Tracking invasive species movements with environmental DNA
How did invasive species spread in the U.S.?
DNA can be used to track the wide variety of aquatic invaders including plants, fish, amphibians, pathogens, and invertebrates like mollusks and snails. Quagga and zebra mussels aren’t yet established in the Northwest but will destroy any ecosystem they populate. (Data Source:USGS-NAS, UGA-EDDMapS)
The six major species threatening Montana
Aquatic invasive species threatening Montana have already arrived with the exception of zebra and quagga mussels. The clickable points represent invasive species observations; some introductions failed, while other locations don’t show the full extent of infested waterways. (Data Source:USGS-NAS, UGA-EDDMapS)
Environmental DNA and Aquatic Invaders
Environmental DNA (eDNA) has the potential to detect any species from a single drop of water.
This power has the potential to vastly improve early detection of invasive species, which is more commonly done through visual microscopy.
eDNA can distinguish plants and animals more readily than the human eye allowing detection of minuscule juvenile dreissenid mussels called veligers that threaten waterways.
The sensitivity of the test also creates potential for errors often through differences in collection methods resulting in changed detection rates. Despite these challenges eDNA is advancing species detection, allowing for quick results and finding species that may be overlooked.
“If you detect a cancer early, like an invasion or tumor, you can excise it early from the body or ecosystem,” says Luikart, who hopes to establish regular testing for invasive species of Montana’s waterways.
Often, invasive species can go years undetected until discovered and by then the chances of removal are nearly impossible due to the rapid ability for species to reproduce.
Lake McDonald in Glacier National Park is a popular recreation area with high potential for invasive species introductions. The park requires self-certification for all boats and manages several seasonal boat inspection stations near entrances, but the system is not without some gaps. Boat ramps are the most likely places for invasive species to pop-up if introduced. Steve Amish and Jenna Schabacker collect filtered water with a fine-meshed plankton tow net for eDNA at the boat launch on Lake McDonald in Glacier National Park in June 2015. Back at the lab they will perform eDNA tests for invasive species and trout that are known to be in the lake. 
At Lake McDonald, Students from Gordon Luikart’s summer conservation ecology course hold a tube of collected sediment that could potentially hold the DNA of many species that have touched or live in the lake. All that is needed is one cell. Environmental DNA, or eDNA, is a way of collecting genetic material without having to find or capture rare or elusive species. A detection process like eDNA can be seen as too sensitive, but that may also be one of its strengths. 
Gordon Luikart, a conservation biologist based at the Flathead Lake Biological Station near Woods Bay, Montana, is working on perfecting environmental DNA, a test to quickly detect aquatic invasive species. “We developed our own test from DNA sequences on zebra and quagga [mussels] and just started applying it,” says Luikart. “So far, the test is sensitive enough to detect invasive species in controlled environments. Outside the laboratory there are many barriers that make accurate tests much more difficult.”
Luikart hopes to monitor large scale lakes and rivers in Montana, including where he works on Flathead Lake. His research group also received funding for a stationary device to collect sediment samples at sites that receive heavy human use to monitor for invasive species.
The state already spends $1.1 million a year on aquatic invasive species prevention, most of it on boat inspection stations that dot Montana highways.
Invasive species can do real damage to lakes and streams by clogging waterways and forcing out native species. However, the strongest argument for preventing invasive species is an economic one.
According to the Pacific Northwest Economic Region Group: Hydroelectric dams, water quality, agriculture, recreation, and fisheries and other ecological systems will all be negatively affected and incur additional costs that are passed on to consumers, electric bills and tourism losses.
To look at what an invasion might look like I headed to a place that had failed to keep mussels out and was now trying to keep them in.
