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  • Writer's pictureKristina Barclay

New Paper: Caprellid amphipods vulnerable to both physiological and habitat-mediated effects of OA

Many ocean acidification (OA) studies on marine organisms have tended to focus on the direct impacts to calcifying organisms, like oysters, snails, corals, and even some types of plankton. Calcifiers are vulnerable to OA, primarily because their calcium carbonate shells, and their ability to grow those shells, are negatively affected by increased ocean acidity. But for other organisms that are not as dependent on calcium carbonate, like crustaceans, the direct impacts of ocean acidification are often less clear. Some may have minimal to no response to ocean acidification, while others may even have positive responses to OA. However, there are other indirect ways in which some organisms may still be vulnerable to OA. For example, what happens when the organism that makes up your habitat is negatively impacted by OA?

We recently spoke with Em Lim, lead-author of a new study that seeks to address both direct and indirect impacts of OA on an important, but lesser-known group of crustaceans called caprellids (skeleton shrimp).

Em Lim is a Master’s student at Simon Fraser University and a scientific diver at Bamfield Marine Sciences Centre. They recently won Regionals for western Canada in this year’s 3MT (Three Minute Thesis) competition, where they presented on their current M.Sc. research examining the effects of animal pee on primary productivity across latitudinal gradients. Before embarking on an M.Sc., Em was a Marine Science Educator at Bamfield Marine Sciences Centre for two years, including during the start of COVID when they had to assist with the development and transition of school field tours into live labs and webinars. No small feat considering the thousands of school groups of children and teenagers that normally visit the centre in person each year.

Em suited up in diving gear on a boat
Em suited up in diving gear on a boat

Em grew up in Vancouver often exploring the coast with their parents, who were avid tidepoolers.

“I was one of those kids in Kindergarten that said ‘I want to be a marine biologist when I grow up’ and I never really changed my mind,” Em admits.

Em stayed true to their dream and pursued an undergraduate degree in Biology. As an undergrad at UBC, one of Em’s first research opportunities came when Dr. Chris Harley said he was looking for someone to help one of his Ph.D. students work on a project examining fouling communities along the coast.

“Fouling communities are made up of these little organisms that live on and cover the bottom surfaces [of the ocean],” Em explains. “They’re the things most people scrape off their boats!”

Em jumped at the opportunity to assist with the project, which was mostly identifying and counting all the organisms that were found on settlement plates (tiles placed out in seawater for a period of time to identify which organisms are settling in the area). On lunchbreaks at the Reed Point marina, Em enjoyed watching the seals and sea lions, and decided to complete a fall program at Bamfield Marine Sciences Centre, focusing on marine invertebrate ecology.

“I think marine ecology is so cool. You get to see how it’s all connected, all these interactions you never would have imagined,” Em says. “There’s also a drive to help these communities that you grow to love, tinkering to see how [these communities] work and how each part is connected.”

Em then received an NSERC USRA (Undergraduate Student Research Award) with Dr. Harley, to develop their own project on caprellid amphipods, one of the many species found in the fouling communities they had come to know.

“Caprellids are these tiny, fascinating crustaceans, sometimes called skeleton shrimp,” Em explains. “They kind of look like a preying mantis, or like someone took a shrimp and stretched it out.”

Caprellids are small, usually no longer than the tip of your thumb, and often much smaller, Em says. Like many other crustaceans, ocean acidification was not expected to have strong direct impacts on caprellids (as they are not as dependent on carbonates to build their skeletons), but Em wanted to know if there were other ways in which caprellids might become negatively impacted by OA. Building off the work of Dr. Jennifer Sunday, a former postdoc in Dr. Harley’s lab, Em wanted to explore the potential for larger scale impacts of OA, such as changes to biogenic habitats. For example, reductions in the complexity and branching of coral reefs due to ocean acidification has negative impacts on the organisms that rely on those corals for habitat. In the case of caprellids, they live in bushy, branching colonies of a hydroid called Obelia. These hydroids, animals related to jellies and sea anemones, respond negatively to OA. Under OA conditions, fouling communities become dominated by encrusting invertebrates, such as bryozoans, resulting in an overall reduction in habitat complexity. Em wanted to know: If Obelia (caprellid habitat) are negatively impacted by OA, will caprellids be impacted, even if OA has no direct impacts on caprellids?

“Our main question was: Are there avenues where OA-resilient organisms may still be impacted by OA?”

A caprellid (Caprella mutica) on a hydroid colony.
A caprellid (Caprella mutica) on a hydroid colony. © Hans Hillewaert

“Convention says that many crustaceans, including caprellids, are likely unaffected by OA, but we suspected there was this greater potential for indirect impacts,” Em explains. “We know that there are likely both direct and indirect effects of ocean acidification [on marine organisms], but often studies are not looking at both aspects in the same study or on the same species.”

The goal of the paper was to test both direct and indirect effects of OA in the same study.

“Our main question was: Are there avenues where OA-resilient organisms may still be impacted by OA?”

The study was conducted in two parts. First, Em examined direct effects of OA by exposing caprellids to acidified treatments, and determining their response. Second, Em tested for indirect effects by examining habitat complexity by counting the number of caprellids in several different types of habitats.

Testing for direct impacts seemed straightforward enough: place the caprellids in one of three treatments of increasing acidity for 72 hours (pH = 8.3, 7.9, 7.5), then measure their heartrate, a commonly used proxy for metabolism and stress level. But Em says they ran into several challenges that made collecting the data rather tricky.

