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Whole-genome sequencing of Bacillus subtilis XF-1 reveals mechanisms for biological control and multiple beneficial properties in plants

  • Genetics and Molecular Biology of Industrial Organisms
  • Published:
Journal of Industrial Microbiology & Biotechnology

Abstract

Bacillus subtilis XF-1 is a gram-positive, plant-associated bacterium that stimulates plant growth and produces secondary metabolites that suppress soil-borne plant pathogens. In particular, it is especially highly efficient at controlling the clubroot disease of cruciferous crops. Its 4,061,186-bp genome contains an estimated 3853 protein-coding sequences and the 1155 genes of XF-1 are present in most genome-sequenced Bacillus strains: 3757 genes in B. subtilis 168, and 1164 in B. amyloliquefaciens FZB42. Analysis using the Cluster of Orthologous Groups database of proteins shows that 60 genes control bacterial mobility, 221 genes are related to cell wall and membrane biosynthesis, and more than 112 are genes associated with secondary metabolites. In addition, the genes contributed to the strain’s plant colonization, bio-control and stimulation of plant growth. Sequencing of the genome is a fundamental step for develo** a desired strain to serve as an efficient biological control agent and plant growth stimulator. Similar to other members of the taxon, XF-1 has a genome that contains giant gene clusters for the non-ribosomal synthesis of antifungal lipopeptides (surfactin and fengycin), the polyketides (macrolactin and bacillaene), the siderophore bacillibactin, and the dipeptide bacilysin. There are two synthesis pathways for volatile growth-promoting compounds. The expression of biosynthesized antibiotic peptides in XF-1 was revealed by matrix-assisted laser desorption/ionization-time of flight mass spectrometry.

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References

  1. Asaka O, Shoda M (1996) Biocontrol of Rhizoctonia solani dam**-off of tomato with Bacillus subtilis RB14. Appl Environ Microbiol 62(11):4081–4085

    PubMed Central  CAS  PubMed  Google Scholar 

  2. Atkins T, Prior R, Mack K, Russell P, Nelson M, Oyston P, Dougan G, Titball R (2002) A mutant of Burkholderia pseudomallei, auxotrophic in the branched chain amino acid biosynthetic pathway, is attenuated and protective in a murine model of melioidosis. Infect Immun 70(9):5290

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  3. Badger JH, Olsen GJ (1999) CRITICA: coding region identification tool invoking comparative analysis. Mol Biol Evol 16(4):512

    Article  CAS  PubMed  Google Scholar 

  4. Bais HP, Fall R, Vivanco JM (2004) Biocontrol of Bacillus subtilis against infection of Arabidopsis roots by Pseudomonas syringae is facilitated by biofilm formation and surfactin production. Plant Physiol 134(1):307–319

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  5. Bird C, Wyman M (2003) Nitrate/nitrite assimilation system of the marine picoplanktonic cyanobacterium Synechococcus sp. strain WH 8103: effect of nitrogen source and availability on gene expression. Appl Environ Microbiol 69(12):7009–7018

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  6. Branda SS, Gonzalez-Pastor JE, Dervyn E, Ehrlich SD, Losick R, Kolter R (2004) Genes involved in formation of structured multicellular communities by Bacillus subtilis. J Bacteriol 186(12):3970–3979

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  7. Buczacki S, Moxham SE (1983) Structure of the resting spore wall of Plasmodiophora brassicae revealed by electron microscopy and chemical digestion. T Brit Mycol Soc 81(2):221–231

    Article  Google Scholar 

  8. Candela T, Fouet A (2006) Poly-gamma-glutamate in bacteria. Mol Microbiol 60(5):1091–1098

    Article  CAS  PubMed  Google Scholar 

  9. Cassán F, Maiale S, Masciarelli O, Vidal A, Luna V, Ruiz O (2009) Cadaverine production by Azospirillum brasilense and its possible role in plant growth promotion and osmotic stress mitigation. Eur J Soil Biol 45(1):12–19

    Article  Google Scholar 

  10. Cavaglieri L, Orlando J, Rodriguez M, Chulze S, Etcheverry M (2005) Biocontrol of Bacillus subtilis against Fusarium verticillioides in vitro and at the maize root level. Res Microbiol 156(5):748–754

