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

Abstract

Deep-sea sediments represent the largest but least known ecosystem on earth. With increasing anthropogenic pressure, it is now a matter of urgency to improve our understanding of deep-sea biodiversity. Traditional morpho-taxonomic studies suggest that the ocean floor hosts extraordinarily diverse benthic communities. However, due to both its remoteness and a lack of expert taxonomists, assessing deep-sea diversity is a very challenging task. Environmental DNA (eDNA) metabarcoding offers a powerful tool to complement morpho-taxonomic studies. Here we use eDNA to assess benthic metazoan diversity in 39 deep-sea sediment samples from bathyal and abyssal depths worldwide. The eDNA dataset was dominated by meiobenthic taxa and we identified all animal phyla commonly found in the deep-sea benthos; yet, the diversity within these phyla remains largely unknown. The large numbers of taxonomically unassigned molecular operational taxonomic units (OTUs) were not equally distributed among phyla, with nematodes and platyhelminthes being the most poorly characterized from a taxonomic perspective. While the data obtained here reveal pronounced heterogeneity and vast amounts of unknown biodiversity in the deep sea, they also expose the difficulties in exploiting metabarcoding datasets resulting from the lack of taxonomic knowledge and appropriate reference databases. Overall, our study demonstrates the promising potential of eDNA metabarcoding to accelerate the assessment of deep-sea biodiversity for pure and applied deep-sea environmental research but also emphasizes the necessity to integrate such new approaches with traditional morphology-based examination of deep-sea organisms.

Biodiversity estimates and ecological interpretations of meiofaunal communities are biased by the taxonomic approach

“…Moreover, while morphological taxonomy allows identification at low taxonomic ranks (generally genus or species), most of the meiofaunal taxa represented in general reference libraries for DNA sequence data remain poorly classified and some represent misidentifications or contaminations 30 . Hence, although metabarcoding enables untangling of great phylogenetic diversity, it is not possible in most cases to classify species, and most remain known only at the phylum level 6,31 .…”

A Multidisciplinary Approach for Generating Globally Consistent Data on Mesophotic, Deep-Pelagic, and Bathyal Biological Communities

“…Through their activities, sediment-dwelling organisms create a unique mosaic of biogenic microenvironments that strongly influence carbon and nitrogen burial and remineralization rates, thus playing a key role in global biogeochemical cycles (Dunlop et al, 2016) and marine ecosystem functioning (Danovaro et al, 2008). The microfauna (i.e., protozoa) and microbes have traditionally been problematic to sample because of challenges in identification, but genetic techniques suggest massive undocumented diversity (Sinniger et al, 2016).…”

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

“…This technique, albeit still subject to some limitations, will likely become a cornerstone in decision making of management bodies in the near future (Kelly et al, 2014a;Danovaro et al, 2016). In the marine realm, eukaryotic diversity has been analysed using metabarcoding in plankton and sediment communities (reviewed in Carugati et al, 2015;Bucklin et al, 2016;Sinniger et al, 2016). These studies aimed at diverse applications, including community description, beta-diversity patterns, impact assessment, or study of ecological interactions, among others (e.g., Bik et al, 2012;Fonseca et al, 2014;Pawlowski et al, 2016;Brannock et al, 2016;Guardiola et al, 2015Guardiola et al, , 2016.…”