Data from: Ecosystem biomonitoring with eDNA: metabarcoding across the tree of life in a tropical marine environment

Effective marine management requires comprehensive data on the status of
marine biodiversity. However, efficient methods that can document
biodiversity in our oceans are currently lacking. Environmental DNA (eDNA)
sourced from seawater offers a new avenue for investigating the biota in
marine ecosystems. Here, we investigated the potential of eDNA to inform
on the breadth of biodiversity present in a tropical marine environment.
Directly sequencing eDNA from seawater using a shotgun approach resulted
in only 0.34% of 22.3 million reads assigning to eukaryotes, highlighting
the inefficiency of this method for assessing eukaryotic diversity. In
contrast, using ‘tree of life’ (ToL) metabarcoding and 20-fold fewer
sequencing reads, we could detect 287 families across the major divisions
of eukaryotes. Our data also show that the best performing ‘universal’ PCR
assay recovered only 44% of the eukaryotes identified across all assays,
highlighting the need for multiple metabarcoding assays to catalogue
biodiversity. Lastly, focusing on the fish genus Lethrinus, we recovered
intra- and inter-specific haplotypes from seawater samples, illustrating
that eDNA can be used to explore diversity beyond taxon identifications.
Given the sensitivity and low cost of eDNA metabarcoding we advocate this
approach be rapidly integrated into biomonitoring programs.