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      Deltaproteobacterium Strain KaireiS1, a Mesophilic, Hydrogen-Oxidizing and Sulfate-Reducing Bacterium From an Inactive Deep-Sea Hydrothermal Chimney

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          Abstract

          A novel deltaproteobacterial, mesophilic, hydrogen-oxidizing, and sulfate-reducing bacterium (strain KaireiS1) was highly enriched from an inactive chimney located in the active zone of the Kairei hydrothermal vent field (Central Indian Ridge) in the Indian Ocean. Based on 16S rRNA gene analyses, strain KaireiS1 is the currently only cultured representative of a cluster of uncultured Deltaproteobacteria, positioned within the Desulfobulbaceae family, between the Desulfobulbus genus and the “Cable Bacteria.” A facultative autotrophic lifestyle of KaireiS1 is indicated by its growth in the absence of organic compounds, measurements of CO 2-fixation rates, and activity measurements of carbon monoxide dehydrogenase, the key enzyme of the reductive Acetyl-CoA pathway. Apart from hydrogen, strain KaireiS1 can also use propionate, lactate, and pentadecane as electron donors. However, the highest cell numbers were reached when grown autotrophically with molecular hydrogen. Hydrogen uptake activity was found in membrane and soluble fractions of cell-free extracts and reached up to 2,981±129 nmol H 2*min −1*mg −1 of partially purified protein. Commonly, autotrophic sulfate-reducing bacteria from the Deltaproteobacteria class, thriving in hydrothermal vent habitats are described as thermophiles. Given its physiological characteristics and specific isolation source, strain KaireiS1 demonstrates a previously unnoticed potential for microbial sulfate reduction by autotrophs taking place at moderate temperatures in hydrothermal vent fields.

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          The Molecular Evolutionary Genetics Analysis (Mega) software implements many analytical methods and tools for phylogenomics and phylomedicine. Here, we report a transformation of Mega to enable cross-platform use on Microsoft Windows and Linux operating systems. Mega X does not require virtualization or emulation software and provides a uniform user experience across platforms. Mega X has additionally been upgraded to use multiple computing cores for many molecular evolutionary analyses. Mega X is available in two interfaces (graphical and command line) and can be downloaded from www.megasoftware.net free of charge.
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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
                22 September 2021
                2021
                : 12
                : 686276
                Affiliations
                [1] 1GEOMAR and Molecular Biology of Microbial Consortia, GEOMAR Helmholtz Center for Ocean Research Kiel , Kiel, Germany
                [2] 2GEOMAR and Molecular Biology of Microbial Consortia, Biocenter Klein Flottbek, University of Hamburg , Hamburg, Germany
                [3] 3Microbiology and Biotechnology, Biocenter Klein Flottbek, University of Hamburg , Hamburg, Germany
                [4] 4Federal Institute for Geosciences and Natural Resources (BGR) , Hannover, Germany
                [5] 5International Seabed Authority , Kingston, Jamaica
                Author notes

                Edited by: Daniel P. R. Herlemann, Estonian University of Life Sciences, Estonia

                Reviewed by: Heide N. Schulz-Vogt, Leibniz Institute for Baltic Sea Research (LG), Germany; Wolfgang Buckel, University of Marburg, Germany

                *Correspondence: Mirjam Perner, mperner@ 123456geomar.de

                These authors have contributed equally to this work and share first authorship

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

                Article
                10.3389/fmicb.2021.686276
                8494109
                34630341
                9b3d31dd-9f9e-408e-bdd3-ddd5be7bce18
                Copyright © 2021 Adam, Han, Laufer-Meiser, Bährle, Schwarz-Schampera, Schippers and Perner.

                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
                : 26 March 2021
                : 24 August 2021
                Page count
                Figures: 7, Tables: 2, Equations: 0, References: 88, Pages: 16, Words: 10871
                Funding
                Funded by: Federal Institute for Geosciences and Natural Resources (BGR)
                Categories
                Microbiology
                Original Research

                Microbiology & Virology
                deltaproteobacteria,desulfobulbaceae,hydrogen oxidation,sulfate reduction,hydrothermal deep-sea vent

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