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      Grazing-induced microbiome alterations drive soil organic carbon turnover and productivity in meadow steppe

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          Abstract

          Background

          Grazing is a major modulator of biodiversity and productivity in grasslands. However, our understanding of grazing-induced changes in below-ground communities, processes, and soil productivity is limited. Here, using a long-term enclosed grazing meadow steppe, we investigated the impacts of grazing on the soil organic carbon (SOC) turnover, the microbial community composition, resistance and activity under seasonal changes, and the microbial contributions to soil productivity.

          Results

          The results demonstrated that grazing had significant impacts on soil microbial communities and ecosystem functions in meadow steppe. The highest microbial α-diversity was observed under light grazing intensity, while the highest β-diversity was observed under moderate grazing intensity. Grazing shifted the microbial composition from fungi dominated to bacteria dominated and from slow growing to fast growing, thereby resulting in a shift from fungi-dominated food webs primarily utilizing recalcitrant SOC to bacteria-dominated food webs mainly utilizing labile SOC. Moreover, the higher fungal recalcitrant-SOC-decomposing activities and bacterial labile-SOC-decomposing activities were observed in fungi- and bacteria-dominated communities, respectively. Notably, the robustness of bacterial community and the stability of bacterial activity were associated with α-diversity, while this was not the case for the robustness of fungal community and its associated activities. Finally, we observed that microbial α-diversity rather than SOC turnover rate can predict soil productivity.

          Conclusions

          Our findings indicate the strong influence of grazing on soil microbial community, SOC turnover, and soil productivity and the important positive role of soil microbial α-diversity in steering the functions of meadow steppe ecosystems.

          Electronic supplementary material

          The online version of this article (10.1186/s40168-018-0544-y) contains supplementary material, which is available to authorized users.

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          Most cited references54

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          The diversity and biogeography of soil bacterial communities.

          For centuries, biologists have studied patterns of plant and animal diversity at continental scales. Until recently, similar studies were impossible for microorganisms, arguably the most diverse and abundant group of organisms on Earth. Here, we present a continental-scale description of soil bacterial communities and the environmental factors influencing their biodiversity. We collected 98 soil samples from across North and South America and used a ribosomal DNA-fingerprinting method to compare bacterial community composition and diversity quantitatively across sites. Bacterial diversity was unrelated to site temperature, latitude, and other variables that typically predict plant and animal diversity, and community composition was largely independent of geographic distance. The diversity and richness of soil bacterial communities differed by ecosystem type, and these differences could largely be explained by soil pH (r(2) = 0.70 and r(2) = 0.58, respectively; P < 0.0001 in both cases). Bacterial diversity was highest in neutral soils and lower in acidic soils, with soils from the Peruvian Amazon the most acidic and least diverse in our study. Our results suggest that microbial biogeography is controlled primarily by edaphic variables and differs fundamentally from the biogeography of "macro" organisms.
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            Diversity and productivity in a long-term grassland experiment.

            Plant diversity and niche complementarity had progressively stronger effects on ecosystem functioning during a 7-year experiment, with 16-species plots attaining 2.7 times greater biomass than monocultures. Diversity effects were neither transients nor explained solely by a few productive or unviable species. Rather, many higher-diversity plots outperformed the best monoculture. These results help resolve debate over biodiversity and ecosystem functioning, show effects at higher than expected diversity levels, and demonstrate, for these ecosystems, that even the best-chosen monocultures cannot achieve greater productivity or carbon stores than higher-diversity sites.
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              Fast UniFrac: Facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data

              Next-generation sequencing techniques, and PhyloChip, have made simultaneous phylogenetic analyses of hundreds of microbial communities possible. Insight into community structure has been limited by the inability to integrate and visualize such vast datasets. Fast UniFrac overcomes these issues, allowing integration of larger numbers of sequences and samples into a single analysis. Its new array-based implementation offers orders of magnitude improvements over the original version. New 3D visualization of principal coordinates analysis (PCoA) results, with the option to view multiple coordinate axes simultaneously, provides a powerful way to quickly identify patterns that relate vast numbers of microbial communities. We demonstrate the potential of Fast UniFrac using examples from three data types: Sanger-sequencing studies of diverse free-living and animal-associated bacterial assemblages and from the gut of obese humans as they diet, pyrosequencing data integrated from studies of the human hand and gut, and PhyloChip data from a study of citrus pathogens. We show that a Fast UniFrac analysis using a reference tree recaptures patterns that could not be detected without considering phylogenetic relationships and that Fast UniFrac, coupled with BLAST-based sequence assignment, can be used to quickly analyze pyrosequencing runs containing hundreds of thousands of sequences, revealing patterns relating human and gut samples. Finally, we show that the application of Fast UniFrac to PhyloChip data could identify well-defined subcategories associated with infection. Together, these case studies point the way towards a broad range of applications and demonstrate some of the new features of Fast UniFrac.
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                Author and article information

                Contributors
                86-10-82109618 , xinxiaoping@caas.cn
                86-25-84396477 , rfzhang@njau.edu.cn
                Journal
                Microbiome
                Microbiome
                Microbiome
                BioMed Central (London )
                2049-2618
                20 September 2018
                20 September 2018
                2018
                : 6
                : 170
                Affiliations
                [1 ]ISNI 0000 0000 9750 7019, GRID grid.27871.3b, Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, , Nanjing Agricultural University, ; Nanjing, 210095 China
                [2 ]ISNI 0000 0001 0526 1937, GRID grid.410727.7, Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, , Chinese Academy of Agricultural Sciences, ; Beijing, 100081 China
                [3 ]ISNI 0000 0001 0526 1937, GRID grid.410727.7, National Hulunber Grassland Ecosystem Observation and Research Station, Institute of Agricultural Resources and Regional Planning, , Chinese Academy of Agricultural Sciences, ; Beijing, 100081 China
                Article
                544
                10.1186/s40168-018-0544-y
                6149009
                30236158
                c4337b11-34ee-4308-a0a8-c2dae466cd86
                © The Author(s). 2018

                Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

                History
                : 29 June 2018
                : 29 August 2018
                Funding
                Funded by: National Natural Science Foundation for Young Scientists of China
                Award ID: 41601252
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/501100001809, National Natural Science Foundation of China;
                Award ID: 41471093
                Award Recipient :
                Funded by: Major State Research Development Program of China
                Award ID: 2016YFC0500601
                Award Recipient :
                Funded by: General and Special Financial Grant from the China Postdoctoral Science Foundation
                Award ID: 2016M601833 & 2017T100379
                Award Recipient :
                Funded by: support of China Agriculture Research System
                Award ID: CARS-34
                Award Recipient :
                Categories
                Research
                Custom metadata
                © The Author(s) 2018

                temperate meadow steppe,cattle grazing,microbial composition,soil incubation,soc-decomposition enzymatic activity,soil productivity

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