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      Phylogenetic Diversity of aprA Genes in Subseafloor Sediments on the Northwestern Pacific Margin off Japan

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          Abstract

          Markedly diverse sequences of the adenosine-5′-phosphosulfate reductase alpha subunit gene ( aprA), which encodes a key enzyme in microbial sulfate reduction and sulfur oxidation, were detected in subseafloor sediments on the northwestern Pacific off Japan. The aprA gene sequences were grouped into 135 operational taxonomic units (90% sequence identity), including genes related to putative sulfur-oxidizing bacteria predominantly detected in sulfate-depleted deep sediments. Our results suggest that microbial ecosystems in the subseafloor biosphere have phylogenetically diverse genetic potentials to mediate cryptic sulfur cycles in sediments, even where sulfate is rarely present.

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          Distributions of microbial activities in deep subseafloor sediments.

          S D'Hondt (2004)
          Diverse microbial communities and numerous energy-yielding activities occur in deeply buried sediments of the eastern Pacific Ocean. Distributions of metabolic activities often deviate from the standard model. Rates of activities, cell concentrations, and populations of cultured bacteria vary consistently from one subseafloor environment to another. Net rates of major activities principally rely on electron acceptors and electron donors from the photosynthetic surface world. At open-ocean sites, nitrate and oxygen are supplied to the deepest sedimentary communities through the underlying basaltic aquifer. In turn, these sedimentary communities may supply dissolved electron donors and nutrients to the underlying crustal biosphere.
          Article 0 comments Cited 285 times – based on 0 reviews     Review now
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            Potential for chemolithoautotrophy among ubiquitous bacteria lineages in the dark ocean.

            Brandon Swan, Manuel Martínez-García, Christina M Preston … (2011)
            Recent studies suggest that unidentified prokaryotes fix inorganic carbon at globally significant rates in the immense dark ocean. Using single-cell sorting and whole-genome amplification of prokaryotes from two subtropical gyres, we obtained genomic DNA from 738 cells representing most cosmopolitan lineages. Multiple cells of Deltaproteobacteria cluster SAR324, Gammaproteobacteria clusters ARCTIC96BD-19 and Agg47, and some Oceanospirillales from the lower mesopelagic contained ribulose-1,5-bisphosphate carboxylase-oxygenase and sulfur oxidation genes. These results corroborated community DNA and RNA profiling from diverse geographic regions. The SAR324 genomes also suggested C(1) metabolism and a particle-associated life-style. Microautoradiography and fluorescence in situ hybridization confirmed bicarbonate uptake and particle association of SAR324 cells. Our study suggests potential chemolithoautotrophy in several uncultured Proteobacteria lineages that are ubiquitous in the dark oxygenated ocean and provides new perspective on carbon cycling in the ocean's largest habitat.
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              Feast and famine--microbial life in the deep-sea bed.

              Bo Jørgensen, Antje Boetius (2007)
              The seabed is a diverse environment that ranges from the desert-like deep seafloor to the rich oases that are present at seeps, vents, and food falls such as whales, wood or kelp. As well as the sedimentation of organic material from above, geological processes transport chemical energy--hydrogen, methane, hydrogen sulphide and iron--to the seafloor from the subsurface below, which provides a significant proportion of the deep-sea energy. At the sites on the seafloor where chemical energy is delivered, rich and diverse microbial communities thrive. However, most subsurface microorganisms live in conditions of extreme energy limitation, with mean generation times of up to thousands of years. Even in the most remote subsurface habitats, temperature rather than energy seems to set the ultimate limit for life, and in the deep biosphere, where energy is most depleted, life might even be based on the cleavage of water by natural radioisotopes. Here, we review microbial biodiversity and function in these intriguing environments.
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                Author and article information

                Journal
                Journal ID (nlm-ta): Microbes Environ
                Journal ID (iso-abbrev): Microbes Environ
                Title: Microbes and Environments
                Publisher: the Japanese Society of Microbial Ecology (JSME)/the Japanese Society of Soil Microbiology (JSSM)/the Taiwan Society of Microbial Ecology (TSME)/the Japanese Society of Plant Microbe Interactions (JSPMI)
                ISSN (Print): 1342-6311
                ISSN (Electronic): 1347-4405
                Publication date (Print): September 2015
                Publication date (Electronic): 04 July 2015
                Volume: 30
                Issue: 3
                Pages: 276-280
                Affiliations
                [1 ]Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC) , 2–15 Natsushima-cho, Yokosuka, Kanagawa 237–0061, Japan
                [2 ]Department of Environmental Systems Engineering, Nagaoka University of Technology , 1603–1 Kamitomioka, Nagaoka, Niigata 940–2188, Japan
                [3 ]Department of Construction Systems Engineering, Anan National College of Technology , 265 Aoki Minobayashi, Anan, Tokushima 774–0017, Japan
                [4 ]Geomicrobiology Group, Kochi Institute for Core Sample Research, JAMSTEC , Monobe B200, Nankoku, Kochi 783–8502, Japan
                Author notes
                [* ]Correspondence author. E-mail: imachi@ 123456jamstec.go.jp ; Tel: +81–46–867–9709; Fax: +81–46–867–9715.
                Article
                Publisher ID: 30_276
                DOI: 10.1264/jsme2.ME15023
                PMC ID: 4567568
                PubMed ID: 26156553
                SO-VID: c5cc389f-fca0-4ae6-bab1-cdaa1e217d9e
                Copyright © Copyright © 2015 by Japanese Society of Microbial Ecology / Japanese Society of Soil Microbiology / Taiwan Society of Microbial Ecology / Japanese Society of Plant Microbe Interactions.
                License:

                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 work is properly cited.

                History
                Date received : 18 February 2015
                Date accepted : 19 May 2015
                Categories
                Subject: Short Communication

                Keywords: apra gene,sulfate reduction,sulfur oxidation,marine sediment
                Data availability:
                Keywords: apra gene, sulfate reduction, sulfur oxidation, marine sediment

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