If you were hired to find out whether the devastating zebra or quagga mussels had invaded Swan Lake, how might you go about it? What if your job was to discover whether an isolated population of bull trout or pure cutthroat trout was hiding out in some remote headwater? Would you search every cubic meter of water in either system? How?
Lucky for you, you’re off the hook, because there are already folks trying to get answers to questions like these and they’re armed with a new surveillance tool: eDNA.
You probably already know that forensic scientists can help identify human criminals or victims by examining DNA left behind in a physical specimen such as blood or bone. In the field of wildlife biology, it is sometimes preferable to study animals using this type of “non-invasive genetic sampling” which can tell us much without the stress and other drawbacks of capturing and handling.
Over the past decade, to study grizzlies, wolverine, lynx, fisher and other forest carnivores, we’ve fielded crews who search out and collect samples – hair and scat – which later undergo genetic analysis. Now, researchers have the ability to determine the presence of a species from microscopic genetic material floating freely in water and air: no hair, bone, or blood required. The technique essentially concentrates and amplifies loose fragments of DNA existing in the environment, thus the name environmental DNA, or eDNA for short.
Aquatic organisms shed genetic material into the water as they slough off mucous or skin cells, excrete waste or when they spawn or die. For a short time after being shed, perhaps days or weeks, DNA can persist in the environment separate from its parent organism. A population of fish holed up in a high elevation stream reach will send waves of DNA downstream that can be captured and studied.
Think of someone being located by a trained bloodhound that has only a scent trail to follow. In the case of aquatic species, a field tech gathers a sample by pumping a large volume of stream water through a micro-pore filter or towing a plankton net through a lake. The material trapped by the filter in either case is analyzed for the unique genetic signature of the target species.
Without anyone actually capturing or laying eyes on one of these animals, eDNA methods have been used to determine presence of invasive Asian carp, Idaho giant salamanders, sturgeon, mussels, and a variety of salmon and trout: all organisms we’re either trying hard to find or hoping we don’t.
eDNA sampling has revolutionized our ability to detect species invasions in their earliest stages, to locate the remnants of once-robust populations, and to confirm the absence of invasive species after eradication efforts. In each of these examples, biologists are looking for organisms that occur in low densities, ones that are inherently rare. By definition, they take far more effort to find than, say, a whitetail you can glimpse out your car window.
In the case of zebra and quagga mussels that annually cost the US billions of dollars to prevent and manage, it’s critical we find them when they are still at low densities, because early detection of their presence is key to potential elimination. They are nearly impossible to eradicate once they’ve become established in a water body. And the Pacific Northwest is the only place on our continent still free of these organisms that have marched steadily westward since invading the Great Lakes in the late 1980s. eDNA tests are so sensitive that a few cells shed by mussels can be detected in a lake.
Bull trout are a different example of a rare species that is challenging and time-consuming to study in the field. They tend to be more difficult to detect than other trout using the standard search technique of electrofishing. And because they are rare, not to mention listed under the Endangered Species Act, it’s wisely conservative to avoid causing undue stress to individuals from electrofishing and handling. Further, given finite financial and human resources available for fieldwork, alternatives that allow for a relatively rapid and cheap look into a stream are always welcome.
Our own electrofishing crew armed with experience, permits and expensive gear consists of at least three people. And over the past two years, in an effort to get a snapshot of the species assemblage of the Swan River, we’ve fielded a five-person snorkel survey team. On the other hand, a single individual given minimal training can quickly collect and filter water for an eDNA sample which can be archived and even reanalyzed in the future for other research interests.
Often when a new technology is developed, folks are quick to search for ways to justify its use. Is everyone jumping on the eDNA bandwagon? It turns out we currently have nothing that can replace the valuable genetic data obtained by directly collecting tissue samples from multiple individuals in a population.
In the case of aquatic species, that still requires electrofishing or netting, we know that eDNA techniques can’t distinguish living from dead organisms, or give a reliable estimate of the size of a population or its age or genetic structure. And eDNA methods are still in relatively early stages of development so there are questions yet to be resolved. Can eDNA tell us how far away organisms are from the sampling location? Or to what degree their signal is diluted under high flow conditions? Exactly how long can genetic material persist in a stream or lake after being shed?
Despite limitations and unanswered questions, locating aquatic organisms with eDNA methods is a more sensitive tool than others now available, including snorkeling and electrofishing, especially if the primary goal is to determine presence or absence. eDNA doesn’t replace available tools but it can quickly generate information to inform researchers where to focus use of their other tools. And in the case of early detection of aquatic invasive species, it may very well be the best tool we’ve got.
In the next installment of this column, we’ll report on efforts at Lindbergh, Holland and Swan Lakes to combat aquatic invasive species (AIS) using eDNA and other techniques.
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