 as the most likely naphthalene oxidizer. 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This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY) *Correspondence: Hanna Zehnle, aHplaG5sZUBtcGktYnJlbWVuLmRl; Gunter Wegener, Z3dlZ2VuZXJAbWFydW0uZGU= Some of the customers ordering at Broadway’s Tacos Guaymas on September 30th 2014 weren’t there for the affordable Mexican food served inside a bustling but tiny Capitol Hill restaurant space according to the office of Attorney General Bob Ferguson investigators from the Department of Revenue visited the restaurant that Tuesday founder and owner of the Tacos Guaymas chain Salvador Sahagun was charged with six counts of first-degree theft and three counts of possessing and using sales suppression software in what the AG says was a multi-year scheme to pocket more than $5.6 million in sales tax from cash transactions While the statute of limitations has run out on any crimes related to the eight transactions that day on Broadway in 2014 state investigators estimate that some $78,000 in tax revenue went missing from the Capitol Hill location of the restaurant over the years Here is how the AG says the suppression works: Run on a point-of-sale computer or cash register sales suppression software surreptitiously deletes or underreports cash transactions The software then re-balances the company financial records to show a lower sales figure reducing the business’ sales tax obligation The retailer pockets the difference between what the patron paid These unscrupulous retailers often keep “two sets of books.” Prosecutors also say “the majority of sales receipts were missing” from the point of sales system. According to the Attorney General’s announcement of the charges the investigation began after an audit revealed discrepancies between Sahagun’s tax returns and his system’s point of sales records Starting with the Broadway Tacos Guaymas visit DOR employees “visited the seven restaurants on several occasions and paid cash for their meals” — The auditor then compared the employees’ receipts with the receipts on the point-of-sale system to determine whether the transactions existed and the amounts matched The auditor found that three of the restaurants were using sales suppression software to delete or underreport cash transactions In addition to the three locations the AG’s office says were using the software to suppress sales totals,the three other locations also owed sales tax the auditor determined Sahagun owed $5,615,497 to the state No charges were brought for use of suppression software on Broadway the statute of limitations for use of sales suppression software had expired before charges could be filed.” started Tacos Guaymas in West Seattle 25 years ago His Broadway location was forced to move to the 1400 block of Broadway when Chipotle took over the original space in 2012 He has not yet entered a plea on the charges The Broadway Tacos Guaymas was open Monday and other locations continue to operate Thanks for stealing from WA taxpayers….that money could have gone to roads parks – instead just lined their greasy a** pockets The food is nasty af too so :( not even very good at what they set out to do Not even good at deception either because the auditors found them out + SUBSCRIBE TO CHS: Support journalism dedicated to your neighborhood. SUBSCRIBE HERE TODAY Got a tip? E-mail CHS — [email protected] — Call or text (206) 399-5959 — About CHS Three Mexicans are part of a team of 33 scientists from nine countries currently studying the seabed of the Gulf of California off the coast of Guaymas a research vessel that drills into the ocean floor to collect samples of sediments carbon cycling and microbial activity of the Guaymas Basin is part of the International Ocean Discovery Program a researcher at the Institute of Geophysics of the National Autonomous University (UNAM) told the newspaper El Universal that research in the Guaymas Basin is important because the Pacific and North American tectonic plates meet there Manet Estefania Peña of the Autonomous University of Baja California said the ocean floor in the basin is breaking up and that the rupturing process is causing magma to shoot into the ocean from within the earth’s crust it cools and hardens to form a new ocean floor “Drilling the subsoil will allows us to obtain geological records that speak to us about the evolution of our planet,” Peña added It’s like getting books from billions of years ago a 143-meter-long vessel with the capacity to dig 8,235 meters below the seabed will carry out drilling at six different points in the Guaymas Basin Peña said the research will enable greater understanding of the tectonic plates beneath Mexico and that will allow “better planning of our cities in the future,” while Pérez said that the sediments of the Gulf of California are likely to contain a “large quantity of geothermal energy that at some point could be used.” The UNAM researcher said that data collected by scientists could form the base of knowledge to “solve some of the problems we’re going to face on matters of energy.” a scientist at the Center of Scientific Research in Ensenada said the research will benefit the energy industry “We’re going to make maps of the heat flows and in that way we’ll be able to estimate the geothermal potential of the area we will try to identify the quantity of carbon in the basin Source: El Universal (sp)  State Department has issued an advisory for Guaymas and other parts of Sonora A group of armed men in a pickup truck ambushed and opened fired Thursday on six police officers on a main avenue in the center of Guaymas a Sonoran industrial port city about 300 miles south of Tucson Three of the officers died at the scene and another died at a hospital, El Imparcial reported Two others were wounded and transferred to a hospital in Hermosillo A traffic officer was also killed during a separate incident when he tried to stop the gunmen from fleeing The Sonora newspaper identified those who were killed as: Enrique Alamillo Romero The army and federal and municipal forces are searching for the perpetrators but no arrests had been made as of Friday afternoon The attack comes after a video surfaced in late July that appears to show Guaymas municipal police officers handing over four men to people linked to organized crime, the national newspaper El Universal reported The U.S. State Department has issued an advisory for certain parts of Sonora since it prohibits its employees from travel to San Carlos Empalme and all points south of Hermosillo via Federal Highway 15 “Sonora is a key location used by the international drug trade and human trafficking networks,” the advisory says But it adds that northern Sonora experiences lower