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      Salp blooms drive strong increases in passive carbon export in the Southern Ocean

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          Abstract

          The Southern Ocean contributes substantially to the global biological carbon pump (BCP). Salps in the Southern Ocean, in particular Salpa thompsoni, are important grazers that produce large, fast-sinking fecal pellets. Here, we quantify the salp bloom impacts on microbial dynamics and the BCP, by contrasting locations differing in salp bloom presence/absence. Salp blooms coincide with phytoplankton dominated by diatoms or prymnesiophytes, depending on water mass characteristics. Their grazing is comparable to microzooplankton during their early bloom, resulting in a decrease of ~1/3 of primary production, and negative phytoplankton rates of change are associated with all salp locations. Particle export in salp waters is always higher, ranging 2- to 8- fold (average 5-fold), compared to non-salp locations, exporting up to 46% of primary production out of the euphotic zone. BCP efficiency increases from 5 to 28% in salp areas, which is among the highest recorded in the global ocean.

          Abstract

          Gelatinous bloom-forming zooplankton—salps—alter microbial communities and quintuple the flux of sinking particles from the surface to the deep, strongly enhancing the ability of the ocean to sequester CO 2.

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          Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

          In comparative high-throughput sequencing assays, a fundamental task is the analysis of count data, such as read counts per gene in RNA-seq, for evidence of systematic changes across experimental conditions. Small replicate numbers, discreteness, large dynamic range and the presence of outliers require a suitable statistical approach. We present DESeq2, a method for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates. This enables a more quantitative analysis focused on the strength rather than the mere presence of differential expression. The DESeq2 package is available at http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0550-8) contains supplementary material, which is available to authorized users.
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            DADA2: High resolution sample inference from Illumina amplicon data

            We present DADA2, a software package that models and corrects Illumina-sequenced amplicon errors. DADA2 infers sample sequences exactly, without coarse-graining into OTUs, and resolves differences of as little as one nucleotide. In several mock communities DADA2 identified more real variants and output fewer spurious sequences than other methods. We applied DADA2 to vaginal samples from a cohort of pregnant women, revealing a diversity of previously undetected Lactobacillus crispatus variants.
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              The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

              SILVA (from Latin silva, forest, http://www.arb-silva.de) is a comprehensive web resource for up to date, quality-controlled databases of aligned ribosomal RNA (rRNA) gene sequences from the Bacteria, Archaea and Eukaryota domains and supplementary online services. The referred database release 111 (July 2012) contains 3 194 778 small subunit and 288 717 large subunit rRNA gene sequences. Since the initial description of the project, substantial new features have been introduced, including advanced quality control procedures, an improved rRNA gene aligner, online tools for probe and primer evaluation and optimized browsing, searching and downloading on the website. Furthermore, the extensively curated SILVA taxonomy and the new non-redundant SILVA datasets provide an ideal reference for high-throughput classification of data from next-generation sequencing approaches.
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                Author and article information

                Contributors
                mdecima@ucsd.edu
                Journal
                Nat Commun
                Nat Commun
                Nature Communications
                Nature Publishing Group UK (London )
                2041-1723
                2 February 2023
                2 February 2023
                2023
                : 14
                : 425
                Affiliations
                [1 ]GRID grid.419676.b, ISNI 0000 0000 9252 5808, National Institute of Water and Atmospheric Research (NIWA), ; Hataitai, Wellington 6021 New Zealand
                [2 ]GRID grid.266100.3, ISNI 0000 0001 2107 4242, Scripps Institution of Oceanography, , University of California at San Diego, ; San Diego, CA 92093 USA
                [3 ]GRID grid.255986.5, ISNI 0000 0004 0472 0419, Department of Earth, Ocean, and Atmospheric Science, , Florida State University, ; Tallahassee, FL 32304 USA
                [4 ]GRID grid.255986.5, ISNI 0000 0004 0472 0419, Center for Ocean-Atmospheric Prediction Studies, , Florida State University, ; Tallahassee, FL 32310 USA
                [5 ]GRID grid.410389.7, ISNI 0000 0001 0943 6642, Instituto Español de Oceanografía, , Centro Oceanográfico de Gijón, Avenida Príncipe de Asturias, ; 70 bis, 33212 Gijón, Spain
                [6 ]GRID grid.410445.0, ISNI 0000 0001 2188 0957, Department of Oceanography, , University of Hawai’i at Mānoa, ; Honolulu, HI 96822 USA
                [7 ]GRID grid.59025.3b, ISNI 0000 0001 2224 0361, Asian School of the Environment, , Nanyang Technological University, ; 50 Nanyang Avenue, Singapore, 639798 Singapore
                [8 ]GRID grid.419676.b, ISNI 0000 0000 9252 5808, National Institute of Water and Atmospheric Research, ; P.O. Box 11-115, Hamilton, New Zealand
                [9 ]GRID grid.175455.7, ISNI 0000 0001 2206 1080, College of Fisheries and Ocean Sciences, , University of Alaska, ; Fairbanks, AK 99775 USA
                [10 ]GRID grid.29980.3a, ISNI 0000 0004 1936 7830, Department of Microbiology and Immunology, , University of Otago, ; Dunedin, New Zealand
                [11 ]GRID grid.10420.37, ISNI 0000 0001 2286 1424, Department of Functional & Evolutionary Ecology, , University of Vienna, ; Vienna, 1090 Austria
                [12 ]GRID grid.430387.b, ISNI 0000 0004 1936 8796, Environmental Biophysics and Molecular Ecology Program, Department of Marine and Coastal Sciences, Rutgers, , The State University of New Jersey, ; New Brunswick, NJ 08901 USA
                Author information
                http://orcid.org/0000-0003-0340-648X
                http://orcid.org/0000-0002-1963-8907
                http://orcid.org/0000-0003-1274-3752
                http://orcid.org/0000-0001-7281-4706
                http://orcid.org/0000-0001-6285-1925
                http://orcid.org/0000-0002-8549-0250
                http://orcid.org/0000-0002-5862-0726
                http://orcid.org/0000-0001-8907-1494
                http://orcid.org/0000-0002-8202-0923
                Article
                35204
                10.1038/s41467-022-35204-6
                9894854
                36732522
                440fb92a-0062-4549-bf0a-72f519131b92
                © The Author(s) 2023

                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 April 2021
                : 23 November 2022
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                © The Author(s) 2023

                Uncategorized
                ecosystem ecology,carbon cycle,marine biology
                Uncategorized
                ecosystem ecology, carbon cycle, marine biology

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