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Montevideo, May 6th 2025 - 05:54 UTC
The Governors of the Brazilian States of Pernambuco and Alagoas issued separate emergency decrees during the weekend due to heavy rains affecting 12 and 29 cities respectively
Pernambuco Governor Raquel Lyra decreed a situation of emergency in 12 cities in Zona da Mata
heavy rains have affected 2,862 people from 756 families
447 people from 656 families are displaced and 101 families are homeless
The emergency is established in the municipalities of São Benedito do Sul
Thirteen points of landslides were registered in these cities - four in Catende
it took into account the preservation of the welfare of the population and the socioeconomic activities of the affected regions and the fact that the inhabitants of the affected municipalities still do not have satisfactory conditions to overcome the damage and losses caused
The government also announced the availability of emergency funding to municipalities in distress and calamity
including those caused by heavy rains recorded in the metropolitan region of Recife and the areas of Mata and Agreste in recent days
Governor Paulo Dantas Saturday declared a situation of emergency in 29 municipalities
The municipalities reached by the decree are Atalaia
Over 22,000 people have been affected statewide
2,756 people were left homeless and 19,273 people have been displaced
2,862 people have been affected by the rains in the state
of which 447 are homeless and 101 are displaced
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Volume 12 - 2021 | https://doi.org/10.3389/fmicb.2021.659965
Bacteria of the genus Bacillus can colonize endophytically and benefit several crops including the control of some pest orders
In view of the benefits provided by these microorganisms and in order to find out an efficient biotechnological control for the giant borer
our interest in studying the microorganisms in symbiosis with sugarcane and the giant borer has arisen
since there is no efficient chemical or biological control method for this pest
endophytic Bacillus strains were isolated from three sugarcane niches (apoplast fluid
central internode cylinder and roots) and also from the giant borer larvae living inside sugarcane varieties grown in the Northeast region of Brazil
The taxonomical characterization (16S rRNA) of 157 Gram-positive isolates showed that 138 strains belonged to the Bacillus genus
The most representative species were phylogenetically closely related to B
BOX-PCR analyses showed very distinct band pattern profiles suggesting a great diversity of Bacillus species within the sugarcane niches and the digestive tract
cereus group remained very closely clustered in the dendrogram
Additional studies using conserved genes (glp
and tpi) indicated that most of these strains were phylogenetically closely related to B
thuringiensis and may be considered different subspecies
this study suggests that the culturable Bacillus species are greatly diversified within the plant niches and showed Bacillus species in the digestive tract of the giant borer for the first time
These results open new perspectives to understand the role and functions played by these microorganisms in symbiosis with this pest and also the possibility of developing an efficient biological control method for the giant borer using strains identified as the B
This opened new perspectives to find species of Bacillus with a broad range of biopesticide and biofertilizer activities in association with sugarcane with the aim of controlling the pests that attack this crop
this study aimed to isolate and taxonomically identify Bacillus strains that endophytically colonize different sugarcane niches
a pest that causes damage inside the stem of sugarcane plants
we aim to understand their role in sugarcane plants and in the digestive tract of the giant borer
in order to contribute to future investigations into the biological control of this pest
The sugarcane material used for the isolation of endophytic bacteria was collected (June 2016) from three sugarcane mills (young and healthy plant material – winter planting) in the Coruripe, Boca da Mata and São Luís do Quitunde county, Alagoas State, Northeast Brazil (Supplementary Table 1)
Fifteen healthy sugarcane stems were collected per plant (five stems from a subarea of the mill) from the varieties RB92579
RB951541 and “Pé-de-Ferro.”
