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Biofilms in Soil

  • Reference work entry
  • First Online:
Encyclopedia of Agrophysics

Part of the book series: Encyclopedia of Earth Sciences Series ((EESS))

Definition

A biofilm is commonly defined as “a structured community of bacterial cells enclosed in a self-produced polymeric matrix and adherent to an inert or living surface” (Costerton et al., 1999), but this definition has been modified to also include that the cell attachment is irreversible, and that the bacteria living in the biofilm exhibit an altered phenotype with respect to growth rate and gene transcription (Donlan and Costerton, 2002).

Introduction

Biofilms are characterized by being composed of cells that are organized into matrix-enclosed structures that vary in size from smaller microcolonies to large and sometimes “mushroom-shaped” structures, which allow nutrient supply and waste product removal for cells placed in the deeper biofilm layers (Costerton et al., 1987; Donlan and Costerton, 2002; Stoodley et al., 2002; Jefferson, 2004). The biofilm matrix consists of extracellular polymeric substances (EPS), mainly exopolysaccharides, and also of proteins and nucleic...

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Bibliography

  • Almås, A. R., Mulder, J., and Bakken, L. R., 2005. Trace metal exposure of soil bacteria depends on their position in the soil matrix. Environmental Science and Technology, 39, 5927–5932.

    PubMed  Google Scholar 

  • Baldrian, P., 2006. Fungal laccases – occurrence and properties. FEMS Microbiology Reviews, 30, 215–242.

    CAS  PubMed  Google Scholar 

  • Baum, M. M., Kainovic, A., O’Keeffe, T., Pandita, R., McDonald, K., Wu, S., and Webster, P., 2009. Characterization of structures in biofilms formed by a Pseudomonas fluorescens isolated from soil. BMC Microbiology, 9, 103–116.

    PubMed Central  PubMed  Google Scholar 

  • Berg, G., Eberl, L., and Hartmann, A., 2005. The rhizosphere as a reservoir for opportunistic human pathogenic bacteria. Environmental Microbiology, 7, 1673–1685.

    CAS  PubMed  Google Scholar 

  • Burmølle, M., Hansen, L. H., and Sørensen, S. J., 2005. Use of a whole-cell biosensor and flow cytometry to detect AHL production by an indigenous soil community during decomposition of litter. Microbial Ecology, 50, 221–229.

    PubMed  Google Scholar 

  • Burmølle, M., Webb, J. S., Rao, D., Hansen, L. H., Sørensen, S. J., and Kjelleberg, S., 2006. Enhanced biofilm formation and increased resistance towards antimicrobial agents and bacterial invasion are caused by synergistic interactions in multispecies biofilms. Applied and Environmental Microbiology, 72, 3916–3923.

    PubMed Central  PubMed  Google Scholar 

  • Burmølle, M., Hansen, L. H., and Sørensen, S. J., 2007. Establishment and early succession of a multispecies biofilm composed of soil bacteria. Microbial Ecology, 54, 352–362.

    PubMed  Google Scholar 

  • Burmølle, M., Bahl, M. I., Jensen, L. B., Sørensen, S. J., and Hansen, L. H., 2008. Type 3 fimbriae, encoded by the conjugative plasmid pOLA52, enhance biofilm formation and transfer frequencies in Enterobacteriaceae strains. Microbiology, 154, 187–195.

    PubMed  Google Scholar 

  • Costerton, J. W., Cheng, K. J., Geesey, G. G., Ladd, T. I., Nickel, J. C., Dasgupta, M., and Marrie, T. J., 1987. Bacterial biofilms in nature and disease. Annual Reviews of Microbiology, 41, 435–464.

    CAS  Google Scholar 

  • Costerton, J. W., Stewart, P. S., and Greenberg, E. P., 1999. Bacterial biofilms: a common cause of persistent infections. Science, 284, 1318–1322.

    CAS  PubMed  Google Scholar 

  • Donlan, R. M., and Costerton, J. W., 2002. Biofilms: survival mechanisms of clinically relevant microorganisms. Clinical Microbiology Reviews, 15, 167–193.

