Spatio-temporal monitoring of deep-sea communities using metabarcoding of sediment DNA and RNA

Magdalena Guardiola; Owen S Wangensteen; Pierre Taberlet; Eric Coissac; María Jesús Uriz; Xavier Turon

doi:10.7717/peerj.2807

Spatio-temporal monitoring of deep-sea communities using metabarcoding of sediment DNA and RNA

PeerJ. 2016 Dec 21:4:e2807. doi: 10.7717/peerj.2807. eCollection 2016.

Authors

Magdalena Guardiola¹, Owen S Wangensteen², Pierre Taberlet³, Eric Coissac³, María Jesús Uriz¹, Xavier Turon¹

Affiliations

¹ Department of Marine Ecology, Centre for Advanced Studies of Blanes (CEAB-CSIC) , Blanes , Spain.
² Department of Animal Biology and Biodiversity Research Institute (IRBIO), University of Barcelona, Barcelona, Spain; Ecosystems & Environment Research Centre, School of Environment & Life Sciences, University of Salford, Salford, United Kingdom.
³ Laboratoire d'Ecologie Alpine (LECA), Centre National de la Recherche Scientifique and Université Grenoble-Alpes , Grenoble , France.

Abstract

We assessed spatio-temporal patterns of diversity in deep-sea sediment communities using metabarcoding. We chose a recently developed eukaryotic marker based on the v7 region of the 18S rRNA gene. Our study was performed in a submarine canyon and its adjacent slope in the Northwestern Mediterranean Sea, sampled along a depth gradient at two different seasons. We found a total of 5,569 molecular operational taxonomic units (MOTUs), dominated by Metazoa, Alveolata and Rhizaria. Among metazoans, Nematoda, Arthropoda and Annelida were the most diverse. We found a marked heterogeneity at all scales, with important differences between layers of sediment and significant changes in community composition with zone (canyon vs slope), depth, and season. We compared the information obtained from metabarcoding DNA and RNA and found more total MOTUs and more MOTUs per sample with DNA (ca. 20% and 40% increase, respectively). Both datasets showed overall similar spatial trends, but most groups had higher MOTU richness with the DNA template, while others, such as nematodes, were more diverse in the RNA dataset. We provide metabarcoding protocols and guidelines for biomonitoring of these key communities in order to generate information applicable to management efforts.

Keywords: 18S; Biomonitoring; Meiofauna; Sediments; Submarine canyons; eDNA; eRNA.

Grants and funding

The sampling was done in the framework of the DOSMARES project (CTM2010-21810) of the Spanish Government. MG benefitted from a FPI predoctoral contract of the Spanish Government. This research was funded by project CHALLENGEN CTM2013-48163 of the Spanish Government. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.