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Microbiol Resour Announc
Microbiol Resour Announc
mra
Microbiology Resource Announcements
2576-098X
American Society for Microbiology 1752 N St., N.W., Washington, DC

39120103
mra01072-23
10.1128/mra.01072-23
mra.01072-23
Genome Sequences
applied-and-industrial-microbiologyApplied and Industrial MicrobiologyDraft genome sequence of cellulose-degrading Bacillus stercoris BHUJPV-SS7 isolated from soil mixed with wood powder
https://orcid.org/0000-0002-9556-062X
Singh Saurabh 1
https://orcid.org/0000-0001-9402-3243
Pereira Arthur Prudêncio de Araujo 2
https://orcid.org/0000-0001-9386-6273
Pellegrinetti Thierry A. 3
https://orcid.org/0000-0002-2643-9623
Verma Jay Prakash 1 verma_bhu@yahoo.co.in

1 Plant-Microbe Interaction Lab, Institute of Environment and Sustainable Development, Banaras Hindu University , Varanasi, Uttar Pradesh, India
2 Soil Science Department, Soil Microbiology Laboratory, Federal University of Ceará , Fortaleza, Ceará, Brazil
3 University of São Paulo, Centre for Nuclear Energy in Agriculture , Piracicaba, São Paulo, Brazil
Editor Pritchard Leighton University of Strathclyde , Glasgow, United Kingdom

Address correspondence to Jay Prakash Verma, verma_bhu@yahoo.co.in
The authors declare no conflict of interest.

9 2024
09 8 2024
09 8 2024
13 9 e01072-2314 11 2023
24 5 2024
Copyright © 2024 Singh et al.
2024
Singh et al.
https://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

ABSTRACT

We report a complete genome of Bacillus stercoris BHUJPV-SS7 isolated from soil which contains 4,299 predicted genes and 4,012 predicted protein-coding genes within its chromosome (4,115,399 bp), and has 43.51% G + C content and a predicted beta-1,4-glucanase (EC 3.2.1.4) gene.

KEYWORDS

genome sequence
Bacillus stercoris
cellulose-degrading
University Grants Commission (UGC) UGC Ref No. 3819)/(NET-JULY-2018 Singh Saurabh Banaras Hindu University (BHU) IoE Singh Saurabh Department of Science and Technology, Ministry of Science and Technology, India (DST) DST (DST/INT/SL/P-31/2021) Verma Jay Prakash Banaras Hindu University (BHU) BHU-IoE (6031)-incentive grant, RJP-PDF, Trans-Disciplinary project BHU IoE Verma Jay Prakash DST | Science and Engineering Research Board (SERB) EEQ/2021/001083 Verma Jay Prakash cover-dateSeptember 2024
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pmcANNOUNCEMENT

Bacillus spp. commonly found in the rhizosphere soils (1) are known to harbor many beneficial properties including the ability of cellulose degradation (2). The bacteria described could be a potent cellulose degrader and hence whole-genome sequencing of Bacillus stercoris BHUJPV-SS7 was done.

Bacillus stercoris BHUJPV-SS7 was isolated from rhizosphere soil [collection depth 10 cm from surface (25.267270 N, 82.987285 E)], near a mango tree, recently fallen, and trunk degraded from inside leading to wood powder mixing with soil. The soil and pruned wood powder, collected simultaneously, were homogenized using a handheld homogenizer, serially diluted in 0.85% NaCl water, and spread after dilutions (from 10−2 to 10−7) on CMC (carboxymethyl cellulose) agar plates (0.5 g KH2PO4, 0.25 g MgSO4, 2 g CMC, 15 g agar, 0.2 g Congo-Red, and 2 g gelatin; 1,000 mL water at pH 6.8–7.2) and incubated for 5 days at 30°C. Subsequent subculturing (three times) in the same media produced multiple colonies with good zones (>15 mm clearance) of cellulose degradation and were selected for further assessment. Single colonies were cultured in nutrient agar (peptone 5 g/L, beef extract 3 g/L, agar 20 g/L, NaCI 0.5 g/L) media and incubated in a biological oxygen demand incubator for 72 h at 30°C. Enzyme quantification was performed on selected strains to select BHUJPV-SS7 for whole-genome sequencing.

Genomic DNA isolated using QIAGEN kit (cat. no: 51304) was checked using a Qubit 3 Fluorometer with dS DNA HS Dye (Thermo Fisher Scientific, Waltham, MA, USA). DNA samples were purified using AMPure beads, and enriched through PCR amplification (six cycles), using NEBNext Ultra II Q5 Master Mix (New England Biolabs), Illumina universal primer, and sample-specific octamer primers. Fragment analysis was done on Agilent 2100 Bioanalyzer with 1 µL library, sequenced on Illumina HiSeq 4000 (Illumina, Inc., San Diego, CA, USA).

