1887

Abstract

The rhizosphere-isolated bacteria belonging to the subsp. and clades are an important group of strains that are used as plant growth promoters and antagonists of plant pathogens. These properties have made these strains the focus of commercial interest. Here, we present the draft genome sequence of KACC 13105 ( = CBMB205). Comparative genomic analysis showed only minor differences between this strain and the genome of the subsp. type strain, with the genomes sharing approximately 95 % of the same genes. The results of morphological, physiological, chemotaxonomic and phylogenetic analyses indicate that the type strains of these two taxa are highly similar. In fact, our results show that the type strain of subsp. FZB42 ( = DSM 23117 = BGSC 10A6) does not cluster with other members of the taxon. Instead, it clusters well within a clade of strains that are assigned to , including the type strain of that species. Therefore, we propose that the subspecies subsp. should be reclassified as a later heterotypic synonym of .

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2015-07-01
2024-10-11
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References

  1. Auch A.F., von Jan M., Klenk H.-P., Göker M. ( 2010;). Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2 117134. [CrossRef]
    [Google Scholar]
  2. Blom J., Rueckert C., Niu B., Wang Q., Borriss R. ( 2012;). The complete genome of Bacillus amyloliquefaciens subsp. plantarum CAU B946 contains a gene cluster for nonribosomal synthesis of iturin A. J Bacteriol 194 18451846. [CrossRef]
    [Google Scholar]
  3. Borriss R., Chen X.H., Rueckert C., Blom J., Becker A., Baumgarth B., Fan B., Pukall R., Schumann P., other authors. ( 2011;). Relationship of Bacillus amyloliquefaciens clades associated with strains DSM 7T and FZB42T: a proposal for Bacillus amyloliquefaciens subsp. amyloliquefaciens subsp. nov. and Bacillus amyloliquefaciens subsp. plantarum subsp. nov. based on complete genome sequence comparisons. Int J Syst Evol Microbiol 61 17861801. [CrossRef]
    [Google Scholar]
  4. Cai J., Liu F., Liao X., Zhang R. ( 2014;). Complete genome sequence of Bacillus amyloliquefaciens LFB112 isolated from Chinese herbs, a strain of a broad inhibitory spectrum against domestic animal pathogens. J Biotechnol 175 6364. [CrossRef]
    [Google Scholar]
  5. Dunlap C.A., Bowman M.J., Schisler D.A. ( 2013;). Genomic analysis and secondary metabolite production in Bacillus amyloliquefaciens AS 43.3: a biocontrol antagonist of Fusarium head blight. Biol Control 64 166175. [CrossRef]
    [Google Scholar]
  6. Geng W., Cao M., Song C., Xie H., Liu L., Yang C., Feng J., Zhang W., Jin Y., other authors. ( 2011;). Complete genome sequence of Bacillus amyloliquefaciens LL3, which exhibits glutamic acid-independent production of poly-γ-glutamic acid. J Bacteriol 193 33933394. [CrossRef]
    [Google Scholar]
  7. Goris J., Konstantinidis K.T., Klappenbach J.A., Coenye T., Vandamme P., Tiedje J.M. ( 2007;). DNA–DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 57 8191. [CrossRef]
    [Google Scholar]
  8. 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 32643265. [CrossRef]
    [Google Scholar]
  9. He P., Hao K., Blom J., Rückert C., Vater J., Mao Z., Wu Y., Hou M., He P., other authors. ( 2013;). Genome sequence of the plant growth promoting strain Bacillus amyloliquefaciens subsp. plantarum B9601-Y2 and expression of mersacidin and other secondary metabolites. J Biotechnol 164 281291. [CrossRef]
    [Google Scholar]
  10. Jeong H., Jeong D.E., Kim S.H., Song G.C., Park S.Y., Ryu C.M., Park S.H., Choi S.K. ( 2012;). Draft genome sequence of the plant growth-promoting bacterium Bacillus siamensis KCTC 13613T . J Bacteriol 194 41484149. [CrossRef]
    [Google Scholar]
  11. Jolley K.A., Maiden M.C. ( 2010;). BIGSdb: scalable analysis of bacterial genome variation at the population level. BMC Bioinformatics 11 595. [CrossRef]
    [Google Scholar]
  12. Lefort F., Calmin G., Pelleteret P., Farinelli L., Osteras M., Crovadore J. ( 2014;). Whole-genome shotgun sequence of Bacillus amyloliquefaciens strain UASWS BA1, a bacterium antagonistic to plant pathogenic fungi. Genome Announc 2 e00016-14. [CrossRef]
    [Google Scholar]
  13. Madhaiyan M., Poonguzhali S., Kwon S.W., Sa T.M. ( 2010;). Bacillus methylotrophicus sp. nov., a methanol-utilizing, plant-growth-promoting bacterium isolated from rice rhizosphere soil. Int J Syst Evol Microbiol 60 24902495. [CrossRef]
    [Google Scholar]
  14. Manzoor S., Niazi A., Bejai S., Meijer J., Bongcam-Rudloff E. ( 2013;). Genome sequence of a plant-associated bacterium, Bacillus amyloliquefaciens strain UCMB5036. Genome Announc 1 e0011113.
    [Google Scholar]
