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The biofilm matrix

Subjects

Key Points

  • Formation of the biofilm matrix induces a unique environment for bacteria that allows the dynamic biofilm mode of life. Biofilms, and the resulting lifestyle, are built in specific, defined steps, producing a bacterial community that is heterogeneous in space and time.

  • Extracellular polymeric substances (EPS) immobilize biofilm cells, keeping them in long-term close proximity and, thus, allowing intense interactions to occur, including cell–cell communication, horizontal gene transfer and the formation of synergistic microconsortia.

  • Owing to the retention of extracellular enzymes in the matrix, a versatile external digestive system is generated: dissolved and particulate nutrients imported through the water phase of the matrix can be sequestered, accumulated and utilized. The matrix acts as an ultimate recycling yard, keeping all the components of lysed cells available, including DNA, and possibly therefore serving as a large genetic archive. Gradient formation creates a wide range of very different habitats, contributing to biodiversity in biofilms.

  • The matrix protects organisms in the biofilm from desiccation, biocides, antibiotics, heavy metals, ultraviolet radiation, host immune defences and many protozoan grazers.

  • Eventually, EPS can serve as a nutrient source, but — as for many other structural polymers in biology — some EPS components are only slowly biodegradable. The vast variety of EPS components means that their complete degradation requires a wide range of enzymes.

  • Ecologically, competition and cooperation in the confined space of the EPS matrix, and competition for the limited nutrients in particular, lead to constant adaptation of population fitness.

Abstract

The microorganisms in biofilms live in a self-produced matrix of hydrated extracellular polymeric substances (EPS) that form their immediate environment. EPS are mainly polysaccharides, proteins, nucleic acids and lipids; they provide the mechanical stability of biofilms, mediate their adhesion to surfaces and form a cohesive, three-dimensional polymer network that interconnects and transiently immobilizes biofilm cells. In addition, the biofilm matrix acts as an external digestive system by keeping extracellular enzymes close to the cells, enabling them to metabolize dissolved, colloidal and solid biopolymers. Here we describe the functions, properties and constituents of the EPS matrix that make biofilms the most successful forms of life on earth.

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Figure 1: The extracellular polymeric substances matrix at different dimensions.
Figure 2: Dynamics of Pseudomonas aeruginosa biofilm architecture.

References

  1. Wingender, J., Neu, T. & Flemming, H.-C. in Microbial Extracellular Polymeric Substances (eds Wingender, J., Neu, T. & Flemming, H.-C.) 1–19 (Springer, Heidelberg, 1999).

    Book  Google Scholar 

  2. Karatan, E. & Watnik, P. Signals, regulatory networks, and materials that build and break bacterial biofilms. Microbiol. Mol. Biol. Rev. 73, 310–347 (2009). An excellent paper on aspects of the regulation of the biofilm matrix.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Xavier, J. B. & Foster, K. R. Cooperation and conflict in microbial biofilms. Proc. Natl Acad. Sci. USA 104, 876–881 (2007). An important and inspiring discussion on microbial interactions, including the role of the matrix.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Flemming, H. C., Neu, T. R. & Wozniak, D. The EPS matrix: the house of biofilm cells. J. Bacteriol. 189, 7945–7947 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Allison, D. G., Sutherland, I. W. & Neu, T. R. in Biofilm Communities: Order from Chaos? (eds McBain, A. et al.) 381–387 (BioLine, Cardiff, 1998).

    Google Scholar 

  6. Zogaj, X., Nimtz, M., Rohde, M., Bokranz, W. & Römling, U. The multicellular morphotypes of Salmonella typhimurium and Escherichia coli produce cellulose as the second component of the extracellular matrix. Mol. Microbiol. 39, 1452–1463 (2001).

    Article  CAS  PubMed  Google Scholar 

  7. Schooling, S. R. & Beveridge, T. J. Membrane vesicles: an overlooked component of the matrices of biofilms. J. Bacteriol. 188, 5945–5957 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Decho, A. W. Microbial exopolymer secretions in ocean environments: their role(s) in food webs and marine processes. Oceanogr. Mar. Biol. Annu. Rev. 28, 73–153 (1990). A classic review of microbial interactions, including the role of EPS.

    Google Scholar 

  9. Decho, A. W. Microbial biofilms in intertidal systems: an overview. Cont. Shelf Res. 20, 1257–1273 (2000).

    Article  Google Scholar 

  10. Flemming, H.-C. & Wingender, J. in Encyclopedia of Environmental Microbiology (ed. Bitton, G.) 1223–1231 (Wiley, New York, 2002).

