Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Review Article
  • Published:

Biofilms: an emergent form of bacterial life

Nature Reviews Microbiology volume 14, pages 563–575 (2016)Cite this article

Subjects

Key Points

  • Bacterial biofilms can be considered to be an emergent form of bacterial life, in which communal life is completely different from bacteria that live as free-living cells.

  • Emergent properties of bacterial biofilms include social cooperation, resource capture and enhanced survival following exposure to antimicrobials, and cannot be understood and predicted through the study of free-living bacterial cells.

  • The physical scaffold of biofilm life is the matrix of extracellular polymeric substances (EPS) that keeps cells in the biofilm together and attaches them to substrata when colonizing surfaces. The matrix underlies the emergent properties of biofilms.

  • The emergent properties of the biofilm are the reason for the evolutionary success of biofilms and underlie the role of biofilms as global habitat formers.

Abstract

Bacterial biofilms are formed by communities that are embedded in a self-produced matrix of extracellular polymeric substances (EPS). Importantly, bacteria in biofilms exhibit a set of 'emergent properties' that differ substantially from free-living bacterial cells. In this Review, we consider the fundamental role of the biofilm matrix in establishing the emergent properties of biofilms, describing how the characteristic features of biofilms — such as social cooperation, resource capture and enhanced survival of exposure to antimicrobials — all rely on the structural and functional properties of the matrix. Finally, we highlight the value of an ecological perspective in the study of the emergent properties of biofilms, which enables an appreciation of the ecological success of biofilms as habitat formers and, more generally, as a bacterial lifestyle.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Emergent properties of biofilms and habitat formation.
Figure 2: Physical and chemical properties of the biofilm matrix.
Figure 3: Biofilms are characterized by heterogeneity and social interactions.
Figure 4: Tolerance of, and resistance to, antimicrobials.

Similar content being viewed by others

References

  1. Vert, M. et al. Terminology for biorelated polymers and applications (IUPAC Recommendations 2012). Pure Appl. Chem. 84, 377–410 (2012).

    Article  CAS  Google Scholar 

  2. Konopka, A. What is microbial community ecology? ISME J. 3, 1223–1230 (2009).

    Article  PubMed  Google Scholar 

  3. Stoodley, P., Davies, D. G. & Costerton, J. W. Biofilms as complex differentiated communities. Annu. Rev. Microbiol. 56, 187–209 (2002).

    Article  CAS  PubMed  Google Scholar 

  4. Ehrlich, H. L. & Newman, D. K. Geomicrobiology 5th edn (CRC press, 2008).

    Book  Google Scholar 

  5. Meckenstock, R. et al. Biodegradation: updating the concepts of control for microbial cleanup in contaminated aquifers. Environ. Sci. Technol. 49, 7073–7081 (2015).

    Article  CAS  PubMed  Google Scholar 

  6. Halan, B., Bühler, K. & Schmid, A. Biofilms as living catalysts in continuous chemical syntheses. Trends Biotechnol. 30, 453–465 (2012).

    Article  CAS  PubMed  Google Scholar 

  7. De Vos, W. M. Microbial biofilms and the human intestinal microbiome. NPJ Biofilms Microbiomes 1, 15005 (2015).

    Article  PubMed  PubMed Central  Google Scholar 

  8. Costerton, J. W. et al. Bacterial biofilms in nature and disease. Annu. Rev. Microbiol. 41, 435–464 (1987).

    Article  CAS  PubMed  Google Scholar 

  9. Shirtliff, M. & Leid, J. (eds) The Role of Biofilms in Device-Related Infections (Springer, 2009).

    Book  Google Scholar 

  10. Flemming, H.-C. in Biofilm Highlights (eds Flemming, H.-C., Wingender, J. & Szewzyk, U.) 81–109 (Springer, 2011).

    Book  Google Scholar 

  11. Wingender, J. & Flemming, H.-C. Biofilms in drinking water and their role as reservoir for pathogens. Int. J. Hyg. Environ. Health 214, 417–423 (2011).

    Article  PubMed  Google Scholar 

  12. Little, B. J. & Lee, J. S. Microbiologically influenced corrosion: an update. Int. Mat. Rev. 59, 384–393 (2014).

    Article  CAS  Google Scholar 

  13. Balzer, M., Witt, N., Flemming, H.-C. & Wingender, J. Accumulation of fecal indicator bacteria in river biofilms. Water Sci. Technol. 61, 1105–1111 (2010).

    Article  CAS  PubMed  Google Scholar 

  14. Morgan-Sastume, F., Larsen, P., Nielsen, J. L. & Nielsen, P. H. Characterization of the loosely attached fraction of activated sludge bacteria. Water Res. 42, 843–854 (2008).

    Article  CAS  Google Scholar 

  15. Singer, S. W. et al. Posttranslational modification and sequence variation of redox-active proteins correlate with biofilm life cycle in natural microbial communities. ISME J. 4, 1348–1409 (2010).

    Article  CAS  Google Scholar 

  16. Corning, P. A. The re-emergence of “emergence”: a venerable concept in search of a theory. Complexity 7, 18–30 (2002).

