Environmental DNA analysis of river herring in Chesapeake Bay: A powerful tool for monitoring threatened keystone species

Abstract

Environmental DNA (eDNA) sampling has emerged as a powerful tool to detect and quantify species abundance in aquatic environments. However, relatively few studies have compared the performance of eDNA-based abundance estimates to traditional catch or survey approaches in the field. Here, we have developed and field-tested a qPCR assay to detect eDNA from alewife and blueback herring (collectively known as ‘river herring’), comparing eDNA-based presence and abundance data to traditional methods of quantification (ichthyoplankton sampling and adult observations). Overall, the qPCR assay showed very high target specificity in lab trials, and was successful in detecting river herring for 11/12 Chesapeake Bay tributaries in spring 2015 and 2016, with 106 out of 445 samples exhibiting positive eDNA hits. We found a strong correlation between eDNA abundance and ichthyoplankton count data (Spearman’s Rho = 0.52), and Phi-tests (correlation of presence/absence data) showed higher correlation between eDNA and ichthyoplankton data (Phi = 0.45) than adult data (Phi = 0.35). Detection probability was significantly lower on western vs. eastern shore tributaries of Chesapeake Bay, and blueback herring and alewife were more likely detected on the western and eastern shores, respectively. Temporal patterns of eDNA abundance over the spring spawning season revealed that alewife were present in high abundances weeks ahead of blueback herring, which aligns with known differences in spawning behavior of the species. In summary, the eDNA abundance data corresponded well to other field methods and has great potential to assist future monitoring efforts of river herring abundance and habitat use.

Environmental DNA monitoring for short‐term reproductive migration of endemic anadromous species, Shishamo smelt (Spirinchus lanceolatus)

“…A unique biological feature of S. lanceolatus is its short‐lasting migration ecology. In fact, our study addressed the shortest freshwater migration among eDNA studies on the migration of diadromous species (Doi et al, ; Laramie, Pilliod, & Goldberg, ; Maruyama, Sugatani, Watanabe, Yamanaka, & Imamura, ; Plough et al, ; Yamanaka & Minamoto, ). We were able to track short‐term migration dynamics of this species using a newly developed, species‐specific primer and probe set.…”

A comparison of European eel Anguilla anguilla eDNA concentrations to fyke net catches in five Irish lakes

“…Other freshwater eDNA studies comparing eDNA sampling to established sampling methods have also reported an increased sensitivity of detection, including for electrofishing of A. japonica in rivers (Itakura et al, 2019) and for other fish species in both lakes and rivers (Hinlo, Gleeson, Lintermans, & Furlan, 2017;Lacoursière-Roussel et al, 2016;Ogburn et al, 2018;Takahara, Minamoto, Yamanaka, Doi, & Kawabata, 2012).…”

A comparison of droplet digital polymerase chain reaction (PCR), quantitative PCR and metabarcoding for species‐specific detection in environmental DNA

“…The rational for this was to enable a comparison of the quantitative capacities and differences between qPCR and ddPCR (discussed above). However, there are some indications from work on eDNA that there can be relationships between copy numbers detected, and actual organism abundance (Chambert, Pilliod, Goldberg, Doi, & Takaharam, 2018;Dowle et al, 2016;Lacoursière-Roussel, Côté, Leclerc, & Bernatchez, 2016;Plough et al, 2018). Caution is recommended as different life stages often have variable cell numbers, DNA may be shed differentially across life stages or under varying environmental conditions and there may be differing rates of degradation.…”