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      The ecology and biogeochemistry of stream biofilms.

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          Abstract

          Streams and rivers form dense networks, shape the Earth's surface and, in their sediments, provide an immensely large surface area for microbial growth. Biofilms dominate microbial life in streams and rivers, drive crucial ecosystem processes and contribute substantially to global biogeochemical fluxes. In turn, water flow and related deliveries of nutrients and organic matter to biofilms constitute major constraints on microbial life. In this Review, we describe the ecology and biogeochemistry of stream biofilms and highlight the influence of physical and ecological processes on their structure and function. Recent advances in the study of biofilm ecology may pave the way towards a mechanistic understanding of the effects of climate and environmental change on stream biofilms and the biogeochemistry of stream ecosystems.

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          Microbial biofilms.

          J Costerton, Z Lewandowski, D E Caldwell … (1995)
          Direct observations have clearly shown that biofilm bacteria predominate, numerically and metabolically, in virtually all nutrient-sufficient ecosystems. Therefore, these sessile organisms predominate in most of the environmental, industrial, and medical problems and processes of interest to microbiologists. If biofilm bacteria were simply planktonic cells that had adhered to a surface, this revelation would be unimportant, but they are demonstrably and profoundly different. We first noted that biofilm cells are at least 500 times more resistant to antibacterial agents. Now we have discovered that adhesion triggers the expression of a sigma factor that derepresses a large number of genes so that biofilm cells are clearly phenotypically distinct from their planktonic counterparts. Each biofilm bacterium lives in a customized microniche in a complex microbial community that has primitive homeostasis, a primitive circulatory system, and metabolic cooperativity, and each of these sessile cells reacts to its special environment so that it differs fundamentally from a planktonic cell of the same species.
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            Microbial biogeography: putting microorganisms on the map.

            Jennifer Martiny, Brendan J. M. Bohannan, James H Brown … (2006)
            We review the biogeography of microorganisms in light of the biogeography of macroorganisms. A large body of research supports the idea that free-living microbial taxa exhibit biogeographic patterns. Current evidence confirms that, as proposed by the Baas-Becking hypothesis, 'the environment selects' and is, in part, responsible for spatial variation in microbial diversity. However, recent studies also dispute the idea that 'everything is everywhere'. We also consider how the processes that generate and maintain biogeographic patterns in macroorganisms could operate in the microbial world.
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              Physiological heterogeneity in biofilms.

              Philip Stewart, Michael J Franklin (2008)
              Biofilms contain bacterial cells that are in a wide range of physiological states. Within a biofilm population, cells with diverse genotypes and phenotypes that express distinct metabolic pathways, stress responses and other specific biological activities are juxtaposed. The mechanisms that contribute to this genetic and physiological heterogeneity include microscale chemical gradients, adaptation to local environmental conditions, stochastic gene expression and the genotypic variation that occurs through mutation and selection. Here, we discuss the processes that generate chemical gradients in biofilms, the genetic and physiological responses of the bacteria as they adapt to these gradients and the techniques that can be used to visualize and measure the microscale physiological heterogeneities of bacteria in biofilms.
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                Author and article information

                Journal
                Journal ID (iso-abbrev): Nat. Rev. Microbiol.
                Title: Nature reviews. Microbiology
                Publisher: Springer Nature
                ISSN (Electronic): 1740-1534
                ISSN (Print): 1740-1526
                Publication date (Electronic): Apr 2016
                Volume: 14
                Issue: 4
                Affiliations
                [1 ] Stream Biofilm and Ecosystem Research Laboratory, Faculty of Architecture, Civil and Environmental Engineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland.
                [2 ] School of Engineering, University of Glasgow, Glasgow G12 8LT, UK.
                [3 ] Institute of Microbiology, University of Greifswald, Greifswald 17489, Germany.
                [4 ] Institute of Aquatic Ecology and Department of Environmental Sciences, University of Girona, Girona E-17071, Spain.
                [5 ] Department of Civil and Environmental Engineering, Northwestern University, Evanston, Illinois 60208-3109, USA.
                Article
                Publisher Item ID: nrmicro.2016.15
                DOI: 10.1038/nrmicro.2016.15
                PubMed ID: 26972916
                SO-VID: 0c53f1d7-b562-4a43-b4de-17af0b0fe8f8
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