During the annual salmon run last fall, 91̽�� researchers pulled salmon DNA out of thin air and used it to estimate the number of fish that passed through the adjacent river. , a 91̽��research scientist of marine and environmental affairs, began formulating the driving hypothesis for the study while hiking on the Olympic Peninsula.

“I saw the fish jumping and the water splashing and I started thinking — could we recover their genetic material from the air?,” he said.

The researchers placed air filters at several sites on Issaquah Creek, near the Issaquah Salmon Hatchery in Washington. To their amazement, the filters captured Coho salmon DNA, even 10 to 12 feet from the river. Scientists collect environmental DNA, or eDNA, to identify species living in or passing through an area, but few have attempted to track aquatic species by sampling air.

This study, , shows that eDNA can move between air and water — a possibility scientists hadn’t accounted for even though aquatic animal DNA sometimes appears in airborne study data.

The researchers then merged air and water eDNA with the hatchery’s visual counts in a model to track how salmon numbers rose and fell during the fall migration. Although the amount of salmon DNA in the air was 25,000 times less than what was observed in the water, its concentration still varied with observed migratory trends.

“This work is at the edge of what is possible with eDNA,” said senior author , a 91̽��professor of marine and environmental affairs and director of . “It pushes the boundaries way further than I thought we could.”

Researchers have streamlined the process of sampling eDNA over the past decade. Water and air are reservoirs for discarded bits of skin, hair and other DNA-rich detritus. Like a footprint, eDNA flags the presence of a species nearby.

After hatching, young salmon migrate to the ocean for one to several years before returning to the same stream to spawn. They leap and thrash near the surface of the water, likely shedding eDNA in the process. Every year, as the fish pass through migratory bottlenecks, people count them to gauge population health, set catch limits and monitor rehabilitation efforts.

Ip began to wonder about remote monitoring efforts while watching the fish wiggle upstream. eDNA has become a valuable tool for tracking endangered and invasive species. He developed an experiment to test the air for salmon DNA in conjunction with colleagues at the UW.

“This is Aden’s baby,” said Kelly. “He arrived saying ‘I know you can get eDNA from the water, but I want to do something nobody has done before.’”

Researchers placed filters 10 to 12 feet from the stream and left them out for 24 hours on six different days between August and October, testing four filter types each time. Three were vertical filters and the fourth was an open 2-liter tub of deionized water to capture settling particles.

In the lab, they washed eDNA from the filter and measured its concentration with a Coho salmon-specific tag to a DNA amplification method called polymerase chain reaction. They referenced air and water eDNA concentration and visual counts to track population changes, assuming that each method has its own margin of error, and the true number of fish is unknown.

The airborne eDNA concentration fluctuated with the visual counts reported by the hatchery, suggesting that this could become a useful tool for tracking salmon populations. The strategy is more remote-friendly than other methods because it does not require electricity.

“This technique quantitatively links air, water and fish,” Ip said. “Airborne eDNA doesn’t give us a headcount, but it does tell us where salmon are and what their relative abundance is in different streams.”

There are still a number of variables to account for, such as rain, wind, humidity and temperature, that the researchers plan to continue exploring in future studies.

“Right now, we’re pushing the boundaries of possibility,” Kelly said. “Eventually, we will develop the technique, as we have for waterborne eDNA, into something that can help guide management and policy.”

For more information, contact Aden Yincheong Ip at adenip@uw.edu

Co-authors include , a 91̽��postdoctoral researcher in the School of Marine and Environmental Affairs and , chief scientist at the eDNA collaborative in the School of Marine and Environmental Affairs at UW. 

This research was funded by the David and Lucile Packard Foundation and Oceankind.

To help struggling salmon populations, the state of Washington is legally required to replace hundreds of culverts that divert streams under roadways. The state transportation department is replacing old, rusting metal pipes with broad, concrete promenades that provide more gradual gradients and gentler flows for salmon swimming upstream to access more spawning grounds. The of the effort will last 17 years and cost $3.8 billion.

But how successful are these projects at boosting fish traffic? A team from the 91̽�� and the National Oceanic and Atmospheric Administration performed genetic sleuthing during two culvert replacements in 2021-22 near the city of Bellingham. Post-intervention monitoring shows that upgrading one culvert — which went under Interstate-5 — had a big impact, and the other culvert may not have been as much of a barrier. Construction did not disrupt fish populations at either site.