    Google Scholar 

  11. Decho, A. W., Visscher, P. T. & Reid, R. P. Production and cycling of natural microbial exopolymers (EPS) within a marine stromatolite. Paleogeogr. Paleoclimatol. Paleoecol. 219, 71–86 (2005).

    Article  Google Scholar 

  12. Ortega-Morales, B. O. et al. Characterization of extracellular polymers synthesized by tropical intertidal biofilm bacteria. J. Appl. Microbiol. 102, 254–264 (2006).

    Article  CAS  Google Scholar 

  13. Sutherland, I. W. The biofilm matrix – an immobilized but dynamic microbial environment. Trends Microbiol. 9, 222–227 (2001).

    Article  CAS  PubMed  Google Scholar 

  14. De Beer, D., Stoodley, P., Roe, F. & Lewandowski, Z. Effects of biofilm structures on oxygen distribution and mass transport. Biotechnol. Bioeng. 43, 1131–1138 (1994). A classic paper introducing microelectrode techniques to biofilm research.

    Article  CAS  PubMed  Google Scholar 

  15. Lawrence, J. R., Swerhone, G. D. W., Kuhlicke, U. & Neu, T. R. In situ evidence for microdomains in the polymer matrix of bacterial microcolonies. Can. J. Microbiol. 53, 450–458 (2007). The use of lectin-staining analysis for characterizing target structures in the EPS matrix.

    Article  CAS  PubMed  Google Scholar 

  16. Wagner, M., Ivleva, N. P., Haisch, C., Niessner, R. & Horn, H. Combined use of confocal laser scanning microscopy (CLSM) and Raman microscopy (RM): investigations on EPS-matrix. Water Res. 43, 63–76 (2009).

    Article  CAS  PubMed  Google Scholar 

  17. Watnik, P. I. & Kolter, R. Steps in the development of a Vibrio cholerae El Tor biofilm. Mol. Microbiol. 34, 586–595 (1999).

    Article  Google Scholar 

  18. Danese, P. N., Pratt, L. A. & Kolter, R. Exopolysaccharide production is required for development of Escherichia coli K-12 biofilm architecture. J. Bacteriol. 182, 3593–3596 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. 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).

    Article  CAS  PubMed  Google Scholar 

  20. Lux, R., Li, Y., Lu, A. & Shi, W. Detailed three-dimensional analysis of structural features of Myxococcus xanthus fruiting bodies using confocal laser scanning microscopy. Biofilms 1, 293–303 (2004).

    Article  Google Scholar 

  21. Tielen, P., Strathmann, M., Jaeger, K. E., Flemming, H.-C. & Wingender, J. Alginate acetylation influences initial surface colonization by mucoid Pseudomonas aeruginosa. Microbiol. Res. 160, 165–176 (2005).

    Article  CAS  PubMed  Google Scholar 

  22. Franklin, M. J. & Ohman, D. E. Identification of algF in the alginate biosynthetic gene cluster of Pseudomonas aeruginosa which is required for alginate acetylation. J. Bacteriol. 175, 5057–5065 (1993).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Wozniak, D. et al. Alginate is not a significant component of the extracellular polysaccharide matrix of PA14 and PAO1 Pseudomonas aeruginosa biofilms. Proc. Natl Acad. Sci. USA 100, 7907–7912 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Körstgens, V., Flemming, H.-C., Wingender, J. & Borchard, W. Influence of calcium ions on the mechanical properties of a model biofilm of mucoid Pseudomonas aeruginosa. Water Sci. Technol. 43, 49–57 (2001).

    Article  PubMed  Google Scholar 

  25. Nielsen, P. H. & Jahn, A. in Microbial Extracellular Polymeric Substances (eds Wingender, J., Neu, T. & Flemming, H.-C.) 49–72 (Springer, Heidelberg, 1999).

    Book  Google Scholar 

  26. Tapia, J. M. et al. Extraction of extracellular polymeric substances from the acidophilic bacterium Acidophilium. Water Sci. Technol. 59, 1959–1967 (2009).

    Article  CAS  PubMed  Google Scholar 

  27. Brown, M. J. & Lester, J. N. Comparison of bacterial extracellular polymer extraction methods. Appl. Environ. Microbiol. 40, 179–185 (1980).

    CAS  PubMed  PubMed Central  Google Scholar 

  28. Frølund, B., Palmgren, R., Keiding, K. & Nielsen, P.-H. Extraction of extracellular polymers from activated sludge using a cation exchange resin. Water Res. 30, 1749–1758 (1996). The original description of one of the most frequently used and most successful methods of isolating EPS.

