Detecting macroecological patterns in bacterial communities across independent studies of global soils.

Autor: Ramirez KS; Netherlands Institute of Ecology, Wageningen, The Netherlands. k.ramirez@nioo.knaw.nl., Knight CG; Faculty of Science and Engineering, University of Manchester, Manchester, UK., de Hollander M; Netherlands Institute of Ecology, Wageningen, The Netherlands., Brearley FQ; School of Science and the Environment, Manchester Metropolitan University, Manchester, UK., Constantinides B; Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester, UK., Cotton A; Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK., Creer S; Environment Centre Wales, College of Natural Sciences, Bangor University, Bangor, UK., Crowther TW; Netherlands Institute of Ecology, Wageningen, The Netherlands.; Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland., Davison J; Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia., Delgado-Baquerizo M; Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO, USA., Dorrepaal E; Climate Impacts Research Centre, Department of Ecology and Environmental Science, Umeå University, Abisko, Sweden., Elliott DR; School of Science and the Environment, Manchester Metropolitan University, Manchester, UK.; Environmental Sustainability Research Centre, University of Derby, Derby, UK., Fox G; School of Science and the Environment, Manchester Metropolitan University, Manchester, UK., Griffiths RI; Centre for Ecology and Hydrology, Wallingford, UK., Hale C; School of Life Sciences, University of Warwick, Coventry, UK., Hartman K; Division of Agroecology and Environment, Agroscope, Zürich, Switzerland., Houlden A; Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK., Jones DL; Environment Centre Wales, College of Natural Sciences, Bangor University, Bangor, UK., Krab EJ; Climate Impacts Research Centre, Department of Ecology and Environmental Science, Umeå University, Abisko, Sweden., Maestre FT; Departamento de Biología y Geología, Física y Química Inorgánica, Escuela Superior de Ciencias Experimentales y Tecnología, Universidad Rey Juan Carlos, Móstoles, Spain., McGuire KL; Department of Biology, Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA., Monteux S; Climate Impacts Research Centre, Department of Ecology and Environmental Science, Umeå University, Abisko, Sweden., Orr CH; School of Science and Engineering, Teesside University, Middlesbrough, UK., van der Putten WH; Netherlands Institute of Ecology, Wageningen, The Netherlands.; Laboratory of Nematology, Wageningen University, Wageningen, The Netherlands., Roberts IS; Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK., Robinson DA; Centre for Ecology and Hydrology, Bangor, UK., Rocca JD; Department of Biology, Duke University, Durham, NC, USA., Rowntree J; School of Science and the Environment, Manchester Metropolitan University, Manchester, UK., Schlaeppi K; Division of Agroecology and Environment, Agroscope, Zürich, Switzerland., Shepherd M; Natural England, Exeter, UK., Singh BK; Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia., Straathof AL; Faculty of Science and Engineering, University of Manchester, Manchester, UK., Bhatnagar JM; Department of Biology, Boston University, Boston, MA, USA., Thion C; Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, UK., van der Heijden MGA; Division of Agroecology and Environment, Agroscope, Zürich, Switzerland.; Institute for Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland.; Plant-Microbe Interactions, Institute of Environmental Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands., de Vries FT; Faculty of Science and Engineering, University of Manchester, Manchester, UK.
Jazyk: angličtina
Zdroj: Nature microbiology [Nat Microbiol] 2018 Feb; Vol. 3 (2), pp. 189-196. Date of Electronic Publication: 2017 Nov 20.
DOI: 10.1038/s41564-017-0062-x
Abstrakt: The emergence of high-throughput DNA sequencing methods provides unprecedented opportunities to further unravel bacterial biodiversity and its worldwide role from human health to ecosystem functioning. However, despite the abundance of sequencing studies, combining data from multiple individual studies to address macroecological questions of bacterial diversity remains methodically challenging and plagued with biases. Here, using a machine-learning approach that accounts for differences among studies and complex interactions among taxa, we merge 30 independent bacterial data sets comprising 1,998 soil samples from 21 countries. Whereas previous meta-analysis efforts have focused on bacterial diversity measures or abundances of major taxa, we show that disparate amplicon sequence data can be combined at the taxonomy-based level to assess bacterial community structure. We find that rarer taxa are more important for structuring soil communities than abundant taxa, and that these rarer taxa are better predictors of community structure than environmental factors, which are often confounded across studies. We conclude that combining data from independent studies can be used to explore bacterial community dynamics, identify potential 'indicator' taxa with an important role in structuring communities, and propose hypotheses on the factors that shape bacterial biogeography that have been overlooked in the past.
Databáze: MEDLINE
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