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      Spatio-Temporal Patterns of Major Bacterial Groups in Alpine Waters

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          Abstract

          Glacial alpine landscapes are undergoing rapid transformation due to changes in climate. The loss of glacial ice mass has directly influenced hydrologic characteristics of alpine floodplains. Consequently, hyporheic sediment conditions are likely to change in the future as surface waters fed by glacial water (kryal) become groundwater dominated (krenal). Such environmental shifts may subsequently change bacterial community structure and thus potential ecosystem functioning. We quantitatively investigated the structure of major bacterial groups in glacial and groundwater-fed streams in three alpine floodplains during different hydrologic periods. Our results show the importance of several physico-chemical variables that reflect local geological characteristics as well as water source in structuring bacterial groups. For instance, Alpha-, Betaproteobacteria and Cytophaga-Flavobacteria were influenced by pH, conductivity and temperature as well as by inorganic and organic carbon compounds, whereas phosphorous compounds and nitrate showed specific influence on single bacterial groups. These results can be used to predict future bacterial group shifts, and potential ecosystem functioning, in alpine landscapes under environmental transformation.

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          Most cited references14

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          The diversity and biogeography of soil bacterial communities.

          For centuries, biologists have studied patterns of plant and animal diversity at continental scales. Until recently, similar studies were impossible for microorganisms, arguably the most diverse and abundant group of organisms on Earth. Here, we present a continental-scale description of soil bacterial communities and the environmental factors influencing their biodiversity. We collected 98 soil samples from across North and South America and used a ribosomal DNA-fingerprinting method to compare bacterial community composition and diversity quantitatively across sites. Bacterial diversity was unrelated to site temperature, latitude, and other variables that typically predict plant and animal diversity, and community composition was largely independent of geographic distance. The diversity and richness of soil bacterial communities differed by ecosystem type, and these differences could largely be explained by soil pH (r(2) = 0.70 and r(2) = 0.58, respectively; P < 0.0001 in both cases). Bacterial diversity was highest in neutral soils and lower in acidic soils, with soils from the Peruvian Amazon the most acidic and least diverse in our study. Our results suggest that microbial biogeography is controlled primarily by edaphic variables and differs fundamentally from the biogeography of "macro" organisms.
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            Application of a suite of 16S rRNA-specific oligonucleotide probes designed to investigate bacteria of the phylum cytophaga-flavobacter-bacteroides in the natural environment.

            We designed a panel of four 16S rRNA-targeted oligonucleotide probes specific for bacteria of the phylum cytophaga-flavobacter-bacteroides (CFB). Probes CF319a and CF319b are targeted to members of the flavobacteria-cytophaga group and the genus Porphyromonas, whereas probe BAC303 has a target region characteristic for the genera Prevotella and Bacteroides within the bacteroides group. The probe FFE8b was developed for species-specific hybridizations with Flavobacterium ferrugineum. All probes were designed by computer-assisted sequence analysis and compared to all currently accessible 16S and 23S rRNA sequences. The oligonucleotides were further evaluated by whole-cell and non-radioactive dot-blot hybridization against reference strains of the CFB phylum and other major lineages of Bacteria. The newly developed probes were used together with other higher-order probes to analyse the structure and community composition in complex environments. In activated sludge samples, members of the flavobacteria-cytophaga group were revealed by in situ hybridization as important constituents of sludge flocs and characteristic colonizers of filamentous bacteria. By application of fluorescent probe BAC303, members of the genera Bacteroides and Prevotella could be visualized without prior cultivation as an important part of the human faecal microflora.
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              Forward selection of explanatory variables.

              This paper proposes a new way of using forward selection of explanatory variables in regression or canonical redundancy analysis. The classical forward selection method presents two problems: a highly inflated Type I error and an overestimation of the amount of explained variance. Correcting these problems will greatly improve the performance of this very useful method in ecological modeling. To prevent the first problem, we propose a two-step procedure. First, a global test using all explanatory variables is carried out. If, and only if, the global test is significant, one can proceed with forward selection. To prevent overestimation of the explained variance, the forward selection has to be carried out with two stopping criteria: (1) the usual alpha significance level and (2) the adjusted coefficient of multiple determination (Ra(2)) calculated using all explanatory variables. When forward selection identifies a variable that brings one or the other criterion over the fixed threshold, that variable is rejected, and the procedure is stopped. This improved method is validated by simulations involving univariate and multivariate response data. An ecological example is presented using data from the Bryce Canyon National Park, Utah, U.S.A.
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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, USA )
                1932-6203
                2014
                19 November 2014
                : 9
                : 11
                : e113524
                Affiliations
                [1 ]Institute of Molecular Health Sciences, Professorship of Genetics, ETH Zurich, Zurich, Switzerland
                [2 ]Department of Aquatic Ecology, Swiss Federal Institute of Aquatic Science and Technology, Eawag, Dübendorf, Switzerland and Institute of Integrative Biology, ETH-Zurich, Zurich, Switzerland
                [3 ]Department of Surface Waters – Research and Management, Swiss Federal Institute of Aquatic Science and Technology, Eawag, Kastanienbaum, Switzerland
                [4 ]Cary Institute of Ecosystem Studies, Millbrook, New York, United States of America
                Argonne National Laboratory, United States of America
                Author notes

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

                Conceived and designed the experiments: RF HB SF CR. Performed the experiments: RF HB SF CR. Analyzed the data: RF. Contributed reagents/materials/analysis tools: RF SF SF CR. Wrote the paper: RF HB SF CR.

                Article
                PONE-D-14-41144
                10.1371/journal.pone.0113524
                4237416
                25409508
                11e06d88-5e3a-4f0f-a69c-6ecf282d0701
                Copyright @ 2014

                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
                : 15 September 2014
                : 27 October 2014
                Page count
                Pages: 8
                Funding
                Funding provided by Swiss National Science Foundation (No. 31003A-119735) to CR HB SF RF. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Research Article
                Biology and Life Sciences
                Ecology
                Community Ecology
                Community Structure
                Freshwater Ecology
                Limnetic Ecosystems
                Microbial Ecology
                Biofilms
                Bacterial Biofilms
                Global Change Ecology
                Earth Sciences
                Marine and Aquatic Sciences
                Aquatic Environments
                Freshwater Environments
                Rivers
                Limnology
                Ecology and Environmental Sciences
                Habitats
                Custom metadata
                The authors confirm that all data underlying the findings are fully available without restriction. All relevant data are within the paper and its Supporting Information files.

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