eDNA metabarcoding shows highly diverse but distinct shallow, mid-water, and deep-water eukaryotic communities within a marine biodiversity hotspot

As the impact of human activities continues to move beyond shallow coastal waters into deeper ocean layers, it is fundamental to describe how diverse and distinct the eukaryotic assemblages from the deep layers are compared to shallow ecosystems. Environmental DNA (eDNA) metabarcoding has emerged as a molecular tool that can overcome many logistical barriers in exploring remote deep ocean areas. We analyzed thirty-two paired seawater samples collected via SCUBA and Niskin samplers from shallow (< 30 m) and deep ecosystems (40-500 m) within a recognized hotspot of marine biodiversity (Gulf of California, Mexico). We sequenced an eDNA metabarcoding library targeting the COI gene of eukaryotes. We demonstrated that the diversity of operational taxonomic units (OTUs) did not peak at shallow coastal regions and that the deep samples had similar levels of biodiversity to shallow sites but detected a significant vertical zonation between shallow and deeper habitats. Our results suggest that the deep refugia hypothesis applies to about a third of the 5495 OTUs identified that were shared between shallow and deep layer samples. At the same time, most taxa were exclusive from either shallow or deep zones. The observation that deep communities were as rich but quite distinct as shallow communities supports extending spatial management and conservation tools to deeper habitats to include a significant fraction of phylogenetic and functional diversity exclusive of mid and deep-water ecosystems.