    Article  CAS  PubMed  Google Scholar 

  11. Chen L, Helmann JD (1994) The Bacillus subtilis sigma D-dependent operon encoding the flagellar proteins FliD, FliS, and FliT. J Bacteriol 176(11):3093–3101

    PubMed Central  CAS  PubMed  Google Scholar 

  12. Chen XH, Vater J, Piel J, Franke P, Scholz R, Schneider K, Koumoutsi A, Hitzeroth G, Grammel N, Strittmatter AW (2006) Structural and functional characterization of three polyketide synthase gene clusters in Bacillus amyloliquefaciens FZB 42. J Bacteriol 188(11):4024–4036

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  13. 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(1–2):27–37

    Article  CAS  PubMed  Google Scholar 

  14. Chen XH, Koumoutsi A, Scholz R, Eisenreich A, Schneider K, Heinemeyer I, Morgenstern B, Voss B, Hess WR, Reva O, Junge H, Voigt B, Jungblut PR, Vater J, Süssmuth R, Liesegang H, Strittmatter A, Gottschalk G, Borriss R (2007) Comparative analysis of the complete genome sequence of the plant growth–promoting bacterium Bacillus amyloliquefaciens FZB42. Nat Biotechnol 25(9):1007–1014

    Article  CAS  PubMed  Google Scholar 

  15. Compant S, Duffy B, Nowak J, Clément C, Barka EA (2005) Use of plant growth-promoting bacteria for biocontrol of plant diseases: principles, mechanisms of action, and future prospects. Appl Environ Microbiol 71(9):4951–4959

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  16. Cox GN, Kusch M, Edgar RS (1981) Cuticle of Caenorhabditis elegans: its isolation and partial characterization. J Cell Biol 90(1):7–17

    Article  CAS  PubMed  Google Scholar 

  17. Delcher AL, Bratke KA, Powers EC, Salzberg SL (2007) Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23(6):673

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  18. Delcher AL, Harmon D, Kasif S, White O, Salzberg SL (1999) Improved microbial gene identification with GLIMMER. Nucleic Acid Res 27(23):4636

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  19. Duckworth OW, Bargar JR, Sposito G (2009) Coupled biogeochemical cycling of iron and manganese as mediated by microbial siderophores. Biometals 22(4):605–613

    Article  CAS  PubMed  Google Scholar 

  20. Duffy BK, Défago G (1999) Environmental factors modulating antibiotic and siderophore biosynthesis by Pseudomonas fluorescens biocontrol strains. Appl Environ Microbiol 65(6):2429–2438

    PubMed Central  CAS  PubMed  Google Scholar 

  21. Fan B, Carvalhais LC, Becker A, Fedoseyenko D, von Wirén N, Borriss R (2012) Transcriptomic profiling of Bacillus amyloliquefaciens FZB42 in response to maize root exudates. BMC Microbiol 12(1):116

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  22. Ferreira J, Matthee F, Thomas A (1991) Biological control of Eutypa lata on grapevine by an antagonistic strain of Bacillus subtilis. Phytopathology 81(3):283–287

    Article  Google Scholar 

  23. Fredrick KL, Helmann JD (1994) Dual chemotaxis signaling pathways in Bacillus subtilis: a sigma D-dependent gene encodes a novel protein with both CheW and CheY homologous domains. J Bacteriol 176(9):2727–2735

    PubMed Central  CAS  PubMed  Google Scholar 

  24. Hayat R, Ali S, Amara U, Khalid R, Ahmed I (2010) Soil beneficial bacteria and their role in plant growth promotion: a review. Ann Microbiol 60(4):579–598

    Article  Google Scholar 

  25. He P, Hao K, Blom J, Rückert C, Vater J, Mao Z, Wu Y, Hou M, He P, He Y (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(2):281–291

    Article  Google Scholar 

  26. Hecker M, Völker U (2004) Towards a comprehensive understanding of Bacillus subtilis cell physiology by physiological proteomics. Proteomics 4(12):3727–3750

    Article  CAS  PubMed  Google Scholar 

  27. Heymann P, Gerads M, Schaller M, Dromer F, Winkelmann G, Ernst JF (2002) The siderophore iron transporter of Candida albicans (Sit1p/Arn1p) mediates uptake of ferrichrome-type siderophores and is required for epithelial invasion. Infect Immun 70(9):5246–5255

