Data from: Biodiversity assessment of tropical shelf eukaryotic communities via pelagic eDNA metabarcoding

Our understanding of marine communities and their functions in an
ecosystem relies on the ability to detect and monitor species
distributions and abundances. Currently, the use of environmental DNA
(eDNA) metabarcoding is increasingly being applied for the rapid
assessment and monitoring of aquatic species. Most eDNA metabarcoding
studies have either focused on the simultaneous identification of a few
specific taxa/groups or have been limited in geographical scope. Here we
employed eDNA metabarcoding to compare beta diversity patterns of complex
pelagic marine communities in tropical coastal shelf habitats spanning the
whole Caribbean Sea. We screened 68 water samples using a universal
eukaryotic COI barcode region and detected highly diverse communities,
which varied significantly among locations, and proved good descriptors of
habitat type and environmental conditions. Less than 15% of eukaryotic
taxa were assigned to metazoans, most DNA sequences belonged to a variety
of planktonic ‘protists’, with over 50% of taxa unassigned at the phylum
level, suggesting that the sampled communities host an astonishing amount
of micro-eukaryotic diversity yet undescribed or absent from COI reference
databases. Although such a predominance of micro-eukaryotes severely
reduces the efficiency of universal COI markers to investigate vertebrate
and other metazoans from aqueous eDNA, the study contributes to the
advancement of rapid biomonitoring methods, and brings us closer to a full
inventory of extant marine biodiversity.