eDNA Research

River herring

We partner with the University of Maine and the Bigelow Laboratory for Ocean Sciences, technical experts in eDNA, to apply eDNA to our work building sustainable fisheries in the Gulf of Maine. One project builds on the restoration of river herring fisheries in the Bagaduce River watershed, conducted by another partner, the Maine Center for Coastal Fisheries (MCCF). We have joined forces with the MCCF to study the production of juvenile alewives to understand better the impacts of river herring restoration on coastal food webs. We know that the exodus of billions of juvenile river herring from lakes to the ocean each fall is an important source of forage for countless marine organisms, including cod, haddock, and other commercially important species. But rivers, lakes, and watersheds are not all the same. eDNA can help us figure out which river systems produce the most juveniles and why. This information will lead to improved river herring management and help prioritize restoration efforts to focus on those most likely to provide forage and support sustainable fisheries.

Shellfish

A second project is focused on shellfish, specifically, the quahog (or hard clam). Populations of softshell clams have been declining, in large part due to their susceptibility to predation by the voracious and invasive green crab, whose abundance has exploded as water temperatures have warmed. This is devastating to Maine’s softshell clam fishery, the third most valuable in Maine after lobster and elvers (baby eels).

As an adaptation to climate change, harvesters have been shifting their efforts to quahogs. This clam species is increasing in abundance (perhaps due to their tolerance of warmer waters and thick shells that protect them from predation) and growing in value as it becomes common alongside oysters at raw bars and seafood restaurants. In 2018, we supported an effort by the Town of Georgetown’s (Maine) Shellfish Conservation Committee to expand their quahog population by transplanting 50,000 adult quahogs to Robinhood Cove with the goal of establishing a self-sustaining population. In the summer of 2021, we will use eDNA to gauge whether or not the transplanted quahogs are spawning and producing larvae.

Partnerships with the University of Maine and Bigelow Laboratory help us with our work and allow us to contribute to the development of eDNA as a tool. The applications for eDNA in fisheries research have been limited so far, but there are many questions we believe it can help solve. Our research using this new tool will help determine how far an eDNA signal can be detected from its source, how long the signal lasts over time (and with the flushing of tides and currents), and how the quantity of eDNA detected relates to the abundance of the species in question. Our findings will help others apply eDNA to fisheries research and monitoring.

While genome mapping requires sophisticated lab analysis (provided for us by our partners at the University of Maine and Bigelow Laboratory), analysis of water samples can now be accomplished in the field and in real-time. In 2021, we will purchase and put to use an eDNA field reader. Using genomic mapping data provided by our partners, we will be able to generate findings as soon as water samples are collected and run through the field reader. Generating data on the spot strengthens engagement of fishermen and other local stakeholders; seeing presence/absence and other data sustains interest in collaborative research and builds confidence in the data analysis and results that follow. Having an eDNA field reader in our toolkit will also allow for testing different sampling strategies during one sampling trip and allow for input from community partners, most familiar with the dynamics of local water bodies. This can help narrow the number of samples required to address specific research questions and improve the efficiency of monitoring.

Looking ahead, we’re excited about the potential use of eDNA to assess not just single species but entire ecological communities. In a process called metabarcoding, eDNA is used to identify genes common to groups of similar species. Metabarcoding provides a big picture view of an ecosystem’s flora and fauna by capturing data not visible to the human eye. It provides an opportunity to assess biodiversity, important to our fisheries work and research on shorebirds. Finally, metabarcoding can also be used as a screening tool; if an order or family of fish or birds is identified, water samples can be further analyzed to test for the presence of particular species.

Shorebirds

Manomet is piloting a new study to investigate the causes of shifts in distribution and the overall decline in numbers of Red Knots within the Monomoy-Pleasant Bay system. This work will incorporate environmental DNA (eDNA) sampling techniques to examine Red Knot diet and prey distribution. This effort is a collaboration with the Fisheries team and the University of Maine’s eDNA Laboratory. Scientist Emeritus Brian Harrington will also continue his long-standing International Shorebird Surveys (ISS) at Monomoy National Wildlife Refuge. This ISS dataset has helped document the shifts in Red Knot demographics that inspired this more recent research.