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  28. Holtmann G, Bakker EP, Uozumi N, Bremer E (2003) KtrAB and KtrCD: two K+ uptake systems in Bacillus subtilis and their role in adaptation to hypertonicity. J Bacteriol 185(4):1289–1298

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  29. Huber DM (1980) The role of mineral nutrition in defense. In: Horsfall JG, Cowling EB (eds) Plant Disease. AcademicPress, New York, pp 381–406

    Google Scholar 

  30. Jacques P (2011) Surfactin and other lipopeptides from Bacillus spp. In: Soberón-Chávez G (ed) Biosurfactants. Springer, Berlin, pp 57–91

    Chapter  Google Scholar 

  31. Jones JD, Dangl JL (2006) The plant immune system. Nature 444(7117):323–329

    Article  CAS  PubMed  Google Scholar 

  32. Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, Itoh M, Katayama T, Kawashima S, Okuda S, Tokimatsu T (2008) KEGG for linking genomes to life and the environment. Nucleic Acid Res 36(suppl 1):480–484

    Google Scholar 

  33. Kearns DB, Chu F, Branda SS, Kolter R, Losick R (2004) A master regulator for biofilm formation by Bacillus subtilis. Mol Microbiol 55(3):739–749

    Article  Google Scholar 

  34. Kearns DB, Chu F, Rudner R, Losick R (2004) Genes governing swarming in Bacillus subtilis and evidence for a phase variation mechanism controlling surface motility. Mol Microbiol 52(2):357–369

    Article  CAS  PubMed  Google Scholar 

  35. Kent WJ (2002) BLAT-the BLAST-like alignment tool. Genome Res 12(4):656

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  36. Kilian M, Steiner U, Krebs B, Junge H, Schmiedeknecht G, Hain R (2000) FZB24® Bacillus subtilis–mode of action of a microbial agent enhancing plant vitality. Pflanzenschutz-Nachrichten Bayer 1(1):72–93

    Google Scholar 

  37. Kirby JR, Kristich CJ, Saulmon MM, Zimmer MA, Garrity LF, Zhulin IB, Ordal GW (2001) CheC is related to the family of flagellar switch proteins and acts independently from CheD to control chemotaxis in Bacillus subtilis. Mol Microbiol 42(3):573–585

    Article  CAS  PubMed  Google Scholar 

  38. Kloepper JW, Leong J, Teintze M, Schroth MN (1980) Enhanced plant growth by siderophores produced by plant growth-promoting rhizobacteria. Nature 286(5776):885–886

    Article  CAS  Google Scholar 

  39. Kloepper JW, Ryu C-M, Zhang S (2004) Induced systemic resistance and promotion of plant growth by Bacillus spp. Phytopathology 94(11):1259–1266

    Article  CAS  PubMed  Google Scholar 

  40. Kobayashi K (2007) Gradual activation of the response regulator DegU controls serial expression of genes for flagellum formation and biofilm formation in Bacillus subtilis. Mol Microbiol 66(2):395–409

    Article  CAS  PubMed  Google Scholar 

  41. Koumoutsi A, Chen X-H, Henne A, Liesegang H, Hitzeroth G, Franke P, Vater J, Borriss R (2004) Structural and functional characterization of gene clusters directing nonribosomal synthesis of bioactive cyclic lipopeptides in Bacillus amyloliquefaciens strain FZB42. J Bacteriol 186(4):1084–1096

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  42. Lazarevic V, Soldo B, Médico N, Pooley H, Bron S, Karamata D (2005) Bacillus subtilis α-phosphoglucomutase is required for normal cell morphology and biofilm formation. Appl Environ Microbiol 71(1):39–45

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  43. Leclère V, Béchet M, Adam A, Guez JS, Wathelet B, Ongena M, Thonart P, Gancel F, Chollet-Imbert M, Jacques P (2005) Mycosubtilin overproduction by Bacillus subtilis BBG100 enhances the organism’s antagonistic and biocontrol activities. Appl Environ Microbiol 71(8):4577–4584

