Key Points
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Bacillus subtilis is a model non-pathogenic Gram-positive bacterium that has been used to study biofilms. These ubiquitous communities of tightly associated bacteria are encased in a self-produced extracellular matrix that holds the constituent cells together.
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Within a biofilm, genetically identical B. subtilis cells differentiate, and cells expressing different sets of genes have distinct functions.
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B. subtilis cells are able to sense and respond to diverse extracellular cues using a complex regulatory network composed of several overlapping subnetworks, all of which control the genes involved in biofilm formation. These cues range from self-produced signals, such as surfactin, to natural products produced by other organisms found in the soil.
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Several self-produced molecules, such as d-amino acids and polyamines, are secreted late during the life cycle of a biofilm and trigger disassembly of the community. These molecules also seem to be effective in the dissolution of biofilms formed by other bacteria.
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B. subtilis is a natural colonizer of plant roots and is commonly used as a biocontrol agent. Biofilm formation is important for plant root colonization and plant protection.
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Although researchers have uncovered the multiple mechanisms controlling biofilm formation in B. subtilis, understanding how this organism integrates these regulatory inputs is one of the major outstanding challenges in the field.
Abstract
Biofilms are ubiquitous communities of tightly associated bacteria encased in an extracellular matrix. Bacillus subtilis has long served as a robust model organism to examine the molecular mechanisms of biofilm formation, and a number of studies have revealed that this process is regulated by several integrated pathways. In this Review, we focus on the molecular mechanisms that control B. subtilis biofilm assembly, and then briefly summarize the current state of knowledge regarding biofilm disassembly. We also discuss recent progress that has expanded our understanding of B. subtilis biofilm formation on plant roots, which are a natural habitat for this soil bacterium.
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References
Sanderson, J. B. Appendix no. 5 in 13th Report of the Medical Officer of the Privy Council [John Simon], with Appendix, 1870 56–66 (Her Majesty's Stationery Office, London, 1871).
Cohn, F. Untersuchungen über bacterien. IV. Beiträge zur biologie der Bacillen. Beiträge zur biologie der Pflanzen 7, 249–276 (1877).
Hall-Stoodley, L., Costerton, J. W. & Stoodley, P. Bacterial biofilms: from the natural environment to infectious diseases. Nature Rev. Microbiol. 2, 95–108 (2004).
Stewart, P. S. & Franklin, M. J. Physiological heterogeneity in biofilms. Nature Rev. Microbiol. 6, 199–210 (2008).
Davies, D. Understanding biofilm resistance to antibacterial agents. Nature Rev. Drug Discov. 2, 114–122 (2003).
Mah, T. F. & O'Toole, G. A. Mechanisms of biofilm resistance to antimicrobial agents. Trends Microbiol. 9, 34–39 (2001).
Stewart, P. S. Mechanisms of antibiotic resistance in bacterial biofilms. Int. J. Med. Microbiol. 292, 107–113 (2002).
Hall-Stoodley, L. & Stoodley, P. Evolving concepts in biofilm infections. Cell. Microbiol. 11, 1034–1043 (2009).
Erable, B., Duteanu, N. M., Ghangrekar, M. M., Dumas, C. & Scott, K. Application of electro-active biofilms. Biofouling 26, 57–71 (2010).
Logan, B. E. Exoelectrogenic bacteria that power microbial fuel cells. Nature Rev. Microbiol. 7, 375–381 (2009).
Singh, R., Paul, D. & Jain, R. K. Biofilms: implications in bioremediation. Trends Microbiol. 14, 389–397 (2006).
Monds, R. D. & O'Toole, G. A. The developmental model of microbial biofilms: ten years of a paradigm up for review. Trends Microbiol. 17, 73–87 (2009).
Branda, S. S., Chu, F., Kearns, D. B., Losick, R. & Kolter, R. A major protein component of the Bacillus subtilis biofilm matrix. Mol. Microbiol. 59, 1229–1238 (2006). A study showing that TasA and EPS are components of the extracellular matrix and essential for biofilm formation.
Branda, S. S., Gonzalez-Pastor, J. E., Ben-Yehuda, S., Losick, R. & Kolter, R. Fruiting body formation by Bacillus subtilis. Proc. Natl Acad. Sci. USA 98, 11621–11626 (2001). The first paper describing B. subtilis colony and pellicle biofilms.
Kobayashi, K. Bacillus subtilis pellicle formation proceeds through genetically defined morphological changes. J. Bacteriol. 189, 4920–4931 (2007).
