Application of Environmental DNA Metabarcoding to Spatiotemporal Finfish Community Assessment in a Temperate Embayment

Abstract

Environmental DNA (eDNA) metabarcoding was used to characterize finfish communities in the nearshore estuarine environment. Monthly sampling was conducted June – August 2017 at two sites with structured habitats: a natural rock reef and a shellfish aquaculture farm within the same coastal embayment of Long Island Sound (LIS), CT, United States. Seventeen common and 25 rare finfish taxa were detected using eDNA metabarcoding. Incomplete status of reference sequence databases for finfish species was identified as a methodological challenge. Confidence in molecular identification was improved appreciably through the use of publicly available data obtained from local trawling and seining surveys. Comparison between eDNA metabarcoding and trawling surveys on 6/27/2017, the only day when both data types were available, revealed more finfish species detected by eDNA metabarcoding. The high sensitivity of eDNA metabarcoding detected finfish species rarely observed in traditional surveys and showed the potential for this methodology to augment existing literature for finfish species distribution patterns and invasive species detection. Non-metric multidimensional scaling (NMS) analysis of finfish communities achieved a low-stress, 2D solution, and revealed greater variation between samples collected from different months than samples collected from the two habitats. Similarly, permutational analysis of variance (PERMANOVA) found both month and the interaction term (month × site) significant, with the latter identifying site as significant only in July and August. Different finfish assemblages were significantly associated with each axis, axes representing temporal and spatial variations, respectively. Additionally, polycarbonate and nylon filters were compared to optimize the sampling method; finfish communities retrieved using the two types of filters were statistically indistinguishable by NMS analysis, although the filtration time for nylon filters was shorter. If the objective is to detect rare species, nylon filters are recommended over polycarbonate filters because of higher capture rates of rare taxa. Our study demonstrates the potential for applying eDNA metabarcoding as a stand-alone method to conduct finfish surveys with high sensitivity.