Eukaryotic biodiversity and spatial patterns in the Clarion-Clipperton Zone and five other abyssal areas using surface sediment DNA and RNA metabarcoding. This dataset gathers a total of 310 deep-sea sediments samples collected during 8 expeditions. Each sample was sequenced eight times, including 2 PCR replicates for the DNA and the RNA version of each sample, and for each of two 18S rRNA gene markers: 37F targeting Foraminifera V1V2 targeting Eukaryota.

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. Nodule mining will be destructive and thus, baseline data are necessary to measure its impact on benthic communities. Hence, we conduct 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 analysed two 18S rRNA gene regions targeting Foraminifera (37F) and eukaryotes with focus on 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 any taxon. Benthic foraminiferal communities are dominated by clades that are only known from environmental surveys and more common in CCZ samples than metazoans. The most striking result is the uniqueness of CCZ areas, both datasets being characterized by a high number of OTUs exclusive to the CCZ, as well as beta diversity differences 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 modelling 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.