    Article  Google Scholar 

  17. Flemming, H.-C. & Wingender, J. The biofilm matrix. Nat. Rev. Microbiol. 8, 623–633 (2010).

    Article  CAS  PubMed  Google Scholar 

  18. Saville, R. M. et al. Energy-dependent stability of Shewanella oneidensis MR-1 biofilms. J. Bacteriol. 193, 3257–3264 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Neu, T. R. & Lawrence, J. R. Innovative techniques, sensors, and approaches for imaging biofilms at different scales. Trends Microbiol. 23, 233–242 (2014).

    Article  CAS  Google Scholar 

  20. Serra, D. O., Richter, A. M., Klauck, G., Mika, F. & Hengge, R. Cellulose as an architectural element in spatially structured Escherichia coli biofilms. J. Bacteriol. 195, 5540–5554 (2013). A paper that highlights the important and underestimated role of cellulose for biofilm architecture.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Birjiniuk, A. et al. Single particle tracking reveals spatial and dynamic organization of the Escherichia coli biofilm matrix. New J. Phys. 16, 085014 (2014).

    Article  PubMed  PubMed Central  Google Scholar 

  22. Persat, A. et al.: The mechanical world of bacteria. Cell 161, 988–997 (2005).

    Article  CAS  Google Scholar 

  23. Jennings, L. K. et al. Pel is a cationic exopolysaccharide that cross-links extracellular DNA in the Pseudomonas aeruginosa biofilm matrix. Proc. Natl Acad. Sci. USA 112, 11353–11358 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Devaraj, A., Justice, S. S., Bakaletz, L. O. & Goodman, S. D. DNABII proteins play a central role in UPEC biofilm structure. Mol. Microbiol. 96, 1119–1135 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  26. Hobley, L., Harkins, C., MacPhee, C. E. & Stanley-Wall, N. R. Giving structure to the biofilm matrix: an overview of individual strategies and emerging common themes. FEMS Microbiol. Rev. 39, 649–669 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Karimi, A., Karig, D., Kumar, A. & Ardekani, A. M. Interplay of physical mechanisms and biofilm processes: review of microfluidic methods. Lab Chip 15, 23–42 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Wilking, J. N. et al. Liquid transport facilitated by channels in Bacillus subtilis. Proc. Natl Acad. Sci. USA 110, 848–852 (2013).

    Article  PubMed  Google Scholar 

  29. Patel, R. Biofilms and antimicrobial resistance. Clin. Orthop. Relat. Res. 437, 41–47 (2005).

    Article  Google Scholar 

  30. Lovley, D. R. & Malvankar, N. S. Seeing is believing: novel imaging techniques help clarify microbial nanowire structure and function. Environ. Microbiol, 17, 2209–2215 (2015).

    Article  CAS  Google Scholar 

  31. Koch, C. et al. Coupling electric energy and biogas production in anaerobic digesters — impact on the microbiome. RSC Adv. 5, 31329–31340 (2015).

    Article  CAS  Google Scholar 

  32. Secor, P. R. et al. Filamentous bacteriophage promote biofilm assembly and function. Cell Host Microbe 18, 1–11 (2015).

    Article  CAS  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Billings, N., Birjiniuk, A., Samad, T. S., Doyle, P. S. & Ribbeck, K. Material properties of biofilms — a review of methods for understanding permeability and mechanics. Rep. Prog. Phys. 78, 036601 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Raymond, J. & Alsop, E. B. Microbial evolution in extreme environments: microbial migration, genomic highways, and geochemical barriers in hydrothermal ecosystems. Environ. Syst. Res. 4, 14 (2015).

    Article  Google Scholar 

  36. Van Gestel, J., Vlamakis, H. & Kolter, R. From cell differentiation to cell collectives: Bacillus subtilis uses division of labor to migrate. PLoS Biol. 13, e1002141 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Houry, A. et al. Bacterial swimmers that infiltrate and take over the biofilm matrix. Proc. Natl Acad. Sci. USA 109, 13088–13093 (2012). A report of surprisingly fast tunnelling movement of some microorganisms in the biofilm matrix, and an investigation of the consequences of this movement.

    Article  PubMed  PubMed Central  Google Scholar 

  38. Petrova, O. E. & Sauer, K. Escaping the biofilm in more than one way: desorption, detachment or dispersion. Curr. Opin. Microbiol. 30, 67–78 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Whitfield, G. B., Marmont, L. S. & Howell, P. L. Enzymatic modifications of exopolysaccharides enhance bacterial persistence. Front. Microbiol. 6, 471 (2015).

    Article  PubMed  PubMed Central  Google Scholar 

  40. Helm, R. F. & Potts, M. in Ecology of Cyanobacteria II: Their Diversity in Space and Time (ed Whitton, B. A.) 461–480 (Springer, 2012).

    Book  Google Scholar 

  41. Flemming, H.-C. The perfect slime. Colloids Surf. B. Biointerfaces 86, 251–259 (2011).

    Article  CAS  PubMed  Google Scholar 

  42. Weaver, L., Webber, J. B., Hickson, A. C., Abraham, P. M. & Close, M. E. Biofilm resilience to desiccation in groundwater aquifers: a laboratory and field study. Sci. Total Environ. 514, 281–289 (2015).

