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      Spatial Patterns in Biofilm Diversity across Hierarchical Levels of River-Floodplain Landscapes

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          Abstract

          River-floodplain systems are among the most diverse and productive ecosystems, but the effects of biophysical complexity at multiple scales on microbial biodiversity have not been studied. Here, we investigated how the hierarchical organization of river systems (i.e., region, floodplain, zone, habitats, and microhabitats) influences epilithic biofilm community assemblage patterns by characterizing microbial communities using 16S rRNA gene sequence data and analyzing bacterial species distribution across local and regional scales. Results indicate that regional and local environmental filters concurrently sort bacterial species, suggesting that spatial configuration of epilithic biofilms resembles patterns of larger organisms in floodplain ecosystems. Along the hierarchical organization of fluvial systems, floodplains constitute a vector of maximum environmental heterogeneity and consequently act as a major landscape filter for biofilm species. Thus, river basins and associated floodplains may simply reflect very large scale ‘patches’ within which environmental conditions select for community composition of epilithic biofilms.

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          Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample.

          The ongoing revolution in high-throughput sequencing continues to democratize the ability of small groups of investigators to map the microbial component of the biosphere. In particular, the coevolution of new sequencing platforms and new software tools allows data acquisition and analysis on an unprecedented scale. Here we report the next stage in this coevolutionary arms race, using the Illumina GAIIx platform to sequence a diverse array of 25 environmental samples and three known "mock communities" at a depth averaging 3.1 million reads per sample. We demonstrate excellent consistency in taxonomic recovery and recapture diversity patterns that were previously reported on the basis of metaanalysis of many studies from the literature (notably, the saline/nonsaline split in environmental samples and the split between host-associated and free-living communities). We also demonstrate that 2,000 Illumina single-end reads are sufficient to recapture the same relationships among samples that we observe with the full dataset. The results thus open up the possibility of conducting large-scale studies analyzing thousands of samples simultaneously to survey microbial communities at an unprecedented spatial and temporal resolution.
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            Diversity in tropical rain forests and coral reefs.

            The commonly observed high diversity of trees in tropical rain forests and corals on tropical reefs is a nonequilibrium state which, if not disturbed further, will progress toward a low-diversity equilibrium community. This may not happen if gradual changes in climate favor different species. If equilibrium is reached, a lesser degree of diversity may be sustained by niche diversification or by a compensatory mortality that favors inferior competitors. However, tropical forests and reefs are subject to severe disturbances often enough that equilibrium may never be attained.
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              Community diversity: relative roles of local and regional processes.

              The species richness (diversity) of local plant and animal assemblages-biological communities-balances regional processes of species formation and geographic dispersal, which add species to communities, against processes of predation, competitive exclusion, adaptation, and stochastic variation, which may promote local extinction. During the past three decades, ecologists have sought to explain differences in local diversity by the influence of the physical environment on local interactions among species, interactions that are generally believed to limit the number of coexisting species. But diversity of the biological community often fails to converge under similar physical conditions, and local diversity bears a demonstrable dependence upon regional diversity. These observations suggest that regional and historical processes, as well as unique events and circumstances, profoundly influence local community structure. Ecologists must broaden their concepts of community processes and incorporate data from systematics, biogeography, and paleontology into analyses of ecological patterns and tests of community theory.
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                Author and article information

                Contributors
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                2 December 2015
                2015
                : 10
                : 12
                : e0144303
                Affiliations
                [1 ]Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America
                [2 ]Department of Microbiology and Immunology, Montana State University, Bozeman, Montana, United States of America
                INRA, FRANCE
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                Conceived and designed the experiments: MP HMV. Performed the experiments: MP HMV. Analyzed the data: MP RJ. Contributed reagents/materials/analysis tools: RJ. Wrote the paper: MP RJ HMV.

                Article
                PONE-D-15-27903
                10.1371/journal.pone.0144303
                4668062
                26630382
                f4fbf91e-d0c1-4311-8974-83e1efc546b9
                Copyright @ 2015

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited

                History
                : 26 June 2015
                : 15 November 2015
                Page count
                Figures: 6, Tables: 1, Pages: 14
                Funding
                Funding was provided by National Science Foundation EPSCoR Track-1 EPS-1101342 (INSTEP 3) through the Montana Institute on Ecosystems to HM Valett and by Natural Resource Damage Program Contract 900017 Task Order 2.42 to HM Valett. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Research Article
                Custom metadata
                Representative DNA sequences from this study are publicly available in GenBank sequence repository (accession numbers KT908042 - KT918405). Moreover, the mapping file used for QIIME analyses containing the barcode sequence used for each sample, the linker/primer sequence used to amplify the sample, and the environmental data (i.e., explanatory variables) for each sample can be found as a supplementary material in the paper.

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