The will appear in a forthcoming issue of Environmental Applications.

“This was an amazing study to work on, both in terms of the science and the broader implications. We demonstrated that we can measure the impact of management interventions using only DNA recovered from the water,” said lead author , who began the project as a 91̽��postdoctoral researcher in marine and environmental affairs and is now chief scientist at the UW-based .

For the study, the researchers didn’t catch or count a single fish. Instead, from March 2021 to December 2022 — before, during and after the project — they collected water samples each month at locations just upstream and downstream of the culvert. Back in the lab, they sequenced the fragments of floating DNA to identify the type and amount of DNA of salmonid species present.

The study used a new type of monitoring known as “environmental DNA,” or eDNA. Fragments of DNA floating in the environment on scales, scat, fur or other material can help researchers detect which species are nearby, rather than relying on visual counts, cameras or traps.

A fish’s DNA stays in the water for a day or two. The researchers aimed to use the culvert project as a model for the use of eDNA in environmental impact reporting, more generally.

The study focused on along Padden Creek, a roughly 3-mile creek flowing from Padden Lake to Bellingham Bay. One culvert replacement was a major upgrade under I-5. DNA results show improvement for the four species of interest: cutthroat trout, coho salmon, rainbow trout and sockeye salmon. The other project, a smaller culvert replacement under state Route 11, or Old Fairhaven Parkway, had less impact: Trout and salmon DNA were present at similar levels before and after construction, meaning the older culvert may have been passable to fish.

“It is clear that not all things that are marked as a blockage to salmon are, in fact, blockages to salmon,” Allan said. “In the future, DNA sampling upstream of culverts might be something to add to the prioritization process.”

The results could help support across the West Coast and in Alaska.

“Environmental DNA offers a pretty different way of seeing the world,” said co-lead author , a 91̽��associate professor of marine and environmental affairs. “We can see thousands of species in a liter of water, in a way that no other sampling method can. And what makes eDNA really attractive is it’s easily repeatable and scalable.”

Researchers collected water samples using a high-tech backpack donated by Smith-Root, a company based in Vancouver, Washington. They sequenced about 52 million fragments of DNA in total, about half of which were for the four salmonid species of interest.

Researchers also surveyed five other creeks as controls. In the future, the authors say, engineers or surveyors could collect water samples for environmental monitoring more easily than surveying and identifying fish, making it simpler to combine with other measurements.

“If you had to go out there with another method and find and count fish, it would take all day,” Kelly said. “So eDNA offers a real savings in terms of in terms of time and effort in the field.”

Other co-authors are postdoctoral researcher , master’s student and research scientist , all in the 91̽��School of Marine and Environmental Affairs; and and at NOAA. The research was funded by Oceankind, a grantmaking organization based in California, and by the Washington State Department of Transportation.

For more information, contact Allan at eallan@uw.edu or Kelly at rpkelly@uw.edu.

A new effort at the 91̽�� aims to accelerate eDNA research by supporting existing projects and building a network of practitioners to advance the nascent field. Called the , the team is based in the College of the Environment with leadership and program staff from the School of Marine and Environmental Affairs.

For about a decade, scientists have honed the craft of using genetic material in the environment — known as eDNA — to detect and monitor organisms for environmental science and conservation. In a marine environment, for example, scientists can collect water samples from a specific location, then extract DNA to discern which species were present recently in that area, having never seen the animals themselves.

This bit of molecular wizardry is now becoming routine for scientists — even prompting a commitment from the U.S. Navy to use eDNA to map the locations of marine mammals — and the eDNA Collaborative aims to help the technique make the leap into everyday use for people and governments everywhere.

It can be hard to monitor and gather data across large areas using standard techniques of observing and counting various species, and eDNA techniques aim to supplement standard approaches to data collection and monitoring. This data can then inform state and federal decisions about wildlife conservation and management. For example, the team helped roll out a molecular method to help Washington find invasive European green crabs as they threaten to invade the waters of Puget Sound. Such practical applications are what turn a technology from being an interesting niche into a foundational tool on which agencies rely.

