Sequencing the Potomac River

The Potomac River starts small, at a place called Fairfax Stone. 300 miles later–as it passes by Washington DC and enters the Chesapeake Bay estuary, it’s very large.

Along the way the Potomac does more than pick up water. It picks up nutrients from the surrounding lands and the species that inhabit its waters and banks shift, too.

How much nutrient it picks up and how the species in its waters respond has never been worked out that well though. There have been surveys of rivers like the Potomac. People have looked for insects and fish at different spots. But, as the river gets big, it’s hard to use standard techniques to see what’s in the water.

Jonah Ventures, along with friends at the University of Maryland, tried to see if we could use environmental DNA to put together a biodiversity atlas of the river and whether we could put together a bio assessment index based on the relative abundance of the DNA of bacteria, phytoplankton, macroinvertebrates, and vertebrates along the river.


We just published our results up on the pre-print server Biorxiv (see here). Although the research is still undergoing peer review, we feel pretty confident that the results are pretty amazing (at least for a first shot).

The take home point of the paper is that the assemblages of the headwaters, main river, and estuary were distinct. Not only that, we found a good relationship between increases in phosphorus concentrations in the river and the relative abundance of different species. As the waters picked up phosphorus, a whole suite of bacteria, phytoplankton, and animals became more abundant as another suite dropped out.

By no means is the last word on the question. We still have to develop our techniques a bit more, but it’s hard not to see the potential here. Soon, we should be able to suck up a small amount of water from a stream or river and quantify enough of the organisms that are in the water to infer the status of the waters.

*Bonus fact not discussed to much in the paper. In some parts of the river, almost half of the vertebrate DNA was human DNA. We thought the most extreme parts would be down by DC. Not so. All the sites with a lot of human DNA were actually up in the headwaters, not down by DC.

**Bonus fact not in the paper. We found a lot of different species in the water that we didn’t discuss. The list of species we found was fascinating. Fish like trout, carp, eels and shad. Amphibians like red salamanders and spring peepers. Mammals like pigs, cattle, and fox. The coolest animal: mountain lion (!). At site 5, 2.5% of the mammal DNA was identified as Puma concolor. There are no cats with sequences close to that.