Bacillus velezensis strain SGAir0473 (Firmicutes) was isolated from tropical air collected in Singapore. Its genome was assembled using short reads and single-molecule real-time sequencing and comprises one chromosome with 4.18 Mb.
ABSTRACT
Bacillus velezensis strain SGAir0473 (Firmicutes) was isolated from tropical air collected in Singapore. Its genome was assembled using short reads and single-molecule real-time sequencing and comprises one chromosome with 4.18 Mb. The genome consists of 3,937 protein-coding genes, 86 tRNAs, and 27 rRNAs.
GENOME ANNOUNCEMENT
Bacillus velezensis is a Gram-positive rod-shaped aerobic bacterium classified in the phylum Firmicutes. This bacterium was first isolated from a brackish water sample collected from the river Vélez in Spain (1). It was isolated from an extremely high-salt environment (12% [wt/vol]) utilizing a test that screens for surfactant-producing bacteria (1). Since then, B. velezensis has been found in diverse habitats, including cotton waste (2), wheat anthers (3, 4), and soil (5). Past studies have also highlighted the ability of B. velezensis to produce antimicrobial metabolites (6) and antibiotics (7) and have also demonstrated its involvement in a wide spectrum of antifungal activities (8).
B. velezensis strain SGAir0473 was isolated from air in an outdoor seaside location in Singapore (global position system coordinates 1.391°N, 103.992°E). Air was drawn and directly impacted onto brain heart infusion agar (Becton, Dickinson, USA) using the Andersen single-stage impactor (SKC, USA). After initial incubation at 30°C, subsequent colony isolation was carried out by culturing on Trypticase soy agar at 30°C. Finally, the pure culture was grown in Luria-Bertani broth overnight before DNA extraction.
Extraction of genomic DNA was performed using the Wizard genomic DNA purification kit (Promega, USA) according to the manufacturer’s standard protocol. After extraction, library preparation was performed with the SMRTbell template prep kit 1.0 (Pacific Biosciences), followed by single-molecule real-time (SMRT) sequencing on the PacBio RS II (Pacific Biosciences) platform. Short reads were also generated with a MiSeq (Illumina) 300-bp paired-end run using whole-genome shotgun libraries constructed with the TruSeq Nano DNA library preparation kit (Illumina).
De novo assembly of the 26,993 long subreads generated on the PacBio RS II platform was accomplished using Hierarchical Genome Assembly Process (HGAP, version 3), which is included in the PacBio SMRT Analysis 2.3.0 package (9). The assembly was then polished and error corrected with the 770,556 MiSeq reads using Quiver (9) and Pilon version 1.16 (10). The final assembly generated one chromosomal contig with a total size of 4,184,178 bp (38.26-fold coverage) and a G+C content of 45.96% evaluated using QUAST (11). The genome was unable to be circularized using Circlator (12). Average nucleotide identity (ANI) analysis, performed with MiSI (13), indicated a 99.26% match to B. velezensis.
Genome annotation was performed with NCBI’s Prokaryotic Genome Annotation Pipeline (PGAP) version 4.2 (14). A total of 4,198 genes were predicted, including 3,937 protein-coding genes, 9 copies each of 5S, 16S, and 23S rRNA genes, 86 tRNA genes, 5 noncoding RNA genes, and 143 pseudogenes.
Functional annotation with Rapid Annotations using Subsystems Technology (RAST) (15–17) highlighted genes that were associated with osmotic stress response (14 genes) and alkanesulfonate metabolism (8 genes), which could explain how this bacterium survives in high-salt (18) or surfactant-rich (19, 20) environments. Genes related to sporulation and dormancy (116 genes) were also found. This indicates that the species might be capable of surviving in other extreme environments, such as air.
Accession number(s).
The genome sequence of Bacillus velezensis strain SGAir0473 has been deposited in DDBJ/EMBL/GenBank under the accession number CP027868.
ACKNOWLEDGMENT
This work was supported by a Singapore Ministry of Education Academic Research Fund tier 3 grant (MOE2013-T3-1-013).
Footnotes
Citation Lim SBY, Junqueira ACM, Uchida A, Purbojati RW, Houghton JNI, Chénard C, Wong A, Kolundžija S, Clare ME, Kushwaha KK, Panicker D, Putra A, Gaultier NE, Premkrishnan BNV, Heinle CE, Vettath VK, Drautz-Moses DI, Schuster SC. 2018. Genome sequence of Bacillus velezensis SGAir0473, isolated from tropical air collected in Singapore. Genome Announc 6:e00642-18. https://doi.org/10.1128/genomeA.00642-18.