Time-lapse maps of individual species:
Zebra mussels (Dreissena polymorpha)
Quagga mussels (Dreissena bugensis)
Eurasian watermilfoil (Myriophyllum spicatum)
Curlyleaf pondweed (Potamogeton crispus)
Flowering rush (Butomus umbellatus)
New Zealand mudsnails (Potamopyrgus antipodarum)
Lake Powell and Quagga Mussels
A colony of exposed quagga mussels at low water in the winter. By Memorial Day, when most visitors to the lake arrive, the water level has been brought up and the mussels aren’t as visible. Yet the shore of lake beneath the surface is quickly being covered. Estimates place the mussel at taking another 5 years before they are found in every part of the 200-mile-long lake In 2007, an eDNA test pointed to mussels in Lake Powell but the precise test didn’t lead to visual confirmation that mussels were in the vast waterway on the Colorado River in Arizona and Utah. State and park officials endured several years of detection of mussels in genetic testing, but diver surveys that turned up no mussels. In 2012, a small colony of quagga mussels were thought to be eradicated, through treatment of infested areas. In 2013, the National Park Service found hundreds more quagga mussels growing in the waters of the reservoir. They had been there for years. After years of intense eradication, education and monitoring efforts, park officials were forced to admit defeat. The mussels had won. Instead of being a target for incoming mussels from millions of visitors per year, Lake Powell was now on the list of places that might start spreading the mussels to other states. Inspectors now check boats entering for new species, and boats going out are decontaminated and quarantined for up to a month before they can go in another lake. 
A total of 2.4 million people visited the park in 2014 with thousands launching or renting boats. The cost for containment through boat inspections and decontamination of exiting boats may soon reach $16 million a year, not including maintenance and removal of mussels from beaches, docks, boats and the pipes and screens at Glen Canyon Dam. The large number of boats are also responsible for moving the mussels to new parts of the lake. The movements on the lake and in the Colorado River are tracked by tow net samples that collect sediment that is then examined though a microscope. DNA tests are used to confirm visual results. Wayne Gustaveson, a Utah state biologist, manages the sport fishery on Lake Powell and keeps track of how the mussels are colonizing the lake. For him, seeing mussels arrive was only a matter of time. Lake Powell had a target on its back, he says, as the lake was under heavy pressure from visiting boaters. At the Castle Rock Cut, an area once under 150 feet of water, the park service cut a canal into the red-sandstone rocks for boats to pass to the main part of the lake. The cut, built in 2014, is one of the best places to watch how quickly mussels are colonizing the lake. Upon newly exposed rocks flooded in the summer they have formed dense colonies. Wayne Gustaveson looks at the millions of quagga mussels that cling to crevices at the Castle Rock Cut. The cut was built in 2014 to save a 14-mile trip through the canyon’s main waterway. 
Quagga Mussels at Lake Powell, Utah. Larvae of the small bivalve are undetectable with the naked eye. DNA can be a powerful tool for finding what other detection methods miss. Wayne Gustaveson suspects the name Lake Powell will soon be synonymous with mussels, much like Lake Mead and Lake Havasu. “We’re on the naughty list now,” he says. It’s hard for him to watch quagga mussels take over. They are expected to be in every part of the lake within five years. Wayne Gustaveson, a Utah fisheries biologist looks at colonizing quagga mussels at the Castle Rock Cut on Lake Powell. The mussels will take food away from other organisms like fish that feed on the same nutrients. Wayne Gustaveson looks at rental boats near Wahweap Marina for signs of mussels. Lake Powell has an incredible number of boats. Many of the large houseboats that stay in the water or in storage for the winter must be cleaned once or twice a year to reduce buildup of mussel colonies. 
Lake Powell remains a popular destination for international visitors to nearby national parks. The introduction of mussels won’t slow the millions of tourists, but it has already increased costs to boaters. Water levels in Lake Powell have fallen by 150 feet since reaching full capacity in 1980. The lake is now at 50-percent of normal levels, exposing a white calcium bathtub ring and in areas where the lake fluctuates seasonally, the quagga mussels that hide beneath the surface. The Glen Canyon Dam may incur extra costs from mussels clogging pipes. The costs come from removing and clearing mussels from intake systems and also installing mussel prevention systems, such as screens, resistant paint, and UV light filters. Despite these systems being in place, the quagga mussels are now on both sides of the dam and possibly moving into the Colorado River. As the Colorado River sees less runoff, declining water availability puts Lake Powell (and Lake Mead) in jeopardy. Maintaining enough water to operate dams and fulfill the needs of municipal and agricultural water users will be a problem in the future. An influx of mussels may further degrade the value and effectiveness of the dam due to increased maintenance costs. 
