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Metagenomes provide valuable comparative information on soil microeukaryotes

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  • Samuel Jehan Auguste Jacquiod, University of Copenhagen, Denmark
  • Jonas Stenbæk, University of Copenhagen, Denmark
  • Susana Santos
  • ,
  • Anne Winding
  • Søren J. Sørensen, University of Copenhagen, Denmark
  • Anders Priemé, University of Copenhagen
Despite the critical ecological roles of microeukaryotes in terrestrial ecosystems, most descriptive studies of soil microbes published so far
focused only on specific groups. Meanwhile, the fast development of metagenome sequencing leads to considerable data accumulation in public
repositories, providing microbiologists with substantial amounts of accessible information. We took advantage of public metagenomes in order
to investigate microeukaryote communities in a well characterized grassland soil. The data gathered allowed the evaluation of several factors
impacting the community structure, including the DNA extraction method, the database choice and also the annotation procedure. While most
studies on soil microeukaryotes are based on sequencing of PCR-amplified taxonomic markers (18S rRNA genes, ITS regions), this work
represents, to our knowledge, the first report based solely on metagenomic microeukaryote DNA. Choosing the correct annotation procedure and
reference database has proven to be crucial, as it considerably limits the risk of wrong assignments. In addition, a significant and pronounced
effect of the DNA extraction method on the taxonomical structure of soil microeukaryotes has been identified. Our analyses suggest that publicly
available metagenome data can provide valuable information on soil microeukaryotes for comparative purposes when handled appropriately,
complementing the current view provided by ribosomal amplicon sequencing methods.
Original languageEnglish
Article number167
JournalResearch in Microbiology
Pages (from-to)436-450
Publication statusPublished - Mar 2016

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