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      Phylogenetic diversity of stochasticity-dominated predatory myxobacterial community drives multi-nutrient cycling in typical farmland soils

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      Science of The Total Environment
      Elsevier BV

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          Abstract

          Predatory myxobacteria are keystone taxa in the soil microbial food web that potentially regulate soil microbial community structure and ecosystem functions. However, little is known about the community assembly processes of myxobacteria in typical farmland soils over large geographic scales, in addition to their relationship with soil multi-nutrient cycling. Here, we used high-throughput sequencing techniques and phylogenetic null modeling analysis to investigate the distribution patterns and assembly processes of myxobacteria communities, in addition to interactions between myxobacteria communities and soil multi-nutrient cycling. Anaeromyxobacter (28.5 %) and Haliangium (19.6 %) were the dominant myxobacteria genera in all samples, and myxobacteria community similarities exhibited distinct distance-decay relationships. Stochastic processes (~77.8 %) were the dominant ecological processes driving the assembly of predatory myxobacteria communities over large geographical scales and under three fertilization regimes. Myxobacteria community structure was influenced by geographic factors (location and climate), soil factors (soil pH, soil organic carbon, total nitrogen, and total potassium), and fertilization, with myxobacteria community assembly being more sensitive to geographic factors. Organic-inorganic combined fertilization (NPKM) increased the proportions of deterministic processes in myxobacteria community assembly. Moreover, myxobacteria community assembly and diversity were closely associated with soil multi-nutrient cycling. Hence, myxobacteria phylogenetic α-diversity represented by NTI index is a potential bioindicators for soil multi-nutrient cycling. Overall, our findings comprehensively reveal the mechanisms of assembly of myxobacteria communities in soils over large geographic scales, and provide a theoretical basis for further research on the role of predatory bacteria on soil nutrient cycling in agro-ecosystems.

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          QIIME allows analysis of high-throughput community sequencing data.

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            Is Open Access

            Metagenomic biomarker discovery and explanation

            This study describes and validates a new method for metagenomic biomarker discovery by way of class comparison, tests of biological consistency and effect size estimation. This addresses the challenge of finding organisms, genes, or pathways that consistently explain the differences between two or more microbial communities, which is a central problem to the study of metagenomics. We extensively validate our method on several microbiomes and a convenient online interface for the method is provided at http://huttenhower.sph.harvard.edu/lefse/.
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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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                Author and article information

                Journal
                Science of The Total Environment
                Science of The Total Environment
                Elsevier BV
                00489697
                May 2023
                May 2023
                : 871
                : 161680
                Article
                10.1016/j.scitotenv.2023.161680
                36682558
                c07f4ad2-8a38-4b03-b3f7-74501d09b171
                © 2023

                https://www.elsevier.com/tdm/userlicense/1.0/

                https://doi.org/10.15223/policy-017

                https://doi.org/10.15223/policy-037

                https://doi.org/10.15223/policy-012

                https://doi.org/10.15223/policy-029

                https://doi.org/10.15223/policy-004

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