    PubMed Central  CAS  PubMed  Google Scholar 

  • Dunsmore, B. C., Bass, C. J., and Lappin-Scott, H. M., 2004. A novel approach to investigate biofilm accumulation and bacterial transport in porous matrices. Environmntal Microbiology, 6, 183–187.

    Google Scholar 

  • Ekelund, F., and Rønn, R., 1994. Notes on protozoa in agricultural soil with emphasis on heterotrophic flagellates and naked amoebae and their ecology. FEMS Microbiology Reviews, 15, 321–353.

    CAS  PubMed  Google Scholar 

  • Foster, R. C., 1981. Polysaccharides in soil fabrics. Science, 214, 665–667.

    CAS  PubMed  Google Scholar 

  • Foster, R. C., 1988. Microenvironments of soil-microorganisms. Biology and Fertility of Soils, 6, 189–203.

    Google Scholar 

  • Gans, J., Wolinsky, M., and Dunbar, J., 2005. Computational improvements reveal great bacterial diversity and high metal toxicity in soil. Science, 309, 1387–1390.

    CAS  PubMed  Google Scholar 

  • Gilbert, P., Allison, D. G., and McBain, A. J., 2002. Biofilms in vitro and in vivo: do singular mechanisms imply cross-resistance? Journal of Applied Microbiology, 92(Suppl), 98S–110S.

    PubMed  Google Scholar 

  • Gray, M. J., Freitag, N. E., and Boor, K. J., 2006. How the bacterial pathogen Listeria monocytogenes mediates the switch from environmental Dr. Jekyll to pathogenic Mr. Hyde. Infection and Immunity, 74, 2505–2512.

    PubMed Central  CAS  PubMed  Google Scholar 

  • Grundmann, G. L., 2004. Spatial scales of soil bacterial diversity - the size of a clone. FEMS Microbiology Ecology, 48, 119–127.

    CAS  PubMed  Google Scholar 

  • Hansen, L. H., Ferrari, B., Sørensen, A. H., Veal, D., and Sørensen, S. J., 2001. Detection of oxytetracycline production by Streptomyces rimosus in soil microcosms by combining whole-cell biosensors and flow cytometry. Applied and Environmental Microbiology, 67, 239–244.

    PubMed Central  CAS  PubMed  Google Scholar 

  • Holden, P. A., Hunt, J. R., and Firestone, M. K., 1997. Toluene diffusion and reaction in unsaturated Pseudomonas putida biofilms. Biotechnology and Bioengineering, 56, 656–670.

    PubMed Central  CAS  PubMed  Google Scholar 

  • Hu, J. Y., Fan, Y., Lin, Y. H., Zhang, H. B., Ong, S. L., Dong, N., Xu, J. L., Ng, W. J., and Zhang, L. H., 2003. Microbial diversity and prevalence of virulent pathogens in biofilms developed in a water reclamation system. Research in Microbiology, 154, 623–629.

    CAS  PubMed  Google Scholar 

  • Jackson, C. R., 2003. Changes in community properties during microbial succession. Okios, 101, 444–448.

    Google Scholar 

  • Jackson, C. R., Churchill, P. F., and Roden, E. E., 2001. Successional changes in bacterial assemblage structure during epilithic biofilm development. Ecology, 82, 555–566.

    Google Scholar 

  • Jass, J., Roberts, S. K., and Lappin-Scott, H. M., 2002. Microbes and enzymes in biofilms. In Burns, R. G., and Dick, R. D. (eds.), Enzymes in the Environment. Activity, Ecology, and Applications. New York: Marcel Dekker, pp. 307–326.

    Google Scholar 

  • Jean, J., Tsao, C., and Chung, M., 2004. Comparative endoscopic and SEM analyses and imaging for biofilm growth on porous quartz sand. Biogeochemistry, 70, 427–445.

    CAS  Google Scholar 

  • Jefferson, K. K., 2004. What drives bacteria to produce a biofilm? FEMS Microbiology Letters, 236, 163–173.