Branda, S. S., Vik, S., Friedman, L. & Kolter, R. Biofilms: the matrix revisited. Trends Microbiol. 13, 20–26 (2005).
Marvasi, M., Visscher, P. T. & Casillas Martinez, L. Exopolymeric substances (EPS) from Bacillus subtilis: polymers and genes encoding their synthesis. FEMS Microbiol. Lett. 313, 1–9 (2010).
Flemming, H. C. & Wingender, J. The biofilm matrix. Nature Rev. Microbiol. 8, 623–633 (2010).
Lopez, D., Vlamakis, H. & Kolter, R. Biofilms. Cold Spring Harb. Perspect. Biol. 2, a000398 (2010).
Vlamakis, H. & Kolter, R. in Bacterial Stress Responses 2nd edn (eds Storz, G. & Hengge, R.) 365–373 (American Society for Microbiology Press, 2011).
Vlamakis, H., Aguilar, C., Losick, R. & Kolter, R. Control of cell fate by the formation of an architecturally complex bacterial community. Genes Dev. 22, 945–953 (2008). This work describes the spatiotemporal regulation of gene expression within biofilms.
Dubnau, D. & Losick, R. Bistability in bacteria. Mol. Microbiol. 61, 564–572 (2006).
Smits, W. K., Kuipers, O. P. & Veening, J. W. Phenotypic variation in bacteria: the role of feedback regulation. Nature Rev. Microbiol. 4, 259–271 (2006).
Veening, J. W., Smits, W. K. & Kuipers, O. P. Bistability, epigenetics, and bet-hedging in bacteria. Annu. Rev. Microbiol. 62, 193–210 (2008). An excellent review discussing phenotypic variability in clonal bacterial populations.
Lopez, D. & Kolter, R. Extracellular signals that define distinct and coexisting cell fates in Bacillus subtilis. FEMS Microbiol. Rev. 34, 134–149 (2010).
Kolodkin-Gal, I. et al. A self-produced trigger for biofilm disassembly that targets exopolysaccharide. Cell 149, 1–9 (2012). The B. subtilis -produced compound norspermidine is described as an inhibitor of EPS in B. subtilis biofilms.
Kolodkin-Gal, I. et al. d-amino acids trigger biofilm disassembly. Science 328, 627–629 (2010). This work determined that d -amino acids, which are secreted late in biofilm formation, inhibit B. subtilis biofilms, as well as those of other species.
Asally, M. et al. Localized cell death focuses mechanical forces during 3D patterning in a biofilm. Proc. Natl Acad. Sci. USA 109, 18891–18896 (2012).
Epstein, A. K., Pokroy, B., Seminara, A. & Aizenberg, J. Bacterial biofilm shows persistent resistance to liquid wetting and gas penetration. Proc. Natl Acad. Sci. USA 108, 995–1000 (2011).
Chagneau, C. & Saier, M. H. Jr. Biofilm-defective mutants of Bacillus subtilis. J. Mol. Microbiol. Biotechnol. 8, 177–188 (2004).
Seminara, A. et al. Osmotic spreading of Bacillus subtilis biofilms driven by an extracellular matrix. Proc. Natl Acad. Sci. USA 109, 1116–1121 (2012).
Hamon, M. A. & Lazazzera, B. A. The sporulation transcription factor Spo0A is required for biofilm development in Bacillus subtilis. Mol. Microbiol. 42, 1199–1209 (2001). The first paper describing submerged, surface-adhered B. subtilis biofilms.
Kearns, D. B., Chu, F., Branda, S. S., Kolter, R. & Losick, R. A master regulator for biofilm formation by Bacillus subtilis. Mol. Microbiol. 55, 739–749 (2005).
Terra, R., Stanley-Wall, N. R., Cao, G. & Lazazzera, B. A. Identification of Bacillus subtilis SipW as a bifunctional signal peptidase that controls surface-adhered biofilm formation. J. Bacteriol. 194, 2781–2790 (2012).
Branda, S. S. et al. Genes involved in formation of structured multicellular communities by Bacillus subtilis. J. Bacteriol. 186, 3970–3979 (2004).
Lazarevic, V. et al. Bacillus subtilis α-phosphoglucomutase is required for normal cell morphology and biofilm formation. Appl. Environ. Microbiol. 71, 39–45 (2005).