    Article  CAS  PubMed  Google Scholar 

  43. Flemming, H.-C. Biodeterioration of synthetic materials — a brief review. Mat. Corr. 61, 986–992 (2010).

    Article  CAS  Google Scholar 

  44. Flemming, H.-C. & Leis, A. in Encyclopedia of Environmental Microbiology Vol. 5 (ed. Bitton, G.) 2958–2967 (Wiley-Interscience, 2002).

    Google Scholar 

  45. Battin, T. J., Besemer, K., Bengtsson, M. M., Romani, A. M. & Packmann, A. I. The ecology and biogeochemistry of stream biofilms. Nat. Rev. Microbiol. 14, 251–263 (2016).

    Article  CAS  PubMed  Google Scholar 

  46. Métevier, R., Bourven, I., Labanowski, J. & Guibaud, G. Interaction of erythromycin ethylsuccinate and acetaminophen with protein fraction of extracellular polymeric substances (EPS) from various bacterial aggregates. Environ. Sci. Pollut. Res. Int. 20, 7275–7285 (2013).

    Article  CAS  Google Scholar 

  47. Dobor, J., Varga, M. & Záray, G. Biofilm controlled sorption of selected acidic drugs on river sediments characterized by different organic carbon content. Chemosphere 87, 105–110 (2012).

    Article  CAS  PubMed  Google Scholar 

  48. Writer, J. H., Barber, L. B., Ryan, J. N. & Bradley, P. M. Biodegradation and attenuation of steroidal hormones and alkylphenols by stream biofilms and sediments. Environ. Sci. Technol. 45, 4370–4376 (2011).

    Article  CAS  PubMed  Google Scholar 

  49. Späth, R., Flemming, H.-C. & Wuertz, S. Sorption properties of biofilms. Water Sci. Technol. 37, 207–210 (1998).

    Article  Google Scholar 

  50. 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 

  51. Mark Welch, J. L., Rossetti, B. J., Rieken, C. W., Dewhirst, F. E. & Borisky, G. G. Biogeography of a human oral microbiome at the micron scale. Proc. Natl Acad. Sci. USA 113, E791–E800 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. López, D., Vlamakis, H. & Kolter, R. Cannibalism enhances biofilm development in Bacillus subtilis. Mol. Microbiol. 74, 609–618 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Pinchuk, G. E. et al. Utilization of DNA as a sole source of phosphorus, carbon, and energy by Shewanella spp.: ecological and physiological implications for dissimilatory metal reduction. Appl. Environ. Microbiol. 74, 1198–1208 (2008).

    Article  CAS  PubMed  Google Scholar 

  54. Mulcahy, H., Charron-Mazenod, L. & Lewenza, S. Pseudomonas aeruginosa produces an extracellular deoxyribonuclease that is required for utilization of DNA as a nutrient source. Environ. Microbiol. 12, 1621–1629 (2010).

    CAS  PubMed  Google Scholar 

  55. Kaplan, J. B. in Microbial Biofilms: Methods and Protocols (ed Donelli, G.) 203–213 (Springer, 2014).

    Book  Google Scholar 

  56. Zrelli, K. et al. Bacterial biofilm mechanical properties persist upon antibiotic treatment and survive cell death. New J. Phys. 15, 125026 (2013).

    Article  CAS  Google Scholar 

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

    Google Scholar 

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

    Article  PubMed  Google Scholar 

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

    Book  Google Scholar 

  60. Oppenheimer-Shaanan, Y. et al. Spatio-temporal assembly of functional mineral scaffolds within microbial biofilms. NPJ Biofilms Microbiomes 2, 15031 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  61. Decho, A. W. Overview of biopolymer-induced mineralization: what goes on in biofilms? Ecol. Eng. 36, 137–144 (2010).

    Article  Google Scholar 

  62. Braun, B., Richert, I. & Szewzyk, U. Detection of iron-depositing Pedomicrobium species in native biofilms from the Odertal National Park by a new, specific FISH probe. J. Microbiol. Methods 79, 37–43 (2009).

    Article  CAS  PubMed  Google Scholar 

  63. Grumbein, S., Opitz, M. & Lieleg, O. Selected metal ions protect Bacillus subtilis biofilms from erosion. Metallomics 6, 1441–1450 (2014).

    Article  CAS  PubMed  Google Scholar 

  64. Cao, B., Ahmed, B. & Beyenal, H. in Emerging Environmental Technologies Vol. 2 (ed Shah, V.) 1–37 (Springer, 2010).

    Google Scholar 

  65. Hammaini, A., Gonzalez, F., Ballester, A., Bláquez, M. L. & Muñoz, J. A. Biosorption of heavy metals by activated sludge and their desorption characteristics. J. Environ. Manage. 84, 419–426 (2007).

    Article  CAS  PubMed  Google Scholar 

  66. Henze, M., van Loosdrechte, M., Ekama, G. A. & Brdjanovic, D. (eds) Biological Wastewater Treatment: Principles, Modelling and Design (IWA Publishing, 2008).

