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      Carbon, Metals, and Grain Size Correlate with Bacterial Community Structure in Sediments of a High Arsenic Aquifer

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          Abstract

          Bacterial communities can exert significant influence on the biogeochemical cycling of arsenic (As). This has globally important implications since As in drinking water affects the health of over 100 million people worldwide, including in the Ganges–Brahmaputra Delta region of Bangladesh where geogenic arsenic in groundwater can reach concentrations of more than 10 times the World Health Organization’s limit. Thus, the goal of this research was to investigate patterns in bacterial community composition across gradients in sediment texture and chemistry in an aquifer with elevated groundwater As concentrations in Araihazar, Bangladesh. We characterized the bacterial community by pyrosequencing 16S rRNA genes from aquifer sediment samples collected at three locations along a groundwater flow path at a range of depths between 1.5 and 15 m. We identified significant differences in bacterial community composition between locations in the aquifer. In addition, we found that bacterial community structure was significantly related to sediment grain size, and sediment carbon (C), manganese (Mn), and iron (Fe) concentrations. Deltaproteobacteria and Chloroflexi were found in higher proportions in silty sediments with higher concentrations of C, Fe, and Mn. By contrast, Alphaproteobacteria and Betaproteobacteria were in higher proportions in sandy sediments with lower concentrations of C and metals. Based on the phylogenetic affiliations of these taxa, these results may indicate a shift to more Fe-, Mn-, and humic substance-reducers in the high C and metal sediments. It is well-documented that C, Mn, and Fe may influence the mobility of groundwater arsenic, and it is intriguing that these constituents may also structure the bacterial community.

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          Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences.

          In 2001 and 2002, we published two papers (Bioinformatics, 17, 282-283, Bioinformatics, 18, 77-82) describing an ultrafast protein sequence clustering program called cd-hit. This program can efficiently cluster a huge protein database with millions of sequences. However, the applications of the underlying algorithm are not limited to only protein sequences clustering, here we present several new programs using the same algorithm including cd-hit-2d, cd-hit-est and cd-hit-est-2d. Cd-hit-2d compares two protein datasets and reports similar matches between them; cd-hit-est clusters a DNA/RNA sequence database and cd-hit-est-2d compares two nucleotide datasets. All these programs can handle huge datasets with millions of sequences and can be hundreds of times faster than methods based on the popular sequence comparison and database search tools, such as BLAST.
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            Identifying the dominant soil bacterial taxa in libraries of 16S rRNA and 16S rRNA genes.

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              Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex.

              We constructed error-correcting DNA barcodes that allow one run of a massively parallel pyrosequencer to process up to 1,544 samples simultaneously. Using these barcodes we processed bacterial 16S rRNA gene sequences representing microbial communities in 286 environmental samples, corrected 92% of sample assignment errors, and thus characterized nearly as many 16S rRNA genes as have been sequenced to date by Sanger sequencing.
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                Author and article information

                Journal
                Front Microbiol
                Front Microbiol
                Front. Microbio.
                Frontiers in Microbiology
                Frontiers Research Foundation
                1664-302X
                27 December 2011
                23 March 2012
                2012
                : 3
                : 82
                Affiliations
                [1] 1simpleDepartment of Ecology and Evolutionary Biology, The Institute of Arctic and Alpine Research, University of Colorado Boulder, CO, USA
                [2] 2simpleQueens College, City University of New York Flushing, NY, USA
                [3] 3simpleLamont-Doherty Earth Observatory, Columbia University Palisades, NY, USA
                [4] 4simpleDepartment of Civil, Environmental and Architectural Engineering, The Institute of Arctic and Alpine Research, University of Colorado Boulder, CO, USA
                [5] 5simpleThe Institute of Arctic and Alpine Research, University of Colorado Boulder, CO, USA
                [6] 6simpleDepartment of Computer Science, University of Colorado Boulder, CO, USA
                [7] 7simpleBronx High School of Science Bronx, NY, USA
                [8] 8simpleDepartment of Geology, Dhaka University Dhaka, Bangladesh
                [9] 9simpleProgram for Environmental Studies, The Institute of Arctic and Alpine Research, University of Colorado Boulder, CO, USA
                Author notes

                Edited by: Rich Boden, University of Plymouth, UK

                Reviewed by: Hongchen Jiang, China University of Geosciences Beijing, China; Richard S. Winder, Natural Resources Canada, Canada

                *Correspondence: Teresa M. Legg, The Institute of Arctic and Alpine Research, University of Colorado, Campus Box 450, Boulder, CO 80309-0450, USA. e-mail: teresa.legg@ 123456colorado.edu

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

                Article
                10.3389/fmicb.2012.00082
                3311048
                22470368
                561a022b-4228-4196-997c-78870fdb4790
                Copyright © 2012 Legg, Zheng, Simone, Radloff, Mladenov, González, Knights, Siu, Rahman, Ahmed, McKnight and Nemergut.

                This is an open-access article distributed under the terms of the Creative Commons Attribution Non Commercial License, which permits non-commercial use, distribution, and reproduction in other forums, provided the original authors and source are credited.

                History
                : 08 December 2011
                : 17 February 2012
                Page count
                Figures: 7, Tables: 3, Equations: 0, References: 85, Pages: 15, Words: 10379
                Categories
                Microbiology
                Original Research

                Microbiology & Virology
                pyrosequencing,arsenic,bacteria,chloroflexi,deltaproteobacteria,aquifer
                Microbiology & Virology
                pyrosequencing, arsenic, bacteria, chloroflexi, deltaproteobacteria, aquifer

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