Chai, Y., Beauregard, P. B., Vlamakis, H., Losick, R. & Kolter, R. Galactose metabolism plays a crucial role in biofilm formation by Bacillus subtilis. mBio 3, e00184–e00112 (2012).
Ren, D. et al. Gene expression in Bacillus subtilis surface biofilms with and without sporulation and the importance of yveR for biofilm maintenance. Biotechnol. Bioeng. 86, 344–364 (2004).
Nagorska, K., Ostrowski, A., Hinc, K., Holland, I. B. & Obuchowski, M. Importance of eps genes from Bacillus subtilis in biofilm formation and swarming. J. Appl. Genet. 51, 369–381 (2010).
Nagorska, K., Hinc, K., Strauch, M. A. & Obuchowski, M. Influence of the σB stress factor and yxaB, the gene for a putative exopolysaccharide synthase under σB control, on biofilm formation. J. Bacteriol. 190, 3546–3556 (2008).
Blair, K. M., Turner, L., Winkelman, J. T., Berg, H. C. & Kearns, D. B. A molecular clutch disables flagella in the Bacillus subtilis biofilm. Science 320, 1636–1638 (2008). A beautiful example of the multiple levels of regulation which ensure that matrix-producing cells are non-motile.
Guttenplan, S. B., Blair, K. M. & Kearns, D. B. The EpsE flagellar clutch is bifunctional and synergizes with EPS biosynthesis to promote Bacillus subtilis biofilm formation. PLoS Genet. 6, e1001243 (2010).
Aguilar, C., Vlamakis, H., Guzman, A., Losick, R. & Kolter, R. KinD is a checkpoint protein linking spore formation to extracellular-matrix production in Bacillus subtilis biofilms. mBio 1, e00035–e00010 (2010).
Morikawa, M. et al. Biofilm formation by a Bacillus subtilis strain that produces γ-polyglutamate. Microbiology 152, 2801–2807 (2006).
Stanley, N. R. & Lazazzera, B. A. Defining the genetic differences between wild and domestic strains of Bacillus subtilis that affect poly-γ-dl-glutamic acid production and biofilm formation. Mol. Microbiol. 57, 1143–1158 (2005).
Romero, D., Aguilar, C., Losick, R. & Kolter, R. Amyloid fibers provide structural integrity to Bacillus subtilis biofilms. Proc. Natl Acad. Sci. USA 107, 2230–2234 (2010). In this work, TasA is shown to form amyloid-like fibres in the extracellular matrix.
Romero, D., Vlamakis, H., Losick, R. & Kolter, R. An accessory protein required for anchoring and assembly of amyloid fibres in B. subtilis biofilms. Mol. Microbiol. 80, 1155–1168 (2011).
Stover, A. G. & Driks, A. Control of synthesis and secretion of the Bacillus subtilis protein YqxM. J. Bacteriol. 181, 7065–7069 (1999).
Stover, A. G. & Driks, A. Regulation of synthesis of the Bacillus subtilis transition-phase, spore-associated antibacterial protein TasA. J. Bacteriol. 181, 5476–5481 (1999).
Tjalsma, H. et al. Functional analysis of the secretory precursor processing machinery of Bacillus subtilis: identification of a eubacterial homolog of archaeal and eukaryotic signal peptidases. Genes Dev. 12, 2318–2331 (1998).
Hamon, M. A., Stanley, N. R., Britton, R. A., Grossman, A. D. & Lazazzera, B. A. Identification of AbrB-regulated genes involved in biofilm formation by Bacillus subtilis. Mol. Microbiol. 52, 847–860 (2004).
Kobayashi, K. & Iwano, M. BslA(YuaB) forms a hydrophobic layer on the surface of Bacillus subtilis biofilms. Mol. Microbiol. 85, 51–66 (2012). A recent study showing that BslA has a role in conferring hydrophobicity to B. subtilis biofilms.
Kobayashi, K. Gradual activation of the response regulator DegU controls serial expression of genes for flagellum formation and biofilm formation in Bacillus subtilis. Mol. Microbiol. 66, 395–409 (2007).
Kovacs, A. T. & Kuipers, O. P. Rok regulates yuaB expression during architecturally complex colony development of Bacillus subtilis 168. J. Bacteriol. 193, 998–1002 (2011).
Verhamme, D. T., Murray, E. J. & Stanley-Wall, N. R. DegU and Spo0A jointly control transcription of two loci required for complex colony development by Bacillus subtilis. J. Bacteriol. 191, 100–108 (2009).