A total of six internodes were used from each subarea of the mill to isolate endophytic bacteria from the apoplast fluid
the central cylinder region of the internodes was separated for isolation of the endophytic bacteria present in the symplast tissues
The sugarcane roots collected at the three sugarcane mills were used to isolate bacilli endophytic bacteria after root surface disinfestation
The larvae were collected at the same time from the sugarcane field at the Boca da Mata (VAT90212 and RB867515 varieties) and São Luís do Quitunde counties (RB92579 variety) and used to isolate the bacilli endophytic bacteria
the digestive tracts of larvae from the Triunfo mill (Boca da Mata) were removed and divided into four subsamples (10 digestive tracts per subsample) totaling 40 larvae
while a sample containing ten digestive tracts was collected at the Santo Antônio mill (São Luís do Quitunde)
The harvest of the apoplast fluid from the sugarcane stems for bacilli bacterial isolation followed the protocol described by Dong et al. (1994)
the stems were washed with neutral detergent and tap water after which the external layer was peeled off
The internodes were cut into pieces of approximately 5 cm and sterilized superficially by immersion in ethanol and rapid flaming
The internodes were then placed in Falcon tubes containing a 0.5 mL microtube
in order to avoid contact between the extracted fluid and the internode
The tubes were centrifuged at 3,000 g for 20 min at 20°C
conditions designed to avoid the extraction of liquid from the symplast
All fluid extract was removed from the tube with the aid of a pipette and then pasteurized
The internodes used to isolate bacilli bacteria from the central cylinder region were the same as those used for the apoplast fluid extraction. Immediately after the extraction of the apoplast fluid, the outer part of the internodes was cut with a knife and discarded. The remaining central cylinder region was macerated with the aid of a mixer (IKA®, Model: A11 BS1) in saline solution (Baldani et al., 2014)
The macerated materials were then pasteurized
The digestive tract was macerated with sterile saline solution (NaCl 0.85%) using a glass stick
Digestive tract of giant borer (Telchin licus licus) and the diversity of colonies in solid BHI medium used for the isolation of bacteria
(A) The digestive tract being removed with the aid of forceps; (B) (B1) Bacteria obtained from the central region of the internodes
and (B4) digestive tract of the giant borer
To reduce the microbial Gram-negative population of the samples and to isolate mainly endospore-forming bacteria, aliquots of 1.0 mL from the apoplast fluid, the macerate suspension of the central internode region, and the roots were pasteurized following the World Health Organization protocol (World Health Organization [WHO], 1999)
The aliquots were placed in 1.5 mL microtubes and submitted to a temperature of 80°C for 12 min followed by incubation on ice for 5 min
DNA extraction from bacterial isolates was performed using the commercial kit Wizard® Genomic DNA Purification (Promega Corporation
an affiliate of Promega Biotecnologia do Brasil
The extracted DNA was quantified by fluorometry using the QubitTM dsDNA BR Assay kit (Q32853 - Thermo Fisher Scientific) and used as a template for the PCR amplification reactions (Polymerase Chain Reactions)
The BOX-PCR technique (genomic fingerprinting) applied to the isolates was carried out using A1R primer (Versalovic et al., 1994) which amplifies repetitive regions of the genome, and which is described in Table 1
The conditions used for amplifying the DNA of bacterial isolates were: 10 ng/μL of DNA
0.3 mM of dNTP and 5 U of GoTaq® DNA polymerase (Promega)
Incubation in the thermal cycler (SureCycler 8800
United States) was carried out under the following conditions: initial denaturation temperature of 95°C for 10 min
followed by 40 cycles of denaturation at 94°C for 1 min
and polymerization at 65°C for 8 min
the amplified product was submitted to a final extension temperature at 65°C for 16 min
The amplified DNA (10 μL) of the bacterial isolates was evaluated on agarose gel electrophoresis (2%) at 70 v
The amplified DNA band profiles were clustered using the BioNumerics software (Applied Maths NV.) and the dendrogram was generated using the unweighted pair group with the arithmetic mean (UPGMA) clustering method based on Jaccard coefficient (BioNumerics
The tolerance adopted to calculate the similarity coefficient of the bands was 3 and 1% optimization
since they were the parameters that best fit the isolate clustering
Primers used in polymerase chain reactions (PCR) to characterize and identify Bacillus species
using the Neighbor-Joining (NJ) and Bootstrap statistical method of 1000 replicates
taking into account the differences and homologies between sequences in order to know the evolutionary history of the microorganisms
The expected size of the amplified fragment was 246 bp