    CAS  PubMed  Google Scholar 

  • Karamanev, D. G., Chavarie, C., and Samson, R., 1997. Soil immobilization: New concept for biotreatment of soil contaminants. Biotechnology and Bioengineering, 57, 471–476.

    Google Scholar 

  • Klayman, B. J., Volden, P. A., Stewart, P. S., and Camper, A. K., 2009. Escherichia coli O157:H7 requires colonizing partner to adhere and persist in a capillary flow cell. Environmental Science and Technology, 43, 2105–2111.

    CAS  PubMed  Google Scholar 

  • Lünsdorf, H., Erb, R. W., Abraham, W. R., and Timmis, K. N., 2000. ‘Clay hutches’: a novel interaction between bacteria and clay minerals. Environmental Microbiology, 2, 161–168.

    PubMed  Google Scholar 

  • Lünsdorf, H., Strömpl, C., Osborn, A. M., Bennasar, A., Moore, E. R. B., Abraham, W. R., and Timmis, K. N., 2001. Approach to analyze interactions of microorganisms, hydrophobic substrates, and soil colloids leading to formation of composite biofilms, and to study initial events in microbiogeological processes. Methods in Enzymology, 336, 317–331.

    PubMed  Google Scholar 

  • Mah, T. F., and O'Toole, G. A., 2001. Mechanisms of biofilm resistance to antimicrobial agents. Trends in Microbiology, 9, 34–39.

    CAS  PubMed  Google Scholar 

  • Martiny, A. C., Jørgensen, T. M., Albrechtsen, H. J., Arvin, E., and Molin, S., 2003. Long-term succession of structure and diversity of a biofilm formed in a model drinking water distribution system. Applied and Environmental Microbiology, 69, 6899–6907.

    PubMed Central  CAS  PubMed  Google Scholar 

  • Møller, S., Korber, D. R., Wolfaardt, G. M., Molin, S., and Caldwell, D. E., 1997. Impact of nutrient composition on a degradative biofilm community. Applied and Environmental Microbiology, 63, 2432–2438.

    PubMed Central  PubMed  Google Scholar 

  • Nannipieri, P., Kandeler, E., and Ruggiero, P., 2002. Enzyme activities and microbiological and biochemical processes in soil. In Burns, R. G., and Dick, R. P. (eds.), Enzymes in the Environment: Activity, Ecology, and Applications. New York: Marcel Dekker, pp. 1–33.

    Google Scholar 

  • Nunan, N., Wu, K. J., Young, I. M., Crawford, J. W., and Ritz, K., 2003. Spatial distribution of bacterial communities and their relationships with the micro-architecture of soil. FEMS Microbiology Ecology, 44, 203–215.

    CAS  PubMed  Google Scholar 

  • Ophir, T., and Gutnick, D. L., 1994. A role for exopolysaccharides in the protection of microorganisms from desiccation. Applied and Environmental Microbiology, 60, 740–745.

    PubMed Central  CAS  PubMed  Google Scholar 

  • Ou, L. T., and Thomas, J. E., 1994. Influence of soil organic-matter and soil surfaces on a bacterial consortium that mineralizes fenamiphos. Soil Science Society of America Journal, 58, 1148–1153.

    CAS  Google Scholar 

  • Pearce, D., Bazin, M. J., and Lynch, J. M., 1995. The rhizosphere as a biofilm. In Lappin-Scott, H. M., and Costerton, J. W. (eds.), Microbial Biofilms. New York: Cambridge University Press, pp. 207–220.

    Google Scholar 

  • Potera, C., 1996. Biofilms invade microbiology. Science, 273, 1795–1797.

    CAS  PubMed  Google Scholar 

  • Roberson, E. B., and Firestone, M. K., 1992. Relationship between desiccation and exopolysaccharide production in a soil Pseudomonas sp. Applied and Environmental Microbiology, 58, 1284–1291.

    CAS  Google Scholar 

  • Rodriguez, S. J., and Bishop, P. L., 2007. Three-dimensional quantification of soil biofilms using image analysis. Environmental Engineering Science, 24, 96–103.

