Genetic Tool May Help Farmers Find Elusive Larval Mussels

In the last 40 years, blue mussel populations in the Gulf of Maine have declined roughly 60%. The explanations are myriad — from rising ocean temperatures to the arrival of invasive species like green crabs. In recent years, mussel farmers have seen similar declines in their harvests, which have been driven in part by a recurring failure to collect enough young larvae, called spat or seed. Scientists are still speculating the reasons for this issue. What is clear, though, is that there’s an urgent need for monitoring tools that can track the presence and abundance of larvae to enable mussel farmers to optimize their operations.

“We don’t really have a good handle on what’s going on yet, so it’s really important that we try to understand the root causes given the significant financial impact,” said Dave Ernst, a Bigelow Laboratory postdoctoral scientist. “Taking a molecular approach may help us solve some of these problems.”

Ernst is leading a cutting-edge effort to use environmental RNA to detect and quantify the abundance of blue mussel larvae in water samples from Maine. The ultimate goal is to incorporate that technology into user-friendly, field-ready toolkits farmers can use, as Ernst said, to take the “guesswork” out of seed collection.

Mussels are the top imported bivalve shellfish species to the U.S. So, there’s economic interest in increasing domestic production and helping producers adapt to changing conditions. When it comes to commercial mussel aquaculture, though, the biggest bottleneck is that it still relies almost entirely on wild-caught seed.

Farmers dangle ropes from long lines or wooden rafts into the water column for seed collection. Ideally, larval mussels floating through the water will settle onto the ropes, sometime after which, they’ll be transferred to grow-out ropes where they can slowly develop into adults for harvesting. But if the timing isn’t right, and those wild larvae aren’t floating by or don’t settle in large enough numbers, there will be nothing to harvest.

It is possible to cultivate seed in hatcheries, but that requires significant investment and would be near impossible to scale up to the level needed. Another option is to sample water and literally count the number of larvae in each sample under a microscope until there’s enough seed to justify dropping the ropes. That’s also not a feasible solution given how time- and labor-intensive those methods are and how challenging it can be to visually discriminate between different species of larvae.

That’s where molecular tools come in.

Bigelow Laboratory, alongside University of Maine, is leading a five-year, multi-institutional initiative to develop ecological management tools from the DNA organisms shed into the environment. Environmental DNA can be used to detect the presence of a species from its genetic signature left behind in free-floating DNA, lost scales or tissue, or individual cells. A single sample of water can be analyzed to test for everything from bacteria to whales.

But DNA is surprisingly long-lasting after being lost to the environment, so it can be impossible to know if one is detecting an organism that is nearby at that moment or one that swam by hours earlier, perhaps several miles away. Plus, the current technology can only provide species-level information. It can’t even say whether the organism that shed that DNA was alive or dead.

That’s why Ernst is exploring the potential of eRNA. RNA transcripts are the small strands of genetic material produced when a gene is, in essence, “turned on.” Detecting and quantifying the genetic information in those floating bits of RNA is challenging, but it can give one even more information than eDNA. For one, eRNA is able to detect living organisms. In addition, because RNA degrades faster than DNA, it provides a more real-time picture of what’s in a water sample.

Most importantly for Ernst’s purposes, eRNA can be used to detect individual organisms, not just by species, but by developmental stage.

“A given genomic sequence of a larva and an adult is going to be essentially identical, but the gene expression patterns of each stage reflected in the RNA are going to be dramatically different,” Ernst said. “So, we have unique signatures that we can hone in on to discriminate between the two and specifically detect larvae.”

Ernst has been working with the Downeast Institute in Beales, Maine, to collect mussel samples of all ages at their hatchery and then identify unique genetic markers that can be used to identify larvae. This summer, he also collected water samples with Bangs Island Mussels, who operate several farms across Casco Bay, to begin to test out his eRNA method in the field. They’ve preserved a subset of each sample and plan to count bivalve larvae using more traditional microscopic techniques, so they can see how the two methods compare and ground truth the eRNA tools.

Throughout field sampling, Ernst and his collaborators have focused on creating a protocol that doesn’t require a specialized lab. For example, one of the thermocyclers they use to detect and quantify the genetic information in each sample is powered by a small battery and operated by a smartphone.

“We want to incorporate these eRNA tools into simple toolkits so farmers have everything they need to do the testing themselves,” Ernst said. “They can then detect larvae and their abundance at their farm and use that information to make decisions of when to drop ropes for seed collection.”

At the same time, Ernst is also pushing the envelope scientifically and believes there are many more tools that could be developed to tap into the power of eRNA. For example, he’s interested in identifying markers of physiological condition so that eRNA could also be used to assess the health of organisms in a water sample.

“These new larvae-monitoring techniques could help mussel farmers be successful, but eRNA tools are potentially powerful for exploring larval ecology and physiology as well,” Ernst said. “And this doesn’t stop at mussels. This could be really valuable for both fundamental science and for monitoring a host of economically important species.”