  67. Okabe, S., Yasuda, T. & Watanabe, Y. Uptake and release of inert fluorescent particles by mixed population biofilms. Biotechnol. Bioeng. 53, 459–469 (1997).

    Article  CAS  PubMed  Google Scholar 

  68. Kouzuma, A., Kato, S. & Watanabe, K. Microbial interspecies interactions: recent findings in syntrophic consortia. Front. Microbiol. 6, 477 (2015).

    PubMed  PubMed Central  Google Scholar 

  69. Ikuma, K., Decho, A. W. & Lau, B. L. When nanoparticles meet biofilms — interactions guiding the environmental fate and accumulation of nanoparticles. Front. Microbiol. 6, 591 (2015).

    Article  PubMed  PubMed Central  Google Scholar 

  70. Tielen, P. et al. Interaction between extracellular lipase LipA and the polysaccharide alginate of Pseudomonas aeruginosa. BMC Microbiol. 159, 221–228 (2013).

    Google Scholar 

  71. Zobell, C. The effect of solid surfaces upon bacterial activity. J. Bacteriol. 46, 39–56 (1943).

    CAS  PubMed  PubMed Central  Google Scholar 

  72. Wingender, J. & Jaeger, K.-E. in Encyclopedia of Environmental Microbiology Vol. 3 (ed. Bitton, G.) 1207–1223 (Wiley-Interscience, 2002).

    Google Scholar 

  73. Burns, R. G. Enzyme activity in soil: location and possible role in microbial ecology. Soil Biol. Biochem. 15, 423–427 (1982).

    Article  Google Scholar 

  74. Lock, M. A., Wallace, R. R., Costerton, J. W., Ventullo, R. M. & Charlton, S. E. River epilithon: toward a structural–functional model. Oikos 42, 10–22 (1984).

    Article  Google Scholar 

  75. Toyofuku, M., Roschitzki, B., Riedel, K. & Eberl, L. Identification of proteins associated with the Pseudomonas aeruginosa biofilom extracellular matrix. J. Proteome Res. 11, 4906–4915 (2012).

    Article  CAS  PubMed  Google Scholar 

  76. Zhang, W. et al. Extracellular matrix-associated proteins form an integral and dynamic system during Pseudomonas aeruginosa biofilm development. Front. Cell. Infect. Microbiol. 5, 40 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  77. Worm, J., Jensen, L. E., Hansen, T. S., Søndergaard, M. & Nybroe, O. Interactions between proteolytic and non-proteolytic Pseudomonas fluorescens affect protein degradation in a model community. FEMS Microbiol. Ecol. 32, 103–109 (2000).

    Article  CAS  PubMed  Google Scholar 

  78. Smucker, R. A. & Kim, C. K. in Microbial Enzymes in Aquatic Environments (ed Chróst, R. J.) 249–269 (Springer–Verlag,1991).

    Book  Google Scholar 

  79. Chang, Y.-W. et al. Biofilm formation in geometries with different surface curvature and oxygen availability. New J. Phys. 17, 033017 (2015).

    Article  CAS  Google Scholar 

  80. Kalmbach, S., Manz, W. & Szewzyk, U. Isolation of new bacterial species from drinking water biofilms and proof of their in situ dominance with highly specific 16S rRNA probes. Appl. Environ. Microbiol. 63, 4164–4170 (1997).

    CAS  PubMed  PubMed Central  Google Scholar 

  81. Boles, B. R., Thoendel, M. & Singh, P. K. Self-generated diversity produces “insurance effects” in biofilm communities. Proc. Natl Acad. Sci. USA 101, 16630–16635 (2004). This paper reports the important finding that, unlike their planktonic counterparts, individual cells in the biofilm develop clearly distinct phenotypes after 1–2 days, even for biofilms that are formed by monoclonal organisms.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  82. Von Ohle, C. et al. Real-time microsensor measurement of local metabolic activities in ex vivo dental biofilms exposed to sucrose and treated with chlorhexidine. Appl. Environ. Microbiol. 76, 2326–2334 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  83. Kragh, K. N. et al. Role of multicellular aggregates in biofilm formation. mBio 7, e00237-16 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  84. Ward, D. M. et al. Genomics, environmental genomics and the issue of microbial species. Heredity 100, 207–219 (2008).

    Article  CAS  PubMed  Google Scholar 

  85. Neu, T. R. & Lawrence, J. R. Advanced techniques for in situ analysis of the biofilm matrix (structure, composition, dynamics) by means of laser scanning microscopy. Methods Mol. Biol. 1147, 43–64 (2015).

    Article  CAS  Google Scholar 

  86. Parsek, M. R. & Greenberg, E. P. Sociomicrobiology: the connections between quorum sensing and biofilms. Trends Microbiol. 13, 27–33 (2005).

    Article  CAS  PubMed  Google Scholar 

  87. West, S. A., Griffin, A. S., Gardner, A. & Diggle, S. P. Social evolution theory for microorganisms. Nat. Rev. Microbiol. 4, 597–607 (2006).