Ostrowski, A., Mehert, A., Prescott, A., Kiley, T. B. & Stanley-Wall, N. R. YuaB functions synergistically with the exopolysaccharide and TasA amyloid fibers to allow biofilm formation by Bacillus subtilis. J. Bacteriol. 193, 4821–4831 (2011). The first paper to describe BslA as a matrix protein that is required, in addition to TasA, for biofilm formation.
Fujita, M., Gonzalez-Pastor, J. E. & Losick, R. High- and low-threshold genes in the Spo0A regulon of Bacillus subtilis. J. Bacteriol. 187, 1357–1368 (2005).
Molle, V. et al. The Spo0A regulon of Bacillus subtilis. Mol. Microbiol. 50, 1683–1701 (2003).
Jiang, M., Shao, W., Perego, M. & Hoch, J. A. Multiple histidine kinases regulate entry into stationary phase and sporulation in Bacillus subtilis. Mol. Microbiol. 38, 535–542 (2000).
McLoon, A. L., Kolodkin-Gal, I., Rubinstein, S. M., Kolter, R. & Losick, R. Spatial regulation of histidine kinases governing biofilm formation in Bacillus subtilis. J. Bacteriol. 193, 679–685 (2011).
Piggot, P. J. & Hilbert, D. W. Sporulation of Bacillus subtilis. Curr. Opin. Microbiol. 7, 579–586 (2004).
Perego, M. & Hoch, J. A. Cell-cell communication regulates the effects of protein aspartate phosphatases on the phosphorelay controlling development in Bacillus subtilis. Proc. Natl Acad. Sci. USA 93, 1549–1553 (1996).
Lopez, D., Fischbach, M. A., Chu, F., Losick, R. & Kolter, R. Structurally diverse natural products that cause potassium leakage trigger multicellularity in Bacillus subtilis. Proc. Natl Acad. Sci. USA 106, 280–285 (2009).
Chu, F., Kearns, D. B., Branda, S. S., Kolter, R. & Losick, R. Targets of the master regulator of biofilm formation in Bacillus subtilis. Mol. Microbiol. 59, 1216–1228 (2006).
Chu, F. et al. A novel regulatory protein governing biofilm formation in Bacillus subtilis. Mol. Microbiol. 68, 1117–1127 (2008).
Lewis, R. J., Brannigan, J. A., Smith, I. & Wilkinson, A. J. Crystallisation of the Bacillus subtilis sporulation inhibitor SinR, complexed with its antagonist, SinI. FEBS Lett. 378, 98–100 (1996).
Chai, Y., Chu, F., Kolter, R. & Losick, R. Bistability and biofilm formation in Bacillus subtilis. Mol. Microbiol. 67, 254–263 (2008).
Chai, Y., Norman, T., Kolter, R. & Losick, R. Evidence that metabolism and chromosome copy number control mutually exclusive cell fates in Bacillus subtilis. EMBO J. 30, 1402–1413 (2011).
Strauch, M., Webb, V., Spiegelman, G. & Hoch, J. A. The SpoOA protein of Bacillus subtilis is a repressor of the abrB gene. Proc. Natl Acad. Sci. USA 87, 1801–1805 (1990).
Strauch, M. A. et al. Abh and AbrB control of Bacillus subtilis antimicrobial gene expression. J. Bacteriol. 189, 7720–7732 (2007).
Chai, Y., Kolter, R. & Losick, R. Paralogous antirepressors acting on the master regulator for biofilm formation in Bacillus subtilis. Mol. Microbiol. 74, 876–887 (2009).
Kobayashi, K. SlrR/SlrA control the initiation of biofilm formation in Bacillus subtilis. Mol. Microbiol. 69, 1399–1410 (2008).
Chai, Y., Kolter, R. & Losick, R. Reversal of an epigenetic switch governing cell chaining in Bacillus subtilis by protein instability. Mol. Microbiol. 78, 218–229 (2010).
Chai, Y., Norman, T., Kolter, R. & Losick, R. An epigenetic switch governing daughter cell separation in Bacillus subtilis. Genes Dev. 24, 754–765 (2010). This study shows that SlrR binds to and re-purposes the repressor SinR to regulate a different set of genes.
Murray, E. J., Strauch, M. A. & Stanley-Wall, N. R. SigmaX is involved in controlling Bacillus subtilis biofilm architecture through the AbrB homologue Abh. J. Bacteriol. 191, 6822–6832 (2009).
