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

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.

Under the canopy: Community-wide effects of invasive algae in Marine Protected Areas revealed by metabarcoding

“…It has been acknowledged that primer bias and differences in copy number of 18S (or mitochondrial abundance in the case of COI) hinder a direct quantitative relationship between number of reads (usually in the form of relative frequency within samples) and biomass of a given MOTU. Nevertheless, most studies analysing this relationship report a gross correlation, in the sense that more abundant species also tend to be represented by a higher relative or absolute number of reads (reviewed in Lejzerowicz et al, 2015;Barnes and Turner, 2016;Valentini et al, 2016;Bucklin et al, 2016). It can be added here that abundance estimation using traditional methods is not free of biases, either (Shelton et al, 2016).…”

Worldwide Analysis of Sedimentary DNA Reveals Major Gaps in Taxonomic Knowledge of Deep-Sea Benthos

“…These uncertainties should not undermine the potential of metabarcoding to better understand the diversity of poorly known communities. Indeed, the total information obtained from a large number of taxa in parallel provides a good estimator of environmental community diversity that has many practical applications for ecosystem assessment and monitoring (Chariton et al, 2010(Chariton et al, , 2014Czernik et al, 2013;Stephenson et al, 2013;Lallias et al, 2014;Pawlowski et al, 2014;Willerslev et al, 2014;Guardiola et al, 2015;Lejzerowicz et al, 2015;Pochon et al, 2015;Boschen et al, 2016).…”

Benchmarking DNA Metabarcoding for Biodiversity-Based Monitoring and Assessment

“…Consequences of the misinterpretation of the taxonomic composition could result in erroneous biodiversity assessment, which may impede the implementation of DNA metabarcoding in regular biomonitoring programs (Chariton et al, 2015;Cowart et al, 2015;Lejzerowicz et al, 2015;Zaiko et al, 2015). In particular, calculation of biotic indices based on pollution tolerances assigned to the taxa retrieved from the sample (Maurer et al, 1999;Borja et al, 2000) may be affected by the approach used for taxonomic assignment.…”