Eukaryotic eDNA/eRNA From CCZ Benthos

Eukaryotic biodiversity and spatial patterns in the Clarion-Clipperton Zone and other abyssal regions: insights from sediment DNA and RNA metabarcoding doi: 10.3389/fmars.2021.671033 The deep seabed is a vast mosaic of poorly-sampled habitats hosting surprisingly high levels of biodiversity that remains mostly undescribed. The sheer amount of rare, small-size taxa and the vast spatial extent of the abyssal seafloor complicates biodiversity and biogeography studies, but baselines must be established for regions such as the Clarion-Clipperton Zone (CCZ) that may be destroyed by polymetallic nodule mining. Environmental genomics may help for this task and for biomonitoring but needs to be assessed thoroughly. We sequenced environmental DNA and RNA for 310 deep-sea sediments samples (2 PCR replicates/sample) from the CCZ and other regions distributed globally, targeting Foraminifera (37F) and Eukaryota (V1V2).The deep seabed is a vast mosaic of poorly-sampled habitats hosting surprisingly high levels of biodiversity that remains mostly undescribed. The sheer amount of rare, small-size taxa and the vast spatial extent of the abyssal seafloor complicates biodiversity and biogeography studies, but baselines must be established for regions such as the Clarion-Clipperton Zone (CCZ) that may be destroyed by polymetallic nodule mining. Environmental genomics may help for this task and for biomonitoring but needs to be assessed thoroughly. We sequenced environmental DNA and RNA for 310 deep-sea sediments samples (2 PCR replicates/sample) from the CCZ and other regions distributed globally, targeting Foraminifera (37F) and Eukaryota (V1V2). 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. 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 a known taxon. Benthic foraminiferal communities are dominated by clades that are only known from environmental surveys; foraminifera are more common in CCZ samples than are metazoans. 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 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.