Huang, X., Fredrick, K. L. & Helmann, J. D. Promoter recognition by Bacillus subtilis σW: autoregulation and partial overlap with the σX regulon. J. Bacteriol. 180, 3765–3770 (1998).
Huang, X. & Helmann, J. D. Identification of target promoters for the Bacillus subtilis σX factor using a consensus-directed search. J. Mol. Biol. 279, 165–173 (1998).
Luo, Y., Asai, K., Sadaie, Y. & Helmann, J. D. Transcriptomic and phenotypic characterization of a Bacillus subtilis strain without extracytoplasmic function σ factors. J. Bacteriol. 192, 5736–5745 (2010).
Mascher, T., Hachmann, A. B. & Helmann, J. D. Regulatory overlap and functional redundancy among Bacillus subtilis extracytoplasmic function σ factors. J. Bacteriol. 189, 6919–6927 (2007).
Helmann, J. D. The extracytoplasmic function (ECF) sigma factors. Adv. Microb. Physiol. 46, 47–110 (2002).
Diethmaier, C. et al. A novel factor controlling bistability in Bacillus subtilis: the YmdB protein affects flagellin expression and biofilm formation. J. Bacteriol. 193, 5997–6007 (2011).
Winkelman, J. T., Blair, K. M. & Kearns, D. B. RemA (YlzA) and RemB (YaaB) regulate extracellular matrix operon expression and biofilm formation in Bacillus subtilis. J. Bacteriol. 191, 3981–3991 (2009).
Verhamme, D. T., Kiley, T. B. & Stanley-Wall, N. R. DegU co-ordinates multicellular behaviour exhibited by Bacillus subtilis. Mol. Microbiol. 65, 554–568 (2007).
Murray, E. J., Kiley, T. B. & Stanley-Wall, N. R. A pivotal role for the response regulator DegU in controlling multicellular behaviour. Microbiology 155, 1–8 (2009).
Irnov, I. & Winkler, W. C. A regulatory RNA required for antitermination of biofilm and capsular polysaccharide operons in Bacillales. Mol. Microbiol. 76, 559–575 (2010).
Kearns, D. B. A field guide to bacterial swarming motility. Nature Rev. Microbiol. 8, 634–644 (2010).
James, B. L., Kret, J., Patrick, J. E., Kearns, D. B. & Fall, R. Growing Bacillus subtilis tendrils sense and avoid each other. FEMS Microbiol. Lett. 298, 12–19 (2009).
Das, P., Mukherjee, S. & Sen, R. Genetic regulations of the biosynthesis of microbial surfactants: an overview. Biotechnol. Genet. Engineer. Rev. 25, 165–185 (2008).
Lopez, D., Vlamakis, H., Losick, R. & Kolter, R. Paracrine signaling in a bacterium. Genes Dev. 23, 1631–1638 (2009). This work finds that not all of the genes in a clonal population produce quorum sensing signals and that the cells which produce the signal are not the cells that respond to it.
Shank, E. A. & Kolter, R. Extracellular signaling and multicellularity in Bacillus subtilis. Curr. Opin. Microbiol. 14, 741–747 (2011).
Lopez, D. & Kolter, R. Functional microdomains in bacterial membranes. Genes Dev. 24, 1893–1902 (2010).
Shemesh, M., Kolter, R. & Losick, R. The biocide chlorine dioxide stimulates biofilm formation in Bacillus subtilis by activation of the histidine kinase KinC. J. Bacteriol. 192, 6352–6356 (2010).
Laub, M. T. & Goulian, M. Specificity in two-component signal transduction pathways. Annu. Rev. Genet. 41, 121–145 (2007).
Shank, E. A. et al. Interspecies interactions that result in Bacillus subtilis forming biofilms are mediated mainly by members of its own genus. Proc. Natl Acad. Sci. USA 108, E1236–1243 (2011).
Chen, Y. et al. A Bacillus subtilis sensor kinase involved in triggering biofilm formation on the roots of tomato plants. Mol. Microbiol. 85, 418–430 (2012).
Gonzalez-Pastor, J. E., Hobbs, E. C. & Losick, R. Cannibalism by sporulating bacteria. Science 301, 510–513 (2003).
Gonzalez-Pastor, J. E. Cannibalism: a social behavior in sporulating Bacillus subtilis. FEMS Microbiol. Rev. 35, 415–424 (2011).
