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      Fundamentals of Microbial Community Resistance and Resilience

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          Abstract

          Microbial communities are at the heart of all ecosystems, and yet microbial community behavior in disturbed environments remains difficult to measure and predict. Understanding the drivers of microbial community stability, including resistance (insensitivity to disturbance) and resilience (the rate of recovery after disturbance) is important for predicting community response to disturbance. Here, we provide an overview of the concepts of stability that are relevant for microbial communities. First, we highlight insights from ecology that are useful for defining and measuring stability. To determine whether general disturbance responses exist for microbial communities, we next examine representative studies from the literature that investigated community responses to press (long-term) and pulse (short-term) disturbances in a variety of habitats. Then we discuss the biological features of individual microorganisms, of microbial populations, and of microbial communities that may govern overall community stability. We conclude with thoughts about the unique insights that systems perspectives – informed by meta-omics data – may provide about microbial community stability.

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          Most cited references 129

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          Nature, nurture, or chance: stochastic gene expression and its consequences.

          Gene expression is a fundamentally stochastic process, with randomness in transcription and translation leading to cell-to-cell variations in mRNA and protein levels. This variation appears in organisms ranging from microbes to metazoans, and its characteristics depend both on the biophysical parameters governing gene expression and on gene network structure. Stochastic gene expression has important consequences for cellular function, being beneficial in some contexts and harmful in others. These situations include the stress response, metabolism, development, the cell cycle, circadian rhythms, and aging.
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            Quantifying the evidence for biodiversity effects on ecosystem functioning and services.

            Concern is growing about the consequences of biodiversity loss for ecosystem functioning, for the provision of ecosystem services, and for human well being. Experimental evidence for a relationship between biodiversity and ecosystem process rates is compelling, but the issue remains contentious. Here, we present the first rigorous quantitative assessment of this relationship through meta-analysis of experimental work spanning 50 years to June 2004. We analysed 446 measures of biodiversity effects (252 in grasslands), 319 of which involved primary producer manipulations or measurements. Our analyses show that: biodiversity effects are weaker if biodiversity manipulations are less well controlled; effects of biodiversity change on processes are weaker at the ecosystem compared with the community level and are negative at the population level; productivity-related effects decline with increasing number of trophic links between those elements manipulated and those measured; biodiversity effects on stability measures ('insurance' effects) are not stronger than biodiversity effects on performance measures. For those ecosystem services which could be assessed here, there is clear evidence that biodiversity has positive effects on most. Whilst such patterns should be further confirmed, a precautionary approach to biodiversity management would seem prudent in the meantime.
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              Persister cells, dormancy and infectious disease.

               Kim Lewis (2006)
              Several well-recognized puzzles in microbiology have remained unsolved for decades. These include latent bacterial infections, unculturable microorganisms, persister cells and biofilm multidrug tolerance. Accumulating evidence suggests that these seemingly disparate phenomena result from the ability of bacteria to enter into a dormant (non-dividing) state. The molecular mechanisms that underlie the formation of dormant persister cells are now being unravelled and are the focus of this Review.
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                Author and article information

                Journal
                Front Microbiol
                Front Microbiol
                Front. Microbio.
                Frontiers in Microbiology
                Frontiers Media S.A.
                1664-302X
                14 October 2012
                19 December 2012
                2012
                : 3
                Affiliations
                1Department of Molecular, Cellular and Developmental Biology, Yale University New Haven, CT, USA
                2Institute of Ecology/Limnology, University of Innsbruck Innsbruck, Austria
                3Department of Ecology and Evolutionary Biology, University of California Irvine, CA, USA
                4Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences Uppsala, Sweden
                5Department of Ecology and Genetics/Limnology, Uppsala University Uppsala, Sweden
                6Department of Surface Waters – Research and Management, Eawag: Swiss Federal Institute of Aquatic Science and Technology Kastanienbaum, Switzerland
                7Department of Biology and Gus R. Douglass Institute, West Virginia State University Dunbar, WV, USA
                8Department of Biology, Indiana University Bloomington, IN, USA
                9Department of Microbiology and Molecular Genetics, Michigan State University Lansing, MI, USA
                Author notes

                Edited by: Cyrille Violle, CNRS, France

                Reviewed by: Anthony Yannarell, University of Illinois at Urbana-Champaign, USA; Jack Gilbert, University of Chicago, USA

                *Correspondence: Jo Handelsman, Department of Molecular, Cellular and Developmental Biology, Yale University, 219 Prospect Street, New Haven, CT 06520, USA. e-mail: jo.handelsman@ 123456yale.edu

                Ashley Shade and Hannes Peter have contributed equally to this work.

                This article was submitted to Frontiers in Aquatic Microbiology, a specialty of Frontiers in Microbiology.

                Article
                10.3389/fmicb.2012.00417
                3525951
                23267351
                Copyright © 2012 Shade, Peter, Allison, Baho, Berga, Bürgmann, Huber, Langenheder, Lennon, Martiny, Matulich, Schmidt and Handelsman.

                This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in other forums, provided the original authors and source are credited and subject to any copyright notices concerning any third-party graphics etc.

                Page count
                Figures: 6, Tables: 1, Equations: 2, References: 175, Pages: 19, Words: 14715
                Categories
                Microbiology
                Review Article

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