But adopting new technologies requires building familiarity and trust, and this is where the eDNA Collaborative comes in. The Collaborative’s director, , a 91̽��professor of marine and environmental affairs, likened the young field of eDNA research to how various new technologies develop and take off.

“Experimentation is how technologies develop, and as with the early days of any new tech, it’s a soup of ideas with eDNA research,” Kelly said. “While people are still inventing, we don’t want to impose standards in a top-down way. We want to encourage best practices without squelching creativity. That’s what this Collaborative will help do: accelerate the field from the bottom up.”

The initiative will focus on three main areas: Supporting existing eDNA research projects at UW; granting seed money to new eDNA research ventures outside the 91̽��and the United States; and supporting a visiting scholar program to connect eDNA practitioners and encourage networking and information-sharing. The goal is to move more of the techniques developed in the lab out into practice in the field, helping the best ideas rise to the surface faster.

“Environmental DNA is an entirely new way of seeing the living world, and we’re just learning how to take advantage of it for purposes of management and conservation. At the Collaborative, we wake up every day thinking about how to move this technology into routine practice for people and institutions around the world,” said Eily Andruszkiewicz Allan, chief scientist at the Collaborative.

The Collaborative is funded initially with a $1 million grant from the David & Lucile Packard Foundation. The team also recently secured a $7.5 million grant from the U.S. Navy — in collaboration with the National Oceanic and Atmospheric Administration and Scripps Institution of Oceanography — for a five-year project to use eDNA to map the locations of marine mammals in the ocean.

The goal is to help the U.S. Navy reduce harm to marine mammals by better understanding where those animals are in space and time. Most of the eDNA sampling activity will begin this fall and center around Seattle and San Diego. eDNA methods will fold into other existing work, including visual and acoustic surveys, to eventually produce a West Coast-wide estimate of where marine mammals are in the ocean.

Other ongoing projects include:

• Monitoring for the invasive European green crab throughout Puget Sound and Washington’s outer coast
• Developing eDNA as a tool for
• Using eDNA to monitor the presence of salmon in streams to gauge the effectiveness of culvert replacement projects in Washington
• Assessing seasonal changes in Norwegian fjords for the country’s salmon industry

For more information, contact Kelly at rpkelly@uw.edu, Allan at eallan@uw.edu and program manager Cara Sucher at csucher@uw.edu or email the Collaborative at ednacollab@uw.edu. Contact U.S. Navy program officer Mike Weise for questions about the marine mammal monitoring grant: michael.j.weise@navy.mil.

Follow the eDNA Collaborative on Twitter at .

European green crabs feast on shellfish, destroy marsh habitats by burrowing in the mud and obliterate valuable seagrass beds. The invasive species also reproduces quickly, making it a nightmare for wildlife managers seeking to control its spread in Washington’s marine waters.

Last month, Gov. Jay Inslee issued an in response to more than as well as dramatic increases in crab populations on Washington’s outer coast and other locations in Puget Sound in recent years.

As the green crab invasion in the state worsens, a new analysis method developed by 91̽�� and Washington Sea Grant scientists could help contain future invasions and prevent new outbreaks using water testing and genetic analysis. The , published online Feb. 6 in the journal Ecological Applications, show that the DNA-based technique works as well in detecting the presence of green crabs as setting traps to catch the live animals, which is a more laborious process. Results suggest these two methods could complement each other as approaches to learn where the species’ range is expanding.

The new method relies on genetic material in the environment, known as eDNA, that is found in the water after organisms move through. Scientists can collect a bottle of water from a location, extract DNA from the water and discern which species were present recently in that area.

“We have limited resources to be able to combat this problem, and it’s important to think about how to allocate those resources efficiently and effectively,” said lead author , who completed the work as a master’s student in the 91̽��School of Marine and Environmental Affairs. “Knowing the best situations for using eDNA to detect invasive green crabs is important, and that’s what our study tried to tackle.”

The research team relied on data collected over three months in 2020 from green crab traps in 20 locations throughout Puget Sound and the outer coast. Trapping at these locations was done by a large number of partners participating in statewide efforts to monitor and control European green crab, including multiple tribes, Washington Department of Fish and Wildlife — the state lead for green crab management — Washington Sea Grant’s , and other state and federal agencies.

