Is aquatic eDNA ready?

A short note here to share our thinking around the office and lab…

Here, at Jonah Ventures we’ve spent a fair amount of resources working to understand how to apply next generation sequencing technology to aquatic environmental DNA.

Speaking non-technically for now, if someone wants to assess whether an aquatic ecosystem is impaired, they can either measure a large suite of physical and chemical factors, or quantify the fish or insect species in that water. The latter is what is used most frequently, for good reason. Individual species each have their own tolerances of environmental conditions. As such, their relative abundances tend to reflect environmental conditions.

The hard part is that it isn’t easy to measure the abundances of fish or insects in water. Also mapping individual fish or insect species to environmental conditions is also pretty crude. Right now, these species are used as indicators of “water quality”, but that typically means biological oxygen demand. And the mappings aren’t that tight. Ideally, we’d also be able to use indicator species to assess not only organic pollution, but also availability of different nutrients like nitrogen or phosphorus, pH, salinity, temperature, and heavy metals. All of these deserve to be assessed over time and over broad spatial scales.

In general, it seems clear that measuring fish or insects is not up to (or going to be up to) the task of being able to deliver all of this information. Leaving out details here, it can do some, but not all. And after 50 years of the traditional approaches, no one expects thing to change drastically any time soon.

If traditional approaches are limited, the question then becomes, can eDNA be used to assess environmental conditions better than quantifying the abundances of fish or insects? Is eDNA ready for this?

We think it is…almost.**

**We think bacteria and phytoplankton eDNA is ready for wide-scale use. Insects and fish, not quite.

Regardless of where we are right now, the important part is thinking about what the future might look like.

We think the future of bioassessment is going to be different than what it is today. And we aren’t going to try to do the same things we are doing now with a newer technique. We are going to try to do more.

In the future, we’ll rely on fish and insects/macroinvertebrates as we do today, but also routinely phytoplankton and bacteria.

And we’re not going to get a simple “water quality” index, but an oxygen demand index, a pH index, a phosphorus index, a salinity index, and a heavy metals index.

The databases that we use to assess water quality are going to span across state and country lines, too. Until rivers stop crossing state lines, our assessments will have to cross political lines, too.

And the days of measuring a river every 7 years to assess its quality will be replaced with much more frequent sampling.

We’re writing this today, because at Jonah Ventures we’ll be able to do some things with our modest resources. We’ll figure out how to measure the relative abundance of species in water with eDNA. We’ll put together the infrastructure to collect, analyze and distribute these data.

But, it’s going to take a lot more than that.

We’ll need better reference libraries. That means we’ll need a lot of taxonomists to identify and culture phytoplankton or sort and identify insects on a national scale. We’ll need ecologists to identify reference conditions that can be used to calibrate new indices. We’ll need regulators to determine how to operationalize new indices and determine sampling schemes.

The future of how we use this technique is going to be interesting, but the most important first step is for people to realize that we are largely going to have to start from scratch. Once people commit to that, eDNA’s future will come quicker than people expect.