    Article  Google Scholar 

  29. Wingender. J., Strathmann, M., Rode, A., Leis, A. & Flemming, H.-C. Isolation and biochemical characterization of extracellular polymeric substances from Pseudomonas aeruginosa. Methods Enzymol. 336, 302–314 (2001).

    Article  CAS  PubMed  Google Scholar 

  30. Römling, U. Molecular biology of cellulose production in bacteria. Res. Microbiol. 153, 205–212 (2002).

    Article  PubMed  Google Scholar 

  31. Ude, S., Arnold, D. L., Moon, C. D., Timms-Wilson, T. & Spiers, A. J. Biofilm formation and cellulose expression among diverse environmental Pseudomonas isolates. Environ. Microbiol. 8, 1997–2011 (2006).

    Article  CAS  PubMed  Google Scholar 

  32. Wang, X. et al. Impact of biofilm matrix components on interaction of commensal Escherichia coli with the gastrointestinal cell line HT-29. Cell. Mol. Life Sci. 63, 2352–2363 (2007).

    Article  CAS  Google Scholar 

  33. Sutherland, I. W. in Comprehensive Glycoscience Vol. 2 (ed. Kamerling, J. P.) 521–558 (Elsevier, Doordrecht, 2007). The best and most comprehensive overview of the polysaccharide moiety of EPS.

    Book  Google Scholar 

  34. Götz, F. Staphylococcus and biofilms. Mol. Microbiol. 43, 1367–1378 (2002).

    Article  PubMed  Google Scholar 

  35. Jefferson, K. K. in Bacterial Polysaccharides. Current Innovations and Future Trends (ed. Ullrich, M.) 175–186 (Caister Academic, Norfolk, UK, 2009).

    Google Scholar 

  36. Vaningelgem, F. et al. Biodiversity of exopolysaccharides produced by Streptococcus thermophilus strains is reflected in their production and their molecular and functional characteristics. Appl. Environ. Microbiol. 70, 900–912 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Ryder, C., Byrd, M., Wozniak, D. J. Role of exopolysaccharides in Pseudomonas aeruginosa biofilm development. Curr. Opin. Microbiol. 10, 644–648 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Byrd, M. S. et al. Genetic and biochemical analyses of the Pseudomonas aeruginosa Psl exopolysaccharide reveal overlapping roles for polysaccharide synthesis enzymes in Psl and LPS production. Mol. Microbiol. 73, 622–638 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Ma, L. et al. Assembly and development of the Pseudomonas aeruginosa biofilm matrix. PLoS Pathog. 5, e1000354 (2009).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  40. Skillman, L., Sutherland, I. W. & Jonse, M. V. The role of exopolysaccharides in dual species biofilm development. J. Appl. Microbiol. 85, S13–S18 (1999).

    Article  Google Scholar 

  41. Conrad, A. et al. Fatty acid lipid fractions in extracellular polymeric substances of activated sludge flocs. Lipids 38, 1093–1105 (2003).

    Article  CAS  PubMed  Google Scholar 

  42. Jahn, A. & Nielsen, P. H. Cell biomass and exopolymer composition in sewer biofilms. Water Sci. Technol. 37, 17–24 (1998).

    Article  CAS  Google Scholar 

  43. Wingender, J., Jaeger, K.-E. & Flemming, H.-C. in Microbial Extracellular Polymeric Substances (eds Wingender, J., Neu, T. & Flemming, H.-C.) 231–251 (Springer, Heidelberg, 1999).

    Book  Google Scholar 

  44. Shimao, M. Biodegradation of plastics. Curr. Opin. Biotechnol. 12, 242–247 (2001).

    Article  CAS  PubMed  Google Scholar 

  45. Busalmen, J. P., Vázquez, M. & de Sánchez, S. R. New evidences on the catalase mechanism of microbial corrosion. Electrochim. Acta 47, 1857–1865 (2002).

    Article  CAS  Google Scholar 

  46. Wingender, J. & Jaeger, K.-E. in Encyclopedia of Environmental Microbiology (ed. Bitton, G.) 1207–1223 (Wiley, New York, 2002).

    Google Scholar 

  47. Mayer, C. et al. The role of intermolecular interactions studies on model systems for bacterial biofilms. Int. J. Biol. Macromol. 26, 3–16 (1999).

    Article  CAS  PubMed  Google Scholar 

  48. Zhang, X. & Bishop, P. Biodegradability of biofilm extracellular polymeric substances. Chemosphere 50, 63–69 (2003).

    Article  CAS  PubMed  Google Scholar 

  49. Russell, R. R. B. in Bacterial Polysaccharides. Current Innovations and Future Trends (ed. Ullrich, M.) 143–156 (Caister Academic, Norfolk, UK, 2009).