French and Chinese tourists driving between Bryce Canyon and the Grand Canyon take a tour of Glen Canyon Dam in December. The chill of winter doesn’t deter thousands of international tourists from visiting the region a few days after Christmas. The Colorado River below Glen Canyon Dam reveals what the canyon now under Lake Powell once looked like. Some advocates say the declining water levels are here to stay and that the dam should be removed. One thing is clear: the reservoir at full capacity is not likely to be seen again as millions of gallons of water are lost to evaporation each year. The loss of more water will make the lake harder to navigate and launch boats on and threatens effective operation of the dam. The mussels will endure rising temperatures and, even without the dam and reservoir, could thrive in the river. The future of Lake Powell’s water is uncertain, but one with quagga mussels is guaranteed.
San Justo Reservoir and Zebra Mussels
Closed for 9 years, future treatment may be first large-scale eradication
San Justo Reservoir near Hollister, California is one of the only Western sites of zebra mussels. In 2007, a fisherman came across a few mussels in the lake. Within a few weeks officials permanently closed the small lake to the public; it has remained so ever since. The reservoir was closed to prevent further spread of zebra mussels (seen on the shore), particularly to larger nearby waterways such as San Luis Reservoir and the California Aqueduct. The mussels are thought to have been introduced from fishing bait sold from out of state. Kelley Aubushon, California Department of Fish and Wildlife Environmental Scientist, inspects tiny zebra mussels growing on the underside of rocks, as Dave Meraz of San Benito County Water District looks on at San Justo Reservoir near Hollister, California. The small size of the reservoir makes possible treatment with potash, a non-chemical method for killing bivalves, while still using the water for agriculture in the surrounding valleys. The water is very important to agriculture in the area during the current drought. 
San Justo was closed in 2007 to prevent further spread of the mussels to canals and waterways. “The risk of these getting out was too great. They’re too afraid that if they got into the Central Valley Project we’d be billions of dollars in the hole,” says Kelley Aubushon, a California Department of Fish and Wildlife Environmental Scientist. Dave Meraz of San Benito County Water District leans in to look at Zebra Mussels in San Justo Reservoir. As manager for the agricultural district, Meraz keeps the reservoir levels low to kill off the mussels in the winter, starving them in oxygen-poor water that limits growth. Despite being closed for many years, San Justo still serves agricultural and municipal water users. Juvenile zebra mussels, shown here at San Justo reservoir near Hollister, California, are often the first visible sign of a new invasive species introduction. By focusing on detecting mussels before they become established, including the use of eDNA, scientists may be able to stop invasive species before it is too late to extirpate them. Kelley Aubushon holds a juvenile zebra mussel, shown here at San Justo reservoir near Hollister, California. These are often the first visible sign of a new invasive species introduction. When the mussels were found in San Justo they may have already been established for three to four years. Aubushon works in the Quagga-Zebra Mussel Program to prevent mussel introduction, but hasn’t found eDNA helpful in detecting in the 12 counties she serves. Lab results often come up with false positives that can’t be confirmed. Instead, her lab uses microscopy from plankton tow-nets to look for small mussels. The goal is to keep invasive species from spreading. Southern California has the quagga mussel from Lake Mead; another mussel would come at a huge cost to agriculture and other resources in the area. By focusing on detecting mussels before they become established, scientists may be able to stop invasive species before it is too late to extirpate them. The boat launch of the popular local fishing and recreation area has been closed for nine years due to an introduction of zebra mussels. There is no timeline for treating, eradicating, and reopening the area, but a treatment plan is now drafted. Once funding is available, officials will treat the lake, knowing that they only have one chance for eradication. The first successful treatment of mussels was at Christmas Lake, a small pond in Minnesota.
In Montana
‘looking for a needle in a haystack’
Flathead Lake, one of the largest freshwater lakes in the American West, remains a particularly clean water source and one of the most popular recreation areas in Montana. Introduction of an aquatic invasive species might change the lake forever. “Flathead Lake is by far the most likely location of invasion,” says scientist Gordon Luikart. 
