Pairing Environmental DNA with Acoustic Monitoring of Anadromous Fish in the Penobscot River, Maine.

Sunnarborg, Julia¹ *, Justin Stevens², Kristina Cammen³, Michael Kinnison⁴, ¹School of Marine Sciences, University of Maine, Orono, ME, ²Maine Sea Grant, Orono, ME, ³School of Marine Sciences, University of Maine, Orono, ME, Maine Center for Genetics in the Environment, University of Maine, Orono, ⁴School of Biology and Ecology, University of Maine, Orono, ME, Maine Center for Genetics in the Environment, University of Maine, Orono, ME

The improvement of fish passage through the Penobscot River Restoration Project has led to increased numbers of migratory fish in the Penobscot River, Maine, including forage fish such as river herring (alewife Alosa pseudoharengus and blueback herring Alosa aestivalis) that support local bird and marine mammal populations. Current efforts to monitor the recovery of this system include hydroacoustic surveys and fish trap counts, but such efforts are burdened by the inherent limits and pitfalls of traditional methods (e.g., taxonomic misidentification, insufficient effort, or bias), as well as the need to involve significant manpower and infrastructure. The implementation of environmental DNA (eDNA) sampling into ongoing survey efforts can expand sampling capacity in a cost-effective and non-invasive manner, but requires that eDNA tools are validated for capturing fish abundance, distribution, and community composition in a dynamic estuarine setting. To achieve this goal, eDNA samples were collected at 8 points along the Penobscot River Estuary during a biweekly acoustic survey conducted from April to November 2021. The eDNA concentration of river herring was quantified using quantitative PCR, and the broader vertebrate community was characterized using 12S rRNA metabarcoding. These data were compared to acoustic estimations of biomass to evaluate how well eDNA approaches capture changes in fish abundance over the course of a migration. The relative composition of fish sequences in each sample were also compared to size distributions obtained in the acoustic survey, to evaluate the utility of eDNA for characterizing fish assemblages and assessing the ecological impacts of restoration efforts.