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      Degradation reduces the diversity of nitrogen-fixing bacteria in the alpine wetland on the Qinghai-Tibet Plateau

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          Abstract

          Biological nitrogen fixation is a key process in the nitrogen cycle and the main source of soil available nitrogen. The number and diversity of nitrogen-fixing bacteria directly reflect the efficiency of soil nitrogen fixation. The alpine wetland on the Qinghai-Tibet Plateau (QTP) is degrading increasingly, with a succession toward alpine meadows. Significant changes in soil physicochemical properties accompany this process. However, it is unclear how does the soil nitrogen-fixing bacteria change during the degradation processes, and what is the relationship between these changes and soil physicochemical properties. In this study, the nifH gene was used as a molecular marker to further investigate the diversity of nitrogen-fixing bacteria at different stages of degradation (none, light, and severe degeneration) in the alpine wetland. The results showed that wetland degradation significantly reduced the diversity, altered the community composition of nitrogen-fixing bacteria, decreased the relative abundance of Proteobacteria, and increased the relative abundance of Actinobacteria. In addition to the dominant phylum, the class, order, family, and genus of nitrogen-fixing bacteria had significant changes in relative abundance. Analysis of Mantel test showed that most soil factors (such as pH, soil water content (SWC), the organic carbon (TOC), total nitrogen (TN), and soil C:P ratio) and abundance had a significant positive correlation. TOC, TN, total phosphorus (TP), soil C:P ratio and Shannon had a significant positive correlation with each other. The RDA ranking further revealed that TOC, SWC, and TN were the main environmental factors influencing the community composition of nitrogen-fixing bacteria. It is found that the degradation of the alpine wetland inhibited the growth of nitrogen-fixing bacteria to a certain extent, leading to the decline of their nitrogen-fixing function.

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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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            UPARSE: highly accurate OTU sequences from microbial amplicon reads.

            Amplified marker-gene sequences can be used to understand microbial community structure, but they suffer from a high level of sequencing and amplification artifacts. The UPARSE pipeline reports operational taxonomic unit (OTU) sequences with ≤1% incorrect bases in artificial microbial community tests, compared with >3% incorrect bases commonly reported by other methods. The improved accuracy results in far fewer OTUs, consistently closer to the expected number of species in a community.
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              Embracing the unknown: disentangling the complexities of the soil microbiome

              Soil contains a vast diversity of microorganisms that can directly or indirectly modulate soil processes and terrestrial ecosystems. In this Review, Fierer summarizes the challenges in characterizing the composition and functions of the soil microbiome, and discusses key future research directions.
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                Author and article information

                Contributors
                Journal
                Front Plant Sci
                Front Plant Sci
                Front. Plant Sci.
                Frontiers in Plant Science
                Frontiers Media S.A.
                1664-462X
                04 August 2022
                2022
                : 13
                : 939762
                Affiliations
                [1] 1College of Agriculture and Animal Husbandry, Qinghai University , Xining, China
                [2] 2State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University , Xining, China
                [3] 3School of Environment, The University of Auckland , Auckland, New Zealand
                Author notes

                Edited by: Yangong Du, Northwest Institute of Plateau Biology (CAS), China

                Reviewed by: Tao Zhang, Northeast Normal University, China; Lu Wen, Inner Mongolia University, China; Ning Chen, Lanzhou University, China

                *Correspondence: Xilai Li xilai-li@ 123456163.com

                This article was submitted to Functional Plant Ecology, a section of the journal Frontiers in Plant Science

                Article
                10.3389/fpls.2022.939762
                9386517
                35991434
                d6de0f26-894b-478f-b261-e4f64cb04a7e
                Copyright © 2022 Li, Li, Yang, Shi and Li.

                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
                : 09 May 2022
                : 06 July 2022
                Page count
                Figures: 7, Tables: 0, Equations: 0, References: 60, Pages: 13, Words: 7433
                Categories
                Plant Science
                Original Research

                Plant science & Botany
                qinghai-tibet plateau,alpine wetland,wetland succession,nifh gene,nitrogen-fixing bacteria

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