    Google Scholar 

  50. Laue, H. et al. Contribution of alginate and levan production to biofilm formation by Pseudomonas syringae. Microbiology 152, 2909–2918 (2006).

    Article  CAS  PubMed  Google Scholar 

  51. Sauer, K. et al. Characterization of nutrient-induced dispersion in Pseudomonas aeruginosa PAO1 biofilm. J. Bacteriol. 186, 7312–7326 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Gjermansen, M. Ragas, P., Sternberg, C., Molin, S. & Tolker-Nielsen, T. Characterization of starvation-induced dispersion in Pseudomonas putida biofilms. Environ. Microbiol. 7, 894–906 (2005).

    Article  CAS  PubMed  Google Scholar 

  53. Kaplan, J. B. et al. Genes involved in the synthesis and degradation of matrix polysaccharide in Actinobacillus actinomycetemcomitans and Actinobacillus pleuropneumoniae biofilms. J. Bacteriol. 186, 8213–8220 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  54. Lynch, D. J., Fountain, T. L. & Mazurkiewicz, Banas, J. A. Glucan-binding proteins are essential for shaping Streptococcus mutans biofilm architecture. FEMS Microbiol. Lett. 268, 158–165 (2007).

    Article  CAS  PubMed  Google Scholar 

  55. Higgins, M. J. & Novak, J. T. Characterization of exocellular protein and its role in bioflocculation. J. Environ. Eng. (New York) 123, 479–485 (1997).

    Article  CAS  Google Scholar 

  56. Mora, P., Rosconi, F., Franco Fraguas, L. & Castro-Sowinski, S. Azospirillum brasilense Sp7 produces an outer-membrane lectin that specifically binds to surface-exposed extracellular polysaccharide produced by the bacterium. Arch. Microbiol. 189, 519–524 (2008).

    Article  CAS  PubMed  Google Scholar 

  57. Tielker, D. et al. Pseudomonas aeruginosa lectin LecB is located in the outer membrane and is involved in biofilm formation. Microbiology 151, 1313–1323 (2005).

    Article  CAS  PubMed  Google Scholar 

  58. Diggle, S. P. et al. The galactophilic lectin, LecA, contributes to biofilm development in Pseudomonas aeruginosa. Environ. Microbiol. 8, 1095–1104 (2006).

    Article  CAS  PubMed  Google Scholar 

  59. Johansson, E. M. V. et al. Inhibition and dispersion of Pseudomonas aeruginosa biofilms by glycopeptide dendrimers targeting the fucose-specific lectin LecB. Chem. Biol. 15, 1249–1257 (2008).

    Article  CAS  PubMed  Google Scholar 

  60. Lasa, I. & Penadés, J. R. Bap: a family of surface proteins involved in biofilm formation. Res. Microbiol. 157, 99–107 (2006). A description of the role of non-enzymatic proteins in the biofilm matrix.

    Article  CAS  PubMed  Google Scholar 

  61. Otzen, D. & Nielsen, P. H. We find them here, we find them there: functional bacterial amyloid. Cell. Mol. Life Sci. 65, 910–927 (2007).

    Article  CAS  Google Scholar 

  62. van Schaik, E. J. et al. DNA binding: a novel function of Pseudomonas aeruginosa type IV pili. J. Bacteriol. 187, 1455–1464 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  63. Izano, E. A., Amarante, M. A., Kher, W. B. & Kaplan, J. B. Differential roles of poly-N-acetylglucosamine surface polysaccharide and extracellular DNA in Staphylococcus aureus and Staphylococcus epidermidis biofilms. Appl. Environ. Microbiol. 74, 470–476 (2008).

    Article  CAS  PubMed  Google Scholar 

  64. Molin, S. & Tolker-Nielsen, T. Gene transfer occurs with enhanced efficiency in biofilms and induces enhanced stabilisation of the biofilm structure. Curr. Opin. Biotechnol. 14, 255–261 (2003).

    Article  CAS  PubMed  Google Scholar 

  65. Watanabe, M. et al. Growth and flocculation of a marine photosynthetic bacterium Rhodovulum sp. Appl. Microbiol. Biotechnol. 50, 682–691 (1998).

    Article  CAS  Google Scholar 

  66. Yang, L. et al. Effects of iron on DNA release and biofilm development by Pseudomonas aeruginosa. Microbiology 153, 1318–1328 (2007).

    Article  CAS  PubMed  Google Scholar 

  67. Whitchurch, C. B., Tolker-Nielsen, T., Ragas, P. S. & Mattick, J. S. Extracellular DNA required for bacterial biofilm formation. Science 295, 1487 (2002). The first report on the functional relevance of eDNA to biofilms.

