Abstract
The abyssal seafloor is a mosaic of highly diverse habitats that represent the least known marine ecosystems on Earth. Some regions enriched in natural resources, such as polymetallic nodules in the Clarion-Clipperton Zone (CCZ), attract much interest because of their huge commercial potential. Since nodule mining will be destructive, baseline data are necessary to measure its impact on benthic communities. Hence, we conducted an environmental DNA and RNA metabarcoding survey of CCZ biodiversity targeting microbial and meiofaunal eukaryotes that are the least known component of the deep-sea benthos. We analyzed two 18S rRNA gene regions targeting eukaryotes with a focus on Foraminifera (37F) and metazoans (V1V2), sequenced from 310 surface-sediment samples from the CCZ and other abyssal regions. Our results confirm huge unknown deep-sea biodiversity. Over 60% of benthic foraminiferal and almost a third of eukaryotic operational taxonomic units (OTUs) could not be assigned to a known taxon. Benthic Foraminifera are more common in CCZ samples than metazoans and dominated by clades that are only known from environmental surveys. The most striking results are the uniqueness of CCZ areas, both datasets being characterized by a high number of OTUs exclusive to the CCZ, as well as greater beta diversity compared to other abyssal regions. The alpha diversity in the CCZ is high and correlated with water depth and terrain complexity. Topography was important at a local scale, with communities at CCZ stations located in depressions more diverse and heterogeneous than those located on slopes. This could result from eDNA accumulation, justifying the interim use of eRNA for more accurate biomonitoring surveys. Our descriptions not only support previous findings and consolidate our general understanding of deep-sea ecosystems, but also provide a data resource inviting further taxon-specific and large-scale modeling studies. We foresee that metabarcoding will be useful for deep-sea biomonitoring efforts to consider the diversity of small taxa, but it must be validated based on ground truthing data or experimental studies.
Highlights
The deep seabed encompasses a vast mosaic of poorly sampled habitats, many of them characterized by fine-grained sediments that, for more than 50 years, have been known to host surprisingly high levels of biodiversity (Hessler and Sanders, 1967; Ramirez-Llodra et al, 2010; Rex and Etter, 2010)
The sheer scale of undescribed deepsea biodiversity, combined with the rarity of many species and the vast spatial extent and chronic under-sampling of the deep seabed, make it very difficult to establish geographical ranges and the prevalence of endemicity, for species that are small in size
High-Level Taxonomic Composition We summarized the taxonomic composition of benthic foraminifera and eukaryotes in terms of operational taxonomic units (OTUs) proportions and sequence read relative abundances in each area (Figure 2)
Summary
The deep seabed encompasses a vast mosaic of poorly sampled habitats, many of them characterized by fine-grained sediments that, for more than 50 years, have been known to host surprisingly high levels of biodiversity (Hessler and Sanders, 1967; Ramirez-Llodra et al, 2010; Rex and Etter, 2010). It conceals a variety of material resources, services and history that are of cultural value to human societies (Wenhai et al, 2019; Turner et al, 2020) as well as ecosystems of considerable and growing economic importance (Armstrong et al, 2012; Thurber et al, 2014). The sheer scale of undescribed deepsea biodiversity, combined with the rarity of many species and the vast spatial extent and chronic under-sampling of the deep seabed, make it very difficult to establish geographical ranges and the prevalence of endemicity, for species that are small in size
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