The PCR conditions for amplification of the XRE biomarker were: DNA concentration of 50 ng
1 X buffer and 2 mM of MgCl2 for a final volume of 20 μL reaction
The amplification conditions were an initial denaturation temperature of 95°C for 5 min
followed by 35 cycles of denaturation at 95°C for 30 s
annealing at 47°C for 30 s and polymerization at 72°C for 30 s
the amplification was submitted to a final extension temperature of 72°C for 5 min
The amplified fragment was run on agarose gel electrophoresis (1.5%) at 100 v for 2 h
Sequences of species within the Bacillus genus deposited in the NCBI database were used to cluster the bacterial isolates within the dendrogram
Great diversity of bacterial colony morphology was observed on BHI plate medium spread with the suspension of sugarcane plant tissues after exposure to the first pasteurization process (Figure 1B). In contrast, colonies from the giant borer digestive tract did not show visual morphological diversity (Figure 1B)
The second round of pasteurization carried out with the 796 purified strains which had been isolated after the first process
showed colonies with morphological characteristics of Bacillus
A total of 425 isolates were then selected
175 from the central cylinder region of the internodes
and 48 from the digestive tract of the giant borer
These 425 isolates were then subjected to Gram staining test and 161 isolates turned blue
which is a characteristic of Gram-positive bacteria
when submitted to phase contrast microscopic analysis
46 from the central cylinder region of the internodes
50 from surface disinfested roots and 19 from the digestive tract of the giant borer
The BOX-PCR fingerprinting analysis was performed for 157 Gram-positive isolates
Four isolates were not analyzed because they did not show product of amplification
The analysis showed the presence of 127 distinct band patterns
The number of detected bands varied from 1 to 28 and the size ranged from 100 to 5000 bp
Regarding the isolating niches, most bacteria did not show pattern profiles similar to those of other analyzed isolates, as demonstrated in the dendrogram (Figure 2)
these different band profiles indicate that the bacilli isolated from the sugarcane niches and giant borer digestive tract belong to different Bacillus species and/or subspecies
UPGMA similarity dendrogram of BOX-PCR fingerprinting
The dendrogram was generated of fingerprinting patterns of 157 bacterial isolates from sugarcane niches (apoplast
roots) and the digestive tract of the giant borer (Telchin licus licus)
The similarity analysis based on the 16S rRNA sequences was performed for 157 bacterial strains. The sequences were compared with sequences deposited in the GenBank enabled the isolates to be phylogenetically clustered into 22 species within the genus Bacillus (138 isolates) (Supplementary Table 2)
some isolates were phylogenetically clustered with other Gram-positive genera/species: Brevibacillus invocatus (one isolate)
Lysinibacillus cresolivorans (one isolate)
and Terribacillus saccharophilus (two isolates)
The built phylogenetic tree showed the bacterial strains clustered within 18 groups (Figure 3)
Group 13 appeared to be the most interesting one since it was formed by 34 isolates phylogenetically related to species B
which has interesting characteristics related to the biological control of pests
Phylogenetic relationships of bacteria isolated from different sugarcane niches estimated based on the 16S rRNA sequence
The tree was obtained using the Neighbor-Joining (NJ) statistical method and the Tamura 3-parameter model as indicated by the model test function of the MEGA 7.0 program
Bootstrap values are shown when the represented relationships have been observed in at least 50% of 1000 replicates
Escherichia/Shigella flexneri was used as an external group
The numbers 1–18 indicate the groups formed
The most representative species were phylogenetically closely related to B. megaterium (11.5%) followed by B. safensis (10.8%), B. cereus (8.9%), B. oleronius (8.9%), B. amyloliquefaciens (7.0%), and B. pacificus (6.4%) (Table 2)
Concerning the niche of bacterial isolation
it was observed that approximately 17.4% of strains
31.8% from the central cylinder region of the internodes showed 99% similarity to B
22.9% from disinfested roots showed greater similarity (99%) to B
amyloliquefaciens sequences and 47.4% obtained from the giant borer digestive tract showed 99/100% similarity to B
Number of isolates representing species and percentage of species in all niches
Species phylogenetically identified in the different sugarcane niches (apoplast
central cylinder region of the internodes and roots) and in the digestive tract of the giant borer (Telchin licus licus)
The diagram shows species inhabiting different niches
Two species, B. australimaris and Paenibacillus illinoisensis, were able to inhabit the apoplast and digestive tract of the giant borer (Figure 4), showing the ability to adapt to quite different conditions. In addition, the species B. cereus and B. safensis were found in all niches (Figure 4)
