High-throughput environmental DNA analysis informs a biological assessment of an urban stream

There is growing interest in the use of DNA barcoding and metabarcoding approaches to aid biological assessments and monitoring of waterbodies. While biodiversity measured by morphology and by DNA often has been found correlated, few studies have compared DNA data to established measures of impairment such as multimetric pollution tolerance indices used by many bioassessment programs. We incorporated environmental DNA (eDNA) metabarcoding of seston into a rigorous watershed-scale biological assessment of an urban stream to examine the extent to which eDNA richness and diversity patterns were correlated with multimetric indices and ecological impairment status designations. We also evaluated different filtering approaches and taxonomic classifications to identify best practices for environmental assessments. Seston eDNA revealed a wide diversity of eukaryotic taxa but was dominated by diatoms (36%). Differentiation among sites in alpha and beta diversity was greater when operational taxonomic units (OTUs) were classified taxonomically, but coarse resolution taxonomy (kingdom) was more informative than finer resolution taxonomy (family, genus). Correlations of DNA richness and diversity with multimetric indices for fish and macroinvertebrates were generally weak, possibly because Metazoa were not highly represented in our DNA dataset. Nonetheless, sites could be differentiated based on ecological impairment status, with more impaired sites having lower eDNA diversity as measured by the Shannon index, but higher taxonomic richness. Significant environmental drivers of community structure, as inferred from constrained ordination analyses, differed among kingdoms within the eDNA dataset, as well as from fish and macrobenthos, suggesting that eDNA provides novel environmental information. These results suggest that even a simple seston eDNA filtering protocol can provide biodiversity information of value to stream bioassessment programs. The approach bears further investigation as a potentially useful rapid assessment protocol to supplement more intensive field sampling efforts.