    CAS  Google Scholar 

  • Sørensen, S. J., Bailey, M., Hansen, L. H., Kroer, N., and Wuertz, S., 2005. Studying plasmid horizontal transfer in situ: a critical review. Nature Reviews Microbiology, 3, 700–710.

    PubMed  Google Scholar 

  • Stach, J. E. M., and Burns, R. G., 2002. Enrichment versus biofilm culture: a functional and phylogenetic comparison of polycyclic aromatic hydrocarbon-degrading microbial communities. Environmental Microbiology, 4, 169–182.

    PubMed  Google Scholar 

  • Stewart, P. S., Camper, A. K., Handran, S. D., Huang, C., and Warnecke, M., 1997. Spatial distribution and coexistence of Klebsiella pneumoniae and Pseudomonas aeruginosa in biofilms. Microbial Ecology, 33, 2–10.

    PubMed  Google Scholar 

  • Stoodley, P., Sauer, K., Davies, D. G., and Costerton, J. W., 2002. Biofilms as complex differentiated communities. Annual Reviews of Microbiology, 56, 187–209.

    CAS  Google Scholar 

  • Sutherland, I., 2001. Biofilm exopolysaccharides: a strong and sticky framework. Microbiology, 147, 3–9.

    CAS  PubMed  Google Scholar 

  • Torsvik, V., Goksöyr, J., and Daae, F. L., 1990. High diversity in DNA of soil bacteria. Applied and Environmental Microbiology, 56, 782–787.

    PubMed Central  CAS  PubMed  Google Scholar 

  • Verbruggen, N., Hermans, C., and Schat, H., 2009. Mechanisms to cope with arsenic or cadmium excess in plants. Current Opinion in Plant Biology, 12, 364–372.

    CAS  PubMed  Google Scholar 

  • von Canstein, H., Kelly, S., Li, Y., and Wagner-Dobler, I., 2002. Species diversity improves the efficiency of mercury-reducing biofilms under changing environmental conditions. Applied and Environmental Microbiology, 68, 2829–2837.

    Google Scholar 

  • Walther, B. A., and Ewald, P. W., 2004. Pathogen survival in the external environment and the evolution of virulence. Biological Reviews of the Cambridge Philosophical Society, 79, 849–869.

    PubMed  Google Scholar 

  • Wilson, B. A., and Salyers, A. A., 2003. Is the evolution of bacterial pathogens an out-of-body experience? Trends in Microbiology, 11, 347–350.

    CAS  PubMed  Google Scholar 

  • Winfield, M. D., and Groisman, E. A., 2003. Role of nonhost environments in the lifestyles of Salmonella and Escherichia coli. Applied and Environmental Microbiology, 69, 3687–3694.

    PubMed Central  CAS  PubMed  Google Scholar 

  • Xavier, K. B., and Bassler, B. L., 2003. LuxS quorum sensing: more than just a numbers game. Current Opinion in Microbiology, 6, 191–197.

    CAS  PubMed  Google Scholar 

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Acknowledgments

The authors would like to thank Prof. James I. Prosser (University of Aberdeen) and Dr. Regin Rønn (University of Copenhagen) for providing useful information.

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Authors and Affiliations

  1. Section of Microbiology, Department of Biology, University of Copenhagen, Sølvgade 83H, 1307, Copenhagen K, Denmark

    Mette Burmølle, Annelise Kjøller & Søren J. Sørensen

Authors
  1. Mette Burmølle
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  2. Annelise Kjøller
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  3. Søren J. Sørensen
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Corresponding author

Correspondence to Mette Burmølle .

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Editors and Affiliations

  1. Institute of Agrophysics, Polish Academy of Sciences, Lublin, Poland

    Jan Gliński , Józef Horabik  & Jerzy Lipiec ,  & 

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Burmølle, M., Kjøller, A., Sørensen, S.J. (2011). Biofilms in Soil. In: Gliński, J., Horabik, J., Lipiec, J. (eds) Encyclopedia of Agrophysics. Encyclopedia of Earth Sciences Series. Springer, Dordrecht. https://doi.org/10.1007/978-90-481-3585-1_260

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