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      Methylotrophic Communities Associated with a Greenland Ice Sheet Methane Release Hotspot

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          Abstract

          Subglacial environments provide conditions suitable for the microbial production of methane, an important greenhouse gas, which can be released from beneath the ice as a result of glacial melting. High gaseous methane emissions have recently been discovered at Russell Glacier, an outlet of the southwestern margin of the Greenland Ice Sheet, acting not only as a potential climate amplifier but also as a substrate for methane consuming microorganisms. Here, we describe the composition of the microbial assemblage exported in meltwater from the methane release hotspot at Russell Glacier and its changes over the melt season and as it travels downstream. We found that a substantial part (relative abundance 27.2% across the whole dataset) of the exported assemblage was made up of methylotrophs and that the relative abundance of methylotrophs increased as the melt season progressed, likely due to the seasonal development of the glacial drainage system. The methylotrophs were dominated by representatives of type I methanotrophs from the Gammaproteobacteria; however, their relative abundance decreased with increasing distance from the ice margin at the expense of type II methanotrophs and/or methylotrophs from the Alphaproteobacteria and Betaproteobacteria. Our results show that subglacial methane release hotspot sites can be colonized by microorganisms that can potentially reduce methane emissions.

          Supplementary Information

          The online version contains supplementary material available at 10.1007/s00248-023-02302-x.

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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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            Cutadapt removes adapter sequences from high-throughput sequencing reads

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              RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

              Motivation: Phylogenies are increasingly used in all fields of medical and biological research. Moreover, because of the next-generation sequencing revolution, datasets used for conducting phylogenetic analyses grow at an unprecedented pace. RAxML (Randomized Axelerated Maximum Likelihood) is a popular program for phylogenetic analyses of large datasets under maximum likelihood. Since the last RAxML paper in 2006, it has been continuously maintained and extended to accommodate the increasingly growing input datasets and to serve the needs of the user community. Results: I present some of the most notable new features and extensions of RAxML, such as a substantial extension of substitution models and supported data types, the introduction of SSE3, AVX and AVX2 vector intrinsics, techniques for reducing the memory requirements of the code and a plethora of operations for conducting post-analyses on sets of trees. In addition, an up-to-date 50-page user manual covering all new RAxML options is available. Availability and implementation: The code is available under GNU GPL at https://github.com/stamatak/standard-RAxML. Contact: alexandros.stamatakis@h-its.org Supplementary information: Supplementary data are available at Bioinformatics online.
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                Author and article information

                Contributors
                matej.znaminko@uef.fi
                marek.stibal@natur.cuni.cz
                Journal
                Microb Ecol
                Microb Ecol
                Microbial Ecology
                Springer US (New York )
                0095-3628
                1432-184X
                16 October 2023
                16 October 2023
                2023
                : 86
                : 4
                : 3057-3067
                Affiliations
                [1 ]Department of Ecology, Faculty of Science, Charles University, ( https://ror.org/024d6js02) Prague, Czechia
                [2 ]Current address: Department of Environmental and Biological Sciences, University of Eastern Finland, ( https://ror.org/00cyydd11) Kuopio, Finland
                [3 ]Department of Geoscience and Natural Resource Management, University of Copenhagen, ( https://ror.org/035b05819) Copenhagen, Denmark
                [4 ]Department of Ecoscience, Arctic Environment, Aarhus University, ( https://ror.org/01aj84f44) Roskilde, Denmark
                Article
                2302
                10.1007/s00248-023-02302-x
                10640400
                37843656
                f5ff81dc-8be4-471d-ad71-7a9ea9d87459
                © 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 licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence 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 licence, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 4 April 2023
                : 9 September 2023
                Funding
                Funded by: FundRef http://dx.doi.org/10.13039/501100009910, Hartmann Fonden;
                Award ID: A32524
                Award ID: A32524
                Award Recipient :
                Funded by: Danish Independent Research Fund
                Award ID: 0135-00229B
                Award ID: 0135-00229B
                Award Recipient :
                Funded by: Czech Ministry of Education, Youth and Sports
                Award ID: LL2004 ‘MARCH4G’
                Award Recipient :
                Funded by: University of Eastern Finland (including Kuopio University Hospital)
                Categories
                Research
                Custom metadata
                © Springer Science+Business Media, LLC, part of Springer Nature 2023

                Microbiology & Virology
                methylotrophs,methanotrophs,subglacial environment,greenland ice sheet
                Microbiology & Virology
                methylotrophs, methanotrophs, subglacial environment, greenland ice sheet

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