TY - JOUR

T1 - Metagenomes provide valuable comparative information on soil microeukaryotes

AU - Jacquiod, Samuel Jehan Auguste

AU - Stenbæk, Jonas

AU - Santos, Susana S.

AU - Winding, Anne

AU - Sørensen, Søren Johannes

AU - Priemé, Anders

N1 - Copyright © 2016 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

PY - 2016

Y1 - 2016

N2 - 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.

AB - 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.

U2 - 10.1016/j.resmic.2016.03.003

DO - 10.1016/j.resmic.2016.03.003

M3 - Journal article

C2 - 27020245

VL - 167

SP - 436

EP - 450

JO - Research in Microbiology

JF - Research in Microbiology

SN - 0923-2508

IS - 5

ER -