    Article  CAS  PubMed  Google Scholar 

  68. Vilain, S., Pretorius, J. M., Theron J. & Broezel, V. S. DNA as an adhesion: Bacillus cereus requires extracellular DNA to form biofilms. Appl. Environ. Microbiol. 75, 2861–2868 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  69. Mulcahy, H., Charron-Mazenod, L. & Lewenza, S. Extracellular DNA chelates and induces antibiotic resistance in Pseudomonas aeruginosa biofilms. PLoS Pathog. 4, e1000213 (2008).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  70. Allesen-Holm, M. et al. A characterization of DNA release in Pseudomonas aeruginosa cultures and biofilms. Mol. Microbiol. 59, 1114–1128 (2006).

    Article  CAS  PubMed  Google Scholar 

  71. Böckelmann, U. et al. Bacterial extracellular DNA forming a defined network-like structure. FEMS Microbiol. Lett. 262, 31–38 (2006).

    Article  PubMed  CAS  Google Scholar 

  72. Jurcisek, J. A. & Bakaletz, L. O. Biofilms formed by nontypeable Haemophilus influenzae in vivo contain both double-stranded DNA and type IV pilin protein. J. Bacteriol. 189, 3868–3875 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  73. Steinberger, R. E. & Holden, P. A. Extracellular DNA in single- and multiple-species unsaturated biofilms. Appl. Environ. Microbiol. 71, 5404–5410 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  74. Neu, T. R. & Poralla, K. An amphiphilic polysaccharide from an adhesive Rhodococcus strain. FEMS Microbiol. Lett. 49, 389–392 (1988).

    Article  CAS  Google Scholar 

  75. Neu, T. R., Dengler, T., Jann, B. & Poralla, K. Structural studies of an emulsion-stabilizing exopolysaccharide produced by an adhesive, hydrophobic Rhodococcus strain. J. Gen. Microbiol. 138, 2531–2537 (1992).

    Article  CAS  PubMed  Google Scholar 

  76. Sand, W. & Gehrke, T. Extracellular polymeric substances mediate bioleaching/biocorrosion via interfacial processes involving iron(III) ions and acidophilic bacteria. Res. Microbiol. 157, 49–56 (2006).

    Article  CAS  PubMed  Google Scholar 

  77. Matsuyama, T. & Nakagawa, Y. Surface-active exolipids: analysis of absolute chemical structures and biological functions. J. Microbiol. Methods 25, 165–175 (1996).

    Article  CAS  Google Scholar 

  78. Ron, E. Z. & Rosenberg, E. Natural role of biosurfactants. Environ. Microbiol. 3, 229–236 (2001).

    Article  CAS  PubMed  Google Scholar 

  79. Neu, T. Significance of bacterial surface-active compounds in interactions of bacteria with interfaces. Microbiol. Rev. 60, 151–166 (1996). A valuable and comprehensive overview of the concept and ecological role of biosurfactants as part of the EPS matrix.

    CAS  PubMed  PubMed Central  Google Scholar 

  80. Panilaitis, B., Castro, G. R., Solaiman, D. & Kaplan, D. L. Biosynthesis of emulsan biopolymers from agro-based feedstocks. J. Appl. Microbiol. 102, 531–537 (2007).

    Article  CAS  PubMed  Google Scholar 

  81. Leck, C. & Bigg, E. K. Biogenic particles in the surface microlayer and overlaying atmosphere in the central Arctic Ocean during summer. Tellus B 57, 305–316 (2005).

    Article  Google Scholar 

  82. Davey, M. E., Cajazza, N. C. & O´Toole, G. A. Rhamnolipid surfactant production affects biofilm architecture in Pseudomonas aeruginosa PAO1. J. Bacteriol. 185, 1027–1036 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  83. Boles, B. R., Thoendel, M & Singh, P. K. Self-generated diversity produces “insurance effects” in biofilms communities Proc. Natl Acad. Sci. USA 101, 16630–16635 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  84. Pamp, S. J., Gjermansen, M. & Tolker-Nielsen, T. in The Biofilm Mode of Life. Mechanisms and Adaptations (eds Kjelleberg, S. & Givskov, M.) 37–69 (Horizon Bioscience, Norfolk, UK, 2007).

    Google Scholar 

  85. Or, D., Phutane, S. & Dechesne, A. Extracellular polymeric substances affecting pore-scale hydrologic conditions for bacterial activity in unsaturated soils. Vadose Zone J. 6, 298–305 (2007).