For this study, the researchers visited each location and collected water samples, then ran genetic analyses to detect both the presence and quantity of European green crab in each location. In this way they could validate the eDNA data with the actual presence and numbers of crabs. They found that using eDNA to detect the presence and abundance of the species was as sensitive as trapping and counting live crabs.

This is significant, the researchers said, because eDNA as a detection method is new, and it hasn’t always been clear how to interpret eDNA detections in past scenarios. This study shows how conventional monitoring methods — in this case, trapping and counting crabs — can be combined with eDNA techniques to more effectively find and control invasive species outbreaks.

“Here’s a really well-validated example of how to use eDNA in the real world. To me that’s really exciting,” said co-author , a 91̽��associate professor in the School of Marine and Environmental Affairs. “There are lots of invasive species, and many imperiled and endangered species that are hard to monitor, so this is one significant way forward on all of those fronts.”

The study also evaluates when eDNA would add value in monitoring for invasive crabs, and when conventional trapping and counting still make the most sense. For example, taking water samples and testing for green crab DNA in remote locations — or in areas where outbreaks haven’t yet been identified — could save time and resources instead of deploying traps. Alternatively, eDNA probably wouldn’t be helpful in locations where large numbers of green crabs are already living and where community scientists and managers are already trapping and controlling those populations, the researchers explained.

“From a management perspective, the value of this tool just really comes to life in places that are more remote or have a lot of shoreline to cover, like Alaska, where green crabs haven’t yet been detected,” said co-author , a marine ecologist who leads the Washington Sea Grant Crab Team. “I see eDNA as another tool in the toolkit, and we can imagine scenarios where it can be used alongside trapping, especially as an early detection method.”

Finding these crabs soon after they have occupied a new location is important for controlling the population and protecting native habitats. Managers could get ahead of new invasions by testing water from multiple locations, and then follow up with more water testing, on-the-ground monitoring and trapping if green crab DNA is detected.

The paper identified green crab DNA in one location where the species hasn’t yet been captured, near Vashon Island. The research team followed up a year later with intensive trapping and retested the water; no green crabs or additional green crab DNA were found. The researchers think the earlier positive sample likely was picking up green crab larvae, which weren’t present in that location a year later. Notably, the effort represented an important test case for how eDNA and traditional trapping can be implemented together for green crab management.

“The reason we pursued this project in the beginning is that early detection of green crabs is difficult — it’s like finding a needle in a haystack,” said co-author , a 91̽��associate teaching professor in environmental studies and aquatic and fishery sciences and the 91̽��principal investigator for Crab Team research. “So if adding eDNA to our toolkit helps us detect those needles, then that’s great to have at our disposal.”

of the Cooperative Institute for Climate, Ocean and Ecosystem Studies is an additional co-author. This research was funded by Washington Sea Grant.

Contact the co-authors for more information. Contact info and expertise listed below:

• Abigail Keller (lead author, eDNA, European green crab): g.keller1@gmail.com
• Ryan Kelly (eDNA): rpkelly@uw.edu
• Emily Grason (European green crab; Crab Team efforts): egrason@uw.edu
• Sean McDonald (European green crab; Crab Team efforts): psean@uw.edu
• Chase Gunnell, WDFW communications (policy and state funding questions related to green crabs): gunnell@dfw.wa.gov or 360-704-0258 (cell)

Grant number: NOAA Award No. NA18OAR4170095

Eelgrass, a species of seagrass named for its long slippery texture, is one of nature’s superheroes. It offers shade and camouflage for young fish, helps anchor shorelines, and provides food and habitat for many marine species.

A 91̽�� study adds one more superpower to the list of eelgrass abilities: warding off the toxin-producing algae that regularly close beaches to shellfish harvests. Researchers found evidence that there are significantly fewer of the single-celled algae that produce harmful toxins in an area more than 45 feet, or 15 meters, around an eelgrass bed.

“We’re not in the laboratory. The effect we’re seeing is happening in nature, and it’s an effect that’s really widespread within this group of harmful algae. What we see is this halo of reduced abundance around the eelgrass beds,” said , a research scientist at the UW. She is the lead author of the published this spring in the open-access journal PeerJ.