The raw sequences were quality controlled using Fastqc v.0.11.9 (3) and Multiqc v.1.10.1 (4) and the sequence adapters were removed using Trimgalore v.0.6.6 (5). Default parameters were employed for all softwares in this study. The trimmed reads were assembled de novo using the Unicycler v.0.4.8 assembler (6). The final assembly was functionally annotated using RASTtk v.1.073 (7) and by NCBI Prokaryotic Genome Pipeline v.6.6 (8). Genome quality and taxonomic validation, including average nucleotide identity (ANI), were conducted using CheckM v.1.2.2 (9) and fastANI v.1.33 (10). The presence of beta-1,4-glucanase gene was predicted using dbCAN2 HMMs of CAZy v.1.9.1 families—v.10 in the KBase platform (11–13).

17,727,601 paired-reads of 151 bp were generated in this project. The draft genome measured 4,117,388 bp with 43.51% of average G + C content and median coverage of 1,110×. Genome assembly revealed 29 contigs with N50 value of 912.3 kilobases. The taxonomic annotation of the draft genome of strain BHUJPV-SS7 was most closely affiliated to Bacillus stercoris (ASM2055188v1) with 98.76% identical by ANI results. A total of 62 genes linked to carbohydrate degradation were predicted, including glycoside hydrolases, one gene for polyphenolic degradation, one for lignin degradation, and 11 lignin degradation auxiliary genes indicating potential for cellulose degradation and biomass biovalorization.

ACKNOWLEDGMENTS

S.S. is grateful to University Grants Commission (India) for providing a Senior Research fellowship (UGC ref no. 3819)/(NET-JULY-2018) and IoE (Teach for BHU Fellowship) for financial assistance. J.P.V. is highly thankful to DST (DST/INT/SL/P-31/2021), SERB (EEQ/2021/001083) and BHU-IoE (6031) incentive grant, RJP-PDF, and Trans-Disciplinary project BHU IoE for help in carrying out research work. T.A.P. is thankful to the PRPI-USP (22.1.08498.01.0).

DATA AVAILABILITY

The Bacillus stercoris BHUJPV-SS7 genome sequence has been deposited in DDBJ/EMBL/GenBank under accession number JALHBN000000000. Reads are available at the Sequence Read Archive (SRA) under accession number SRX14868609 and BioSample number SAMN26982665 (SRA accession number PRJNA820196). Genome annotations, including those generated by RAST and CAZy, are available at https://doi.org/10.5281/zenodo.7869037 .
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REFERENCES

1 Meena VS, Maurya B, Meena SK, Meena RK, Kumar A, Verma J, Singh N. 2016. Can Bacillus species enhance nutrient availability in agricultural soils?, p 367–395. In Bacilli and Agrobiotechnology. doi:10.1007/978-3-319-44409-3_16.
2 Li Y-H, Ding M, Wang J, Xu G-J, Zhao F. 2006. A novel thermoacidophilic endoglucanase, Ba-EGA, from a new cellulose-degrading bacterium, Bacillus sp. AC-1. Appl Microbiol Biotechnol 70 :430–436. doi:10.1007/s00253-005-0075-x 16142468
3 Andrews SF, Krueger F, Seconds-Pichon A, Biggins F, Wingett SF. 2014. A quality control tool for high throughput sequence data. Babraham Bioinformatics
4 Ewels P, Magnusson M, Lundin S, Käller M. 2016. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics 32 :3047–3048. doi:10.1093/bioinformatics/btw354 27312411
5 Krueger F. 2012. Trim Galore: a wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries. Available from: http://www. bioinformatics.babraham.ac.uk/projects/trim_galore/. Retrieved 3 Sep 2023.
6 Wick RR, Judd LM, Gorrie CL, Holt KE. 2017. Unicycler: resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol 13 :e1005595. doi:10.1371/journal.pcbi.1005595 28594827
7 Brettin T, Davis JJ, Disz T, Edwards RA, Gerdes S, Olsen GJ, Olson R, Overbeek R, Parrello B, Pusch GD, Shukla M, Thomason JA, Stevens R, Vonstein V, Wattam AR, Xia F. 2015. RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. Sci Rep 5 :8365. doi:10.1038/srep08365 25666585
8 Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP, Zaslavsky L, Lomsadze A, Pruitt KD, Borodovsky M, Ostell J. 2016. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 44 :6614–6624. doi:10.1093/nar/gkw569 27342282
9 Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. 2015. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 25 :1043–1055. doi:10.1101/gr.186072.114 25977477
10 Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, Aluru S. 2018. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun 9 :5114. doi:10.1038/s41467-018-07641-9 30504855
11 Zhang H, Yohe T, Huang L, Entwistle S, Wu P, Yang Z, Busk PK, Xu Y, Yin Y. 2018. dbCAN2: a meta server for automated carbohydrate-active enzyme annotation. Nucleic Acids Res 46 :W95–W101. doi:10.1093/nar/gky418 29771380
12 Eddy SR. 2011. Accelerated profile HMM searches. PLOS Comput Biol 7 :e1002195. doi:10.1371/journal.pcbi.1002195 22039361
13 Arkin AP, Cottingham RW, Henry CS, Harris NL, Stevens RL, Maslov S, Dehal P, Ware D, Perez F, Canon S, et al. . 2018. KBase: the United States department of energy systems biology knowledgebase. Nat Biotechnol 36 :566–569. doi:10.1038/nbt.4163 29979655
