Biodiversity assessment of tropical shelf eukaryotic communities via pelagic eDNA metabarcoding

Abstract

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 focussed 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.

Environmental DNA survey captures patterns of fish and invertebrate diversity across a tropical seascape

“…In combination with a traditional visual survey, eDNA allowed for a more comprehensive survey of the biodiversity contained in the Bocas del Toro lagoon. Overall, over 8,500 metazoan OTUs were detected in the eDNA, which is comparable to previous estimates of marine metazoan diversity for the entire Caribbean region (10,676 animal species reported in a 2010 study of georeferenced species records and taxonomic lists 13 ) and is consistent with other eDNA results from the Caribbean 30 . We detected over 200 metazoan OTUs with species-level identifications that had not been previously recorded in the Bocas or OBIS databases.…”

DNA Metabarcoding of Deep-Sea Sediment Communities Using COI: Community Assessment, Spatio-Temporal Patterns and Comparison with 18S rDNA

“…At the species level, 52.32% of assignments belonged to organisms of only one super-group, Amoebozoa, which had been the object of remarkable barcoding efforts (e.g., [57][58][59]). All this evidence confirms previous reports that there are major gaps in reference databases that use COI as a marker regarding sediment communities from both marine and freshwater environments [23,60], or even regarding marine organisms in general [33,61]. Notwithstanding, one of the advantages of metabarcoding is that taxonomic identification can only improve as reference databases are updated.…”

More Than Expected From Old Sponge Samples: A Natural Sampler DNA Metabarcoding Assessment of Marine Fish Diversity in Nha Trang Bay (Vietnam)

“…However, Jeunen et al (2019) demonstrated that eDNA was able to discriminate diverse marine habitats within a small spatial scale subject to tidal and water currents. Indeed, some studies have already shown that eDNA surveys are able to detect fine-scale community composition patterns in heterogeneous aquatic habitats (Port et al, 2016;O'Donnell et al, 2017;Pont et al, 2018;Bakker et al, 2019;Stat et al, 2019;Nguyen et al, 2020;Oka et al, 2020). In our study, the residency time and degradation rate of nsDNA in the sponge tissues is an important factor that can hamper the detection of community patterns.…”