    Article  CAS  PubMed  Google Scholar 

  88. Fredrickson, J. K. Ecological communities by design. Science 348, 1425–1427 (2015).

    Article  CAS  PubMed  Google Scholar 

  89. Zelezniak, A. et al. Metabolic dependencies drive species co-occurrence in diverse microbial communities. Proc. Natl Acad. Sci. USA 112, 6449–6454 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  90. Elias, S. & Banin, E. Multi-species biofilms: living with friendly neighbours. FEMS Microbiol. Rev. 36, 990–1004 (2012).

    Article  CAS  PubMed  Google Scholar 

  91. Koch, H. et al. Expanded metabolic versatility of ubiquitous nitrite-oxidizing bacteria from the genus Nitrospira. Proc. Natl Acad. Sci. USA 112, 11371–11376 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  92. Gorbushina, A. A. & Broughton, W. J. Microbiology of the atmosphere–rock interface: how biological reactions and physical stress modulate a sophisticated microbial ecosystem. Annu. Rev. Microbiol. 63, 431–450 (2009).

    Article  CAS  PubMed  Google Scholar 

  93. Lee, K. W. et al. Biofilm development and enhanced stress resistance of a model, mixed species community biofilm. ISME J. 8, 894–907 (2014).

    Article  CAS  PubMed  Google Scholar 

  94. Breugelmans, P. et al. Architecture and spatial organization in a triple-species bacterial biofilm synergistically degrading the phenylurea herbicide linuron. FEMS Microbiol. Ecol. 64, 271–282 (2008).

    Article  CAS  PubMed  Google Scholar 

  95. Hansen, S. K., Rainey, P. B., Haagensen, J. A. & Molin, S. Evolution of species interactions in a biofilm community. Nature 445, 533–536 (2007).

    Article  CAS  PubMed  Google Scholar 

  96. Ren, D., Madsen, J. S., Sørensen, S. & Burmølle, M. High prevalence of biofilm synergy among bacterial soil isolates in cocultures indicates bacterial interspecific cooperation. ISME J. 9, 81–89 (2015).

    Article  CAS  PubMed  Google Scholar 

  97. Burmølle, M., Ren, D., Bjarnsholt, T. & Soerensen, S. J. Interactions in multispecies biofilms: do they actually matter? Trends Microbiol. 22, 84–90 (2014).

    Article  CAS  PubMed  Google Scholar 

  98. Foster, K. R. & Bell, T. Competition, not cooperation dominates interactions among microbial species. Curr. Biol. 19, 1845–1850 (2012).

    Article  CAS  Google Scholar 

  99. Rendueles, O. & Ghigo, J.-M. Mechanisms of competition in biofilm communities. Microbiol. Spectr. 3, MB-0009-2014 (2015).

    Article  Google Scholar 

  100. McIntyre, D. L., Miyata, S. T., Kitaoka, M. & Pukazki, S. The Vibrio cholera type VI secretion system displays antimicrobial properties. Proc. Natl Acad. Sci. USA 107, 19520–19524 (2010).

    Article  Google Scholar 

  101. Brauner, A., Fridman, O., Gefen, O. & Balaban, N. Distinguishing between resistance, tolerance and persistence to antibiotic treatment. Nat. Rev. Microbiol. 14, 320–330 (2016).

    Article  CAS  PubMed  Google Scholar 

  102. Olsen, I. Biofilm-specific antibiotic tolerance and resistance. Eur. J. Clin. Microbiol. Infect. Dis. 34, 877–886 (2015).

    Article  CAS  PubMed  Google Scholar 

  103. Thuptimdang, P., Limpiyakorn, T., McEvoy, J., Prüß, B. M. & Khan, E. Effect of silver nanoparticles on Pseudomonas putida biofilms at different stages of maturity. J. Hazard. Mater. 290, 127–133 (2015).

    Article  CAS  PubMed  Google Scholar 

  104. Königs, A. M., Flemming, H.-C. & Wingender, J. Nanosilver induces a non-culturable but metabolically active state in Pseudomonas aeruginosa. Front. Microbiol. 6, 395 (2015).

    Article  PubMed  PubMed Central  Google Scholar 

  105. Oubekka, S. D., Briandet, R., Fontaine-Aupart, M.-P. & Steenkeste, K. Correlative time-resolved fluorescence microscopy to assess antibiotic diffusion-reaction in biofilms. Antimicrob. Agents Chemother. 56, 3349–3358 (2012). A paper that studies, in detail, the interactions between antibiotics and EPS components.

    Article  CAS  Google Scholar 

  106. Ordax, M., Marco-Noales, E., López, M. M. & Biscoa, E. G. Exopolysaccharides favor the survival of Erwinia amylovora under copper stress through different strategies. Res. Microbiol. 161, 549–555 (2010).

    Article  CAS  PubMed  Google Scholar 

  107. Harrison, J., Ceri, H. & Turner, R. J. Multimetal resistance and tolerance in microbial biofilms. Nat. Rev. Microbiol. 5, 928–939 (2007).