level of crime than cities closer to its neighboring state Sinaloa and other parts of Mexico In March, a commander in Guaymas was also shot and killed following a pursuit through the historic downtown The gunmen shot Francisco Genaro Bogarín Gutiérrez multiple times while he was driving his Nissan Pathfinder The vehicle came to a stop after crashing against a stoplight Andrés Manuel López Obrador promised to cut taxes and double the minimum wage in the border region to make it more competitive Dozens of people await refunds for flights that never materialized Commercial air service from Tucson to begin next month; airfare Between calls for building a concrete barrier A new auxiliary team aims to make tourists feel safe This weekend's arrival of spring breakers will test it The best chance for rain in southeastern Arizona will be from late Sunday afternoon through Monday morning clipped out the banner news article … The vote gave Trump his second appointee to the court tilting it further to the right and pleasing conservative voters who might have revolte… A 30 percent chance of rain was given for Sunday by the National Weather Service Two people have been arrested in connection with three murders and two arson attacks in San Carlos a 31-year-old recently-married man with a doctorate was murdered in his car in the car park of Hammerhead’s restaurant last Friday Those homicides came after a security guard at the La Bartina bar was murdered on June 19 in an armed attack that wounded one other person was wounded in Tuesday’s attack and taken to hospital for treatment The same two people accused of the murders are also allegedly responsible for setting fire to La Bartina and a restaurant and beach club called Maukaa according to the Sonora Attorney General’s Office (FGJE) The FGJE said in a statement Wednesday that it deployed a special team of investigators to respond to the events detaining two people in possession of firearms and drugs The FGJE said the unnamed people possibly participated in the criminal acts San Carlos – a beach town 20 kilometers northwest of the city of Guaymas – is currently amidst a crisis of insecurity It said that rival criminal groups are fighting for control of the town and that – despite the recent arrests – authorities haven’t acted to solve the crisis The recent wave of violence appears related to extortion demands made by criminals in San Carlos A local businessman told Tribuna that criminal groups are asking many businesses to make regular payments Other business owners have taken to social media to denounce the crime and highlight authorities’ failure to combat it One business owner pleaded for people to “pray for San Carlos,” Tribuna said said that extortion usually occurs because organized “crime acts as a franchise business.” “So local groups tend to look for sources of financing by resorting to these actions,” he said “The … victims selected by these criminals are usually Mexican business people,” said Rafael López Criminals target them because “it’s known their families are here” and they have “vulnerable points,” he said Foreign-owned businesses – of which there are some in San Carlos – are “the least affected by this kind of crime because they don’t have these vulnerable points,” López said local businessman Luis Zaragoza questioned the inaction of authorities “There was an attack that resulted in the death of a person … it’s a very serious situation because families with children and tourists were walking around,” he said in a radio interview “[It happened] at a relatively early hour; it’s an increasingly delicate situation … [but] there’s no reaction [from authorities] I don’t understand what authorities are thinking and what they’re waiting for to act.” Tribuna reported that Guaymas Mayor Karla Córdova hasn’t made a public appearance since the latest outbreak of violence began, but noted that isn’t surprising because she has kept a low profile since witnessing an armed attack on the municipal police chief, which claimed the lives of three other people last November Sonora Security Minister María Dolores del Río has asserted that authorities are concerned about what’s happening in San Carlos and working to combat crime in the town The recent arrests lend some credence to those words said the absence of the mayor creates the impression that the problems in San Carlos are not being addressed by local authorities “Mayors are the visible faces of municipal governments they’re the first responders [to local problems] and if that face isn’t there if citizens don’t see an interest in resolving problems … [they believe] they’ve been abandoned by an indolent authority,” he said in an armed attack Thursday that targeted the city’s police chief Navy Minister José Rafael Ojeda said Friday The attack occurred outside the municipal palace in the northern port city as women were protesting against gender violence One of the victims was an 18-year-old protester who Ojeda identified as the daughter of a member of the navy were a member of the Guaymas mayor’s security team and a wanted criminal suspect another young protester and a municipal official were wounded and taken to hospital for treatment Speaking at President López Obrador’s morning press conference Ojeda said municipal police Chief Andrés Humberto Cano Ahuir He described the three fatalities as “collateral damage.” The minister ruled out the possibility that the gunmen intended to kill Morena party Mayor Karla Córdova She and Cano had come out of the municipal palace to speak with protesters “It was not an attack directed at the mayor … they were going for the captain,” he said Ojeda said an arrest warrant had previously been issued for the slain suspect “… We’re going to try to obtain intelligence information to go after this group that is in the region,” Ojeda said Sonora Attorney General Claudia Indira Contreras Córdova said in a video message early Friday that state authorities were considering the possibility that the attack targeted Cano a 33-year veteran of the navy who became Guaymas police chief in August 2019 She said that the navy captain had been the subject of threats “That these attacks occur is unacceptable; we especially regret that it occurred at the end of a protest for the International Day for the Elimination of Violence against Women,” Contreras said The attorney general said police seized a pickup truck without registration plates that was abandoned near the scene of the crime Two army-grade firearms and other weapons paraphernalia were found in the Nissan Titan Contreras and Sonora Governor Alfonso Durazo vowed to apprehend the perpetrators An act of violence that offends and hurts society will not go unpunished,” Durazo said With reports from Milenio