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      Generation of zero-valent sulfur from dissimilatory sulfate reduction in sulfate-reducing microorganisms

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          Significance

          Dissimilatory sulfate reduction (DSR) is one of the oldest and most prominent microbial metabolic pathways on Earth. It is generally accompanied by zero-valent sulfur (ZVS) that is involved in several cryptic pathways in marine and terrestrial environments. In this study, we identified a to-date unknown DSR pathway or sulfate-to-ZVS conversion mediated by sulfate-reducing microorganisms. This finding provides further insights into the sulfur cycle, which may help reveal details about cryptic element cycling pathways and improve our understanding of the sulfur metabolism in early Archaean microorganisms.

          Abstract

          Dissimilatory sulfate reduction (DSR) mediated by sulfate-reducing microorganisms (SRMs) plays a pivotal role in global sulfur, carbon, oxygen, and iron cycles since at least 3.5 billion y ago. The canonical DSR pathway is believed to be sulfate reduction to sulfide. Herein, we report a DSR pathway in phylogenetically diverse SRMs through which zero-valent sulfur (ZVS) is directly generated. We identified that approximately 9% of sulfate reduction was directed toward ZVS with S 8 as a predominant product, and the ratio of sulfate-to-ZVS could be changed with SRMs’ growth conditions, particularly the medium salinity. Further coculturing experiments and metadata analyses revealed that DSR-derived ZVS supported the growth of various ZVS-metabolizing microorganisms, highlighting this pathway as an essential component of the sulfur biogeochemical cycle.

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          Most cited references75

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          Trimmomatic: a flexible trimmer for Illumina sequence data

          Motivation: Although many next-generation sequencing (NGS) read preprocessing tools already existed, we could not find any tool or combination of tools that met our requirements in terms of flexibility, correct handling of paired-end data and high performance. We have developed Trimmomatic as a more flexible and efficient preprocessing tool, which could correctly handle paired-end data. Results: The value of NGS read preprocessing is demonstrated for both reference-based and reference-free tasks. Trimmomatic is shown to produce output that is at least competitive with, and in many cases superior to, that produced by other tools, in all scenarios tested. Availability and implementation: Trimmomatic is licensed under GPL V3. It is cross-platform (Java 1.5+ required) and available at http://www.usadellab.org/cms/index.php?page=trimmomatic Contact: usadel@bio1.rwth-aachen.de Supplementary information: Supplementary data are available at Bioinformatics online.
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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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              HTSeq—a Python framework to work with high-throughput sequencing data

              Motivation: A large choice of tools exists for many standard tasks in the analysis of high-throughput sequencing (HTS) data. However, once a project deviates from standard workflows, custom scripts are needed. Results: We present HTSeq, a Python library to facilitate the rapid development of such scripts. HTSeq offers parsers for many common data formats in HTS projects, as well as classes to represent data, such as genomic coordinates, sequences, sequencing reads, alignments, gene model information and variant calls, and provides data structures that allow for querying via genomic coordinates. We also present htseq-count, a tool developed with HTSeq that preprocesses RNA-Seq data for differential expression analysis by counting the overlap of reads with genes. Availability and implementation: HTSeq is released as an open-source software under the GNU General Public Licence and available from http://www-huber.embl.de/HTSeq or from the Python Package Index at https://pypi.python.org/pypi/HTSeq. Contact: sanders@fs.tum.de
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                Author and article information

                Contributors
                Journal
                Proc Natl Acad Sci U S A
                Proc Natl Acad Sci U S A
                PNAS
                Proceedings of the National Academy of Sciences of the United States of America
                National Academy of Sciences
                0027-8424
                1091-6490
                8 May 2023
                16 May 2023
                8 November 2023
                : 120
                : 20
                : e2220725120
                Affiliations
                [1] aEnvironmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University , Guangzhou 510006, China
                [2] bState Key Laboratory of Isotope Geochemistry and CAS Center for Excellence in Deep Earth Science, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences , Guangzhou 510640, China
                [3] cSouthern Marine Science and Engineering Guangdong Laboratory , Guangzhou 511458, China
                [4] dUniversity of Chinese Academy of Sciences , Beijing 100039, China
                [5] eGuangdong Laboratory for Lingnan Modern Agriculture, College of Natural Resources and Environment, South China Agricultural University , Guangzhou 510642, China
                [6] fInstitute of Ecological Science, School of Life Sciences, South China Normal University , Guangzhou 510631, China
                [7] gDepartment of Biochemistry, University of Missouri-Columbia , Columbia, MO 65211
                [8] hDepartment of Molecular Microbiology & Immunology, University of Missouri-Columbia , Columbia, MO 65211
                Author notes
                2To whom correspondence may be addressed. Email: wangshanquan@ 123456mail.sysu.edu.cn .

                Edited by Bo Barker Jorgensen, Aarhus Universitet, Aarhus C, Denmark; received December 6, 2022; accepted April 14, 2023

                1S.W., Q.L., and Z.L. contributed equally to this work.

                Author information
                https://orcid.org/0000-0002-4292-950X
                https://orcid.org/0000-0001-8904-7697
                https://orcid.org/0000-0002-8743-1705
                https://orcid.org/0000-0002-9152-5544
                Article
                202220725
                10.1073/pnas.2220725120
                10194018
                37155857
                ae72f70d-6e40-46b5-afda-e64b1541a995
                Copyright © 2023 the Author(s). Published by PNAS.

                This article is distributed under Creative Commons Attribution-NonCommercial-NoDerivatives License 4.0 (CC BY-NC-ND).

                History
                : 06 December 2022
                : 14 April 2023
                Page count
                Pages: 8, Words: 5342
                Funding
                Funded by: MOST | National Natural Science Foundation of China (NSFC), FundRef 501100001809;
                Award ID: 41922049
                Award Recipient : Shanquan Wang
                Funded by: MOST | National Natural Science Foundation of China (NSFC), FundRef 501100001809;
                Award ID: 42161160306
                Award Recipient : Shanquan Wang
                Funded by: Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai);
                Award ID: SML2021SP317
                Award Recipient : Shanquan Wang Award Recipient : Mang Lin
                Funded by: Key Research Program of Frontier Sciences from the Chinese Academy of Sciences;
                Award ID: ZDBS-LY-DQC035
                Award Recipient : Shanquan Wang Award Recipient : Mang Lin
                Funded by: Guangdong Pearl River Talents Program;
                Award ID: 2019QN01L150
                Award Recipient : Shanquan Wang Award Recipient : Mang Lin
                Categories
                research-article, Research Article
                env-sci-bio, Environmental Sciences
                earth-sci, Earth, Atmospheric, and Planetary Sciences
                413
                417
                Biological Sciences
                Environmental Sciences
                Physical Sciences
                Earth, Atmospheric, and Planetary Sciences

                zero-valent sulfur,dissimilatory sulfate reduction,sulfate-reducing microorganism,sulfate reduction pathway,sulfur cycle

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