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Environ Microbiol. 2018 Jan;20(1):30-43. doi: 10.1111/1462-2920.13941. Epub 2017 Nov 24.

Protists are an integral part of the Arabidopsis thaliana microbiome.

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Institute of Population Genetics, Universitätstrasse 1, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, Universitätstrasse 40225 Düsseldorf, Germany.
Institute of Zoology, Department of Terrestrial Ecology, Zülpicher Str 47b, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Zülpicher Strasse 50674 Köln, Germany.
Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, 60325 Frankfurt am Main, Germany.


Although protists occupy a vast range of habitats and are known to interact with plants among other things via disease suppression, competition or growth stimulation, their contributions to the 'phytobiome' are not well described. To contribute to a more comprehensive picture of the plant holobiont, we examined cercozoan and oomycete taxa living in association with the model plant Arabidopsis thaliana grown in two different soils. Soil, roots, leaves and wooden toothpicks were analysed before and after surface sterilization. Cercozoa were identified using 18S rRNA gene metabarcoding, whereas the Internal Transcribed Spacer 1 was used to determine oomycetes. Subsequent analyses revealed strong spatial structuring of protist communities between compartments, although oomycetes appeared more specialized than Cercozoa. With regards to oomycetes, only members of the Peronosporales and taxa belonging to the genus Globisporangium were identified as shared members of the A. thaliana microbiome. This also applied to cercozoan taxa belonging to the Glissomonadida and Cercomonadida. We identified a strong influence by edaphic factors on the rhizosphere, but not for the phyllosphere. Distinct differences of Cercozoa found preferably in wood or fresh plant material imply specific niche adaptations. Our results highlight the importance of micro-eukaryotes for the plant holobiont.

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