    Article  CAS  PubMed  Google Scholar 

  86. Tamaru, Y., Takami, Y., Yoshida, T. & Sakamoto, T. Crucial role of extracellular polysaccharides in desiccation and freezing tolerance in the terrestrial cyanobacterium Nostoc commune. Appl. Environ. Microbiol. 71, 7327–7333 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  87. Roberson, E. B., Firestone, M. K. Relationship between desiccation and exopolysaccharide production in a soil Pseudomonas sp. Appl. Environ. Microbiol. 58, 1284–1291 (1992).

    CAS  PubMed  PubMed Central  Google Scholar 

  88. Potts, M. Desiccation tolerance of prokaryotes. Microbiol. Rev. 58, 755–805 (1994).

    CAS  PubMed  PubMed Central  Google Scholar 

  89. Flemming, H.-C. & Leis, A. in Encyclopedia of Environmental Microbiology (ed. Bitton, G.) 2958–2967 (Wiley, New York, 2002).

    Google Scholar 

  90. Van Hullebusch, E. D., Zandvoord, M. H. & Lens, P. N. L. Metal immobilization by biofilms: mechanisms and analytical tools. Rev. Environ. Sci. Biotechnol. 2, 9–33 (2004).

    Article  Google Scholar 

  91. Wuertz, S. et al. A new method for extraction of extracellular polymeric substances from biofilms and activated sludge suitable for direct quantification of sorbed metals. Water Sci. Technol. 43, 25–34 (2001).

    Article  CAS  PubMed  Google Scholar 

  92. Schmitt, J., Nivens, D., White, D. C. & Flemming, H.-C. Changes of biofilm properties in response to sorbed substances — an FTIR-ATR-study. Water Sci. Technol. 32, 149–155 (1995).

    Article  CAS  Google Scholar 

  93. Stoodley, P., Cargo, R., Rupp, C. J., Wilson, S. & Klapper, I. Biofilm material properties as related to shear-induced deformation and detachment phenomena. J. Ind. Microbiol. Biotechnol. 29, 361–367 (2003). A seminal article about the measurement and ecological role of biofilm stability.

    Article  CAS  Google Scholar 

  94. Klausen, M. M., Thomsen, T. R., Nielsen, J. L., Mikkelsen, L. H. & Nielsen, P. H. Variations in microcolony strength of probe-defined bacteria in activated sludge flocs. FEMS Microbiol. Ecol. 50, 123–132 (2004).

    Article  CAS  PubMed  Google Scholar 

  95. Gerbersdorf, S. U., Jancke, T., Westrich, B. & Paterson, D. M. Microbial stabilization of riverine sediments by extracellular polymeric substances. Geobiology 6, 57–69 (2008).

    CAS  PubMed  Google Scholar 

  96. Jaeger-Zuern, I. & Gruberg, M. Podostemaceae depend on sticky biofilms with respect to attachment to rocks in waterfalls. Int. J. Plant Sci. 161, 599–607 (2000).

    Article  Google Scholar 

  97. Rupp, C. J., Fux, C. A. & Stoodley, P. Viscoelasticity of Staphylococcus aureus biofilms in response to fluid shear allows resistance to detachment and facilitates rolling migration. Appl. Environ. Microbiol. 71, 2175–2178 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  98. Shaw, T., Winston, M., Rupp, C. J., Klapper, I. & Stoodley, P. Commonality of elastic relaxation times in biofilms. Phys. Rev. Let. 93, 098102 (2004).

    Article  CAS  Google Scholar 

  99. Hohne, D. N., Younger, G. J. & Solomon, M. J. Flexible multifluidic device for mechanical property characterization of soft viscoelastic solids such as bacterial biofilms. Langmuir 25, 7743–7751 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  100. Webb, J. et al. Cell death in Pseudomonas aeruginosa biofilm development. J. Bacteriol. 185, 4585–4592 (2003). A thorough discussion of the dynamics of the EPS matrix and the concept of a microbial analogue to programmed cell death that leads to alterations of the matrix architecture.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  101. Borlee, B. R. et al. Pseudomonas aeruginosa uses a cyclic-di-GMP-regulated adhesin to reinforce the biofilm extracellular matrix. Mol. Microbiol. 75, 827–842 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  102. De Kievit, T. R. Quorum sensing in Pseudomonas aeruginosa biofilms. Environ. Microbiol. 11, 279–288 (2009).

    Article  CAS  PubMed  Google Scholar 

  103. Cooksey, K. E. & Wigglesworth-Cooksey, B. in Encyclopedia of Environmental Microbiology (ed. Bitton, G.) 1051–1063 (Wiley, New York, 2002).

