Mark Y. Stoeckle and Jesse H. Ausubel
Animals shed environmental DNA (eDNA) into the environment. Sources include cells sloughed from body surfaces, body wastes, and tissue remnants following predation, death, or injury. eDNA is a bit like dandruff. DNA of course consists of long strands of four chemical compounds: cytosine (C), adenine (A), guanine (G), and thymine (T). Researchers use strands of about 100 “letters” from variable parts of the genome, like a long telephone number, to identify the species of animal from which the DNA comes. Acidity, heat, and light can speed eDNA degradation, and bacteria eat eDNA. A rule of thumb is that eDNA sufficient for reliable identification lasts about 24 hours and thus gives a good current portrait of life in a water body.
As seen in these 5 slides, the PHE’s Mark Stoeckle regularly collects a half liter of water from the East River adjacent to the Rockefeller campus (slide 1) with a bucket on a string, filters the water, extracts the DNA from the sediment on the filter using special chemicals called primers to grab only the DNA that came from vertebrates, sequences these pieces of eDNA, and matches the sequences against genetic libraries. The number of copies for each species corresponds well to the recent abundance of that animal in the East River.
Our vertebrate eDNA studies show that that the East River abounds in fishes (slide 2), with tautog most common but also herring, bass, and eel. The presence of water from sewage treatment plants and rains that wash city streets also brings DNA of urban wildlife into the East River. A cup of water from the East River reports the abundance of rats, pigeons, dogs, and cats (slide 3). It also reports the presence in the River or nearby of additional wildlife ranging from deer and beaver to seal and dolphin (slide 4). Finally, the eDNA in the East River neatly tracks the diet of humans of New York (slide 5). The fractions of aquatic eDNA of commonly consumed meats such as chicken and cow match nicely with national data on meat consumption. An exception is sea bass (branzino), widely served in New York City restaurants and thus common in East River water samples but a tiny proportion of the national fish diet.
eDNA revolutionizes the ability for people to know, affordably, what animals live in or use the waters near them. eDNA will be a routine component of fish stock assessment, detection of invasive species, and monitoring effects of coastal storms and climate change. Genomics enables a cup of water to tell the natural history of the East River.