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      Microbial community and geochemical analyses of trans-trench sediments for understanding the roles of hadal environments

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          Abstract

          Hadal trench bottom (>6000 m below sea level) sediments harbor higher microbial cell abundance compared with adjacent abyssal plain sediments. This is supported by the accumulation of sedimentary organic matter (OM), facilitated by trench topography. However, the distribution of benthic microbes in different trench systems has not been well explored yet. Here, we carried out small subunit ribosomal RNA gene tag sequencing for 92 sediment subsamples of seven abyssal and seven hadal sediment cores collected from three trench regions in the northwest Pacific Ocean: the Japan, Izu-Ogasawara, and Mariana Trenches. Tag-sequencing analyses showed specific distribution patterns of several phyla associated with oxygen and nitrate. The community structure was distinct between abyssal and hadal sediments, following geographic locations and factors represented by sediment depth. Co-occurrence network revealed six potential prokaryotic consortia that covaried across regions. Our results further support that the OM cycle is driven by hadal currents and/or rapid burial shapes microbial community structures at trench bottom sites, in addition to vertical deposition from the surface ocean. Our trans-trench analysis highlights intra- and inter-trench distributions of microbial assemblages and geochemistry in surface seafloor sediments, providing novel insights into ultradeep-sea microbial ecology, one of the last frontiers on our planet.

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          FLASH: fast length adjustment of short reads to improve genome assemblies.

          Next-generation sequencing technologies generate very large numbers of short reads. Even with very deep genome coverage, short read lengths cause problems in de novo assemblies. The use of paired-end libraries with a fragment size shorter than twice the read length provides an opportunity to generate much longer reads by overlapping and merging read pairs before assembling a genome. We present FLASH, a fast computational tool to extend the length of short reads by overlapping paired-end reads from fragment libraries that are sufficiently short. We tested the correctness of the tool on one million simulated read pairs, and we then applied it as a pre-processor for genome assemblies of Illumina reads from the bacterium Staphylococcus aureus and human chromosome 14. FLASH correctly extended and merged reads >99% of the time on simulated reads with an error rate of <1%. With adequately set parameters, FLASH correctly merged reads over 90% of the time even when the reads contained up to 5% errors. When FLASH was used to extend reads prior to assembly, the resulting assemblies had substantially greater N50 lengths for both contigs and scaffolds. The FLASH system is implemented in C and is freely available as open-source code at http://www.cbcb.umd.edu/software/flash. t.magoc@gmail.com.
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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

                Contributors
                hiraokas@jamstec.go.jp
                takuron@jamstec.go.jp
                Journal
                ISME J
                ISME J
                The ISME Journal
                Nature Publishing Group UK (London )
                1751-7362
                1751-7370
                11 December 2019
                11 December 2019
                March 2020
                : 14
                : 3
                : 740-756
                Affiliations
                [1 ]ISNI 0000 0001 2191 0132, GRID grid.410588.0, Research Center for Bioscience and Nanoscience (CeBN), , Japan Agency for Marine-Earth Science and Technology (JAMSTEC), ; 2–15 Natsushima-cho, Yokosuka, 237–0061 Kanagawa Japan
                [2 ]ISNI 0000 0001 2191 0132, GRID grid.410588.0, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), , Japan Agency for Marine-Earth Science and Technology (JAMSTEC), ; 2–15 Natsushima-cho, Yokosuka, 237–0061 Kanagawa Japan
                [3 ]ISNI 0000 0001 2191 0132, GRID grid.410588.0, Project Team for Development of New-generation Research Protocol for Submarine Resources, , Japan Agency for Marine-Earth Science and Technology (JAMSTEC), ; 2–15 Natsushima-cho, Yokosuka, 237–0061 Kanagawa Japan
                [4 ]ISNI 0000 0001 2191 0132, GRID grid.410588.0, Research and Development Center for Submarine Resources, , Japan Agency for Marine-Earth Science and Technology (JAMSTEC), ; 2–15 Natsushima-cho, Yokosuka, 237–0061 Kanagawa Japan
                [5 ]ISNI 0000 0004 1758 0806, GRID grid.6401.3, Stazione Zoologica Anton Dohrn, Villa Comunale, ; Naples, 80121 Italy
                [6 ]ISNI 0000 0001 1017 3210, GRID grid.7010.6, Department of Life and Environmental Sciences, , Polytechnic University of Marche, ; Ancona, 60131 Italy
                [7 ]ISNI 0000 0001 1017 3210, GRID grid.7010.6, Department of Materials, Environmental Sciences and Urban Planning, , Polytechnic University of Marche, ; Ancona, 60131 Italy
                [8 ]ISNI 0000 0001 2191 0132, GRID grid.410588.0, Marine Biodiversity and Environmental Assessment Research Center (BioEnv), , Japan Agency for Marine-Earth Science and Technology (JAMSTEC), ; 2–15 Natsushima-cho, Yokosuka, 237–0061 Kanagawa Japan
                [9 ]ISNI 0000 0001 2151 536X, GRID grid.26999.3d, Present Address: Atmosphere and Ocean Research Institute, , The University of Tokyo, ; 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8564 Japan
                [10 ]ISNI 0000 0004 1762 8507, GRID grid.265125.7, Present Address: Faculty of Science and Engineering, , Toyo University, ; 2100 Kujirai, Kawagoe, 350-8585 Saitama Japan
                Author information
                http://orcid.org/0000-0001-5008-0916
                http://orcid.org/0000-0001-7690-0222
                http://orcid.org/0000-0002-6467-670X
                http://orcid.org/0000-0003-4043-376X
                http://orcid.org/0000-0003-2323-0880
                Article
                564
                10.1038/s41396-019-0564-z
                7031335
                31827245
                006c3442-c91d-4f20-9342-0a16cb3859a0
                © The Author(s) 2019

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 9 August 2019
                : 20 November 2019
                : 28 November 2019
                Funding
                Funded by: FundRef https://doi.org/10.13039/501100000646, Japan Society for the Promotion of Science London (JSPS London);
                Award ID: JP18H06080
                Award Recipient :
                Categories
                Article
                Custom metadata
                © International Society for Microbial Ecology 2020

                Microbiology & Virology
                microbial ecology,environmental sciences,biogeochemistry
                Microbiology & Virology
                microbial ecology, environmental sciences, biogeochemistry

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