    Article  CAS  PubMed  Google Scholar 

  108. Khan, W. et al. Aminoglycoside resistance of Pseudomonas aeruginosa biofilms modulated by extracellular polysaccharide. Int. Microbiol. 13, 207–212 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  109. Fux, C. A., Costerton, J. W., Stewart, P. S. & Stoodley, P. Survival strategies of infectious biofilms. Trends Microbiol. 13, 34–40 (2005).

    Article  CAS  PubMed  Google Scholar 

  110. Brown, M. R., Allison, D. G. & Gilbert, P. Resistance of bacterial biofilms: a growth-related effect? J. Antimicrob. Chemother. 22, 777–783 (1988).

    Article  CAS  PubMed  Google Scholar 

  111. Amato, S. M. et al. The role of metabolism in bacterial persistence. Front. Microbiol. 5, 70 (2014).

    Article  PubMed  PubMed Central  Google Scholar 

  112. Maisonneuve, E. & Gerdes, K. Molecular mechanisms underlying bacterial persisters. Cell 157, 539–548 (2014).

    Article  CAS  PubMed  Google Scholar 

  113. Monzón, M., Oteiza, C., Leiva, J., Lamata, M. & Amorena, B. Biofilm testing of Staphylococcus epidermidis clinical isolates: low performance of vancomycin in relation to other antibiotics. Diagn. Microbiol. Infect. Dis. 44, 319–324 (2002).

    Article  PubMed  Google Scholar 

  114. Li, L., Mendis, N., Trigui, H., Oliver, J. D. & Faucher, S. P. The importance of the viable-but-nonculturable state in human bacterial pathogens. Front. Microbiol. 5, 258 (2014).

    PubMed  PubMed Central  Google Scholar 

  115. Conlon, B. P., Rowe, S. E. & Lewis, K. Persister cells in biofilm associated infections. Adv. Exp. Med. Biol. 831, 1–9 (2015).

    Article  PubMed  Google Scholar 

  116. Ayrapetyan, M., Williams, T. C. & Oliver, J. D. Bridging the gap between viable but non-culturable and antibiotic persistent bacteria. Trends Microbiol. 23, 7–13 (2015).

    Article  CAS  PubMed  Google Scholar 

  117. Helaine, S. & Kugelberg, E. Bacterial persisters: formation, eradication, and experimental systems. Trends Microbiol. 22, 417–424 (2014).

    Article  CAS  PubMed  Google Scholar 

  118. Keren, I., Minami, S., Rubin, E. & Lewis, K. Characterization and transcriptome analysis of Mycobacterium tuberculosis persisters. mBio 2, e00100-11 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  119. Mah, T.-F. Biofilm-specific antibiotic resistance. Future Microbiol. 7, 1061–1072 (2012).

    Article  CAS  PubMed  Google Scholar 

  120. Madsen, J. S., Burmølle, M., Hansen, H. L. & Sørensen, S. J. The interconnection between biofilm formation and horizontal gene transfer. FEMS Immunol. Med. Microbiol. 65, 183–195 (2012).

    Article  CAS  PubMed  Google Scholar 

  121. van Meervenne, E. et al. Biofilm models for the food industry: hot spots for plasmid transfer? Pathog. Dis. 70, 332–338 (2014).

    Article  CAS  PubMed  Google Scholar 

  122. Król, J. E. et al. Invasion of E. coli biofilms by antibiotic resistance plasmids. Plasmid 70, 110–119 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  123. Savage, V. J., Chopra, I. & O'Neill, A. J. Staphylococcus aureus biofilms promote horizontal transfer of antibiotic resistance. Antimicrob. Agents Chemother. 57, 1968–1970 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  124. Borgeaud, S., Metzger, L. C., Scrignari, T. Blokesch, M. The type VI secretion system of Vibrio cholerae fosters horizontal gene transfer. Science 347, 63–67 (2015).

    Article  CAS  PubMed  Google Scholar 

  125. Wang, B. Y., Chi, B. & Kuramitsu, H. K. Genetic exchange between Treponema denticola and Streptococcus gordonii in biofilms. Oral Microbiol. Immunol. 17, 108–112 (2002).

    Article  CAS  PubMed  Google Scholar 

  126. Merod, R. T. & Wuertz, S. Extracellular polymeric substance architecture influences natural genetic transformation of Acinetobacter baylyi in biofilms. Appl. Environ. Microbiol. 80, 7752–7757 (2014). An important paper regarding the role of EPS in facilitating horizontal gene transfer.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  127. Karatan, E. & Watnick, P. Signals, regulatory networks, and materials that build and break bacterial biofilms. Microbiol. Mol. Biol. Rev. 73, 310–347 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  128. Thomsen, M. S. et al. Habitat cascades: The conceptual context and global relevance of facilitation cascades via habitat formation and modification. Integr. Comp. Biol. 50, 158–175 (2010).

    Article  PubMed  Google Scholar 

  129. Jones, C. G., Lawton, J. H. & Shachak, M. Organisms as ecosystem engineers. Oikos 69, 373–386 (1994).

    Article  Google Scholar 

  130. Bennett, S. R. et al. The 'Great Southern Reef': social, ecological and economic value of Australia's neglected kelp forests. Mar. Freshw. Res. 67, 47–56 (2015).