Researchers sampled five coastal sites three times in the spring and summer of 2017. Four sites were within Puget Sound and one was in Willapa Bay, on Washington’s outer coast.

In addition to a traditional visual ecological survey at each site, the researchers used a type of genetic forensics to detect species that might not be easily seen or present at the time of the survey.

Scientists put on waders and walked parallel to shore in water less than knee deep while scooping up seawater samples to analyze the environmental DNA, or eDNA, present. This method collects fragments of genetic material to identify organisms living in the seawater.

The researchers sampled water from each site at the same point in the tidal cycle both inside the eelgrass bed and at regular intervals up to 45 feet away from the edge. For comparison they also surveyed a location farther away over bare seabed.

“In the DNA fragments we saw everything from shellfish to marine worms, osprey, bugs that fell in the water,” Jacobs-Palmer said. “It’s quite fascinating to just get this potpourri of organisms and then look for patterns, rather than deciding on a pattern that we think should be there and then looking for that.”

The researchers analyzed the eDNA results to find trends among 13 major groups of organisms. They discovered that , a broad class of single-celled organism, were scarcer in and around the eelgrass beds than in surrounding waters with bare seabed.

“We were asking how the biological community changes inside eelgrass beds, and this result was so strong that it jumped out at us, even though we weren’t looking for it specifically,” said senior author , a 91̽��associate professor of marine and environmental affairs.

The result has practical applications, since certain species of dinoflagellate populations can spike and produce toxins that accumulate in shellfish, making the shellfish dangerous or even deadly to eat.

The phrase “harmful algal bloom” has a formal definition that was not measured for this study. But authors say the trend appeared when the overall dinoflagellate populations were high.

“I have heard people talk about a trade-off between shellfish and eelgrass, in terms of land use in Puget Sound. Now, from our perspective, there’s not a clean trade-off between those things — these systems might be able to complement one another,” Kelly said.

To explore the reasons for the result, the authors looked at differences in water chemistry or current motion around the bed. But neither could explain why dinoflagellate populations were lower around the eelgrass.

Instead, the authors hypothesize that the same biological reasons why dinoflagellates don’t flourish inside eelgrass beds — likely bacteria that occur with eelgrass and are harmful to dinoflagellates — may extend past the bed’s edge.

“It was known that there is some antagonistic relationship between eelgrass and algae, but it’s really important that this effect seems to span beyond the bounds of the bed itself,” Jacobs-Palmer said.

The discovery of a “halo effect” by which eelgrass discourages the growth of potentially harmful algae could have applications in shellfish harvesting, ecological restoration or shoreline planning.

“These beds are often really large, and that means that their perimeter is also really large,” Jacobs-Palmer said. “That’s a lot of land where eelgrass is potentially having an effect.”

In follow-up work, researchers chose two of the sites, in Port Gamble on the Kitsap Peninsula and Skokomish on Hood Canal, to conduct weekly sampling from late June through October 2019. They hope to verify the pattern they discovered and learn more about the environmental conditions that might allow the halo to exist.

Other co-authors on the recent paper are postdoctoral researcher and master’s student in the 91̽��School of Marine and Environmental Affairs; Micah Horwith, a former 91̽��graduate student and Washington State Department of Natural Resources scientist now with the state Department of Ecology; Ana Ramón-Laca at the National Oceanic and Atmospheric Administration; and Emily Kunselman at the University of California, San Diego. This research was funded by the Washington State Department of Natural Resources. The Skokomish Tribe provided access to one of the study sites.

For more information, contact Jacobs-Palmer at ejacobspalmer@gmail.com and Kelly at rpkelly@uw.edu.

In a published Dec. 15 in the journal PLOS ONE, researchers from the 91̽�� looked at the abstracts from more than 700 scientific papers about climate change to find out what makes a paper influential in its field. But instead of focusing on content, they looked at writing style, which is normally more the province of humanities professors rather than scientists.

Their idea was that papers written in a more narrative style — those that tell a story — might be more influential than those with a drier, more expository style. Psychology and literary theory have long held that if you want someone to remember something, you should communicate it in the form of a story. The 91̽��researchers — led by , a recent graduate from the UW’s School of Marine and Environmental Affairs, and professors and — wondered whether this theory would hold up in the realm of peer-reviewed scientific literature.

