GENOME ANNOUNCEMENT
Draft Genome Sequence of the Biocontrol Bacterium Bacillus amyloliquefaciens Strain M27 Sang-Yeob Lee,a Byung-Yong Kim,a Jae-Hyung Ahn,a Jaekyeong Song,a Young-Joo Seol,b Wan-Gyu Kim,a and Hang-Yeon Weona Agricultural Microbiology Divisiona and Genomics Division,b National Academy of Agricultural Science, Rural Development Administration, Suwon, Republic of Korea
Bacillus amyloliquefaciens strain M27 is a biocontrol agent with antagonistic activities against a wide range of fungal pathogens. Here we present the 3.86-Mb draft genome sequence of the bacterium with the aims of providing insights into the genomic basis of its antifungal mechanism and facilitating its application in the biocontrol of plant diseases.
A
fter the name Bacillus amyloliquefaciens was revived and validly published (10), Borriss et al. (4) subdivided the species into two subspecies, B. amyloliquefaciens subsp. amyloliquefaciens and plantarum, on the basis of whole-genome comparisons, as well as classical bacterial taxonomy. They reported that B. amyloliquefaciens subsp. plantarum could be a promising candidate for use as a potential biofertilizer or biopesticide to improve crop yield and quality, owing to its plant growth-promoting activity and its antagonistic activities against pathogenic fungi (3, 4). Recently, the genomes of plant-associated strains of the genus Bacillus, including type strain FZB42T, have been completely sequenced (2, 5–7, 12). Strain M27, isolated from cotton waste compost that was used in the cultivation of oyster mushrooms (Pleurotus ostreatus), was identified as a strain of B. amyloliquefaciens by 16S rRNA gene sequencing and physiological and biochemical analyses. The strain suppresses a broad spectrum of pathogenic fungi, including Fusarium oxysporum, Phytophthora capsici, Rhizoctonia solani, Sclerotinia sclerotiorum, Trichoderma harzianum, Trichoderma koningii, and Trichoderma viridescens (8, 9). Because of these antifungal properties, strain M27 has been extensively field tested against sclerotinia rot caused by S. sclerotiorum in lettuce (Lactuca sativa L.) and registered as a biofungicide (Danjjak) in Korea (S.-Y. Lee, unpublished data). Here we analyzed the genome sequence of this strain to explore the genomic features responsible for its effectiveness as a biocontrol agent. The genome of B. amyloliquefaciens strain M27 was sequenced at Chunlab Inc. (Korea) by using a combination of the Roche 454 GS-FLX Titanium and Illumina GAIIx instruments. A total of 41.18 Mb (coverage, 10.7⫻) in 197,347 paired-end reads containing 8-kb inserts was generated by using the 454 GS-FLX Titanium system. The Illumina GAIIx system generated sequence data that contained 2.14 Gb (coverage, 553.4⫻) in 21,147,524 reads. All generated reads were assembled into 21 contigs by using a GS De Novo Assembler 2.6 (Newbler; Roche) and CLC Genomics Workbench 4.5 (CLC bio). Automatic gene prediction and functional annotation of the assemblies were carried out by using the NCBI Prokaryotic Genomes Automatic Annotation Pipeline and the RAST server (1). The average nucleotide identity value was calculated by using JSpecies (11). The assembly contained 3,860,959 bp in 21 large contigs that were over 500 bp long (N50, 927,071 bp) with a 46.6% G⫹C content. The maximum and average contig sizes were 1,076,358 and 183,855 bp, respectively. A total of 3,811 protein coding sequences, seven rRNA operons (polymorphism may exist), and 51
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tRNAs were predicted. The strain M27 genome was found to be closely related to that of B. amyloliquefaciens subsp. plantarum FZB42T, with an average nucleotide identity of 97.7% based on BLAST, and the identity between strain M27 and B. amyloliquefaciens subsp. amyloliquefaciens DSM 7T was 93.3%. Thus, strain M27 is most likely a strain of B. amyloliquefaciens subsp. plantarum. The strain M27 genome also contains several genes related to the biosynthesis of antimicrobial products that are similar to those found in the genomes of B. amyloliquefaciens subsp. plantarum (4). These include genes related to the productions of cyclic lipopeptides (bacillomycin D, fengycin, iturin, and surfactin), a dipeptide (bacilysin), a siderophore (bacillibactin), and polyketides (bacillaene, difficidin, and macrolactin). Nucleotide sequence accession numbers. The draft genome sequence of strain M27 has been deposited at DDBJ/EMBL/ GenBank under accession no. AMPK00000000. The version described in this paper is the first version, AMPK01000000. ACKNOWLEDGMENT This study was made possible by the support of the Research Program for Agricultural Science & Technology Development (project PJ008976032012) from the National Academy of Agricultural Science, Rural Development Administration, Republic of Korea.
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Received 28 September 2012 Accepted 1 October 2012 Address correspondence to Hang-Yeon Weon,
[email protected]. Copyright © 2012, American Society for Microbiology. All Rights Reserved. doi:10.1128/JB.01835-12
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5. Chen XH, et al. 2009. Genome analysis of Bacillus amyloliquefaciens FZB42 reveals its potential for biocontrol of plant pathogens. J. Biotechnol. 140:27–37. 6. Hao K, et al. 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. 7. Kim BK, et al. 2012. Genome sequence of the leaf-colonizing bacterium Bacillus sp. strain 5B6, isolated from a cherry tree. J. Bacteriol. 194:3758 – 3759. 8. Kim W-G, Weon H-Y, Lee S-Y. 2008. In vitro antagonistic effects of bacilli isolates against four soilborne plant pathogenic fungi. Plant Pathol. J. 24:52–57.
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9. Kim W-G, Weon H-Y, Seok S-J, Lee K-H. 2008. In vitro antagonistic characteristics of bacilli isolates against Trichoderma spp. and three species of mushrooms. Mycobiology 36:266 –269. 10. Priest FG, Goodfellow M, Shute LA, Berkeley RCW. 1987. Bacillus amyloliquefaciens sp. nov., nom. rev. Int. J. Syst. Evol. Microbiol. 37:69 – 71. 11. Richter M, Rossello-Mora R. 2009. Shifting the genomic gold standard for the prokaryotic species definition. Proc. Natl. Acad. Sci. U. S. A. 106: 19126 –19131. 12. Wang X, Luo C, Chen Z. 2012. Genome sequence of the plant growthpromoting rhizobacterium Bacillus sp. strain 916. J. Bacteriol. 194:5467– 5468.
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