Abstract
Bacillus subtilis is a nonpathogenic bacterium that lives in soil and has long been used as biological control agent in agriculture. Here, we report the genome sequence of a B. subtilis strain isolated from rhizosphere of onion that shows strong biological activity against the soilborne fungal pathogen Setophoma terrestris.
GENOME ANNOUNCEMENT
Biocontrol is a reliable alternative to chemical fungicides, which have raised serious concerns regarding food contamination and environmental pollution. Biocontrol is eco-friendly, safe, and may provide long-term protection to a crop (1). Plant growth-promoting rhizobacteria (PGPR) are naturally occurring soil microorganisms that colonize plant roots and benefit plants by increasing growth and/or reducing disease impact. Several Bacillus spp. representing typical PGPR have been widely studied and applied as efficient and stable biocontrol agents due to their ability to form heat- and desiccation-resistant spores (2). Bacteria belonging to the genus Bacillus are considered to be safe microorganisms that hold the remarkable ability to synthesize a vast array of beneficial substances for agronomical and industrial purposes (3). We have isolated a strain of Bacillus subtilis subsp. subtilis from the rhizosphere of onion plants (Bahía Blanca, Argentina) that was capable of strongly inhibiting the growth of Setophoma terrestris in vitro. We named it B. subtilis strain ALBA01. Interestingly, we observed a high growth inhibition of S. terrestris on plates containing cell-free supernatant of B. subtilis ALBA01 previously grown in the presence of the fungus (4). No antagonistic activity against two other onion pathogens, Fusarium oxysporum f. sp. cepae and Fusarium proliferatum, was observed. To gain insight into the features of B. subtilis ALBA01, we sequenced and annotated its genome sequence. Whole-genome sequencing was performed using a paired-end (PE) 2 × 100-bp library on an Illumina HiSeq 1500 (INDEAR Genome Sequencing facility, Argentina). The A5 pipeline (5) was used to execute de novo assembly. Reads were assembled into 28 scaffolds, with an average scaffold size of 147,128 bp. Annotation of the genome was done by uploading the scaffolds to the Rapid Annotations using Subsystems Technology (RAST) server (6) and by using the SEED-based method on this server. The genome sequence of B. subtilis ALBA01 is composed of 4,119,571 bp, with a mean G+C content of 44%. The annotation revealed 4,303 open reading frames (ORFs). Three families of Bacillus lipopeptides (surfactins, iturins, and fengycins) have mostly been studied for their antagonistic activity against a wide range of potential phytopathogens, including fungi (7). Then, we decided to analyze the genome for the presence of genes encoding antimicrobial peptide synthetases. Four ORFs showed high identity levels to those from the srfA locus required for the production of the lipopeptide antibiotic surfactin. We also found an ORF with 98.77% identity to pksD, a gene encoding an enzyme involved in polyketide synthesis, and another with 80.66% identity to the fengycin synthetase gene, fenB. No coding sequences were found to be related to ituD (iturin A synthetase D), bamA (bacillomycin D synthetase A), bmyA (bacillomycin L. synthetase A), and mycA (mycosubtilin synthase subunit A).
Nucleotide sequence accession numbers.
This whole-genome shotgun project has been deposited at DDBJ/ENA/GenBank under the accession no. LVYH00000000. The version described in this paper is version LVYH01000000.
ACKNOWLEDGMENTS
We thank the Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Agencia Nacional de Promoción Científica y Tecnológica (ANPCyT, grant PICT 2013-2592 to A.G.A.O.), and Santiago Revale (Indear) for bioinformatics support.
Footnotes
Citation Albarracín Orio AG, Tobares RA, Ducasse DA, Smania AM. 2016. Draft genome sequence of Bacillus subtilis ALBA01, a strain with antagonistic activity against the soilborne fungal pathogen of onion Setophoma terrestris. Genome Announc 4(3):e00455-16. doi:10.1128/genomeA.00455-16.
REFERENCES
- 1.Fernando WGD, Ramarathnam R, Krishnamoorthy AS, Savchuk SC. 2005. Identification and use of potential bacterial organic antifungal volatiles in biocontrol. Soil Biol Biochem 37:955–964. doi: 10.1016/j.soilbio.2004.10.021. [DOI] [Google Scholar]
- 2.Xie S-S, Wu H-J, Zang H-Y, Wu L-M, Zhu Q-Q, Gao X-W. 2014. Plant growth promotion by spermidine-producing Bacillus subtilis OKB105. Mol Plant Microbe Interact 27:655–663. doi: 10.1094/MPMI-01-14-0010-R. [DOI] [PubMed] [Google Scholar]
- 3.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]
- 4.Albarracín Orio AG, Brücher E, Ducasse DA. 2016. A strain of Bacillus subtilis subsp. subtilis shows a specific antagonistic activity against the soil-borne pathogen of onion Setophoma terrestris. Eur J Plant Pathol 144:217–223. doi: 10.1007/s10658-015-0762-0. [DOI] [Google Scholar]
- 5.Tritt A, Eisen JA, Facciotti MT, Darling AE. 2012. An integrated pipeline for de novo assembly of microbial genomes. PLoS One 7:e42304. doi: 10.1371/journal.pone.0042304. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 6.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]
- 7.Ongena M, Jacques P. 2008. Bacillus lipopeptides: versatile weapons for plant disease biocontrol. Trends Microbiol 16:115–125. doi: 10.1016/j.tim.2007.12.009. [DOI] [PubMed] [Google Scholar]