Remarkably, it did. The most highly cited papers tended to include elements like sensory language, a greater degree of language indicating cause-and-effect and a direct appeal to the reader for a particular follow-up action.

“The results were especially surprising given that we often think of scientific influence as being driven by science itself, rather than the form in which it is presented,” Hillier said.

Perhaps even more surprising, the researchers noted, was the finding that the highest-rated journals tended to feature articles that had more narrative content.

“We don’t know if the really top journals pick the most readable articles, and that’s why those articles are more influential, or if the more narrative papers would be influential no matter what journal they are in,” Kelly said.

The researchers used a crowdsourcing website to evaluate the narrative content of the journal articles. Online contributors were asked a series of questions about each abstract to measure whether papers had a narrative style, including elements like language that appeals to one’s senses and emotions.

The researchers hope this work might lead to advances in scientific communication, improving the odds that science might lead the way to better decisions in the policy realm.

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For more information, contact Ryan Kelly at rpkelly@uw.edu or 206-616-0185.

Every living thing leaves a genetic trail in its wake. As animals, plants and microbes shed cells and produce waste, they drop traces of their DNA everywhere — in the air, soil and water.

Researchers are now able to capture the cells of animals, sequence their DNA and identify which species were present at a point in time. Think of it as genetic fingerprints that leave a trace of past activity.

New 91̽�� and Northwest Fisheries Science Center research has applied this technique to broadly measure the effects of human activity on the environment. Their , appearing this week in the journal , used DNA in the waters of Puget Sound to characterize the amount of animal life along highly urbanized shorelines, such as Piper’s Creek in Seattle, and in more remote areas with fewer humans, like Vashon Island.

This is believed to be the first study that uses genetic markers to understand the impact urbanization has on the environment — specifically, whether animal diversity flourishes or suffers.

“It is now possible to use genetic traces in water samples to look at the effects of human activities on ecosystems,” said lead author , a 91̽��assistant professor of marine and environmental affairs. “It’s totally remarkable to me that what appears to be plain water can tell you all of this information about what animals are present.”

Using environmental DNA — or eDNA, for short — the researchers found that urban Puget Sound shorelines support a denser array of animals than in remote areas. In particular, clams and other mud-dwellers congregate more densely along urban beaches — a surprising finding, Kelly said.

“Clams and other things that live in mud seem to like living near cities, which is really interesting,” Kelly said. “It suggests that maybe humans are subsidizing mudflats, or it may just as well be the converse — maybe humans tend to live in really protected areas that are the same environment clams happen to like.”

While urban beaches in Puget Sound had more abundant fauna, these areas were also more homogenous in the kinds of species that lived there, the researchers found, suggesting a tradeoff between different kinds of diversity between more- and less-urban areas.

Genetic tools allow researchers to paint a representative mosaic of animal life in particular areas without having to physically count critters. In conventional ways of measuring environmental impacts, scientists choose a select number of species and count how many they see before and after development. Or they might survey a small section of shoreline and try to document everything they find.

These methods are inherently time-consuming and probably don’t fully capture what is present, Kelly explained.

“We can go out, take a sample of water, and the DNA from thousands of species appears,” Kelly said. “This way, we don’t have to decide if we are going to count snails or orcas when we look at environmental impacts. Instead, we can just look at what’s there.”

The researchers collected liters of water from urbanized and remote beaches around Puget Sound, then filtered out cells larger than bacteria. They then extracted DNA from these cells, using a molecular tool to detect animal genes.

After sequencing the DNA, they could identify specific animals present where the water was collected. They detected more than 1,600 unique genetic signatures — many representing different species — across Puget Sound, including porpoises, salmon, starfish, barnacles, eagles — and even humans.

Kelly and his collaborators have spent years testing and refining the process of obtaining eDNA in water. They first worked in the Monterey Bay Aquarium, a controlled setting where they could make sure their DNA sampling was actually . In subsequent work, they found that an animal’s DNA tends to stay within a few hundred feet of where it was initially deposited; it remains in the water for one to two days.

The methods described in this study could be used to evaluate the effects of humans and development in other urban waterways, such as Chesapeake Bay or the Hudson River. Scientists in the Midwest have started using to monitor lakes for invasive Asian carp.