  15. Meier-Kolthoff J.P., Auch A.F., Klenk H.P., Göker M. ( 2013;). Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 14 60. [CrossRef]
    [Google Scholar]
  16. Mekjian K.R., Bryan E.M., Beall B.W., Moran C.P. Jr ( 1999;). Regulation of hexuronate utilization in Bacillus subtilis . J Bacteriol 181 426433.
    [Google Scholar]
  17. Nelson B.A., Ramaiya P., Lopez de Leon A., Kumar R., Crinklaw A., Jolkovsky E., Crane J.M., Bergstrom G.C., Rey M.W. ( 2014;). Complete genome sequence for the Fusarium head blight antagonist Bacillus amyloliquefaciens strain TrigoCor 1448. Genome Announc 2 e00219-14. [CrossRef]
    [Google Scholar]
  18. Niazi A., Manzoor S., Bejai S., Meijer J., Bongcam-Rudloff E. ( 2014a;). Complete genome sequence of a plant associated bacterium Bacillus amyloliquefaciens subsp. plantarum UCMB5033. Stand Genomic Sci 9 718725. [CrossRef]
    [Google Scholar]
  19. Niazi A., Manzoor S., Asari S., Bejai S., Meijer J., Bongcam-Rudloff E. ( 2014b;). Genome analysis of Bacillus amyloliquefaciens subsp. plantarum UCMB5113: a rhizobacterium that improves plant growth and stress management. PLoS One 9 e104651. [CrossRef]
    [Google Scholar]
  20. Ongena M., Jacques P. ( 2008;). Bacillus lipopeptides: versatile weapons for plant disease biocontrol. Trends Microbiol 16 115125. [CrossRef]
    [Google Scholar]
  21. Palazzini J.M., Ramirez M.L., Torres A.M., Chulze S.N. ( 2007;). Potential biocontrol agents for Fusarium head blight and deoxynivalenol production in wheat. Crop Prot 26 17021710. [CrossRef]
    [Google Scholar]
  22. Pérez-García A., Romero D., de Vicente A. ( 2011;). Plant protection and growth stimulation by microorganisms: biotechnological applications of Bacilli in agriculture. Curr Opin Biotechnol 22 187193. [CrossRef]
    [Google Scholar]
  23. Priest F.G., Goodfellow M., Shute L.A., Berkeley R.C.W. ( 1987;). Bacillus amyloliquefaciens sp. nov., nom. rev. Int J Syst Bacteriol 37 6971. [CrossRef]
    [Google Scholar]
  24. Rooney A.P., Price N.P., Ehrhardt C., Swezey J.L., Bannan J.D. ( 2009;). Phylogeny and molecular taxonomy of the Bacillus subtilis species complex and description of Bacillus subtilis subsp. inaquosorum subsp. nov.. Int J Syst Evol Microbiol 59 24292436. [CrossRef]
    [Google Scholar]
  25. Rückert C., Blom J., Chen X., Reva O., Borriss R. ( 2011;). Genome sequence of B. amyloliquefaciens type strain DSM7T reveals differences to plant-associated B. amyloliquefaciens FZB42. J Biotechnol 155 7885. [CrossRef]
    [Google Scholar]
  26. Schisler D.A., Khan N.I., Boehm M.J. ( 2002;). Biological control of Fusarium head blight of wheat and deoxynivalenol levels in grain via use of microbial antagonists. Adv Exp Med Biol 504 5369. [CrossRef]
    [Google Scholar]
  27. Schönert S., Buder T., Dahl M.K. ( 1999;). Properties of maltose-inducible α-glucosidase MalL (sucrase-isomaltase-maltase) in Bacillus subtilis: evidence for its contribution to maltodextrin utilization. Res Microbiol 150 167177. [CrossRef]
    [Google Scholar]
  28. Shan H., Zhao M., Chen D., Cheng J., Li J., Feng Z., Ma Z., An D. ( 2013;). Biocontrol of rice blast by the phenaminomethylacetic acid producer of Bacillus methylotrophicus strain BC79. Crop Prot 44 2937. [CrossRef]
    [Google Scholar]
  29. Sharma A., Satyanarayana T. ( 2013;). Comparative genomics of Bacillus species and its relevance in industrial microbiology. Genomics Insights 6 2536.
    [Google Scholar]
  30. Shi C., Yan P., Li J., Wu H., Li Q., Guan S. ( 2014;). Biocontrol of Fusarium graminearum growth and deoxynivalenol production in wheat kernels with bacterial antagonists. Int J Environ Res Public Health 11 10941105. [CrossRef]
    [Google Scholar]
  31. Tamura K., Nei M. ( 1993;). Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 10 512526.
    [Google Scholar]
  32. Tamura K., Stecher G., Peterson D., Filipski A., Kumar S. ( 2013;). mega6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30 27252729. [CrossRef]
    [Google Scholar]
  33. Yang H., Liao Y., Wang B., Lin Y., Pan L. ( 2011;). Complete genome sequence of Bacillus amyloliquefaciens XH7, which exhibits production of purine nucleosides. J Bacteriol 193 55935594. [CrossRef]
    [Google Scholar]
  34. Zhang G., Deng A., Xu Q., Liang Y., Chen N., Wen T. ( 2011;). Complete genome sequence of Bacillus amyloliquefaciens TA208, a strain for industrial production of guanosine and ribavirin. J Bacteriol 193 31423143. [CrossRef]
    [Google Scholar]
  35. Zhang W., Gao W., Feng J., Zhang C., He Y., Cao M., Li Q., Sun Y., Yang C., other authors. ( 2014;). A markerless gene replacement method for B. amyloliquefaciens LL3 and its use in genome reduction and improvement of poly-γ-glutamic acid production. Appl Microbiol Biotechnol 98 89638973. [CrossRef]
    [Google Scholar]
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