REFERENCES
- 1.Ruiz-García C, Béjar V, Martínez-Checa F, Llamas I, Quesada E. 2005. Bacillus velezensis sp. nov., a surfactant-producing bacterium isolated from the river Vélez in Málaga, southern Spain. Int J Syst Evol Microbiol 55:191–195. doi: 10.1099/ijs.0.63310-0. [DOI] [PubMed] [Google Scholar]
- 2.Kim SY, Lee SY, Weon H-Y, Sang MK, Song J. 2017. Complete genome sequence of Bacillus velezensis M75, a biocontrol agent against fungal plant pathogens, isolated from cotton waste. J Biotechnol 241:112–115. doi: 10.1016/j.jbiotec.2016.11.023. [DOI] [PubMed] [Google Scholar]
- 3.Palazzini JM, Ramirez ML, Torres AM, Chulze SN. 2007. Potential biocontrol agents for Fusarium head blight and deoxynivalenol production in wheat. Crop Prot 26:1702–1710. doi: 10.1016/j.cropro.2007.03.004. [DOI] [Google Scholar]
- 4.Kang X, Zhang W, Cai X, Zhu T, Xue Y, Liu C. 2018. Bacillus velezensis CC09: a potential “vaccine” for controlling wheat diseases. Mol Plant Microbe Interact 31:623–632. doi: 10.1094/MPMI-09-17-0227-R. [DOI] [PubMed] [Google Scholar]
- 5.Krebs B, Höding B, Kübart S, Workie MA, Junge H, Schmiedeknecht G, Grosch R, Bochow H, Hevesi M. 1998. Use of Bacillus subtilis as biocontrol agent. I. Activities and characterization of Bacillus subtilis strains/Anwendung von Bacillus subtilis als Mittel für den Biologischen Pflanzenschutz. I. Aktivitten und Charakterisierung von Bacillus subtilis-Stämmen. J Plant Dis Prot 105:181–197. [Google Scholar]
- 6.Chen XH, Koumoutsi A, Scholz R, Schneider K, Vater J, Süssmuth R, Piel J, Borriss R. 2009. Genome analysis of Bacillus amyloliquefaciens FZB42 reveals its potential for biocontrol of plant pathogens. J Biotechnol 140:27–37. doi: 10.1016/j.jbiotec.2008.10.011. [DOI] [PubMed] [Google Scholar]
- 7.Hao K, He P, Blom J, Rueckert C, Mao Z, Wu Y, He Y, Borriss R. 2012. The genome of plant growth-promoting Bacillus amyloliquefaciens subsp. plantarum strain YAU B9601-Y2 contains a gene cluster for mersacidin synthesis. J Bacteriol 194:3264–3265. doi: 10.1128/JB.00545-12. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 8.Stein T. 2005. Bacillus subtilis antibiotics: structures, syntheses and specific functions. Mol Microbiol 56:845–857. doi: 10.1111/j.1365-2958.2005.04587.x. [DOI] [PubMed] [Google Scholar]
- 9.Chin C-S, Alexander DH, Marks P, Klammer AA, Drake J, Heiner C, Clum A, Copeland A, Huddleston J, Eichler EE, Turner SW, Korlach J. 2013. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods 10:563–569. doi: 10.1038/nmeth.2474. [DOI] [PubMed] [Google Scholar]
- 10.Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A, Sakthikumar S, Cuomo CA, Zeng Q, Wortman J, Young SK, Earl AM. 2014. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One 9:e112963. doi: 10.1371/journal.pone.0112963. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 11.Gurevich A, Saveliev V, Vyahhi N, Tesler G. 2013. QUAST: quality assessment tool for genome assemblies. Bioinformatics 29:1072–1075. doi: 10.1093/bioinformatics/btt086. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 12.Hunt M, De Silva N, Otto TD, Parkhill J, Keane JA, Harris SR. 2015. Circlator: automated circularization of genome assemblies using long sequencing reads. Genome Biol 16:294. doi: 10.1186/s13059-015-0849-0. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 13.Varghese NJ, Mukherjee S, Ivanova N, Konstantinidis KT, Mavrommatis K, Kyrpides NC, Pati A. 2015. Microbial species delineation using whole genome sequences. Nucleic Acids Res 43:6761–6771. doi: 10.1093/nar/gkv657. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 14.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. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 15.Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O. 2008. The RAST server: Rapid Annotations using Subsystems Technology. BMC Genomics 9:75. doi: 10.1186/1471-2164-9-75. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 16.Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ, Disz T, Edwards RA, Gerdes S, Parrello B, Shukla M, Vonstein V, Wattam AR, Xia F, Stevens R. 2014. The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Res 42:D206–D214. doi: 10.1093/nar/gkt1226. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 17.Brettin T, Davis JJ, Disz T, Edwards RA, Gerdes S, Olsen GJ, Olson R, Overbeek R, Parrello B, Pusch GD, Shukla M, Thomason JA III, 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. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 18.Zhang X, Gao J, Zhao F, Zhao Y, Li Z. 2014. Characterization of a salt-tolerant bacterium Bacillus sp. from a membrane bioreactor for saline wastewater treatment. J Environ Sci 26:1369–1374. doi: 10.1016/S1001-0742(13)60613-0. [DOI] [PubMed] [Google Scholar]
- 19.Liu X, Ren B, Chen M, Wang H, Kokare CR, Zhou X, Wang J, Dai H, Song F, Liu M, Wang J, Wang S, Zhang L. 2010. Production and characterization of a group of bioemulsifiers from the marine Bacillus velezensis strain H3. Appl Microbiol Biotechnol 87:1881–1893. doi: 10.1007/s00253-010-2653-9. [DOI] [PubMed] [Google Scholar]
- 20.Makkar RS, Cameotra SS, Banat IM. 2011. Advances in utilization of renewable substrates for biosurfactant production. AMB Express 1:5. doi: 10.1186/2191-0855-1-5. [DOI] [PMC free article] [PubMed] [Google Scholar]