    Article  Google Scholar 

  131. Steneck, R. S. et al. Kelp forest ecosystems: biodiversity, stability, resilience and future. Environ. Conserv. 29, 436–459 (2002).

    Article  Google Scholar 

  132. Lawrence, D. & Vandecar, K. Effects of tropical deforestation on climate change and agriculture. Nat. Clim. Chang. 5, 27–36 (2015).

    Article  Google Scholar 

  133. Bruno, J. F., Stachowicz, J. J. & Bertness, M. D. Inclusion of facilitation into ecological theory. Trends Ecol. Evol. 18, 119–125 (2003).

    Article  Google Scholar 

  134. Cornwall, C. E. et al. Diffusion boundary layers ameliorate the negative effects of ocean acidification on the temperate coralline macroalga Arthrocardia corymbosa. PLoS ONE 9, e97235 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  135. 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. Nat. Rev. Microbiol. 10, 39–50 (2012).

    Article  CAS  Google Scholar 

  136. Whitham, T. G. et al. A framework for community and ecosystem genetics: from genes to ecosystems. Nat. Rev. Genet. 7, 510–523 (2006).

    Article  CAS  PubMed  Google Scholar 

  137. Ponge, J.-F. Emergent properties from organisms to ecosystems: towards a realistic approach. Biol. Rev. 80, 403–411 (2005).

    Article  PubMed  Google Scholar 

  138. Lowman, M. D. & Schowalter, T. D. Plant science in forest canopies — the first 30 years of advances and challenges (1980-2010). New Phytol. 194, 12–27 (2012).

    Article  PubMed  Google Scholar 

  139. Matz, C. & Kjelleberg, S. Off the hook — how bacteria survive protozoan grazing. Trends Microbiol. 13, 302–307 (2005).

    Article  CAS  PubMed  Google Scholar 

  140. Aikens, K. R., Timms, L. L. & Buddle, C. M. Vertical heterogeneity in predation pressure in a temperate forest canopy. PeerJ 1, e138 (2013).

    Article  PubMed  PubMed Central  Google Scholar 

  141. Hubbell, S. P. et al. Light-gap disturbances, recruitment limitation, and tree diversity in a neotropical forest. Science 283, 554–557 (1999).

    Article  CAS  PubMed  Google Scholar 

  142. Nealson, K. H. Autoinduction of bacterial luciferase. Arch. Microbiol. 112, 73–79 (1977). A pioneering and seminal study of intercellular communication in bacteria.

    Article  CAS  PubMed  Google Scholar 

  143. Keller, L. & Surette, M. G. Communication in bacteria: an ecological and evolutionary perspective. Nat. Rev. Microbiol. 4, 249–258 (2006).

    Article  CAS  PubMed  Google Scholar 

  144. Seviour, T. et al. Functional amyloids keep quorum sensing molecules in check. J. Biol. Chem. 290, 6457–6469 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  145. Redfield, R. Is quorum sensing a side effect of diffusion sensing? Trends Microbiol. 10, 365–370 (2002).

    Article  CAS  PubMed  Google Scholar 

  146. Hense, B. A. et al. Does efficiency sensing unify diffusion and quorum sensing? Nat. Rev. Microbiol. 5, 230–239 (2007).

    Article  CAS  PubMed  Google Scholar 

  147. Charlton, T. S. et al. A novel and sensitive method for the quantification of N-3-oxoacyl homoserine lactones using gas chromatography-mass spectrometry: application to a model bacterial biofilm. Environ. Microbiol. 2, 530–541 (2000).

    Article  CAS  PubMed  Google Scholar 

  148. Tan, C. H. et al. Community quorum sensing signalling and quenching: microbial granular biofilm assembly. NPJ Biofilms Microbiomes 1, 15006 (2015).

    Article  PubMed  PubMed Central  Google Scholar 

  149. Kim, M., Ingremeau, F., Zhao, A., Bassler, B. L. & Stone, H. A. Local and global consequences of flow on bacterial quorum sensing. Nat. Microbiol. 1, 15005 (2016). This study reports a very interesting correlation between the activation of quorum sensing and external flow, explaining the spatially and temporally non-uniform responses to quorum sensing signals that are observed in natural environments.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  150. Liu, J. et al. Metabolic co-dependence gives rise to collective oscillations within biofilms. Nature 523, 550–554 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  151. Prindle, A. et al. Ion channels enable electrical communication in bacterial community. Nature 527, 59–65 (2015). The discovery of an exciting alternative signalling mechanism to chemical communication among bacteria in biofilms.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  152. Kato, S., Hashimoto, K. & Watanabe, K. Microbial interspecies electron transfer via electric currents through conductive materials. Proc. Natl Acad. Sci. USA 109, 10042–10046 (2012).

    Article  PubMed  PubMed Central  Google Scholar 

  153. Balsalobre, C. et al. Release of the type I secreted α-haemolysin via outer membrane vesicles from Escherichia coli. Mol. Microbiol. 59, 99–112 (2006).

