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      Microbial Communities Under Distinct Thermal and Geochemical Regimes in Axial and Off-Axis Sediments of Guaymas Basin

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          Abstract

          Cold seeps and hydrothermal vents are seafloor habitats fueled by subsurface energy sources. Both habitat types coexist in Guaymas Basin in the Gulf of California, providing an opportunity to compare microbial communities with distinct physiologies adapted to different thermal regimes. Hydrothermally active sites in the southern Guaymas Basin axial valley, and cold seep sites at Octopus Mound, a carbonate mound with abundant methanotrophic cold seep fauna at the Central Seep location on the northern off-axis flanking regions, show consistent geochemical and microbial differences between hot, temperate, cold seep, and background sites. The changing microbial actors include autotrophic and heterotrophic bacterial and archaeal lineages that catalyze sulfur, nitrogen, and methane cycling, organic matter degradation, and hydrocarbon oxidation. Thermal, biogeochemical, and microbiological characteristics of the sampling locations indicate that sediment thermal regime and seep-derived or hydrothermal energy sources structure the microbial communities at the sediment surface.

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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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              MUSCLE: multiple sequence alignment with high accuracy and high throughput.

              We describe MUSCLE, a new computer program for creating multiple alignments of protein sequences. Elements of the algorithm include fast distance estimation using kmer counting, progressive alignment using a new profile function we call the log-expectation score, and refinement using tree-dependent restricted partitioning. The speed and accuracy of MUSCLE are compared with T-Coffee, MAFFT and CLUSTALW on four test sets of reference alignments: BAliBASE, SABmark, SMART and a new benchmark, PREFAB. MUSCLE achieves the highest, or joint highest, rank in accuracy on each of these sets. Without refinement, MUSCLE achieves average accuracy statistically indistinguishable from T-Coffee and MAFFT, and is the fastest of the tested methods for large numbers of sequences, aligning 5000 sequences of average length 350 in 7 min on a current desktop computer. The MUSCLE program, source code and PREFAB test data are freely available at http://www.drive5. com/muscle.
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                Author and article information

                Contributors
                Journal
                Front Microbiol
                Front Microbiol
                Front. Microbiol.
                Frontiers in Microbiology
                Frontiers Media S.A.
                1664-302X
                12 February 2021
                2021
                : 12
                : 633649
                Affiliations
                [1] 1Department of Marine Sciences, University of North Carolina at Chapel Hill , Chapel Hill, NC, United States
                [2] 2Max-Planck-Institute for Marine Microbiology , Bremen, Germany
                [3] 3MARUM, Center for Marine Environmental Sciences, University of Bremen , Bremen, Germany
                [4] 4Department of Earth, Ocean and Atmospheric Sciences, Florida State University , Tallahassee, FL, United States
                [5] 5Department of Earth and Environmental Sciences, University of Minnesota , St. Paul, MI, United States
                [6] 6Department of Organismic and Evolutionary Biology, Harvard University , Cambridge, MA, United States
                [7] 7United States Environmental Protection Agency , Research Triangle Park, NC, United States
                [8] 8Frontiers Science Centre for Deep Ocean Multispheres and Earth System (FDOMES)/Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China , Qingdao, China
                [9] 9Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Ocean University of China , Qingdao, China
                [10] 10Department of Marine Sciences, University of Georgia , Athens, GA, United States
                [11] 11Department of Biological Sciences, Miami University , Oxford, OH, United States
                [12] 12Geology & Geophysics Department, Woods Hole Oceanographic Institution , Woods Hole, MA, United States
                [13] 13Marine Biological Laboratory, The Ecosystems Center , Woods Hole, MA, United States
                [14] 14Marine Biological Laboratory, The Josephine Bay Paul Center for Comparative Molecular Biology and Evolution , Woods Hole, MA, United States
                Author notes

                Edited by: Axel Schippers, Federal Institute for Geosciences and Natural Resources, Germany

                Reviewed by: Takuro Nunoura, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Japan; Gordon Webster, Cardiff University, United Kingdom

                *Correspondence: Andreas Teske, teske@ 123456email.unc.edu

                This article was submitted to Extreme Microbiology, a section of the journal Frontiers in Microbiology

                Article
                10.3389/fmicb.2021.633649
                7906980
                33643265
                39dea478-7da5-4302-b916-ca7917e025d0
                Copyright © 2021 Teske, Wegener, Chanton, White, MacGregor, Hoer, de Beer, Zhuang, Saxton, Joye, Lizarralde, Soule and Ruff.

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                History
                : 25 November 2020
                : 12 January 2021
                Page count
                Figures: 11, Tables: 1, Equations: 0, References: 111, Pages: 23, Words: 13790
                Funding
                Funded by: NSF Biological Oceanography
                Award ID: 1357238
                Award ID: 1357360
                Funded by: Marine Biological Laboratory 10.13039/100006049
                Categories
                Microbiology
                Original Research

                Microbiology & Virology
                cold seep,hydrothermal sediment,porewater profiles,bacteria,archaea,guaymas basin

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