As genetic traces become more reliable, they could take the place of expensive, time-intensive environmental impact statements or environmental monitoring, the researchers said.

“I’m excited because I think if you can make it easier for people to do these sorts of broad scale surveys, they will do it. It’s a much more powerful method,” Kelly said.

Other co-authors are James O’Donnell, a 91̽��postdoctoral researcher in marine and environmental affairs; Natalie Lowell, a 91̽��doctoral student in aquatic and fishery sciences; , a former 91̽��student in aquatic and fishery sciences now at Oregon State University; and , , and of the National Oceanic and Atmospheric Administration’s Northwest Fisheries Science Center.

This study was funded by the David and Lucile Packard Foundation.

###

For more information, contact Kelly at rpkelly@uw.edu or 206-616-0185.

Researchers also for the first time used DNA from water samples to discern which of the species were most plentiful in the tank.

Being able to determine the relative abundance of fish species in a body of water is the next step in possibly using modern DNA identification techniques to census fish in the open ocean, according to , 91̽�� assistant professor of , and lead author of a in the Jan. 15 issue of PLOS ONE.

Currently most scientists net, see or in other ways count fish to determine what species are present and in what proportions in marine environments.

“It might be unpleasant to think about when going for a swim in the ocean, but the water is a soup of cells shed by what lives there,” Kelly said. Fish shed cells from their skin, damaged tissues and as body wastes.

“Every one of those cells has DNA and if you have the right tools you can tell what species the cell came from. Now we’re working to find the relative abundance of each species present,” he said.

It was barely two years ago that an influential paper was published by scientists who determined the presence of an endangered species they were seeking in a river using this “environmental DNA” or “eDNA.” Since then the technique has been used to look for other specific species in both freshwater and one marine setting.

“Clearly this is an effective tool in the wild when you know what you’re looking for,” Kelly said.

He and his co-authors, , and with Stanford University’s , took the work another step further with funding from the David and Lucile Packard Foundation. The researchers wanted to see how well they could detect DNA using a single set of “primers,” molecular probes designed by another group just the year before this study, that zero in on portions of DNA that indicate an animal has a backbone and is a vertebrate.

The sea tank at was suggested because the inhabitants are known and could be compared to what the new technique revealed was present, giving the authors a way to judge the technique’s accuracy. The researchers analyzed about two pint glasses worth of water in the course of their project and Ryan said the DNA data of what’s in the tank likely could have been revealed by an even smaller sample.

The approach proved effective by both identifying the eight bony fishes in the tank and determining that tuna and sardines made up the greatest amount of biomass in the tank, which tank managers could document. The technique turned out to be so finely tuned that it also picked up DNA from long-dead menhaden from the Atlantic Ocean, fish that had been processed, transported and added to the tank as food. It was a surprise when an Atlantic species turned up, until the researchers realized where the DNA was coming from, and then they made calculations to take that into account.

The primers were unable to detect DNA from two groups of vertebrates in the tank: the turtles and the fish with cartilage in place of bones, such as rays and sharks. Kelly said that these kinds of biases in detection are inevitable, highlighting the need to focus on the design of additional general primers.

Being able to determine what’s living in a body of water in the ocean using environmental DNA could be less expensive and time consuming than traditional census methods. The process could help scientists charged with monitoring and managing aquatic habitats, could reveal the arrival of invasive species before they become a major problem, or provide ways to look at food webs and other basic ecosystem functions, Kelly said.

The mixing of ocean waters by tides, currents or other forces is one hurdle to using this technique in the open ocean. But the group’s preliminary work in Monterey Bay revealed DNA differences between areas of near-shore sea grass areas and kelp beds farther out but still within sight of each other. Additional field testing is planned in San Francisco Bay.

While fish research using environmental DNA only started in recent years, the revolution using DNA to detect what’s present in particular habitats started in the early 2000s. Since then the cost of gene sequencing has plummeted, with what was $5,300 in 2001 costing about 6 cents today, Kelly said. Microbiologists developed and used techniques to survey bacteria, viruses and other microorganisms in everything from the human gut to the ocean for a decade before any research group published results using it for fish and other aquatic organisms that could actually be seen.

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For more information:
Ryan, 206-616-0185, rpkelly@uw.edu