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

H.-C.F., S.K., S.R. and P.S. gratefully acknowledge the influence of the inspiring and motivating atmosphere during the Singapore Centre on Environmental Life Sciences Engineering (SCELSE) Summer Course while preparing this Review article. The authors thank J. Froesler for assistance with the figures. H.-C.F. appreciates the long-term support of the IWW Water Centre (Muelheim, Germany) to his work, and the support of P. Wilderer, his first mentor. The authors also thank SCELSE for supporting this work.

Author information

Authors and Affiliations

  1. University of Duisburg-Essen, Faculty of Chemistry, Biofilm Centre, Universitätsstrasse 5, Essen, D-45141, Germany

    Hans-Curt Flemming & Jost Wingender

  2. Department of Environmental Microbiology, Technical University of Berlin, Ernst-Reuter-Platz 1, D-10587, Berlin, Germany

    Ulrich Szewzyk

  3. The School of Biological, Earth and Environmental Sciences and The Centre for Marine Bio-Innovation, University of New South Wales, Sydney, 2052, NSW, Australia

    Peter Steinberg

  4. The Singapore Centre for Environmental Life Sciences Engineering and the School of Biological Sciences, Nanyang Technological University, 637551, Singapore

    Scott A. Rice & Staffan Kjelleberg

Authors
  1. Hans-Curt Flemming
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Jost Wingender
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Ulrich Szewzyk
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Peter Steinberg
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Scott A. Rice
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Staffan Kjelleberg
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Hans-Curt Flemming.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

PowerPoint slides

Glossary

Grazing

A form of predation, such as when protozoa feed on bacteria.

Macrophytes

Aquatic photosynthetic organisms that are visible to the naked eye. In marine systems, 'macrophytes' is often used as a general term that includes macroalgae, such as kelps, and coastal plants, such as seagrasses or mangroves.

Bromeliads

A family of flowering plants that has leaves that often form in such a way so as to enable the persistence of pools of water that form distinct habitats and ecological communities.

Microrheology

The study of the rheological properties of a material at the micrometre scale.

Desiccation tolerance

The ability to survive water limitation.

Nanowires

Electrically conductive structures that are produced by microorganisms.

Rheologocial

Pertaining to the study of the flow of matter, primarily in a liquid state but also as 'soft solids' or solids under conditions in which they respond to an applied force with plastic flow rather than elastic deformation.

Ecomechanics

The biomechanical mechanisms by which organisms interact with their environment.

Electrogenic

Capable of generating an electric current.

Microbial mats

A coherent, layered organization of microorganisms with complementary metabolic capacities. Microbial mats are typically found in aquatic environments, anchored to a surface.

Mass transfer

The net movement of compounds or chemical species from one position to another.

Streamers

Portions of the biofilm extracellular polymeric substances (EPS) that extend out from the biofilm surface into the liquid flow.

Sorption

Adsorption or absorption, or a combination of both processes.

Oligotrophic

An environment that is characterized by low nutrient concentrations.

Lithification

A process in which sediments compact under pressure and gradually become solid rock. The biogenesis of carbonate can support this process.

Activated sludge

The microbial biomass in the aerobic portion of a wastewater treatment system.

Carbon cloth

A soft, flexible cloth-like material made from carbon fibre.

Planktonic cells

Free-living cells (that is, not in a biofilm) in the liquid phase.

Humic substances

The combination of compounds, generally humic acids, that make up the organic components of soils, peat and coal.

Molecular modelling

Methods that encompass theoretical methods and computational techniques that are used to model or mimic the behaviour of molecules.

Copiotrophic

An environment that is characterized by high nutrient concentrations.

Heterotrophic

Refers to the use of organic compounds for nutrition.

Type VI secretion systems

Multiprotein complexes that use a one-step mechanism to inject effector proteins, such as virulence factors, from the interior of a bacterial cell into a target cell. These systems have been found in a quarter of all proteobacterial genomes, including those that encode animal, plant and human pathogens, as well as soil, environmental and marine bacteria.

Aminoglycosides

A class of antibiotics that typically have a cyclohexane ring and amino sugars.

Stationary phase

A slow or non-growth phase of the bacterial growth cycle that typically results from a lack of electron donors or acceptors.

Viable-but-nonculturable state

(VBNC state). A state of dormancy that is defined by failure of an organism to be cultured on media that normally supports its growth, while retaining measurable indications of viability, such as respiratory activity, the presence of rRNA and integrity of the cell membrane.

Plasmid conjugation

The transfer of a specialized type of plasmid from one cell to another by a pilus that is encoded within the plasmid genome.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Flemming, HC., Wingender, J., Szewzyk, U. et al. Biofilms: an emergent form of bacterial life. Nat Rev Microbiol 14, 563–575 (2016). https://doi.org/10.1038/nrmicro.2016.94

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nrmicro.2016.94

This article is cited by

Search

Advanced search

Quick links

Nature Briefing Microbiology

Sign up for the Nature Briefing: Microbiology newsletter — what matters in microbiology research, free to your inbox weekly.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing: Microbiology