which suggests that the same species can present variable Gram staining results
Phylogenetic relationships of isolated bacteria from the digestive tract of the giant borer estimated by 16S rRNA sequence
The tree was obtained using the Neighbor-Joining (NJ) statistical method and the Kimura 2-parameter model as indicated by the model test function of the MEGA 7.0 program
The scale bar represents the number of base pair substitutions per site
Escherichia coli was used as an external group
The PCR amplification of the XRE transcriptional regulator with B. thuringiensis specific primers revealed that, among the 34 bacterial strains phylogenetically related to B. cereus group, 11 strains (FORCN005, 007, 008, 011, 012, 014, 067, 076, 092, 093, and 135) presented amplified product of the expected size (∼246 bp) as shown in Figure 6
and 135 were tentatively included in the B
All these strains have the capacity to induce the spore formation during growth for 72 h in HCT medium (data not shown)
and 139) presented neither one band nor bands of different sizes and therefore may belong to different species
Agarose gels (1.5%) showing the 246 bp PCR amplification product amplified using the specific primers for the XRE transcriptional regulator
The arrows indicate the strains with a positive result
A comparison of the XRE transcriptional regulator results with the dendrogram generated by the BOX-PCR pattern profiles showed that strains FORCN005, 007, 008, 012, 014, 067, 076, 092, 093, and 135 presented very similar band patterns (Figure 2)
forming a group of bacilli or part of a closely related group
A few strains were not included in these analyses because the sequences were neither of high quality nor amplified for certain housekeeping genes
Phylogenetic tree using the Neighbor-Joining method estimated from the concatenated sequences of four conserved genes (glp
The evolutionary distances were calculated using the Tamura 3-parameter model as indicated by the model test function of the MEGA 7.0 program
Bootstrap values are shown when the relationships represented have been observed in at least 50% of 500 replicates
Sequences of species of the genus Bacillus deposited in the NCBI database were used to group the bacterial isolates in the dendrogram
The arrows indicate the strains with positive results for the amplification of XRE transcriptional regulator
The strains FORCN005, 007, 008, 011, 012, 014, 067, 076, 092, 093, and 135 that presented positive PCR product for the transcriptional regulator XRE (corresponding to the B. thuringiensis species) may be considered different Bacillus subspecies or serovars. According to the conserved gene analysis, these strains were clustered in the same group (Cluster 1), but in different subgroups in the evolutionary trees for the different genes (Figure 7)
indicating that it is not possible to use only this test for characterization of bacilli microorganisms
since it can generate false negative results
hydrolytic enzyme activities and the ability to solubilize inorganic phosphate and zinc
The endophytic community of Bacillus associated with different plants is quite diverse and a similar result was obtained in our work
confirmed by the molecular analyses of Gram-positive bacilli isolates based on the 16S rRNA gene sequences
This analysis allowed the 157 bacterial strains to be clustered
within 32 species isolated from the sugarcane niches (apoplast fluid
central internodes region and roots) and 12 species from the digestive tract of the giant borer
The apoplast fluid was the niche with the highest number of bacterial species, 17 species identified among the genera Bacillus, Brevibacillus, Paenibacillus, and Terribacillus. The reason for this high species diversity is unknown, although the amount of nutrients available in the internal tissues of sugarcane may have favored the establishment of microorganisms (Karthik et al., 2017)
according to the taxonomical characterization (16S rRNA region)
All these studies point out the importance of the interaction of endophytic microorganisms with plants
since they promote plant growth and have interesting characteristics for biocontrol of pests and diseases
The BOX-PCR fingerprinting from our Gram-positive isolates showed diversified profiles
Most of the bacterial isolates with similar phylogenetic characterization (16S rRNA) presented different band profiles in the fingerprinting analysis and were grouped differently in the dendrogram
The fingerprinting analysis for these strains indicated that they belong to other species or subspecies of Bacillus
the results of the fingerprint analysis of some strains corroborated the phylogenetic characterization (16S rRNA) and were kept clustered together
cereus and found that some strains presented few amplified bands
the HD-1 strain also presented a low number of bands
which may be a characteristic of the bacterial strain
