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      Sustained bacterial N 2O reduction at acidic pH

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          Abstract

          Nitrous oxide (N 2O) is a climate-active gas with emissions predicted to increase due to agricultural intensification. Microbial reduction of N 2O to dinitrogen (N 2) is the major consumption process but microbial N 2O reduction under acidic conditions is considered negligible, albeit strongly acidic soils harbor nosZ genes encoding N 2O reductase. Here, we study a co-culture derived from acidic tropical forest soil that reduces N 2O at pH 4.5. The co-culture exhibits bimodal growth with a Serratia sp. fermenting pyruvate followed by hydrogenotrophic N 2O reduction by a Desulfosporosinus sp. Integrated omics and physiological characterization revealed interspecies nutritional interactions, with the pyruvate fermenting Serratia sp. supplying amino acids as essential growth factors to the N 2O-reducing Desulfosporosinus sp. Thus, we demonstrate growth-linked N 2O reduction between pH 4.5 and 6, highlighting microbial N 2O reduction potential in acidic soils.

          Abstract

          Microbial reduction of nitrous oxide to dinitrogen is considered negligible under acidic conditions. However, Guang He et al. show that a co-culture of two bacterial species derived from acidic tropical forest soil can reduce nitrous oxide at pH 4.5.

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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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              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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                Author and article information

                Contributors
                frank.loeffler@utk.edu
                Journal
                Nat Commun
                Nat Commun
                Nature Communications
                Nature Publishing Group UK (London )
                2041-1723
                15 May 2024
                15 May 2024
                2024
                : 15
                : 4092
                Affiliations
                [1 ]Department of Biosystems Engineering and Soil Science, The University of Tennessee, Knoxville, ( https://ror.org/020f3ap87) Knoxville, TN 37996 USA
                [2 ]Department of Civil and Environmental Engineering, The University of Tennessee, Knoxville, ( https://ror.org/020f3ap87) Knoxville, TN 37996 USA
                [3 ]Center for Environmental Biotechnology, The University of Tennessee, Knoxville, ( https://ror.org/020f3ap87) Knoxville, TN 37996 USA
                [4 ]Department of Microbiology, The University of Tennessee Knoxville, ( https://ror.org/020f3ap87) Knoxville, TN 37996 USA
                [5 ]Biosciences Division, Oak Ridge National Laboratory, ( https://ror.org/01qz5mb56) Oak Ridge, TN 37831 USA
                [6 ]School of Civil and Environmental Engineering, Georgia Institute of Technology, ( https://ror.org/01zkghx44) Atlanta, GA 30332 USA
                [7 ]GRID grid.19006.3e, ISNI 0000 0000 9632 6718, Present Address: Department of Chemistry and Biochemistry, , University of California, Los Angeles, ; Los Angeles, CA 90095 USA
                Author information
                http://orcid.org/0000-0003-0061-1373
                http://orcid.org/0000-0002-8767-3130
                http://orcid.org/0000-0002-8878-2419
                http://orcid.org/0000-0002-0954-4755
                http://orcid.org/0000-0002-9797-4279
                Article
                48236
                10.1038/s41467-024-48236-x
                11096178
                38750010
                2930ebc3-f0d8-4201-9b1d-71ba3d83e329
                © The Author(s) 2024

                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
                : 12 January 2024
                : 23 April 2024
                Funding
                Funded by: FundRef https://doi.org/10.13039/100000001, National Science Foundation (NSF);
                Award ID: 1831599
                Award Recipient :
                Categories
                Article
                Custom metadata
                © Springer Nature Limited 2024

                Uncategorized
                environmental sciences,environmental microbiology
                Uncategorized
                environmental sciences, environmental microbiology

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