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      Microbial Ecology of the Dark Ocean above, at, and below the Seafloor

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          SUMMARY

          The majority of life on Earth—notably, microbial life—occurs in places that do not receive sunlight, with the habitats of the oceans being the largest of these reservoirs. Sunlight penetrates only a few tens to hundreds of meters into the ocean, resulting in large-scale microbial ecosystems that function in the dark. Our knowledge of microbial processes in the dark ocean—the aphotic pelagic ocean, sediments, oceanic crust, hydrothermal vents, etc.—has increased substantially in recent decades. Studies that try to decipher the activity of microorganisms in the dark ocean, where we cannot easily observe them, are yielding paradigm-shifting discoveries that are fundamentally changing our understanding of the role of the dark ocean in the global Earth system and its biogeochemical cycles. New generations of researchers and experimental tools have emerged, in the last decade in particular, owing to dedicated research programs to explore the dark ocean biosphere. This review focuses on our current understanding of microbiology in the dark ocean, outlining salient features of various habitats and discussing known and still unexplored types of microbial metabolism and their consequences in global biogeochemical cycling. We also focus on patterns of microbial diversity in the dark ocean and on processes and communities that are characteristic of the different habitats.

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          Most cited references629

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          Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB

          A 16S rRNA gene database ( http://greengenes.lbl.gov ) addresses limitations of public repositories by providing chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies. It was found that there is incongruent taxonomic nomenclature among curators even at the phylum level. Putative chimeras were identified in 3% of environmental sequences and in 0.2% of records derived from isolates. Environmental sequences were classified into 100 phylum-level lineages in the Archaea and Bacteria .
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            Early oxidation of organic matter in pelagic sediments of the eastern equatorial Atlantic: suboxic diagenesis

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              Ubiquity and diversity of ammonia-oxidizing archaea in water columns and sediments of the ocean.

              Nitrification, the microbial oxidation of ammonia to nitrite and nitrate, occurs in a wide variety of environments and plays a central role in the global nitrogen cycle. Catalyzed by the enzyme ammonia monooxygenase, the ability to oxidize ammonia was previously thought to be restricted to a few groups within the beta- and gamma-Proteobacteria. However, recent metagenomic studies have revealed the existence of unique ammonia monooxygenase alpha-subunit (amoA) genes derived from uncultivated, nonextremophilic Crenarchaeota. Here, we report molecular evidence for the widespread presence of ammonia-oxidizing archaea (AOA) in marine water columns and sediments. Using PCR primers designed to specifically target archaeal amoA, we find AOA to be pervasive in areas of the ocean that are critical for the global nitrogen cycle, including the base of the euphotic zone, suboxic water columns, and estuarine and coastal sediments. Diverse and distinct AOA communities are associated with each of these habitats, with little overlap between water columns and sediments. Within marine sediments, most AOA sequences are unique to individual sampling locations, whereas a small number of sequences are evidently cosmopolitan in distribution. Considering the abundance of nonextremophilic archaea in the ocean, our results suggest that AOA may play a significant, but previously unrecognized, role in the global nitrogen cycle.
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                Author and article information

                Journal
                Microbiology and Molecular Biology Reviews
                Microbiol Mol Biol Rev
                American Society for Microbiology
                1092-2172
                1098-5557
                June 2011
                June 2011
                : 75
                : 2
                : 361-422
                Affiliations
                [1 ]Center for Geomicrobiology, Aarhus University, 8000 Aarhus, Denmark
                [2 ]Marine Environmental Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089
                [3 ]Department of Earth Sciences, University of Southern California, Los Angeles, California 90089
                Article
                10.1128/MMBR.00039-10
                3122624
                21646433
                fc76448e-a959-4ac8-a973-a68e6b3a6da6
                © 2011

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

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