This result reinforces the idea that the later methodology is insufficient to distinguish both species within the B
cereus group and that the transcriptional regulator XRE biomarker seems to be a good complementary technique for identification of the B
and was present in more than 70% of 30 analyzed species of lepidopterans
These studies suggest that different species or bacterial genera have the potential for biological control application
further studies should focus not only in the B
thuringiensis species but also in other Bacillus species that may produce different entomopathogenic protein compounds that are toxic to giant borer
In our work, all isolates belonged to the phylum Firmicutes. Bacteria from Firmicutes (59%) were also isolated from the gut of S. littoralis (Lepidoptera: Noctuidae) in early instar larvae and 97% in the advanced instar (Chen et al., 2016). Orozco-Flores et al. (2017) also identified the phyla Proteobacteria (74.4%)
and Actinobacteria (14%) in the intestine of the lepidopteran Plodia interpunctella
It is believed that the pasteurization process applied here contributed to the isolation of only one phylum in contrast to what occurred in the other studies which used a different approach and isolated bacteria from other phyla in symbiosis with the host insects
The presence of bacteria inside the larvae may be due to the ingestion of the diet which would maintain the habitats of these bacteria. Symbiotic bacteria found in the intestinal microbiota can be transmitted horizontally, through the host plant, and vertically, at the egg stage (Paniagua Voirol et al., 2018). In our case, the giant borer enters through the root base and moves up inside the stem by gnawing the cane stalk (Negrisoli Junior et al., 2015)
any bacteria colonizing the internal tissues should pass by the intestinal digestive tract of the larvae including the endophytic Bacillus species
Our results showed that the distinction of closely related Bacillus species such as B
being indicated to use more than one methodology
The 16S rRNA sequencing region was important for identification at the genus level and provided hints about the possibly isolated species
the most suitable methodology to separate species within the B
cereus group was the amplification of the XRE biomarker and sequencing of the housekeeping genes (glp
These tools allowed us to consider the strains FORCN005
it should be emphasized that the complete genomic sequence analysis of representative strains within each clade may provide a better view of the occurring Bacillus species within the sugarcane plant tissues and the living giant borer larvae
The identification of these Bacillus species showed how complex is the symbiosis between plant-microorganism
with a diversified number of species living in association with sugarcane plants
We should keep in mind that this study did not consider non-cultivable bacterial species; therefore the number of species could be much higher than those identified here
By knowing that these microorganisms live inside the plants and in symbiosis with the target pest insects
it is essential to outline new strategic lines of research envisaging the development of bioproduct based on these B
thuringiensis strains to control sugarcane pests
The data presented in the study are deposited in the National Center for Biotechnology Information (NCBI) repository
accession numbers MW363203 to MW363359 and MW402865 to MW402893
AN and JB contributed to conceptualization
GM performed the validation of software analysis
All the authors contributed to manuscript and approved the submitted version
02.14.14.002.00.04.001 – Empresa Brasileira de Pesquisa Agropecuária (Embrapa Agrobiologia and Embrapa Tabuleiros Costeiros) and the Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro – FAPERJ for the partial financial support of this research (Project No
FR was supported with a scholarship from the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior – Brazil (Capes) – Financing Code 001 (Ordinance No
2018 CAPES) while JB thanks CNPq for the fellowship (process No
The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest
The authors are grateful for the collaboration of the mills Santo Antônio
and Coruripe for providing the sugarcane materials
FR thanks the postgraduate course of Crop Science at Federal Rural University of Rio de Janeiro for the study opportunity
The Supplementary Material for this article can be found online at: https://www.frontiersin.org/articles/10.3389/fmicb.2021.659965/full#supplementary-material
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Vidal MS and Baldani JI (2021) Endophytic Bacillus Bacteria Living in Sugarcane Plant Tissues and Telchin licus licus Larvae (Drury) (Lepidoptera: Castniidae): The Symbiosis That May Open New Paths in the Biological Control
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*Correspondence: José Ivo Baldani, aXZvLmJhbGRhbmlAZW1icmFwYS5icg==
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