eDNA for AIS: Demystifying a Tool That Can Watch the Health of our Waters

by ROB RICH

Dragging a meter-long net a meter underwater while putting along at five miles an hour, I understand what it’s like to be a bull trout holding still against the flow. The drag was only a hundred meters and three minutes long, but even with a forearm resting on the gunwales of the aluminum skiff – a well-worn, forest-green vessel dubbed Shrek – there was an isometric intensity to the static pull. This isn't the first time we've collected water samples to scan for aquatic invasive species (AIS), but for most of the season our samples have gone to experts at Montana Fish, Wildlife & Parks who are trained to detect zebra and quagga mussel larvae under microscopic scrutiny. For our most recent survey, in partnership with the US Forest Service’s Beth Gardner, our samples will be scanned with a tool that sees what a microscope can’t: fragments of sloughed-off cells, and within them, the helical strands of DNA that carry the instructions for life.

  Beth keeps time as I drag the net at the outlet of Holland Lake. Inlets, outlets, and boat ramps are common places we sample, because these are the most likely places for invasive species to occur. Because this is the peak season for aquatic plant growth, and because zebra/quagga mussels are the most reproductively active when the water temperature crests 50 degrees, mid-August is the most likely  time to detect invasive species.

Beth keeps time as I drag the net at the outlet of Holland Lake. Inlets, outlets, and boat ramps are common places we sample, because these are the most likely places for invasive species to occur. Because this is the peak season for aquatic plant growth, and because zebra/quagga mussels are the most reproductively active when the water temperature crests 50 degrees, mid-August is the most likely  time to detect invasive species.

If that kind of vision sounds a bit overblown, consider this: there are parts of you everywhere. When you scratch an itch, flecks of your skin scatter through the air. When you take a sneeze or blow your nose, that’s you in the tissue. When you get a haircut, that’s you, all over the floor. You might be swirling around your office or house as you read this right now, or already off on a journey through the water cycle from your recent shower or flush. And of course, you’re not alone: dogs are shedding, birds molting, leaves falling. But each species has a unique genetic code, and if we can extract a pure sequence for that species, we can detect its presence in a sample of the environment. That’s the theory behind eDNA (ie. environmental DNA), and as Fisheries Biologist for the Flathead National Forest, Gardner sees its promise.


While its earliest applications were terrestrial – with genetic data gleaned from extinct plants and creatures sealed in permafrost or caves – eDNA’s success has increasingly been aquatic. Without intervening in the lives of rare or sensitive species, and with maximum efficiency in complex, fluid conditions, eDNA provides scientists a sight-unseen way to explore the mysteries of biodiversity. Gardner’s scans will aim to detect zebra and quagga mussels, Eurasian water-milfoil, and curly leaved pondweed, all of which are troublesome aquatic invaders we hope are non-existent enough to yield negative results on this fine-tuned scan. Because its high degree of precision also creates its vulnerability, Gardner honed the method on tests with common water-milfoil, a native known to occur in the Swan Valley. To avoid sample contamination, Gardner also makes sure we take advanced precautions to cleanse and rinse all the materials we use.

Over three days, Gardner, Luke, Mike and I surveyed a total of twenty-nine sites around Swan,
Lindbergh, Holland, Lakes. Each lake we sampled had a separate net, and each sample we collected was preserved with ethanol, carefully labeled, and cooled for transport to the eDNA lab at Flathead Lake Biological Station. As current leaders in eDNA analysis for Montana, the Bio Station will be processing Gardner’s samples, and hundreds of others, in the coming months. It costs 40 dollars to process one 100mL vial, but the Bio Station is making some impressive discoveries that will make the method accessible and affordable.

 

  On Swan Lake, Mike learns to label our samples – with date, location, and number – so that they can be processed efficiently and effectively.

On Swan Lake, Mike learns to label our samples – with date, location, and number – so that they can be processed efficiently and effectively.

I got more than a few perplexed looks from fishermen, boaters, or swimmers as I dragged the net, and sometimes I could only give a nod to a distant boat passing by as I strained along. Truth be told, if I saw myself scooping water, I’d be concerned for my sanity too. But a lot of people were curious, and some came over to ask “so what are you doing?” One time, in the zone of our work, Luke reflexively uttered that we were just collecting “eDNA for AIS.” “e- for what?” they answered. The humor in that disastrous acronymic phrase sparked talk about how our work linked to the zebra mussel and the check stations and what really mattered: that this tool was but a means to the goal of healthier waters for all.

  Captain Beth at the helm of Shrek on Swan Lake. Always a creative, pragmatic thinker, Beth likes to keep a photo of a mid-20th century computer –the size of her entire office – next to the thing we now call a “desktop,” just as a reminder that we’ll each need a courageously open mind to find durable conservation solutions, some that we have yet to imagine.

Captain Beth at the helm of Shrek on Swan Lake. Always a creative, pragmatic thinker, Beth likes to keep a photo of a mid-20th century computer –the size of her entire office – next to the thing we now call a “desktop,” just as a reminder that we’ll each need a courageously open mind to find durable conservation solutions, some that we have yet to imagine.