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.

Seawater was filtered using Millipore MCE filters 0.45 µm pore size and eDNA was extracted using MoBIO (DNEasy) PowerSoil DNA extraction kit.

We used Leray-XT primers to amplify the Leray 313 bp fragment of mitochondrial cytochrome c oxidase (COI) and sequenced it in an Illumina Miseq V3 2x250 bp.

OBITools were used for paired-end assembly, demultiplexing and quality control. Chimeras were removed with uchime_denovo in VSearch. Swarm 2.0 with d=13 was used for clustering MOTUs. Ecotag was used for taxonomic assignment using custom reference databases for the COI Leray region. LULU was used for removing supernumerary MOTUs arising from pseudogenes. Singleton MOTUs were removed.

COI eDNA metabarcoding of filtered seawater