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      Deep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities

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      1 , , 1 , 1 , 2 , 1 , 3 , 1 , 4 , 1 , 1 , 2 , 2 , 5 , 6 , 7 , 8 , 9 , 25 , 10 , 11 , 12 , 12 , 13 , 14 , 15 , 16 , 17 , 18 , 19 , 20 , 12 , 1 , 21 , 22 , 1 , 23 , 1 , 24
      Communications Biology
      Nature Publishing Group UK
      Microbial ecology, Environmental microbiology, Microbial biooceanography

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          Abstract

          The deep sea, the largest ocean’s compartment, drives planetary-scale biogeochemical cycling. Yet, the functional exploration of its microbial communities lags far behind other environments. Here we analyze 58 metagenomes from tropical and subtropical deep oceans to generate the Malaspina Gene Database. Free-living or particle-attached lifestyles drive functional differences in bathypelagic prokaryotic communities, regardless of their biogeography. Ammonia and CO oxidation pathways are enriched in the free-living microbial communities and dissimilatory nitrate reduction to ammonium and H 2 oxidation pathways in the particle-attached, while the Calvin Benson-Bassham cycle is the most prevalent inorganic carbon fixation pathway in both size fractions. Reconstruction of the Malaspina Deep Metagenome-Assembled Genomes reveals unique non-cyanobacterial diazotrophic bacteria and chemolithoautotrophic prokaryotes. The widespread potential to grow both autotrophically and heterotrophically suggests that mixotrophy is an ecologically relevant trait in the deep ocean. These results expand our understanding of the functional microbial structure and metabolic capabilities of the largest Earth aquatic ecosystem.

          Abstract

          Silvia Acinas et al. report the Malaspina Gene Database, a gene catalogue from deep ocean microbes and the Malaspina Deep Metagenome-Assembled Genomes (MAGs) which is made publicly available. The analysis of the metabolic pathways within these MAGs sheds light on the composition and of the strategies these microbes use to survive the deep ocean microbiome.

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          The Sequence Alignment/Map format and SAMtools

          Summary: The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms. It is flexible in style, compact in size, efficient in random access and is the format in which alignments from the 1000 Genomes Project are released. SAMtools implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments. Availability: http://samtools.sourceforge.net Contact: rd@sanger.ac.uk
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            Fast gapped-read alignment with Bowtie 2.

            As the rate of sequencing increases, greater throughput is demanded from read aligners. The full-text minute index is often used to make alignment very fast and memory-efficient, but the approach is ill-suited to finding longer, gapped alignments. Bowtie 2 combines the strengths of the full-text minute index with the flexibility and speed of hardware-accelerated dynamic programming algorithms to achieve a combination of high speed, sensitivity and accuracy.
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              MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

              We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were implemented after the previous major update. This report shows actual examples to explain how these features work, alone and in combination. Some examples incorrectly aligned by MAFFT are also shown to clarify its limitations. We discuss how to avoid misalignments, and our ongoing efforts to overcome such limitations.
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                Author and article information

