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Sci Rep. 2015 Sep 10;5:13932. doi: 10.1038/srep13932.

High-throughput sequencing and morphology perform equally well for benthic monitoring of marine ecosystems.

Author information

1
Department of Genetics and Evolution, University of Geneva, Switzerland.
2
IRCAM, UMR 9912, Université Pierre et Marie Curie, Paris, France.
3
ADMM UMR 7144, CNRS, Station Biologique de Roscoff, 29682 Roscoff, France.
4
SAMS, Scottish Marine Institute, Oban, Argyll, UK.

Abstract

Environmental diversity surveys are crucial for the bioassessment of anthropogenic impacts on marine ecosystems. Traditional benthic monitoring relying on morphotaxonomic inventories of macrofaunal communities is expensive, time-consuming and expertise-demanding. High-throughput sequencing of environmental DNA barcodes (metabarcoding) offers an alternative to describe biological communities. However, whether the metabarcoding approach meets the quality standards of benthic monitoring remains to be tested. Here, we compared morphological and eDNA/RNA-based inventories of metazoans from samples collected at 10 stations around a fish farm in Scotland, including near-cage and distant zones. For each of 5 replicate samples per station, we sequenced the V4 region of the 18S rRNA gene using the Illumina technology. After filtering, we obtained 841,766 metazoan sequences clustered in 163 Operational Taxonomic Units (OTUs). We assigned the OTUs by combining local BLAST searches with phylogenetic analyses. We calculated two commonly used indices: the Infaunal Trophic Index and the AZTI Marine Biotic Index. We found that the molecular data faithfully reflect the morphology-based indices and provides an equivalent assessment of the impact associated with fish farms activities. We advocate that future benthic monitoring should integrate metabarcoding as a rapid and accurate tool for the evaluation of the quality of marine benthic ecosystems.

PMID:
26355099
PMCID:
PMC4564730
DOI:
10.1038/srep13932
[Indexed for MEDLINE]
Free PMC Article

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