    Article  PubMed Central  PubMed  Google Scholar 

  44. Liu Q, **ong G, Mao Z, Wu Y, He Y (2012) Analyses for the colonization ability of Bacillus subtilis XF-1 in the rhizosphere. Acta phytophylacica sinica 39:425–430

    Google Scholar 

  45. Lopez D, Kolter R (2010) Extracellular signals that define distinct and coexisting cell fates in Bacillus subtilis. FEMS Microbiol Rev 34(2):134–149

    Article  CAS  PubMed  Google Scholar 

  46. Lopez D, Vlamakis H, Kolter R (2009) Generation of multiple cell types in Bacillus subtilis. FEMS Microbiol Rev 33(1):152–163

    Article  CAS  PubMed  Google Scholar 

  47. Marsin S, McGovern S, Ehrlich SD, Bruand C, Polard P (2001) Early steps of Bacillus subtilis primosome assembly. J Biol Chem 276(49):45818

    Article  CAS  PubMed  Google Scholar 

  48. Marvasi M, Visscher PT, Casillas Martinez L (2010) Exopolymeric substances (EPS) from Bacillus subtilis : polymers and genes encoding their synthesis. FEMS Microbiol Lett 313(1):1–9

    Article  CAS  PubMed  Google Scholar 

  49. Merrick M, Edwards R (1995) Nitrogen control in bacteria. Microbiol Rev 59(4):604–622

    PubMed Central  CAS  PubMed  Google Scholar 

  50. Mirel DB, Lauer P, Chamberlin MJ (1994) Identification of flagellar synthesis regulatory and structural genes in a sigma D-dependent operon of Bacillus subtilis. J Bacteriol 176(15):4492–4500

    PubMed Central  CAS  PubMed  Google Scholar 

  51. Moxham SE, Buczacki S (1983) Chemical composition of the resting spore wall of Plasmodiophora brassicae. T British Mycol Soc 80(2):297–304

    Article  CAS  Google Scholar 

  52. Neilands J (1995) Siderophores: structure and function of microbial iron transport compounds. J Biol Chem 270(45):26723–26726

    Article  CAS  PubMed  Google Scholar 

  53. Noguchi H, Park J, Takagi T (2006) MetaGene: prokaryotic gene finding from environmental genome shotgun sequences. Nucleic Acid Res 34(19):5623

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  54. Omoike A, Chorover J (2004) Spectroscopic study of extracellular polymeric substances from Bacillus subtilis: aqueous chemistry and adsorption effects. Biomacromolecules 5(4):1219–1230

    Article  CAS  PubMed  Google Scholar 

  55. ** L, Boland W (2004) Signals from the underground: bacterial volatiles promote growth in Arabidopsis. Trends Plant Sci 9(6):263–266

    Article  CAS  PubMed  Google Scholar 

  56. Rao CV, Glekas GD, Ordal GW (2008) The three adaptation systems of Bacillus subtilis chemotaxis. Trends Microbiol 16(10):480–487

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  57. Ryu CM, Farag MA, Hu C-H, Reddy MS, Wei HX, Paré PW, Kloepper JW (2003) Bacterial volatiles promote growth in Arabidopsis. P Natl A Sci 100(8):4927–4932

    Article  CAS  Google Scholar 

  58. Schultz D, Wolynes PG, Jacob EB, Onuchic JN (2009) Deciding fate in adverse times: sporulation and competence in Bacillus subtilis. P Natl A Sci 106(50):21027

    Article  CAS  Google Scholar 

  59. Sekowska A, Bertin P, Danchin A (1998) Characterization of polyamine synthesis pathway in Bacillus subtilis 168. Mol Microbiol 29(3):851–858

    Article  CAS  PubMed  Google Scholar 

  60. Stein T (2005) Bacillus subtilis antibiotics: structures, syntheses and specific functions. Mol Microbiol 56(4):845–857

    Article  CAS  PubMed  Google Scholar 

  61. Steller S, Vater J (2000) Purification of the fengycin synthetase multienzyme system from Bacillus subtilis b213. J Chroma Togr B: Biomed Sci Appl 737(1):267–275

    Article  CAS  Google Scholar 

  62. Steller S, Vollenbroich D, Leenders F, Stein T, Conrad B, Hofemeister J, Jacques P, Thonart P, Vater J (1999) Structural and functional organization of the fengycin synthetase multienzyme system from Bacillus subtilis b213 and A1/3. Chem Biol 6(1):31–41