    Google Scholar 

  104. de Brouwer, J. F. C., Wolfstein, K., Ruddy, G. K., Jones, T. E. R. & Stal, L. J. Biogenic stabilization of intertidal sediments: the importance of extracellular polymeric substances produced by benthic diatoms. Microbiol. Ecol. 49, 501–512 (2005).

    Article  CAS  Google Scholar 

  105. Dade, W. B. et al. Effects of bacterial exopolymer adhesion on the entrainment of sand. Geomicrobiol. J. 8, 1–16 (1990).

    Article  Google Scholar 

  106. Domozych, D. S., Kort, S., Benton, S. & Yu, T. The extracellular polymeric substance of the green alga Penium margaritaceum and its role in biofilm formation. Biofilms 2, 129–144 (2005).

    Article  Google Scholar 

  107. Baillie, G. S. & Douglas, L. J. Matrix polymers of Candida biofilms and their possible role in biofilm resistance to antifungal agents. J. Antimicrob. Chemother. 46, 397–403 (2000).

    Article  CAS  PubMed  Google Scholar 

  108. Chandra, J. et al. Biofilm formation by the fungal pathogen Candida albicans: development, architecture, and drug resistance. J. Bacteriol. 183, 5385–5394 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  109. Verstrepen, K. J. & Klis, F. M. Flocculation, adhesion and biofilm formation in yeasts. Mol. Microbiol. 60, 5–15 (2006).

    Article  CAS  PubMed  Google Scholar 

  110. Zolghadr, B. et al. Appendage-mediated surface adherence of Sulfolobus solfataricus. J. Bacteriol. 192, 104–110 (2009).

    Article  PubMed Central  CAS  Google Scholar 

  111. Wrangstadh, M., Szewzyk, U., Östling, J. & Kjelleberg, S. Starvation-specific formation of peripheral exopolysaccharide by a marine Pseudomonas sp., strain S9. Appl. Environ. Microbiol. 56, 2065–2072 (1990).

    CAS  PubMed  PubMed Central  Google Scholar 

  112. Neu, T. R., Lawrence, J. R. in Microbial Extracellular Polymeric Substances (eds Wingender, J., Neu, T. & Flemming, H.-C.) 22–47 (Springer, Heidelberg, 1999).

    Google Scholar 

  113. Dow, J. M. et al. Biofilm dispersal in Xanthomonas campestris is controlled by cell–cell signalling and is required for full virulence to plants. Proc. Natl Acad. Sci. USA 100, 10995–11000 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  114. Davies, D. G. & Marques, C. N. H. A fatty acid messenger is responsible for inducing dispersion in microbial biofilms. J. Bacteriol. 191, 1393–1403 (2009).

    Article  CAS  PubMed  Google Scholar 

  115. Kolodkin-Gal, I. et al. D-amino acids trigger biofilm disassembly. Science 328, 627–629 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  116. Tait, K., Skillman, L. C. & Sutherland, I. W. The efficacy of bacteriophage as a method of biofilm eradication. Biofouling 18, 305–311 (2002).

    Article  Google Scholar 

  117. Nardini, M., Lang, D. M., Liebeton, K., Jaeger, K.-E. & Dijkstra, B. W. Crystal structure of Pseudomonas aeruginosa lipase in the open conformation. The prototype for family i.1 of bacterial lipases. J. Biol. Chem. 275, 31219–31225 (2000).

    Article  CAS  PubMed  Google Scholar 

  118. Grobe, S., Wingender, J., Trüper, H. G. Characterization of mucoid Pseudomonas aeruginosa strains isolated from technical water systems. J. Appl. Bacteriol. 79, 94–102 (1995).

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

We are grateful for the inspiring cooperation with partners in the research group on 'Physico-chemistry of Biofilms': W. Borchard, K.-E. Jaeger, H. Kuhn, C. Mayer and W. Veeman. We also acknowledge financial support by the German Research Foundation to various EPS research projects. Furthermore, constructive, critical and stimulating comments and discussions with I. Sutherland are highly appreciated.

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Protein Data Bank

Glossary

Biofilm

A loose definition for microbial aggregates that usually accumulate at a solid–liquid interface and are encased in a matrix of highly hydrated EPS. Included in this definition are cell aggregates such as flocs (floating biofilms) and sludge, which are not attached to an interface but which share the characteristics of biofilms. Multispecies biofilms can form stable microconsortia, develop physiochemical gradients, and undergo horizontal gene transfer and intense cell–cell communication, and these consortia therefore represent highly competitive environments.

Extracellular polymeric substances

Hydrated biopolymers (including polysaccharides, proteins, nucleic acids and lipids) that are secreted by biofilm cells to encase and immobilize microbial aggregates. These biopolymers are responsible for the macroscopic appearance of biofilms, which are frequently referred to as 'slime'.