                Contributors
                sacinas@icm.csic.es
                Journal
                Commun Biol
                Commun Biol
                Communications Biology
                Nature Publishing Group UK (London )
                2399-3642
                21 May 2021
                21 May 2021
                2021
                : 4
                : 604
                Affiliations
                [1 ]GRID grid.428945.6, Department of Marine Biology and Oceanography, , Institute of Marine Sciences (ICM), CSIC, ; Barcelona, Spain
                [2 ]GRID grid.5801.c, ISNI 0000 0001 2156 2780, Department of Biology, , Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zurich, ; Zurich, Switzerland
                [3 ]GRID grid.205975.c, ISNI 0000 0001 0740 6917, Department of Ocean Sciences, , University of California, ; Santa Cruz, CA USA
                [4 ]GRID grid.4521.2, ISNI 0000 0004 1769 9380, Instituto de Oceanografía y Cambio Global, IOCAG, , Universidad de Las Palmas de Gran Canaria, ULPGC, ; Gran Canaria, Spain
                [5 ]GRID grid.5399.6, ISNI 0000 0001 2176 4817, Aix Marseille Univ., Université de Toulon, CNRS, ; Marseille, France
                [6 ]GRID grid.258799.8, ISNI 0000 0004 0372 2033, Institute for Chemical Research, Kyoto University, ; Gokasho, Uji Japan
                [7 ]GRID grid.4989.c, ISNI 0000 0001 2348 0746, Cellular and Molecular Microbiology, Faculté des Sciences, Université libre de Bruxelles (ULB), ; Brussels, Belgium
                [8 ]GRID grid.4989.c, ISNI 0000 0001 2348 0746, Interuniversity Institute for Bioinformatics in Brussels, ULB-VUB, ; Brussels, Belgium
                [9 ]GRID grid.261331.4, ISNI 0000 0001 2285 7943, Department of Microbiology, , The Ohio State University, ; Columbus, OH USA
                [10 ]GRID grid.10041.34, ISNI 0000000121060879, Department of Microbiology, , University of La Laguna, ; La Laguna, Spain
                [11 ]GRID grid.410389.7, ISNI 0000 0001 0943 6642, Spanish Institute of Oceanography (IEO), Oceanographic Center of The Canary Islands, Dársena Pesquera, ; Santa Cruz de Tenerife, Spain
                [12 ]GRID grid.45672.32, ISNI 0000 0001 1926 5090, King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), ; Thuwal, Saudi Arabia
                [13 ]GRID grid.462036.5, Institut de Biologie de l’ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, ; Paris, France
                [14 ]Research Federation for the study of Global Ocean Systems Ecology and Evolution, Paris, France
                [15 ]GRID grid.415751.3, Department of Microbiology and Immunology, , Rega Institute, KU Leuven – University of Leuven, ; Leuven, Belgium
                [16 ]VIB Center for Microbiology, Leuven, Belgium
                [17 ]GRID grid.225360.0, ISNI 0000 0000 9709 7726, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), , Wellcome Genome Campus, ; Hinxton, Cambridge, United Kingdom
                [18 ]GRID grid.7704.4, ISNI 0000 0001 2297 4381, PANGAEA, Data Publisher for Earth and Environmental Science, , University of Bremen, ; Bremen, Germany
                [19 ]GRID grid.4709.a, ISNI 0000 0004 0495 846X, Structural and Computational Biology, European Molecular Biology Laboratory, ; Heidelberg, Germany
                [20 ]GRID grid.45672.32, ISNI 0000 0001 1926 5090, King Abdullah University of Science and Technology (KAUST), Red Sea Research Center (RSRC), ; Thuwal, Saudi Arabia
                [21 ]GRID grid.261331.4, ISNI 0000 0001 2285 7943, Department of Microbiology and Civil Environmental and Geodetic Engineering, , The Ohio State University, ; Columbus, OH USA
                [22 ]GRID grid.428469.5, ISNI 0000 0004 1794 1018, Department of Systems Biology, Centro Nacional de Biotecnología (CNB), CSIC, ; Madrid, Spain
                [23 ]GRID grid.45672.32, ISNI 0000 0001 1926 5090, King Abdullah University of Science and Technology (KAUST), Red Sea Research Center (RSRC) and Computational Bioscience Research Center (CBRC), ; Thuwal, Saudi Arabia
                [24 ]GRID grid.1038.a, ISNI 0000 0004 0389 4302, Centre for Marine Ecosystems Research, School of Sciences, Edith Cowan University, ; Joondalup, WA Australia
                [25 ]GRID grid.451309.a, ISNI 0000 0004 0449 479X, Present Address: U.S. Department of Energy Joint Genome Institute, ; Berkeley, CA USA
                Author information
                http://orcid.org/0000-0002-3439-0428
                http://orcid.org/0000-0003-2787-822X
                http://orcid.org/0000-0002-9786-1493
                http://orcid.org/0000-0001-8431-9278
                http://orcid.org/0000-0001-7175-8941
                http://orcid.org/0000-0002-8213-0604
                http://orcid.org/0000-0003-2966-9093
                http://orcid.org/0000-0003-3065-0314
                http://orcid.org/0000-0001-6594-377X
                http://orcid.org/0000-0002-5309-1845
                http://orcid.org/0000-0002-5831-5895
                http://orcid.org/0000-0002-9926-3323
                http://orcid.org/0000-0002-0190-6950
                http://orcid.org/0000-0001-5306-847X
                http://orcid.org/0000-0002-6659-3713
                http://orcid.org/0000-0003-3835-6187
                http://orcid.org/0000-0002-2627-833X
                http://orcid.org/0000-0003-0536-7293
                http://orcid.org/0000-0002-0420-5914
                http://orcid.org/0000-0001-8398-8234
                http://orcid.org/0000-0001-9172-5418
                http://orcid.org/0000-0002-1213-1361
                http://orcid.org/0000-0001-5238-2387
                Article
                2112
                10.1038/s42003-021-02112-2
                8139981
                34021239
                3327c0cd-4937-40bb-b493-42d2015f012a
                © The Author(s) 2021

                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
                : 25 September 2020
                : 16 April 2021
                Funding
                Funded by: Spanish Ministry of Economy and Competitiveness (MINECO)through the Consolider-Ingenio program (Malaspina 2010 Expedition, ref. CSD2008-00077). U.S. Department of Energy Joint Genome Institute, supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02 05CH11231 to SGA (CSP 612 “Microbial metagenomics and transcriptomics from a global deep-ocean expedition”). The project MAGGY (CTM2017-87736-R) to SGA from the Spanish Ministry of Economy and Competitiveness. Grup de Recerca 2017SGR/1568 from Generalitat de Catalunya. King Abdullah University of Science and Technology (KAUST) under contract OSR #3362. Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S).
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                © The Author(s) 2021

                microbial ecology,environmental microbiology,microbial biooceanography

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