Ellermeier, C. D., Hobbs, E. C., Gonzalez-Pastor, J. E. & Losick, R. A three-protein signaling pathway governing immunity to a bacterial cannibalism toxin. Cell 124, 549–559 (2006).
Lopez, D., Vlamakis, H., Losick, R. & Kolter, R. Cannibalism enhances biofilm development in Bacillus subtilis. Mol. Microbiol. 74, 609–618 (2009).
Nandy, S. K., Bapat, P. M. & Venkatesh, K. V. Sporulating bacteria prefers predation to cannibalism in mixed cultures. FEBS Lett. 581, 151–156 (2007).
Liu, W. T. et al. Imaging mass spectrometry of intraspecies metabolic exchange revealed the cannibalistic factors of Bacillus subtilis. Proc. Natl Acad. Sci. USA 107, 16286–16290 (2010).
Kaplan, J. B. Biofilm dispersal: mechanisms, clinical implications, and potential therapeutic uses. J. Dent. Res. 89, 205–218 (2010).
McDougald, D., Rice, S. A., Barraud, N., Steinberg, P. D. & Kjelleberg, S. Should we stay or should we go: mechanisms and ecological consequences for biofilm dispersal. Nature Rev. Microbiol. 10, 39–50 (2012).
Lam, H. et al. D-amino acids govern stationary phase cell wall remodeling in bacteria. Science 325, 1552–1555 (2009).
Burrell, M., Hanfrey, C. C., Murray, E. J., Stanley-Wall, N. R. & Michael, A. J. Evolution and multiplicity of arginine decarboxylases in polyamine biosynthesis and essential role in Bacillus subtilis biofilm formation. J. Biol. Chem. 285, 39224–39238 (2010).
Hochbaum, A. I. et al. Inhibitory effects of d-amino acids on Staphylococcus aureus biofilm development. J. Bacteriol. 193, 5616–5622 (2011).
Sanchez, Z., Tani, A. & Kimbara, K. Extensive reduction in cell viability and enhanced matrix production in Pseudomonas aeruginosa PAO1 flow biofilms treated with D-amino acid mixture. Appl. Environ. Microbiol. 7 Dec 2012 (doi:10.1128/AEM.02911-12).
Liu, C. I. et al. A cholesterol biosynthesis inhibitor blocks Staphylococcus aureus virulence. Science 319, 1391–1394 (2008).
Richards, J. J. & Melander, C. Controlling bacterial biofilms. Chembiochem 10, 2287–2294 (2009).
Zeigler, D. R. et al. The origins of 168, W23, and other Bacillus subtilis legacy strains. J. Bacteriol. 190, 6983–6995 (2008).
McLoon, A. L., Guttenplan, S. B., Kearns, D. B., Kolter, R. & Losick, R. Tracing the domestication of a biofilm-forming bacterium. J. Bacteriol. 193, 2027–2034 (2011).
Lazazzera, B. A. The intracellular function of extracellular signaling peptides. Peptides 22, 1519–1527 (2001).
Srivatsan, A. et al. High-precision, whole-genome sequencing of laboratory strains facilitates genetic studies. PLoS Genet. 4, e1000139 (2008).
Earl, A. M., Losick, R. & Kolter, R. Ecology and genomics of Bacillus subtilis. Trends Microbiol. 16, 269–275 (2008).
Danhorn, T. & Fuqua, C. Biofilm formation by plant-associated bacteria. Annu. Rev. Microbiol. 61, 401–422 (2007).
Lugtenberg, B. & Kamilova, F. Plant-growth-promoting rhizobacteria. Annu. Rev. Microbiol. 63, 541–556 (2009).
Ramey, B. E., Koutsoudis, M., von Bodman, S. B. & Fuqua, C. Biofilm formation in plant-microbe associations. Curr. Opin. Microbiol. 7, 602–609 (2004).
Morikawa, M. Beneficial biofilm formation by industrial bacteria Bacillus subtilis and related species. J. Biosci. Bioeng. 101, 1–8 (2006).
Emmert, E. A. & Handelsman, J. Biocontrol of plant disease: a (Gram-) positive perspective. FEMS Microbiol. Lett. 171, 1–9 (1999).
Kloepper, J. W., Ryu, C. M. & Zhang, S. Induced systemic resistance and promotion of plant growth by Bacillus spp. Phytopathology 94, 1259–1266 (2004).
