Environmental Sciences Professor Brooke Love and graduate student Rhiannon Holmes explore the link between proteins and resistance to ocean acidification
Rhiannon Holmes holds up two female Dungeness crabs. Photo by Luke Hollister.
Professor Brooke Love was already studying the effects of ocean acidification on sea life, but wanted to look into some new tools to aid her studies. After Love received the National Science Foundation’s Mid-Career Advancement Grant in 2020, she decided to learn molecular tools such as mass spectrometry to explore a microscopic angle.
Soon after, she found a study by Paul McElhany, who was researching Dungeness crabs at the National Oceanic and Atmospheric Administration (NOAA).
McElhany had found a difference in survivability between the offspring, or zoea, of multiple Dungeness crab mothers collected in different regions when living in water with a high concentration of CO2.
Close-ups of some zoea used in the experiment. Photos courtesy of Rhiannon Holmes.
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The NOAA group initially hypothesized that water conditions, such as oxygen and CO2 levels, at the sites where the crab mothers were collected could influence the zoeae’s survivability and resistance to ocean acidification (OA), but ultimately they found that location had less of an impact than matrilineal lineage.
As Love continued the research, she knew she would need more resources. Support from the Washington Ocean Acidification Center allowed her to move ahead and bring WWU undergraduate Rhiannon Holmes onto the project as an intern. Together, they took the first NOAA experiment’s preserved zoea gathered from the Puget Sound and compared all the proteins present in each brood. Of the three Puget Sound females, one mother’s brood had far higher survivability under high CO2 conditions than the other two. The team discovered that these survivors had elevated amounts of a few key proteins. The function of these proteins could indicate the reason why those zoea survived the best.
Now, the team is working towards the next phase of their experiment, which will consist of testing the resistance to OA of additional broods to see if the first experiment’s data is repeatable. Love’s team is working with local tribal fishery experts to collect new egg-bearing females and will use the Shannon Point OA system to test how their offspring survive, and to see if their targeted proteins are once again associated with more resilient broods in the next trial.
“We’ve been using mass spectrometry to look at the different proteins that they produced, and then compare the zoea that were resistant with the vulnerable ones. We identified a group of 33 proteins that were different between the two groups,” said Holmes, who is now a graduate student in Love’s lab. “We’ve only analyzed zoea from one of the three locations so far. They had three females per location, so the sample size is pretty small, but we’re interested in seeing if that trend holds true as we analyze the rest of the samples.”
To understand why Holmes, Love, and NOAA are so focused on Dungeness crabs, you first have to understand the dangers of ocean acidification. According to the State of Washington Ocean Acidification Center, which is also providing grant funding to Love’s project, our oceans absorb around 28% of the carbon dioxide produced by the combustion of fossil fuels into our atmosphere. The absorption of so much additional carbon dioxide alters the chemistry of the seawater, and as a result, the surface ocean has become about 30% more acidic over the past 250 years.
This change in acidity in our Pacific Northwest coastal waters isn’t just a passive chemical imbalance. Shellfish like oysters, clams, and crabs can experience a weakening of their protective shells and skeletons, particularly during larval and developmental life stages.
“Chemistry is a huge part of the ocean. Slight changes can have a huge impact on which species can live in those conditions, and that can trigger a chain reaction with massive ecosystem implications ,” said Holmes. “Acidification has a big impact on organisms that have shells, like crabs, mussels, oysters, all of the shellfish that people really love to eat at seafood restaurants. And, shockingly, just a tiny shift in one of those species out in the wild can have a huge ecosystem impact.”
One of the direct effects OA has on shellfish is due to the calcium carbonate that makes up their shells. When OA rises, the amount of carbonate in the water is reduced, which forces the shellfish to spend more energy drawing carbonate from the ocean to make their shell. This extra energy expense can be extremely dangerous for larval shellfish, as they overextend their energy reserves to construct their first shell.
However, crabs mostly use chitin to construct their shells, not carbonate. Still, current research shows developmental delays and higher mortality rates in Dungeness crabs when OA rises. Thus, advanced research methods like proteomics are necessary to understand why crabs might be struggling in higher CO2 conditions.
Dungeness crabs are the most valuable fishery on the West Coast, and even beat out salmon as the most profitable seafood in Washington state. Thus, they were the ideal specimen for the study.
The first step in running the experiment is gathering female crabs with eggs. Crab mothers keep their eggs stuck to the underside of their bodies until they hatch. When they do, the researchers collect the zoea and place them in environmental chambers with varying levels of CO2, and continue raising them until they’re 30 days old.
The process is incredibly time-intensive and requires a lot of hands-on monitoring. Love’s team currently includes four undergraduate research assistants who helped care for the most recent batch of zoea as the team learns how to best raise the zoea in the lab. Undergraduates Isabella Hummel, Alexandria Jackson, Marissa Steward, and Olivia Smith had to catch each tiny, fast-moving zoea in a thin glass pipette and move them to a new dish of water every few days, as well as keep a brine shrimp farm going to feed them daily.
Thanks to their work, the team has a better understanding of how to best raise the zoea. This will allow the team to hit the ground running when the crabs spawn again next winter.
“We monitor how they’re doing, and how many are surviving, and so forth. But then after 30 days we freeze them, and begin the proteomic analysis,” said Love.
The team uses an enzyme to cut the protein chains in specific spots.
“So instead of having these very long proteins, we have shorter segments that are called peptides,” Love said, “and then we can analyze those peptide mixtures on a mass spectrometer.”
Through this process, the researchers can identify how much of each possible protein is present in each sample. They can then compare the samples to find higher concentrations of specific proteins in broods that show higher OA survivability. If the experiment successfully identifies a biomarker that signals OA resistance, fishery managers could work to increase and spread the crab populations that have the biomarker.
“Based on the data that we have, we did find that out of 2,500 proteins that we identified, there were 33 that were really associated with the one female who had really high survival,” said Love. “Then we can, using some other tools, try to figure out what those proteins actually do based on how similar they are to other proteins that have been researched. So we know that of those 33 proteins, some of them were associated with protein folding, some of them with energy metabolism, and some of them with their exoskeletons. We have hints right now of some specific proteins that might be associated with why those zoea are resilient, and that’s what we’re really trying to follow up on and understand. ”
Western Washington University (WWU), 8 June 2026. Full article.
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