Humic substance

A component of the natural organic matter in soil and water enviroments. Humic substances are mixtures of compounds that are formed by limited degradation and transformation of dead organic matter and that are resistant to complete biodegradation. They can be divided into three main fractions: humic acids, fulvic acids and humin. They usually include phenolic and polyaromatic compounds (containing peptide and carbohydrate moieties with carboxylic substituents), providing the acidic character.

Flagellum

A long, thin, helically shaped bacterial appendage that provides motility. A flagellum consists of several components and moves by rotation, much like a propeller. The motor is anchored in the cytoplasmic membrane and the cell wall.

Pilus

A bacterial surface structure that is similar to a fimbria but is typically a longer structure, and that is present on the cell surface in one or two copies. Pili can be receptors for bacteriophages and also facilitate genetic exchange between bacterial cells during conjugation. Type IV pili mediate twitching motility, which is a flagella-independent form of bacterial translocation over surfaces, and can be involved in biofilm development.

Fimbria

A filamentous structure composed of one or a few proteins that extends from the surface of a cell and can have diverse functions. Fimbriae are involved in attachment to both animate and inanimate surfaces and in the formation of pellicles and biofilms. They assist in the disease process of some pathogens, such as S. enterica, Neisseria gonorrhoea and Bordetella pertussis.

Membrane vesicle

A vesicle that is formed from the outer membrane of Gram-negative bacteria, is secreted from the cell surface and contains extracellular enzymes and nucleic acids. These vesicles may represent mobile elements in the EPS matrix.

Capsule

A discrete polysaccharide (sometimes also protein) layer that is firmly attached to the surface of a bacterial cell, closely surrounding it, in contrast to less compact, amorphous slime that is shed into the more distant extracellular environment.

Lectin

A protein or glycoprotein of plant, animal or microbial origin that binds to carbohydrates with a characteristic specificity. Fluorescently labelled lectins can be used as probes to investigate EPS composition, enabling the microscopic in situ detection of EPS and their distribution in biofilms.

Raman microscopy

A spectroscopic technique based on inelastic light scattering (Raman scattering) of monochromatic laser light in the near-ultraviolet range, revealing vibrational, rotational and other low-frequency modes in a system. The technique is used for the analysis of chemical bonds and is suitable for very small volumes, allowing spectra and chemical information to be obtained for the molecules present in that volume.

Matrix void

A pore or channel in the biofilm matrix that contains liquid water and is not filled with hydrated EPS molecules.

Stromatolite

A laminated microbial mat that is typically built from layers of filamentous cyanobacteria and other microorganisms that become fossilized. Stromatolites are the oldest records of life on Earth, dating back 3.5 billion years.

Surface-active property

The ability of a molecule to alter the interface of two different phases. Substances with surface-active properties (surfactants) are amphipatic molecules with both hydrophilic and hydrophobic (generally hydrocarbon) moieties. They partition preferentially at the interface between fluid phases with different degrees of polarity and hydrogen bonding, such as oil–water interfaces.

Biosurfactant

A substance that is synthesized by living cells (mostly bacteria and yeasts) and that is surface active. Biosurfactants reduce surface tension, stabilize emulsions, promote foaming and are generally non-toxic and biodegradable. When grown on hydrocarbon substrates as a carbon source, microorganisms can synthesize a wide range of biosurfactants, such as glycolipids and phospholipids. These chemicals are apparently synthesized to emulsify the hydrocarbon substrate and facilitate its transport into the cells. In some bacterial species, such as P. aeruginosa, biosurfactants are also involved in a group movement behaviour called swarming motility.

Hydraulic decoupling

The formation of areas that have virtually no exchange of water content with their environment. An example is a desiccated EPS layer that covers an area with a high water content but has very low water transport through the layer, retaining the water underneath.

Elasticity modulus

The tendency of an object or material to reversibly develop an elastic force in response to deformation. Mathematically, the elasticity modulus is the proportionality factor between the force and the deformation, or, in other words, the slope on a plot of stress versus strain in the elastic deformation region. Stiff materials have a higher elasticity modulus, whereas soft materials have a lower one.

Stress relaxation

A deviation from the ideal elastic behaviour of a material due to an internal relief of stress under constant strain. Some materials, when put under mechanical tension, undergo internal flow processes (termed 'creep') that are at least partially irreversible and lead to a constant deformation of the test specimen.

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Flemming, HC., Wingender, J. The biofilm matrix. Nat Rev Microbiol 8, 623–633 (2010). https://doi.org/10.1038/nrmicro2415

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