Instead of clutching magnifying glasses, William & Mary aquatic ecology students hoist 20-pound blue backpacks onto their shoulders. March 22 is World Water Day, and these portable sampling systems allow students to quickly and efficiently collect high-quality data to deepen scientific understanding of water-related issues.
Water and data are two of the four cornerstone initiatives of W&M’s strategic plan, Vision 2026.
Environmental DNA (eDNA) is DNA that organisms shed or secrete into the surrounding environment. Skin cells, hair, mucus and fecal matter are a few examples. The discarded DNA lasts in aquatic and terrestrial environments for about seven-21 days before degrading due to factors like heat, UVB exposure, acidity or enzyme activity.
Recent technological advances allow researchers to collect and analyze eDNA in water and soil samples to determine which species are present at specific sites. Such information is useful to identify the presence of elusive or rare species that may not be detected through more traditional survey methods. It can also provide early identification of invasive species.
“Environmental DNA pulls the veil off of the true diversity out there,” said James Skelton, assistant professor of biology. “It’s typically a much more effective detection method than traditional surveys. It comes with caveats, so you do have to be careful, but we can see things much more clearly than we did before.”
Skelton is a community ecologist who uses molecular methods to answer ecological questions. He specializes in aquatic ecology, and students in his lab have been using eDNA and molecular methods to conduct research that appeals to their specific interests.
Meet Rose and Frank
Rose and Frank are the biology department’s eDNA backpack samplers, and Skelton refers to them as the best investment he’s ever made.
Named in honor of Rosalind Franklin, a British scientist who played a significant role in discovering the structure of DNA, these portable eDNA sampling systems allow researchers to collect samples conveniently and efficiently in the field.
“Going back to the olden days of eDNA technology – about five years ago – researchers collected water samples in plastic containers and lugged them back to the lab for analysis,” said Skelton. He explained that this clumsy method required a walk-in freezer for storage space and carried an elevated risk of sample contamination within the lab.
“But with Rose and Frank,” said Skelton, “it’s a completely different story.”
The backpacks filter water samples onsite at a standardized pressure, rate and volume and even record GPS coordinates and time of collection. During filtration, the water passes through a membrane that catches DNA. After a sample is filtered, the membrane is removed from the apparatus and popped into a sterile tube of DNA preservative, eliminating the need for cumbersome water containers and freezer storage space.
“That way it also never gets opened in the lab,” said Skelton. “There’s much less opportunity for lab-based contamination.”
With earlier methods of eDNA sample collection, it could take months or years to train a student to correctly collect, store and identify samples.
“I can train students to use Rose and Frank in about an hour,” said Skelton. “After that, I can send an undergrad out into the field, and they can collect incredibly rich, high-quality data that we can trust right at day one. Rose and Frank also look like Ghostbuster proton packs, which students really like.”
The versatility of eDNA research
In their four years at W&M, Rose and Frank have been used in a broad range of research.
For example, one of Skelton’s undergraduate students developed an interest in a remarkably diverse and understudied group of organisms.
“I once caught Lauren French (’22) in the lab at 11 o’clock at night reading an arcane text about aquatic fungi, which are the base of aquatic food webs,” said Skelton.
He explained that aquatic fungi are highly diverse and perform a wide array of functions, from converting otherwise inedible algae and tough plant material into food for invertebrates and fish to releasing potentially toxic compounds. The community composition of aquatic fungi plays a key role in the health of aquatic ecosystems.
French wanted to explore whether human activities that affect water quality also impact the composition of aquatic fungal communities. She used eDNA to identify thousands of species of fungi at 17 local pond, stream and tidal creek sites in the Williamsburg area.
Comparing that information with long-term water quality data collected by Randy Chambers, professor of biology, at the Keck Lab, French found a strong correlation between water quality and the community composition and functional diversity of aquatic fungi. Temperature and particulate phosphorus played particularly important roles.
French’s study is important for understanding how freshwater fungal diversity and function is likely to shift as human activity continues to impact aquatic conditions. Her paper has been accepted for publication in the Wiley journal Environmental DNA.
Another recent student, Mindy Spence M.S. ’22, wanted to investigate the effects of dams on fish diversity within the Virginia Peninsula for her master’s thesis. To that end, she collected eDNA samples from 465 sampling points within 34 regional water bodies to track the distribution of 61 species of fish.
Spence found that undammed sites contained approximately twice as many fish species as dammed sites and that non-native species were 2.6 times more likely to be detected at dammed sites.
Many native species are migratory and require several types of habitats throughout their lifecycle. Spence found that these species were less than one tenth as likely to be found at dammed sites.
“It wasn’t a surprise that we don’t see a lot of those highly migratory species upstream of dams,” said Skelton. “The surprising thing was that she also saw reductions in a lot of non-migratory local species, like little swamp darters and our native catfishes.”
The decreased diversity of non-migratory local species is likely due to habitat alterations that occur when dams are constructed.
Spence’s study provides important considerations for proposed projects to build or remove dams. It is under second review for publication in Proceedings of the Royal Society B.
Environmental DNA can also be used to analyze stomach contents, opening yet another avenue of research.
Zoe Hutcheson ’23 wanted to investigate what happens when a native species is replaced by a non-native species that is ecologically similar. Specifically, she was curious as to whether the non-native species fills a similar niche or if there can be dietary differences that result in a broader ecological impact.
Hutcheson chose to study crayfish, often regarded as a keystone species and ecosystem engineer within aquatic environments. Increasingly, native species of crayfish around the world are being outcompeted by introduced species, and more information is needed to determine how broad the ecological impact will be.
Hutcheson analyzed the stomach contents of native and non-native crayfish collected at sites in Southeastern and Southwestern Virginia and used eDNA methodology to sequence the animal and plant components of their diet. She found significant differences between types of leaves and invertebrates eaten by native and non-native species collected from the same sites.
“That suggests that when non-native species replace native species, there are probably going to be community level effects, not just a replacement of one crayfish for another,” said Skelton.
Hutcheson is currently preparing her paper for submission to the journal Freshwater Biology.
These are just a few examples of research in Skelton’s lab. Other eDNA projects in the works include a study of the mycoloop hypothesis in estuarine systems and a collaborative study with Dan Cristol, Chancellor Professor of Biology, to determine whether there is a direct link between the diet of wolf spiders and terrestrial mercury contamination.
“Environmental DNA presents a great teaching opportunity for everything from basic ecology to bioinformatics and statistics to solid molecular methods,” said Skelton. “There are lots of opportunities for students to find what really interests them and gain experience across a broad range of components used in scientific research.”
Laura Grove, Research Writer