Researchers Develop Tools for Unlocking Larval Lobster Diet

The American lobster has indescribable economic, ecological, and cultural value for the Gulf of Maine. Yet, there are significant gaps in scientists’ understanding of these charismatic creatures, especially in their crucial early life stages.

Researchers from Bigelow Laboratory for Ocean Sciences and the University of Maine are trying to fill those gaps.

In a new study published in PLOS One, they’ve provided a novel approach for understanding the diet of newly-hatched lobsters that combines traditional microscopy-based methods with advanced molecular techniques.

Their findings confirm with certainty that larval lobsters consume Calanus finmarchicus — a zooplankton species foundational to the diets of everything from cod to right whales — at a higher proportion, in fact, than expected given the availability of other prey options in the wild. That provides new insight into how plankton abundance in a warming ocean may hinder the survival of larvae.

“Lobsters are an important economic and cultural resource. They’re also important ecologically as a large-bodied crustacean scavenger in the Gulf of Maine,” said the study’s lead author, Alex Ascher, a postdoctoral researcher at Quahog Bay Conservancy and Woods Hole Oceanographic Institution and former University of Maine PhD student. “This means they are well studied, but there are still gaps when it comes to their early life history.”

Traditionally, researchers study diets by dissecting an organism’s stomach under a microscope and identifying the partially digested contents. But that’s challenging with a quarter-inch-long baby lobster that subsists on microscopic, often soft-bodied, prey and has a stomach the size of a pinhead.

The team tested two molecular approaches for studying the gut contents of larval lobsters to see if these newer methods, in concert with microscopy, might help illuminate the lobsters’ eating habits.

The first, DNA metabarcoding, uses a “universal” genetic marker to broadly identify which prey species are present in the lobster’s stomach and has become a widely popular approach for studying environmental DNA.

Metabarcoding is invaluable for providing a more complete picture of the diversity of foods that larval lobsters eat. It also allows researchers to examine the contents of several stomachs at a time and distinguish prey organisms that are hard to identify visually.

Of course, the technique has some challenges the team had to overcome. For one, it relies on having a database of genetic sequences from potential prey species to match to the genetic information pulled from the stomach contents. On top of that, the lobster’s own DNA can overwhelm the signal from its food. That’s especially true since some of what the larval lobsters eat are crustaceans with similar DNA profiles to their own, so the researchers had to develop a specialized “blocker” to reduce the contributions from lobster DNA.

With this technique, the team was able to confirm some of the common, broad prey categories that have been identified by microscopy. But they also identified prey species that have soft body parts, such as worms and fish eggs, and found a strong genetic signal from several single-cell organisms, like microalgae, some of which may be evidence of the food that the lobsters’ prey is eating.

“The potential to reveal not only what the larval lobsters are eating, but also what species of phytoplankton their prey are eating reveals potential pathways back to the base of the marine food-web, and suggests which planktonic species play a role in the survival of early lobster life-stages,” said co-author Peter Countway, a senior research scientist at Bigelow Laboratory.

The team also developed a second molecular technique. Like a Covid test, their Polymerase Chain Reaction approach relies on DNA primers and a fluorescent DNA probe that are unique to a single species of interest, which lights up the test when that species is present in a gut sample. Unlike metabarcoding, which highlights the diversity of prey being consumed, this approach provides an accurate method for targeting a single species, in this case, Calanus finmarchicus. That’s how the team confirmed that Calanus was present, and in a high proportion, in the diet of newly-hatched lobsters.

“The finding that Calanus are a preferred food of lobster larvae provides important insight into the future of the lobster fishery,” said co-author David Fields, a senior research scientist at Bigelow Laboratory and one of Ascher’s PhD advisors. “As the Gulf of Maine warms, the copepod community is reorganizing and moving northward, which will have downstream effects, including on where the lobster larvae can find adequate food and ultimately settle.”

The findings showcase, more broadly, the power of combining these newer molecular approaches with traditional microscopy methods to get a deeper understanding of the feeding habits of hard-to-study organisms like larval lobsters.

“Now we have a bigger tool kit to understand the larval diet that not only takes advantage of visible evidence from traditional microscopy, but also capitalizes on new molecular approaches that open a window on the invisible,” said co-author Richard Wahle, a University of Maine professor and former director of the UMaine Lobster Institute. “This will help us answer long standing questions about how larval lobsters interact with the planktonic food web.”

Going forward, the research team is continuing to apply these methods to further unravel the diet of larval lobsters, as part of a broad, multi-disciplinary project on the role of larval lobsters in the Gulf of Maine’s dynamic food web.

This work was supported by the NSF Established Program to Stimulate Competitive Research Maine-eDNA research program (Grant #OIA-1849227), the Maine Department of Marine Resources, and the Maine Sea Grant American Lobster Initiative.

Photo Captions:

Photo 1: Study authors David Fields and Alex Ascher collect wild larval lobsters (Courtesy of David Fields).

Photo 2: A microscopy image of a larval lobster’s gut contents, highlighting how challenging it can be to visually identify specific prey species (Credit: Alex Ascher).

Photo 3: Lead author, Alex Ascher, holds a vial of larval lobsters (Credit: Holland Haverkamp, University of Maine).