Ryu, C. M., Murphy, J. F., Mysore, K. S. & Kloepper, J. W. Plant growth-promoting rhizobacteria systemically protect Arabidopsis thaliana against Cucumber mosaic virus by a salicylic acid and NPR1-independent and jasmonic acid-dependent signaling pathway. Plant J. 39, 381–392 (2004).
Choudhary, D. K. & Johri, B. N. Interactions of Bacillus spp. and plants – with special reference to induced systemic resistance (ISR). Microbiol. Res. 164, 493–513 (2009).
Perez-Garcia, A., Romero, D. & de Vicente, A. Plant protection and growth stimulation by microorganisms: biotechnological applications of Bacilli in agriculture. Curr. Opin. Biotechnol. 22, 187–193 (2011).
Vessey, J. K. Plant growth promoting rhizobacteria as biofertilizers. Plant Soil 255, 571–586 (2003).
Fall, R., Kinsinger, R. F. & Wheeler, K. A. A simple method to isolate biofilm-forming Bacillus subtilis and related species from plant roots. Syst. Appl. Microbiol. 27, 372–379 (2004).
Chen, Y. et al. Biocontrol of tomato wilt disease by Bacillus subtilis isolates from natural environments depends on conserved genes mediating biofilm formation. Environ. Microbiol. 30 Aug 2012 (doi:10.1111/j.1462-2920.2012.02860.x).
Bais, H. P., Fall, R. & Vivanco, J. M. Biocontrol of Bacillus subtilis against infection of Arabidopsis roots by Pseudomonas syringae is facilitated by biofilm formation and surfactin production. Plant Physiol. 134, 307–319 (2004).
Rudrappa, T., Czymmek, K. J., Pare, P. W. & Bais, H. P. Root-secreted malic acid recruits beneficial soil bacteria. Plant Physiol. 148, 1547–1556 (2008).
Rudrappa, T., Quinn, W. J., Stanley-Wall, N. R. & Bais, H. P. A degradation product of the salicylic acid pathway triggers oxidative stress resulting in down-regulation of Bacillus subtilis biofilm formation on Arabidopsis thaliana roots. Planta 226, 283–297 (2007).
Ongena, M. et al. Surfactin and fengycin lipopeptides of Bacillus subtilis as elicitors of induced systemic resistance in plants. Environ. Microbiol. 9, 1084–1090 (2007).
Donovan, C. & Bramkamp, M. Characterization and subcellular localization of a bacterial flotillin homologue. Microbiology 155, 1786–1799 (2009).
Huang, X., Gaballa, A., Cao, M. & Helmann, J. D. Identification of target promoters for the Bacillus subtilis extracytoplasmic function σ factor, σW. Mol. Microbiol. 31, 361–371 (1999).
Acknowledgements
The authors are grateful to E. Shank for her invaluable feedback on the preparation of this Review. Work in the authors' laboratories related to B. subtilis biofilms was funded by the US National Institutes of Health grants GM58213 (to R.K.) and GM18546 (to R.L.)
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Supplementary Information S1 (movie)
Movie of Bacillus subtilis cells forming a colony biofilm at room temperature over a period of approximately 9 days on MSgg medium. (MOV 12837 kb)
Glossary
- Rhizosphere
-
A narrow region of soil that surrounds the root of a plant and is directly influenced by plant root secretions and associated soil microorganisms.
- Biocontrol
-
The protection of plants against diseases by using biological control agents such as beneficial bacteria.
- Chaining
-
An event that occurs when daughter cells divide but remain connected by polar cell wall peptidoglycans.
- Epigenetic switch
-
A regulatory switch that imposes heritable changes in gene expression by a mechanism that does not involve genetic mutation.
- TetR-type transcriptional repressor
-
A two-domain protein with a DNA-binding domain and a small ligand-binding domain. Normally, repression is relieved when a specific small molecule binds to the ligand-binding domain.
- Cannibalism
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In the context of Bacillus subtilis: killing of siblings through the secretion of a toxin. In a genetically identical population, some cells will secrete a toxin, but these cells also express the genes that confer resistance. Siblings that do not express the toxin or resistance genes will be killed.
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Vlamakis, H., Chai, Y., Beauregard, P. et al. Sticking together: building a biofilm the Bacillus subtilis way. Nat Rev Microbiol 11, 157–168 (2013). https://doi.org/10.1038/nrmicro2960
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DOI: https://doi.org/10.1038/nrmicro2960
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