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.

Restoring and sustaining anadromous fish populations is a grand challenge in the conservation of freshwater ecosystems. Alewife Alosa pseudoharengus and Blueback Herring Alosa aestivalis are two closely related anadromous fish for which responses to fish passage restoration are poorly known. We used a targeted environmental DNA method to sample 17 major tributaries of the Chesapeake Bay, USA, to determine the spatial extent of habitat use during the spawning season and the associations of habitat use with watershed characteristics. To help understand responses to restoration of fish passage, the study included portions of eight watersheds where dam removals, fish ladders, or dam failures provided access to habitats that were previously inaccessible to anadromous fish. Overall, 27.5% of samples showed positive detections for river herring, including at least one sample in 16 of 17 tributaries sampled. The presence of both species combined was negatively associated with elevation (relative influence [RI] = 29.8%) and positively associated with a watershed area (RI = 14.5%) and percent cropland (13.6%) of the watershed. In species-specific analyses, both Alewife (RI = 24.8%) and Blueback Herring (26.2%) presence was negatively associated with elevation, Alewife were more common in watersheds with high percentages of cropland (RI = 19.1%), whereas Blueback Herring were more common in streams with large watersheds (23.2%). The use of formerly blocked spawning habitats was generally greater upstream of sites where dams were removed (2%-100% of habitat used) compared with sites where fish ladders were installed (0%-66.8% of habitat used). The broad-scale sampling enabled by eDNA methods made it possible to identify habitat use patterns that can be applied to prioritize future restoration efforts and predict species-specific responses.

Despite the availability of interdisciplinary academic training programs, the practice of environmental science is often hampered by a lack of convergence across diverse disciplines. This gap is particularly salient in settings characterized by complex environmental issues, such as multiple-use coastal ecosystems. In response, we developed and implemented a training, research, and communication framework to provide undergraduates with an authentic operative experience working at the interface of interdisciplinary science and public decision-making within a case study of marine renewable energy. In our program, students gained hands-on experience with the scientific process and learned how to make information relevant, useful, and accessible to diverse stakeholder groups. Application of this framework demonstrates that the process of integrating data from biological (visual and acoustic monitoring of fish and marine mammals), physical (hydrodynamics), and social (local ecological knowledge) sciences can provide a more complete understanding of complex and turbulent ecosystems for better informed decision-making. We offer several recommendations to facilitate the adaptation and implementation of our interdisciplinary framework to diverse research contexts, with a focus on interdisciplinary training for the next generation of marine scientists.