A glass of seawater is neither half empty nor half full for assistant professor of marine and environmental affairs Ryan Kelly and his lab. Instead, it’s brimming with information about ocean ecosystems in the form of trace DNA.
“The whole idea is that we’re constantly shedding cells out into the environment, and those cells have all our DNA in them,” Kelly said. “We can actually sequence that DNA and trace it back the organism.”
This DNA that is left behind, known as environmental or eDNA, can be used for a range of applications, from determining the presence of individual species to surveying animal diversity. In a recent paper, the Kelly lab is using the latter application to examine how urbanization affects biodiversity in the Puget Sound.
The results were surprising. The biodiversity, or species richness, of clam and other infauna that live in mud, increased in locations of urbanization. However, this may not necessarily mean that urbanization has a positive impact on all species.
“So the richness of those seems to very much increase in humans, but it might mean there’s much more mudflats near humans,” Kelly said. “It’s not obvious that urbanization drives diversity up, it may be that urbanization drives mud
.”Kelly and his team also noted that while species richness increased, the overall diversity of urban communities over distance decreased. Every urban environment had the same selection of species, and less difference between different urban areas.
Kelly explains this with the idea that in less urbanization, the species diversity is more like the downtown of a small town. There will be less shops overall, but each town has its own uniqueness. In contrast, higher urbanization areas are like large malls: There’s a wide selection of shops, but the shops are recognizable and familiar in each mall.
More exciting to Kelly than these results was that this was the first time eDNA has been used to look at the interaction between humans and the ecosystem. Microbiologists have been using eDNA for a decade to take microbial surveys of the ocean, but only recently have scientists started to consider the technique for taking broader surveys of animal biodiversity.
“You can see whales and you can see starfish in the DNA just as well as you can see the microbes,” Kelly said. “It’s just a question of which [DNA tests] you use to aim at the sweet slice of biodiversity that you care about.”
Using eDNA has reduced the amount of fieldwork required, which is something James Kralj, a master’s student in the School of Marine and Environmental Affairs and a member of the Kelly lab, is excited about.
Kralj is running a similar study, and is using eDNA to examine the impact of oyster farming on biodiversity. To collect his water samples, Kralj worked alongside a larger project that was using more traditional survey methods.
“They were doing more of the traps, the nets, and the visual counts,” Kralj said. “That would take a long time to set up and get all that data, and I would almost feel like I was waiting around all day to scoop up a bottle of water.”
The bulk of the work involving eDNA occurs in lab, where that bottle of water undergoes filtering to collect the eDNA, and then rigorous genetic testing.
“For each sample we took, we had different kind of processing replicates down a line so there were hundreds of different things I had to treat,” said Natalie Lowell, co-author and a former master’s student in the Kelly lab. “The beginning just looked like a hundred bottles, but the end was a lot more than that.”
In all, the Kelly lab processed more than 300 million DNA sequences from the Puget Sound.
“Because DNA sequencing is so cheap, we’re no longer limited by genetic data,” Kelly said. “What we’re limited in is the power to process that data, so virtually everyone has become a bioinformatics [scientist].”
The massive amount of data that can be collected from eDNA is incredibly useful, Kelly said, but it does not mean it is necessarily superior to other forms of more traditional surveying. Instead, eDNA is complementary to other techniques. Each technique reveals different information, and Kelly believes that using multiple techniques at once is the best way to examine the ecosystem.
“You might see different patterns in one [technique] versus the other and that is really cool,” Kelly said. “It means you’re seeing the ecosystem in different ways and that’s giving you different answers, all of which is approximating some larger truth about the world hopefully.”
