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      Experimental insights into the importance of aquatic bacterial community composition to the degradation of dissolved organic matter

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          Abstract

          Bacteria play a central role in the cycling of carbon, yet our understanding of the relationship between the taxonomic composition and the degradation of dissolved organic matter (DOM) is still poor. In this experimental study, we were able to demonstrate a direct link between community composition and ecosystem functioning in that differently structured aquatic bacterial communities differed in their degradation of terrestrially derived DOM. Although the same amount of carbon was processed, both the temporal pattern of degradation and the compounds degraded differed among communities. We, moreover, uncovered that low-molecular-weight carbon was available to all communities for utilisation, whereas the ability to degrade carbon of greater molecular weight was a trait less widely distributed. Finally, whereas the degradation of either low- or high-molecular-weight carbon was not restricted to a single phylogenetic clade, our results illustrate that bacterial taxa of similar phylogenetic classification differed substantially in their association with the degradation of DOM compounds. Applying techniques that capture the diversity and complexity of both bacterial communities and DOM, our study provides new insight into how the structure of bacterial communities may affect processes of biogeochemical significance.

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          Most cited references18

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          MTML-msBayes: Approximate Bayesian comparative phylogeographic inference from multiple taxa and multiple loci with rate heterogeneity

          Background MTML-msBayes uses hierarchical approximate Bayesian computation (HABC) under a coalescent model to infer temporal patterns of divergence and gene flow across codistributed taxon-pairs. Under a model of multiple codistributed taxa that diverge into taxon-pairs with subsequent gene flow or isolation, one can estimate hyper-parameters that quantify the mean and variability in divergence times or test models of migration and isolation. The software uses multi-locus DNA sequence data collected from multiple taxon-pairs and allows variation across taxa in demographic parameters as well as heterogeneity in DNA mutation rates across loci. The method also allows a flexible sampling scheme: different numbers of loci of varying length can be sampled from different taxon-pairs. Results Simulation tests reveal increasing power with increasing numbers of loci when attempting to distinguish temporal congruence from incongruence in divergence times across taxon-pairs. These results are robust to DNA mutation rate heterogeneity. Estimating mean divergence times and testing simultaneous divergence was less accurate with migration, but improved if one specified the correct migration model. Simulation validation tests demonstrated that one can detect the correct migration or isolation model with high probability, and that this HABC model testing procedure was greatly improved by incorporating a summary statistic originally developed for this task (Wakeley's ΨW ). The method is applied to an empirical data set of three Australian avian taxon-pairs and a result of simultaneous divergence with some subsequent gene flow is inferred. Conclusions To retain flexibility and compatibility with existing bioinformatics tools, MTML-msBayes is a pipeline software package consisting of Perl, C and R programs that are executed via the command line. Source code and binaries are available for download at http://msbayes.sourceforge.net/ under an open source license (GNU Public License).
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            Measurement of dissolved organic matter fluorescence in aquatic environments: an interlaboratory comparison.

            The fluorescent properties of dissolved organic matter (DOM) are often studied in order to infer DOM characteristics in aquatic environments, including source, quantity, composition, and behavior. While a potentially powerful technique, a single widely implemented standard method for correcting and presenting fluorescence measurements is lacking, leading to difficulties when comparing data collected by different research groups. This paper reports on a large-scale interlaboratory comparison in which natural samples and well-characterized fluorophores were analyzed in 20 laboratories in the U.S., Europe, and Australia. Shortcomings were evident in several areas, including data quality-assurance, the accuracy of spectral correction factors used to correct EEMs, and the treatment of optically dense samples. Data corrected by participants according to individual laboratory procedures were more variable than when corrected under a standard protocol. Wavelength dependency in measurement precision and accuracy were observed within and between instruments, even in corrected data. In an effort to reduce future occurrences of similar problems, algorithms for correcting and calibrating EEMs are described in detail, and MATLAB scripts for implementing the study's protocol are provided. Combined with the recent expansion of spectral fluorescence standards, this approach will serve to increase the intercomparability of DOM fluorescence studies.
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              Molecular architecture and electrostatic properties of a bacterial porin.

              The integral membrane protein porin from Rhodobacter capsulatus consists of three tightly associated 16-stranded beta barrels that give rise to three distinct diffusion channels for small solutes through the outer membrane. The x-ray structure of this porin has revealed details of its shape, the residue distributions within the pore and at the membrane-facing surface, and the location of calcium sites. The electrostatic potential has been calculated and related to function. Moreover, potential calculations were found to predict the Ca2+ sites.
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                Author and article information

                Journal
                ISME J
                ISME J
                The ISME Journal
                Nature Publishing Group
                1751-7362
                1751-7370
                March 2016
                21 August 2015
                1 March 2016
                : 10
                : 3
                : 533-545
                Affiliations
                [1 ]Department of Biology/Aquatic Ecology, Lund University , Lund, Sweden
                [2 ]Science for Life Laboratory , Solna, Sweden
                [3 ]National Institute for Aquatic Resources, Technical University of Denmark , Charlottenlund, Denmark
                [4 ]Department of Ecology and Genetics/Limnology, Uppsala University , Uppsala, Sweden
                [5 ]Department of Plant and Environmental Sciences, University of Copenhagen , Copenhagen, Denmark
                [6 ]Division of Gene Technology, Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology , Solna, Sweden
                [7 ]Department of Forest Ecology and Management, Swedish University of Agricultural Sciences , Umeå, Sweden
                Author notes
                [* ]Department of Biology/Aquatic Ecology, Lund University , Sölvegatan 37, Lund 22362, Sweden. E-mail: Jurg_Brendan.Logue@ 123456biol.lu.se
                Author information
                http://orcid.org/0000-0002-3627-6899
                Article
                ismej2015131
                10.1038/ismej.2015.131
                4817675
                26296065
                bb5ff03e-323e-4cfa-8424-8c1a4189e06b
                Copyright © 2016 International Society for Microbial Ecology

                This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivs 4.0 International License. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-nd/4.0/

                History
                : 11 December 2014
                : 13 April 2015
                : 01 July 2015
                Categories
                Original Article

                Microbiology & Virology
                Microbiology & Virology

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