Fruit DNA in Invasive Flies’ Guts Could Help Track Their Dispersal

By Laura Kraft

Research does not cut a straight path toward eureka moments, as science textbooks may lead you to believe. It involves a lot of failure and requires someone dedicated to keep coming back to the same problem and trying something new. Lauren Diepenbrock, Ph.D., a postdoctoral researcher at North Carolina State University and soon to be an assistant professor at the University of Florida, has an energy and enthusiasm that drives her forward, even when she encounters roadblock after roadblock. (She was also featured recently in a “Standout Early Career Professionals” Q&A post here on Entomology Today.)

Diepenbrock studies spotted-wing drosophila (Drosophila suzukii), the fruit fly cousin to the ones hanging around your bananas. This fly differs from the innocuous banana-loving variety in that it has a saw-like egg-laying organ allowing it to lay eggs in ripening brambles, strawberries, blueberries, and cherries. Buyers for grocery stores have zero tolerance for the pest and will turn away an entire truckload of berries if it has even one insect in or on the fruit. This not only causes financial losses to the growers, to the tune of $1.3 billion in potential losses in the United States annually, but also is wasteful when such large quantities of fruit are thrown out.

Even after berry season ends, spotted-wing drosophila (SWD) persists near host fields in winter, harboring in wild bramble, pokeweed, and other wild berries until the first crop of summer is available: strawberries. In North Carolina, the flies build their populations on strawberries, from which they then attack blueberries, blackberries, and raspberries as each becomes available later in the season, reaching staggering numbers in the latter two crops, where it does the most damage.

Diepenbrock was frustrated with the existing data on SWD movement because it involved trapping, which attracts flies away from other cues or intercepts them in some way. “The only way that I could think of to really document a tried-and-true interaction was to look at their gut so you know what they’re feeding on,” she says.

Diepenbrock proposed studying how adult flies disperse by testing what they ate. She first became interested in the idea of using molecular tools to study feeding behaviors while working with ladybird beetles in the lab of Deborah Finke, Ph.D., at the University of Missouri. In predator-prey systems, like with ladybird beetles, scientists analyze the DNA from digestive systems of predators to find out what prey they have recently consumed. Diepenbrock wanted to try the same concept in the berry-feeding flies. She wrote a large grant to the U.S. Department of Agriculture National Institute of Food and Agriculture to support her postdoctoral research and was “rejected brutally,” in her own words. The grant reviewers repeatedly commented that “You have no proof that you can do this with a phytophagous [plant-eating] insect.”

Undeterred, she contacted a colleague in South Dakota, Jonathan Lundgren of Blue Dasher Farm, who had evaluated DNA in the guts of predators and stored grain beetles but not with fruit-feeding flies. He agreed that the project was feasible and helped her write a new grant for the Southern Region Small Fruit Consortium. This time, the project got funded. She flew up to South Dakota for a week where, together, they had tentative success detecting DNA when flies fed on strawberries.

Lauren Diepenbrock, Ph.D., shows off the dissecting scissors used to decapitate adult spotted-wing drosophila flies (Drosophila suzukii) prior to DNA testing for gut contents. The flies’ heads contain enzymes that chop up DNA, inhibiting DNA extraction. (Photo credit: Laura Kraft, Lauren Diepenbrock, Ph.D.)

The life of a scientist isn’t always easy. At times, Diepenbrock had to wake up in the wee hours of the morning to place strawberry-fed adult spotted-wing drosophila flies (Drosophila suzukii) in the freezer. (Photo credit: Lauren Diepenbrock, Ph.D.)

“But, when I came back to NC State, nothing worked,” Diepenbrock says. In hindsight, she notes that she did not have enough of a grasp of the technology used, and the machine in South Dakota was a different make from the one at NC State, further confounding the issue.

Needing help to move forward, Diepenbrock reached out to the Department of Entomology and Plant Pathology at NC State and received an email back from an unlikely collaborator, Tim Sit, Ph.D. Sit studies viruses in plants and had no experience working with flies, but he was excited about the project and the prospect of collaborating with someone new. Together, he and Diepenbrock analyzed fly after fly for traces of strawberry DNA.

When you test DNA, samples are inserted into a machine that presents successful DNA matches as distinct peaks on a graph. Says Diepenbrock: “The frustrating thing about working with DNA is you cannot see it until some machine tells you it’s there. Then, all of the sudden, I had peaks! On everything! And it was beautiful!” Together, Sit and Diepenbrock were able to show that, yes, you can detect strawberry DNA after a fly has eaten it.

“Then we wanted to know how long after consumption you could detect the food,” she says. Flies were fed strawberry puree and then held for a 24-hour period before being frozen to test their DNA. Twenty-four hours seemed reasonable based on other studies.

“It turns out the DNA was still very strongly detected after 24 hours,” Diepenbrock says. So, she held them for 36 hours before DNA extraction. Then 48 hours. Then 72. A collaborator at University of California, Davis, shared that they were collecting high-quality fly DNA samples from flies trapped in a preserving solution up to seven days later. Diepenbrock figured, “Well, if you can get fly DNA for seven days, maybe you can get fruit DNA for seven days.” She fed strawberry puree to the flies and held them for a full seven days in the lab on a cornmeal-based diet and still found traces of strawberry DNA. The results of this work were published this month in the Journal of Economic Entomology.

The extended period at which strawberry DNA can be detected within the flies increases the chances of the lab-based experiment being deployed successfully in the field. In the meantime, other berry hosts should be added to the experiment to be able to answer larger questions about how flies are moving. Luckily, a blackberry breeder working at NC State is sequencing the blackberry genome, potentially making it possible to find a unique piece of blackberry DNA to analyze in flies.

“From there, you need to take it to the field … and validate field-trapping methodologies to look at fly movement,” Diepenbrock says. “I have some ideas of that, but they probably won’t be what ends up happening. But you’ve got to have an idea to start with.” She has enough experience with science to be tentative but tenacious in her pursuit of the data that may help growers better manage their berry crops.

This week, Diepenbrock will take on a new role, a faculty position at the University of Florida’s Lake Alfred Citrus Research and Education Station working on Integrated Pest Management in citrus crops.

Laura Kraft is a Ph.D. student at North Carolina State University and a National Science Foundation Graduate Research Fellow. When she isn’t traveling the world, she spends her time making science more accessible through science writing and outreach. Email: ljkraft@ncsu.edu