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      Fungal-bacterial diversity and microbiome complexity predict ecosystem functioning

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          Abstract

          The soil microbiome is highly diverse and comprises up to one quarter of Earth’s diversity. Yet, how such a diverse and functionally complex microbiome influences ecosystem functioning remains unclear. Here we manipulated the soil microbiome in experimental grassland ecosystems and observed that microbiome diversity and microbial network complexity positively influenced multiple ecosystem functions related to nutrient cycling (e.g. multifunctionality). Grassland microcosms with poorly developed microbial networks and reduced microbial richness had the lowest multifunctionality due to fewer taxa present that support the same function (redundancy) and lower diversity of taxa that support different functions (reduced  functional uniqueness). Moreover, different microbial taxa explained different ecosystem functions pointing to the significance of functional diversity in microbial communities. These findings indicate the importance of microbial interactions within and among fungal and bacterial communities for enhancing ecosystem performance and demonstrate that the extinction of complex ecological associations belowground can impair ecosystem functioning.

          Abstract

          There is ongoing interest in linking soil microbial diversity to ecosystem function. Here the authors manipulate the diversity and composition of microbial communities and show that complex microbial networks contribute more to ecosystem multifunctionality than simpler or low-diversity networks.

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          Most cited references38

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          Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample.

          The ongoing revolution in high-throughput sequencing continues to democratize the ability of small groups of investigators to map the microbial component of the biosphere. In particular, the coevolution of new sequencing platforms and new software tools allows data acquisition and analysis on an unprecedented scale. Here we report the next stage in this coevolutionary arms race, using the Illumina GAIIx platform to sequence a diverse array of 25 environmental samples and three known "mock communities" at a depth averaging 3.1 million reads per sample. We demonstrate excellent consistency in taxonomic recovery and recapture diversity patterns that were previously reported on the basis of metaanalysis of many studies from the literature (notably, the saline/nonsaline split in environmental samples and the split between host-associated and free-living communities). We also demonstrate that 2,000 Illumina single-end reads are sufficient to recapture the same relationships among samples that we observe with the full dataset. The results thus open up the possibility of conducting large-scale studies analyzing thousands of samples simultaneously to survey microbial communities at an unprecedented spatial and temporal resolution.
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            A global atlas of the dominant bacteria found in soil

            The immense diversity of soil bacterial communities has stymied efforts to characterize individual taxa and document their global distributions. We analyzed soils from 237 locations across six continents and found that only 2% of bacterial phylotypes (~500 phylotypes) consistently accounted for almost half of the soil bacterial communities worldwide. Despite the overwhelming diversity of bacterial communities, relatively few bacterial taxa are abundant in soils globally. We clustered these dominant taxa into ecological groups to build the first global atlas of soil bacterial taxa. Our study narrows down the immense number of bacterial taxa to a "most wanted" list that will be fruitful targets for genomic and cultivation-based efforts aimed at improving our understanding of soil microbes and their contributions to ecosystem functioning.
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              Soil biodiversity and soil community composition determine ecosystem multifunctionality.

              Biodiversity loss has become a global concern as evidence accumulates that it will negatively affect ecosystem services on which society depends. So far, most studies have focused on the ecological consequences of above-ground biodiversity loss; yet a large part of Earth's biodiversity is literally hidden below ground. Whether reductions of biodiversity in soil communities below ground have consequences for the overall performance of an ecosystem remains unresolved. It is important to investigate this in view of recent observations that soil biodiversity is declining and that soil communities are changing upon land use intensification. We established soil communities differing in composition and diversity and tested their impact on eight ecosystem functions in model grassland communities. We show that soil biodiversity loss and simplification of soil community composition impair multiple ecosystem functions, including plant diversity, decomposition, nutrient retention, and nutrient cycling. The average response of all measured ecosystem functions (ecosystem multifunctionality) exhibited a strong positive linear relationship to indicators of soil biodiversity, suggesting that soil community composition is a key factor in regulating ecosystem functioning. Our results indicate that changes in soil communities and the loss of soil biodiversity threaten ecosystem multifunctionality and sustainability.
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                Author and article information

                Contributors
                cameron.wagg@canada.ca
                marcel.vanderheijden@agroscope.admin.ch
                Journal
                Nat Commun
                Nat Commun
                Nature Communications
                Nature Publishing Group UK (London )
                2041-1723
                24 October 2019
                24 October 2019
                2019
                : 10
                : 4841
                Affiliations
                [1 ]ISNI 0000 0004 4681 910X, GRID grid.417771.3, Plant Soil Interactions, Division Agroecology and Environment, , Agroscope, ; Reckenholzstrasse 191, CH-8046 Zürich, Switzerland
                [2 ]ISNI 0000 0004 1937 0650, GRID grid.7400.3, Department of Evolutionary Biology and Environmental Studies, , University of Zürich, ; Winterthurerstrasse 190, Zürich, CH-8057 Switzerland
                [3 ]ISNI 0000 0001 1302 4958, GRID grid.55614.33, Fredericton Research and Development Center, , Agriculture and Agri-Food Canada, ; 850 Lincoln Rd, Fredericton, NB E3B 4Z7 Canada
                [4 ]ISNI 0000 0001 0726 5157, GRID grid.5734.5, Institute of Plant Sciences, , University of Bern, ; Altenbergrain 21, CH-3013 Bern, Switzerland
                [5 ]ISNI 0000 0001 1013 0288, GRID grid.418375.c, Department of Microbial Ecology, , Netherlands Institute of Ecology (NIOO-KNAW), ; 6708 PB Wageningen, The Netherlands
                [6 ]ISNI 0000 0004 1937 0650, GRID grid.7400.3, Department of Plant and Microbial Biology, , University of Zurich, ; Zollikerstrasse 107, CH-8008 Zurich, Switzerland
                Author information
                http://orcid.org/0000-0003-3620-0875
                http://orcid.org/0000-0002-1402-0171
                http://orcid.org/0000-0001-6701-8668
                http://orcid.org/0000-0001-7040-1924
                Article
                12798
                10.1038/s41467-019-12798-y
                6813331
                31649246
                38353843-af6c-4c22-bc33-6a26e16352c8
                © The Author(s) 2019

                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 license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license 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 license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 20 March 2019
                : 1 October 2019
                Categories
                Article
                Custom metadata
                © The Author(s) 2019

                Uncategorized
                microbial ecology,ecosystem ecology
                Uncategorized
                microbial ecology, ecosystem ecology

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