Leveraging eDNA metabarcoding to characterize nearshore fish communities in Southeast Alaska: Do habitat and tide matter?

Abstract

Nearshore marine habitats are critical for a variety of commercially important fish species, but assessing fish communities in these habitats is costly and time‐intensive. Here, we leverage eDNA metabarcoding to characterize nearshore fish communities near Juneau, Alaska, USA, a high‐latitude environment with large tidal swings, strong currents, and significant freshwater input. We investigated whether species richness and community composition differed across three habitat types (sand beaches, eelgrass beds, and rocky shorelines) and between high and low tides. Additionally, we tested whether replication of field samples and PCR reactions influenced either species richness or composition. We amplified a 12S mitochondrial locus in our samples and identified 167 fish amplicon sequence variants, which were grouped into 24 unique taxa based on sequence similarity, with approximately half of these taxa resolved to single species. Species richness and composition inferred from eDNA differed substantially among habitats, with rock habitats containing fewer taxa and fewer overall detections than sand and eelgrass habitats. The effect of tide was not significant on its own, but a significant habitat‐tide interaction was documented, with the most pronounced differences in taxa between tides found in sand habitats. Power analyses indicated that additional field sampling is useful to detect small changes in species richness such as those due to tide. PCR replicates typically identified few additional taxa. Our results provide important information that can be used to guide future studies, most notably, that the influence of tide on eDNA results appears to be minimal and potentially isolated to certain habitats. This suggests that replication across tides may not be vital for future eDNA studies and that additional replication across space—particularly across heterogeneous environments—likely is a better allocation of sampling effort.

Capturing drifting species and molecules—Lessons learned from integrated approaches to assess marine metazoan diversity in highly dynamic waters

“…In our study, the tidal flow had no significant effect on the species assemblage recovered from the eDNA approach, although water movement is driven by the tide at Helgoland Roads. The same was found in other studies examining the tidal influence on species detection (Bleijswijk et al, 2020; Kelly et al, 2018; Lafferty et al, 2021; Larson et al, 2022). However, one study identified a significant effect of tides but this explained only 8% of the observed variation (Ely et al, 2021).…”

Two for the price of one: eDNA metabarcoding reveals temporal and spatial variability of mussel and fish co‐distributions in Michigan riverine systems

“…Data were processed using methods similar to Larson et al (2022). Raw sequencing reads were trimmed of primers using Cutadapt (Martin, 2011).…”

“…Other ASVs that were assigned to fish or mussel species not present in Michigan based on distributional information from the FishBase (https://www.fishb ase.org) and Nature Explorer databases (https://explo rer.natur eserve.org) were removed. Full taxonomy of the remaining ASVs was determined from NCBI taxonomy using custom scripts (Larson et al, 2022). Any ASVs that matched a single species at ≥98% similarity was assigned to that species.…”

Using qPCR of environmental DNA (eDNA) to estimate the biomass of juvenile Pacific salmon (Oncorhynchus spp.)

“…Environmental impact on shedding and degradation of DNA must be further investigated for a more accurate interpretation of eDNA concentrations for biomass estimation. While DNA shedding and degradation rates alone could be used to estimate fish biomass, an optimal approach would include an oceanographic model framework that accounts for DNA dispersal and exposure to conditions affecting degradation (Larson et al, 2021).…”