Interview with Pete Countway of Bigelow Laboratory

What is your background?

I’m a microbiologist and oceanographer by training. Most of my work is focused on phytoplankton communities, the diversity of these communities, and their change over time. And not just one or two functional groups, but we try to look at them as high resolution as possible, meaning that we do a lot of genetic analysis of these communities. Essentially, we use high-throughput DNA sequencing to kind of tease apart these microbial communities. And by comparing one sequence to another, we can figure out how many different unique types there are in an ecosystem and how these organisms change over time. Maybe, these changes are in response to temperature or nutrient availability or just changes with the seasons, depth in the water column, or even geographic distance.

The tools that I utilize have broad applicability, especially to a lot of questions that the aquaculture industry will be thinking about as the Gulf of Maine continues to change and warm, as it appears to be doing.

I’m finding that my work is starting to focus more on some of these real-world problems that the aquaculture industry faces. In particular, I’ve worked with harmful algal blooms; in the Maine eDNA project, that’s my primary role. I’m leading a project on developing molecular toolkits to monitor not just one harmful algal blooms species but half a dozen species. We’re also expanding work into freshwater ecosystems. Broadly speaking, many of us at the lab are getting more involved with aquaculture-based issues, marine conservation, and how climate change may be impacting things.

Can you tell us more about how eDNA is being used for research?

A couple of years ago, some folks over at the Darling Marine Center asked me if we could apply these same techniques to shellfish communities. And so I thought about it for a few minutes and thought, I suppose we could, and so they were interested in tracking the reproductive events of deep sea scallops.

The idea was that instead of putting divers in the field and conducting experiments to examine the duration and timing of the spawning of the scallops, you could just collect a water sample and look for a DNA signature. So we did that, and it worked surprisingly well. Instead of taking this approach of large-scale DNA sequencing, we developed a species-specific assay  for the deep sea scallops. And so then, instead of looking for a needle in a haystack or the particular sequence that matched up with scallops, we could actually know that every time we saw amplification with this particular test, it meant that there was scallop DNA in the water. The analogy that everybody can relate to these days is that this is very similar to the kind of test that’s done for COVID.

I’m part of a research initiative that’s a collaboration between Bigelow Laboratory and the University of Maine, partner organizations, and other research and teaching institutions in the state. We are trying to broadly utilize these DNA-based techniques to understand better coastal marine resources’ connectivity between freshwater ecosystems and coastal marine ecosystems. We can use these tools to detect species that pose some kind of harmful threat or are new to the Gulf of Maine because of changing climate.

So broadly, we’re applying these molecular tools across many different trophic levels and asking lots of different questions. We feel that these approaches are really useful for figuring out the ecology of some of these organisms that we don’t know very much about because certain stages of their lifecycle are hard to capture or have remained invisible for a long time prior to these methods.

Just going back to the scallop example, we’re able to demonstrate both the magnitude and the duration of these reproductive events. So, Manomet is working to seed Robin Hood Cove with hard clams and would like to know something about the ongoing restoration or introduction of the hard clams to Robin Hood Cove. The thinking is that we can design an assay, very similar to the scalp assay, to look at hard clam DNA in the water column. That should also tell us something about the size of the population and when that population is reproducing.

What work have you done with Manomet?

We’ve been out sampling a couple of times, and so far, the training has been on how we collect our samples in the field and how we ensure the collection is not contaminated by something else from the environment. Then we’ve processed water samples back at Bigelow.

In terms of the genetic testing, we haven’t gotten to that stage yet, but we’ve started filtering water samples. I think that the frequency of that sample collection is about to step up a little bit because we are approaching the time of year when these hard clams are thought to be reproducing. So we will be looking for signals of the gametes in the water.

Another aspect of this is actually developing the genetic assay. That’s something that I’ve just started within the past couple of weeks. Essentially, that involves looking at the DNA sequence from the hard clam and comparing it to other bivalve taxa. You want to detect only the signal from the hard clams, not from soft clams or any other bivalve or any other mollusk. So when you look at DNA sequences, the challenge is finding a region, a really short region, within the genome that is unique to the hard clam. And to that species, only. Comparing this to COVID, you don’t want to pick up all the other coronaviruses out there; you want to know if you have that one particular type. But, some of the groundwork that I had done for the scallop eDNA project feeds in directly to this project, so we are pretty close on the assay. Then we can begin testing with some genomic DNA extracts from the hard clams.

Once we have that assay in hand, Manomet can come to my lab to learn how to utilize it. This tool is basically a molecular lab that will fit in a suitcase and is easy to use out in the field for any particular genetic test that you would be interested in doing. This project is probably just a jumping-off point for further molecular work that you guys might be interested in. It’s kind of limitless what you can do with this technology.