Two boats arriving at Flathead Lake in March each had a single mussel on the bottom of their hulls. The boat and mussel pictured above were traveling from Lake Havasu. Within the first two weeks of operation a boat inspection station in Pablo, Montana found the mussels as part of a pilot project to intercept boats that travel to the state before Memorial Day. Currently, the only way boats will be stopped is if an inspector sees them or if trained mussel dogs deployed in a few places throughout the state sniff them out. If boats carrying invaders reach Flathead Lake, a mussel colonization is possible. eDNA could be another tool to monitor for invasive species that get past boat inspections or travel when the stations are closed. (© Flathead Basin Commission) 
Virgil Dupuis, Extension Director at Salish Kootenai College, looks at an invasive flowering rush plant that forms dense mats in parts of Flathead Lake. The plants are visible on the south shore of the lake as they emerge from the water. “I hate this stuff,” he says with a laugh. Flowering rush, seen here, can be identified by a triangular stem section and flowers. By late summer, the plant has entirely overtaken the boat launch on the south shore of Flathead Lake near Polson, Montana. “This kind of a habitat favors invasive fish like bass and perch,” says Dupuis. These fish are not native to the lake, but they thrive by breeding in the flowering rush. They outcompete native fish like endangered bull trout and declining westslope cutthroat trout, Dupuis says. Eurasian watermilfoil has overtaken sections of the Lower Clark Fork River where it runs wide behind a dam. The waterway is unnavigable by boat as large swaths of the shoreline and shallow backwaters are overtaken with dense chains growing in the Cabinet Gorge and Lake Pend Oreille and at Noxon Reservoir, seen here. 
Eurasian watermilfoil on the Clark Fork River blocks the light and growth of other plants by forming a dense drifting mat. Parts of a flowering rush plant break loose and float away. Each floating piece, called a rhizome, is a potential rooting plant that will drift to a new location and take root. The non-native milfoil can potentially choke an entire waterway if left unchecked, and can stretch up to 30 feet from the floor of a lake to the surface. In 2007, invasive Eurasian watermilfoil was discovered by accident in Beaver Lake, an isolated lake northwest of Whitefish, Montana. Since then, the lake has been treated yearly to eliminate infested areas, and the unwanted plant is thought to be nearly eradicated. eDNA was able to successfully confirm the difference between a native milfoil and the invasive version in the lake and to ensure that it wasn’t traveling to other lakes in the region.
Invasive aquatic plants don’t get as much attention as mussels, pathogens or fish, but the potential for damage is great.
Invasive plants, like Eurasian watermilfoil, have been blending into Montana’s waters for decades. Many people miss the early signs often thinking a plant was there to begin with and cannot do as much damage.
Still aquatic plants can be detected by eDNA just the same as any other, but the response to finding them may be different.
An introduction of an invasive mussels effectively means the end of an aquatic ecosystem. Mussels will rapidly alter water quality and changing species composition and habitat forever.
This brings back the importance of early detection for all invasive species, plant or animal, especially for Luikart and his team.
Caryn Miske director of Flathead Basin Commission is optimistic the future of eDNA and looks forward to putting it to use in protecting the Flathead Lake.
“You’re looking for a needle in a haystack,” says Miske “with mussels, even if you detect early, you’re often not able to save that lake, but you can save other lakes, and with invasive plants there is likelihood that we can actually do something.”
Luikart and fellow scientists currently test lakes and rivers in the region at the request of many groups with an interest in preserving water quality and ecosystems. The tests they run from sampled water always include a known species like a trout, a possible one like Eurasian watermilfoil and quagga or zebra mussels, just to be sure.
Part 3: The True Home of Alaskan Salmon
For more on invasive species in Montana and eDNA, see the story originally published in Solutions Journal and the Daily Inter Lake Part 1
© KEN RAND 2016 – images and text COPYRIGHTED unless otherwise noted. All rights reserved. (Published May 12th, 2016)