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      Dehalogenation Activities and Distribution of Reductive Dehalogenase Homologous Genes in Marine Subsurface Sediments

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          ABSTRACT

          Halogenated organic compounds serve as terminal electron acceptors for anaerobic respiration in a diverse range of microorganisms. Here, we report on the widespread distribution and diversity of reductive dehalogenase homologous ( rdhA ) genes in marine subsurface sediments. A total of 32 putative rdhA phylotypes were detected in sediments from the southeast Pacific off Peru, the eastern equatorial Pacific, the Juan de Fuca Ridge flank off Oregon, and the northwest Pacific off Japan, collected at a maximum depth of 358 m below the seafloor. In addition, significant dehalogenation activity involving 2,4,6-tribromophenol and trichloroethene was observed in sediment slurry from the Nankai Trough Forearc Basin. These results suggest that dehalorespiration is an important energy-yielding pathway in the subseafloor microbial ecosystem.

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          CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice

          Julie D Thompson, Desmond Higgins, Toby J Gibson (1994)
          Article 0 comments Cited 1715 times – based on 0 reviews     Review now
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            MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0.

            K Tamura, J. Dudley, M Nei … (2007)
            We announce the release of the fourth version of MEGA software, which expands on the existing facilities for editing DNA sequence data from autosequencers, mining Web-databases, performing automatic and manual sequence alignment, analyzing sequence alignments to estimate evolutionary distances, inferring phylogenetic trees, and testing evolutionary hypotheses. Version 4 includes a unique facility to generate captions, written in figure legend format, in order to provide natural language descriptions of the models and methods used in the analyses. This facility aims to promote a better understanding of the underlying assumptions used in analyses, and of the results generated. Another new feature is the Maximum Composite Likelihood (MCL) method for estimating evolutionary distances between all pairs of sequences simultaneously, with and without incorporating rate variation among sites and substitution pattern heterogeneities among lineages. This MCL method also can be used to estimate transition/transversion bias and nucleotide substitution pattern without knowledge of the phylogenetic tree. This new version is a native 32-bit Windows application with multi-threading and multi-user supports, and it is also available to run in a Linux desktop environment (via the Wine compatibility layer) and on Intel-based Macintosh computers under the Parallels program. The current version of MEGA is available free of charge at (http://www.megasoftware.net).
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              Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation.

              Ivica Letunic, Peer Bork (2007)
              Interactive Tree Of Life (iTOL) is a web-based tool for the display, manipulation and annotation of phylogenetic trees. Trees can be interactively pruned and re-rooted. Various types of data such as genome sizes or protein domain repertoires can be mapped onto the tree. Export to several bitmap and vector graphics formats is supported. iTOL is available at http://itol.embl.de
              Article 0 comments Cited 612 times – based on 0 reviews     Review now
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                Author and article information

                Journal
                Title: Applied and Environmental Microbiology
                Abbreviated Title: Appl Environ Microbiol
                Publisher: American Society for Microbiology
                ISSN (Print): 0099-2240
                ISSN (Electronic): 1098-5336
                Publication date Created: November 2009
                Publication date (Print): November 2009
                Volume: 75
                Issue: 21
                Pages: 6905-6909
                Affiliations
                [1 ]Geomicrobiology Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Monobe B200, Nankoku, Kochi 783-8502, Japan
                [2 ]Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Hakozaki 6-10-1, Fukuoka 812-8581, Japan
                [3 ]Marine Works Japan Ltd., Kamariya-higashi 2-16-32-5F, Yokohama 236-0042, Japan
                [4 ]Department of Chemistry and Bioengineering, Tampere University of Technology, FIN-33101 Tampere, Finland
                Article
                DOI: 10.1128/AEM.01124-09
                PMC ID: 2772448
                PubMed ID: 19749069
                SO-VID: b3b839c5-83c5-412f-98ae-c7cce79927db
                Copyright © © 2009
                License:

                https://journals.asm.org/non-commercial-tdm-license

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