Metagenomes provide valuable comparative information on soil microeukaryotes

TY - JOUR

T1 - Metagenomes provide valuable comparative information on soil microeukaryotes

AU - Jacquiod, Samuel Jehan Auguste

AU - Stenbæk, Jonas

AU - Santos, Susana

AU - Winding, Anne

AU - Sørensen, Søren J.

AU - Priemé, Anders

PY - 2016/3

Y1 - 2016/3

N2 - Despite the critical ecological roles of microeukaryotes in terrestrial ecosystems, most descriptive studies of soil microbes published so farfocused only on specific groups. Meanwhile, the fast development of metagenome sequencing leads to considerable data accumulation in publicrepositories, providing microbiologists with substantial amounts of accessible information. We took advantage of public metagenomes in orderto investigate microeukaryote communities in a well characterized grassland soil. The data gathered allowed the evaluation of several factorsimpacting the community structure, including the DNA extraction method, the database choice and also the annotation procedure. While moststudies on soil microeukaryotes are based on sequencing of PCR-amplified taxonomic markers (18S rRNA genes, ITS regions), this workrepresents, to our knowledge, the first report based solely on metagenomic microeukaryote DNA. Choosing the correct annotation procedure andreference database has proven to be crucial, as it considerably limits the risk of wrong assignments. In addition, a significant and pronouncedeffect of the DNA extraction method on the taxonomical structure of soil microeukaryotes has been identified. Our analyses suggest that publiclyavailable 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 farfocused only on specific groups. Meanwhile, the fast development of metagenome sequencing leads to considerable data accumulation in publicrepositories, providing microbiologists with substantial amounts of accessible information. We took advantage of public metagenomes in orderto investigate microeukaryote communities in a well characterized grassland soil. The data gathered allowed the evaluation of several factorsimpacting the community structure, including the DNA extraction method, the database choice and also the annotation procedure. While moststudies on soil microeukaryotes are based on sequencing of PCR-amplified taxonomic markers (18S rRNA genes, ITS regions), this workrepresents, to our knowledge, the first report based solely on metagenomic microeukaryote DNA. Choosing the correct annotation procedure andreference database has proven to be crucial, as it considerably limits the risk of wrong assignments. In addition, a significant and pronouncedeffect of the DNA extraction method on the taxonomical structure of soil microeukaryotes has been identified. Our analyses suggest that publiclyavailable 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.

KW - Metagenome

KW - Microeukaryote

KW - Soil

UR - http://www.scopus.com/inward/record.url?scp=84964330324&partnerID=8YFLogxK

U2 - 10.1016/j.resmic.2016.03.003

DO - 10.1016/j.resmic.2016.03.003

M3 - Journal article

C2 - 27020245

SN - 0923-2508

VL - 167

SP - 436

EP - 450

JO - Research in Microbiology

JF - Research in Microbiology

IS - 5

M1 - 167

ER -