    Article  CAS  PubMed  Google Scholar 

  63. Stragier P, Losick R (1996) Molecular genetics of sporulation in Bacillus subtilis. Annu Rev Genet 30(1):297–341

    Article  CAS  PubMed  Google Scholar 

  64. Tabor CW, Tabor H (1984) Polyamines. Annu Rev Biochem 53(1):749–790

    Article  CAS  PubMed  Google Scholar 

  65. Tatusov RL, Galperin MY, Natale DA, Koonin EV (2000) The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acid Res 28(1):33–36

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  66. Tatusova TA, Madden TL (2006) BLAST 2 sequences, a new tool for comparing protein and nucleotide sequences. FEMS Microbiol Lett 174(2):247–250

    Article  Google Scholar 

  67. Timmusk S, Grantcharova N, Wagner EGH (2005) Paenibacillus polymyxa invades plant roots and forms biofilms. Appl Environ Microbiol 71(11):7292

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  68. Tosato V, Albertini AM, Zotti M, Sonda S, Bruschi CV (1997) Sequence completion, identification and definition of the fengycin operon in Bacillus subtilis 168. Microbiology 143(11):3443–3450

    Article  CAS  PubMed  Google Scholar 

  69. Walsh CT (2004) Polyketide and nonribosomal peptide antibiotics: modularity and versatility. Science 303(5665):1805

    Article  CAS  PubMed  Google Scholar 

  70. Weilharter A, Mitter B, Shin MV, Chain PS, Nowak J, Sessitsch A (2011) Complete genome sequence of the plant growth-promoting endophyte Burkholderia phytofirmans strain PsJN. J Bacteriol 193(13):3383–3384

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  71. Werhane H, Lopez P, Mendel M, Zimmer M, Ordal G, Márquez-Magaña L (2004) The last gene of the fla/che operon in Bacillus subtilis, ylxL, is required for maximal σD function. J Bacteriol 186(12):4025–4029

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  72. Witte G, Hartung S, Buttner K, Hopfner KP (2008) Structural biochemistry of a bacterial checkpoint protein reveals diadenylate cyclase activity regulated by DNA recombination intermediates. Mol Cell 30(2):167–178

    Article  CAS  PubMed  Google Scholar 

  73. Wolff S, Antelmann H, Albrecht D, Becher D, Bernhardt J, Bron S, Büttner K, van Dijl JM, Eymann C, Otto A (2007) Towards the entire proteome of the model bacterium Bacillus subtilis by gel-based and gel-free approaches. J Chroma Togr B 849(1–2):129–140

    Article  CAS  Google Scholar 

  74. Wray L, Atkinson MR, Fisher SH (1994) The nitrogen-regulated Bacillus subtilis nrgAB operon encodes a membrane protein and a protein highly similar to the Escherichia coli glnB-encoded PII protein. J Bacteriol 176(1):108–114

    PubMed Central  CAS  PubMed  Google Scholar 

  75. **ong G, Zhao G, Fan C, He Y (2009) Identification and fungistatic effect of a biocontrol strain. J Yunnan Agr U 24:190–194

    CAS  Google Scholar 

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Acknowledgments

We thank the Ministry of Agriculture, China, and the Department of Science and Technologies, Yunnan Province, China, for their financial support through the Special Fund for Agroscientific Research in the Public Interest (201003029) and the Natural Science Foundation of Yunnan Province (2008CC024).

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The authors declare that they have no conflict of interest.

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This article does not contain any studies with human participants or animals performed by any of the authors. Informed consent was obtained from all individual participants included in the study.

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  1. Faculty of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China

    Shengye Guo, **ngyu Li, Pengfei He, Yixin Wu & Yueqiu He

  2. Department of Biology, State University of New York, New Paltz, NY, 12561, USA

    Honhing Ho

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Guo, S., Li, X., He, P. et al. Whole-genome sequencing of Bacillus subtilis XF-1 reveals mechanisms for biological control and multiple beneficial properties in plants. J Ind Microbiol Biotechnol 42, 925–937 (2015). https://doi.org/10.1007/s10295-015-1612-y

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