title: Metatranscriptomic census of active protists in soils.
abstract: The high numbers and diversity of protists in soil systems have long been presumed, but their true diversity and community composition have remained largely concealed. Traditional cultivation-based methods miss a majority of taxa, whereas molecular barcoding approaches employing PCR introduce significant biases in reported community composition of soil protists. Here, we applied a metatranscriptomic approach to assess the protist community in 12 mineral and organic soil samples from different vegetation types and climatic zones using small subunit ribosomal RNA transcripts as marker. We detected a broad diversity of soil protists spanning across all known eukaryotic supergroups and revealed a strikingly different community composition than shown before. Protist communities differed strongly between sites, with Rhizaria and Amoebozoa dominating in forest and grassland soils, while Alveolata were most abundant in peat soils. The Amoebozoa were comprised of Tubulinea, followed with decreasing abundance by Discosea, Variosea and Mycetozoa. Transcripts of Oomycetes, Apicomplexa and Ichthyosporea suggest soil as reservoir of parasitic protist taxa. Further, Foraminifera and Choanoflagellida were ubiquitously detected, showing that these typically marine and freshwater protists are autochthonous members of the soil microbiota. To the best of our knowledge, this metatranscriptomic study provides the most comprehensive picture of active protist communities in soils to date, which is essential to target the ecological roles of protists in the complex soil system.
authors.affiliation: Department of Terrestrial Ecology, Institute of Zoology, University of Cologne, Cologne, Germany.|Department of Terrestrial Ecology, Netherlands Institute for Ecology, (NIOO-KNAW), Wageningen, The Netherlands.
authors.forename: Stefan
authors.identifier: http://orcid.org/0000-0003-0734-727X
authors.initials: S
authors.lastname: Geisen
authors.affiliation: Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway.
authors.forename: Alexander T
authors.initials: AT
authors.lastname: Tveit
authors.affiliation: Department of AgroEcology, Rothamsted Research, Harpenden, Hertfordshire, UK.
authors.forename: Ian M
authors.initials: IM
authors.lastname: Clark
authors.affiliation: Department of Microbiology and Ecosystem Sciences, University of Vienna, Vienna, Austria.
authors.forename: Andreas
authors.initials: A
authors.lastname: Richter
authors.affiliation: Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway.
authors.forename: Mette M
authors.initials: MM
authors.lastname: Svenning
authors.affiliation: Department of Terrestrial Ecology, Institute of Zoology, University of Cologne, Cologne, Germany.
authors.forename: Michael
authors.initials: M
authors.lastname: Bonkowski
authors.affiliation: Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria.
authors.forename: Tim
authors.initials: T
authors.lastname: Urich
mesh_terms: D044822:Biodiversity; D056890:Eukaryota / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*; D020869:Gene Expression Profiling / Q000379:methods; D010802:Phylogeny; D012335:RNA, Ribosomal / Q000032:analysis; D012987:Soil / Q000737:chemistry / Q000469:parasitology*
chemical_list: D012335:RNA, Ribosomal; D012987:Soil
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