Boardman River 2019 eDNA metabarcoding water sample data

Understanding biodiversity in aquatic systems is critical to ecological
research and conservation efforts, but accurately measuring species
richness using traditional methods can be challenging. Environmental DNA
(eDNA) metabarcoding, which uses high-throughput sequencing and universal
primers to amplify DNA from multiple species present in an environmental
sample, has shown great promise for augmenting results from traditional
sampling to characterize fish communities in aquatic systems. Few studies,
however, have compared exhaustive traditional sampling with eDNA
metabarcoding of corresponding water samples at a small spatial scale. We
intensively sampled Boardman Lake (1.4 km2) in Michigan, USA from May to
June in 2019 using gill and fyke nets and paired each net set with lake
water samples collected in triplicate. We analyzed water samples using
eDNA metabarcoding with 12S and 16S fish-specific primers and compared
estimates of fish diversity among methods. In total, we set 60 nets and
analyzed 180 1 L lake water samples. We captured a total of 12 fish
species in our traditional gear and detected 40 taxa in the eDNA water
samples, which included all the species observed in nets. The 12S and 16S
assays detected a comparable number of taxa, but taxonomic resolution
varied between the two genes. In our traditional gear, there was a clear
difference in the species selectivity between the two net types, and there
were several species commonly detected in the eDNA samples that were not
captured in nets. Finally, we detected spatial heterogeneity in fish
community composition across relatively small scales in Boardman Lake with
eDNA metabarcoding, but not with traditional sampling. Our results
demonstrated that eDNA metabarcoding was substantially more efficient than
traditional gear for estimating community composition, highlighting the
utility of eDNA metabarcoding for assessing species diversity and
informing management and conservation.