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

Frédéric Sinniger,Simon Creer,Tomas Cedhagen,Gary Carvalho,Hiroyuki Yamamoto,Saki Harii,Jan Pawlowski,Pierre Chevaldonné,Andrew J Gooday

doi:10.3389/fmars.2016.00092

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 emphasises the necessity to integrate such new approaches with traditional morphology-based examination of deep-sea organisms.

Highlights

Prior to global industrialisation, the deep sea was protected from human influence by its remoteness
operational taxonomic units (OTUs) richness data showed less variation between locations compared to abundance data (Figure 3)
At a clustering threshold of 97%, metazoan OTUs represented between 8.4% (S Brazil Basin, abyssal) and 34.8% (Antarctic Peninsula) of the total eukaryotic richness for each site

Summary

Introduction

The deep sea was protected from human influence by its remoteness. The mining of metal-rich minerals in environments ranging from abyssal plains to hydrothermal vents and seamounts is a serious prospect in the fairly near future (e.g., Wedding et al, 2013; Fisher et al, 2014; Schlacher et al, 2014; Van Dover, 2014) Such combinations of different direct anthropogenic stressors will likely exacerbate multiple interacting stressors arising from climatic changes acting at a global scale (Mora et al, 2013; Jones et al, 2014), creating major threats to the largest environment on Earth (Ramirez-Llodra et al, 2011). Environmental stresses on whole ecosystems led to a loss of biodiversity observed worldwide, with consequences to ecosystem functioning (Worm et al, 2006; Hooper et al, 2012) It is, essential to acquire baseline information on deep-sea diversity in order to establish reference data reflecting near pristine or less impacted habitats. Such baseline studies are crucial to the assessment of changes in deep-sea ecosystems resulting from the increasing human activity

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Conclusion