Area of Research: Aquatic environmental DNA (eDNA)

Today begins our National Conference on Marine Environmental DNA.

A press release describes the purposes and previews some findings.

The meeting is part of the continuing Monmouth University-Rockefeller University Marine Science and Policy Initiative.

Over 200 news outlets so far, including the Washington Post and New York Times published the Associated Press story that opens with reference to Mark Stoeckle’s East River eDNA work.

https://ktar.com/story/2194560/telltale-bits-of-dna-help-track-past-and-elusive-wildlife/

Mark Stoeckle is interviewed in an AP Television segment about searching for the Loch Ness monster using eDNA.  Mark’s interview and footage begins about 2 minutes 50 seconds into the 8-minute segment.

https://www.youtube.com/watch?v=d5UPXmP5YE0

https://www.youtube.com/watch?v=nj8qoHoa0Vg

We (Mark Stoeckle and Jesse Ausubel) post new results from water sampling in October 2017 for eDNA on the island of Martha’s Vineyard.  We tested for freshwater fish (light green rows), saltwater fish (blue rows), and other vertebrates (taupe rows).  We tested in four more locations, Upper Lagoon Pond (Oak Bluffs), Mill Brook just below Mill Pond (West Tisbury), Old Millpond (West Tisbury), and Priester’s Pond (North Tisbury).  Priester’s Pond is about two miles north of Mill Pond and feeds into it.  We compared these four locations to two places we tested in 2016, Look’s Pond (freshwater, West Tisbury) and Tisbury Great Pond (saltwater) into which it feeds.

In each case, we sieved DNA from about a cup of water scooped within reach of the shore. The numbers in the columns are the number of DNA “reads” obtained from each sample for each species.  One can think of the number of reads or fragments of DNA as indicative of the abundance of DNA of that species and probably indicative of the abundance of the species itself, although different species of animals shed DNA at different rates.

The first two columns on the left show the results from 2016, for example, lots of American eel DNA in Look’s Pond.  In 2017 the Bella Bennett of the Martha’s Vineyard Times covered our initial findings about eDNA on the Island: https://www.mvtimes.com/2017/08/02/fishing-for-dna/

We found some cool things in the new locations.  For example, Mill Pond has DNA of river otters, which are hard critters to see.  The Mill Brook, Millpond, and Priester’s Pond all have muskrat DNA, and all abound in frog DNA.  DNA from all the fish in Priester’s Pond also occurs downstream in Millpond but Millpond has pickerel and eel DNA absent from Priester’s.   The brook has DNA for small stream species such as darters and killifish but not for brown bullhead (similar to catfish) or pickerel, which may need the pond habitat.

We found a mix of DNA for salt and freshwater fish in Upper Lagoon Pond.  We were happy to find menhaden and herring DNA, which means the “herring ladder” gets used.  Most remarkably, we found striped bass DNA in Upper Lagoon Pond, confirming a wild “fish” story from 2016: https://www.mvtimes.com/2016/06/01/late-night-splash-dark-holds-surprise/

We continue to be thrilled by ways that eDNA allows us to discover the animals in the water around us.  For more, see https://phe.rockefeller.edu/blog/2018/01/11/edna-seasonal-fish-abundance-study/ and  https://phe.rockefeller.edu/blog/2017/04/12/fishing-for-dna-paper-published/ .

As part of the Monmouth U-Rockefeller U Marine Science and Policy Initiative, Mark Stoeckle and Jesse Ausubel participated in a lively seminar at the Urban Coast Institute about discovering aquatic life with environmental DNA (eDNA).

Mark Stoeckle, together with co-authors Lyubov Soboleva (Hunter College) and Zachary Charlop-Powers (Rockefeller University), update their 2017 paper “Aquatic environmental DNA detects seasonal fish abundance and habitat preference in an urban estuary” (PLOS ONE e0175186). They extended their original six-month study to twelve months, making this one of the longest time series of fish monitoring by eDNA to date. The new analysis shows how little bits of DNA shed by fish track the seasonal movements of fish populations in and out of New York Harbor. eDNA also gives a picture of how the relative abundance of species differs from one habitat to another. These results help open our eyes to how eDNA can improve monitoring of ocean life.