Abstract
Environmental DNA (eDNA) metabarcoding could facilitate rapid and comprehensive biotic surveys in the deep ocean, yet many aspects of the sources and distribution of eDNA in the deep sea are still poorly understood. In order to examine the influence of the water column on benthic eDNA surveys in regions targeted for deep-sea polymetallic nodule mining, we investigated the occurrence of pelagic eDNA across: (1) two different deep-sea habitat types, abyssal plains and seamounts, (2) benthic sample types, including nodules, sediment, and seawater within the benthic boundary layer (BBL), and (3) sediment depth horizons (0-2 cm, 3-5 cm). Little difference was observed between seamounts and the adjacent abyssal plains in the proportion of legacy pelagic eDNA sampled in the benthos, despite an > 1000 m depth difference for these habitats. In terms of both reads and amplicon sequence variants (ASVs), pelagic eDNA was minimal within sediment and nodule samples (< 2 %), and is unlikely to affect benthic surveys that monitor resident organisms at the deep seafloor. However, pelagic eDNA was substantial within the BBL (up to 13 % ASVs, 86% reads), derived both from the high-biomass upper ocean as well as deep pelagic residents. While most pelagic metazoan eDNA found in sediments and on nodules could be sourced from the epipelagic, protist legacy eDNA sampled on these substrates appeared to originate across a range of depths in the water column. Some evidence of eDNA degradation across a vertical sediment profile was observed for protists, with higher diversity in the 0-2 cm layer and a significantly lower proportion of legacy pelagic eDNA in deeper sediments (3-5 cm). Study-wide, our estimated metazoan sampling coverage ranged from 40 % to 74 %, despite relatively large sample size. Future deep-sea eDNA surveys should examine oceanographic influences on eDNA transport and residence times, consider habitat heterogeneity at a range of spatial scales in the abyss, and aim to process large amounts of material per sample (with replication) in order to increase the sampling coverage in these diverse deep ocean communities.
Highlights
Deep sea ecosystems are facing increasing pressure from anthropogenic activities, including climate change and future seabed mining (Boschen et al, 2013; Halpern et al, 2015; Sweetman et al, 2017)
Biodiversity assessments in the deep ocean are essential prior to large-scale anthropogenic impacts, such as polymetallic nodule mining proposed for the Clarion Clipperton Zone (Smith et al, 2008a; Wedding et al, 2013, 2015). Environmental DNA (eDNA) metabarcoding methods are increasingly being applied as a biomonitoring tool for ecosystem health in marine systems (e.g., Danovaro et al, 2016; Goodwin et al, 2017; Stat et al, 2017), but have seen limited application in the deep sea (e.g., Dell’Anno et al, 2015; Guardiola et al, 2015, 2016; Sinniger et al, 2016)
Our results show that detrital pelagic eDNA represents a very small fraction of the diversity sampled in sediments and nodules at the abyssal seafloor (
Summary
Deep sea ecosystems are facing increasing pressure from anthropogenic activities, including climate change and future seabed mining (Boschen et al, 2013; Halpern et al, 2015; Sweetman et al, 2017). Regional species diversity is enhanced by habitat heterogeneity at a range of spatial scales, including the presence of polymetallic nodules that serve as hard substrates in a predominantly soft sediment ecosystem (Amon et al, 2016; Vanreusel et al, 2016; De Smet et al, 2017; Kaiser et al, 2017; Simon-Lledó et al, 2019; Laroche et al, 2020a), as well as deep seamounts (relief >1,000 m above the surrounding seafloor; Clark et al, 2010; Leitner et al, 2017) that may alter nutrient and particle fluxes and influence associated biological communities (Genin and Dower, 2007; Samadi et al, 2007; Lavelle and Mohn, 2010; Rowden et al, 2010). Biodiversity and species ranges remain poorly characterized across the CCZ, making predictions of the impacts of large-scale mining problematic
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