For one, caprellids are tiny, and Em could only see their hearts beating through a microscope. Small hearts also beat really quickly, so Em had to find a way to record the heart beats and slow the film down to be able to count them properly.

A person looking under a dissecting microscope at a hydroid colony with caprellids
Em looking at a caprellid under the microscope

“I had to build a homemade microscope camera out of a toilet paper tube with an old phone case attached to it. I’d film the caprellids, then slow down the video so I could count and calculate BPM (beats per minute),” Em explains. “One of the reviewers suggested I put a picture of my set-up in the paper, so you can see a figure of it in the paper.”

Another challenge was that the caprellids didn’t want to sit still, which made counting their heart beats even harder.

“I’d be almost finished and then they’d move out of scope, so I’d have to start all over again,” Em says, chuckling.

(A) The caprellid heart rate monitoring set up and (B) sample footage recorded by the smart phone. An iPhone was secured to a dissection microscope using a cardboard tube glued to a phone case in order to film the caprellid’s heart rate. The black arrow indicates where the heart rate was most clearly visible on the pictured C. mutica.
Figure 1 (Lim and Harley 2018). (A) The caprellid heart rate monitoring set up and (B) sample footage recorded by the smart phone. An iPhone was secured to a dissection microscope using a cardboard tube glued to a phone case in order to film the caprellid’s heart rate. The black arrow indicates where the heart rate was most clearly visible on the pictured C. mutica. Photo credit: (A) Christopher Harley and (B) Emily Lim.

Em also tried to be conscious of sex biases that are often seen in biological studies, but this also proved to be challenging.

“Many studies only look at the males because researchers don’t want to deal with or disturb fecund females [that are reproductive or carrying offspring],” Em points out.

Em explains that they had originally conducted experiments on both females and males, but it was too challenging to measure the heartrates of the females. Only data for the males ended up being included in the final paper.

“The females have brood pouches, which makes them have big round bellies, and I couldn’t get them to lay flat enough. They would just roll around,” Em says.

To examine indirect effects, Em first had to test for habitat preferences of caprellids to see if they would prefer the OA-vulnerable hydroids (Obelia) over other habitat types. Em put out settlement plates and then counted the caprellids on the different habitat types, consisting of either mussels, tunicates, or hydroids, after 10 weeks. Then, Em examined the role of habitat complexity on caprellid abundance. Em manipulated hydroid colony complexity by taking clumps of between one and four colonies, picking off all the caprellids, and then hung them from bricks off a dock. After eight weeks, Em counted all the caprellids on each hydroid clump, and then laid out each clump to trace the branchiness as a means of quantifying habitat complexity when comparing it to caprellid abundance.

Person standing on an oyster raft holding two ziplock bags full of water and hydroids with caprellids
Em proudly showing off their bags of caprellids, collected on an oyster raft

One of Em’s favourite moments of the study was when a family happened upon Em while they were working on their project at the marina.

“I was covered in grime and laying on the dock, which must have looked interesting,” Em admits.

The father asked Em what they were doing, so Em took the opportunity to engage the whole family in their research project.

“It’s my favourite part of doing science in public spaces,” Em says. “It’s a great way to do outreach.”

A person lying on their belly on a dock turns to smile at the camera. They are in the middle of checking on their experiment with their arms over the side of the dock.
Em checking on their experiment while a family approaches on the dock.
A person on a dock holding out a clicker counter to a curious toddler in a lifejacket who is touching the buttons. A parent (only legs and lower torso visible) holds the toddler's other hand.
Engaging in scientific outreach with a curious family

Em found that, contrary to what they had expected, caprellids experienced direct negative impacts from OA.

“I was a bit surprised, but OA increased caprellid heartrates, so maybe they were stressed, or their bodies were working harder due to OA,” Em explains.

In terms of habitat, as Em expected, caprellids preferred hydroids over mussels or tunicates (sea squirts).

“Caprellid appendages look kind of like a hand, which they use to grab onto things,” Em says. “Sea squirts are smooth and squishy, and hard for caprellids to grab.”

Hydroids, on the other hand, are branchy, providing an easy structure on which caprellids can cling. Caprellids are detritivores, and the bushy, branching structures of hydroid colonies also provide a means of capturing and collecting more food than other habitat types.

An example of a bushier hydroid clump with many branches coming off the main stalk
An example of a bushier hydroid clump
An example of a less bushy hydroid clump (fewer branches off main stalk)
An example of a less bushy hydroid clump

So what happens when hydroid colonies become reduced in size and complexity as a consequence of ocean acidification?

In the final part of their experiment, Em found that there was a strong relationship between the complexity or bushiness of hydroid colonies and the number of caprellids found amongst them.

“Basically, more hydroids meant more caprellids,” Em says.

With an expected reduction in hydroids due to continued ocean acidification, caprellids will have less habitat, and corresponding food sources, available to them. Essentially, not only will OA negatively impact caprellids in terms of their physiology (heartrates), but OA may also reduce their abundances as less habitat becomes available.

And it won’t just be caprellids that are impacted by a loss of hydroid habitat. Many other organisms live in hydroid colonies too.

Em points out that the results of this research highlight the need to examine both direct and indirect impacts of ocean acidification on marine organisms.

“If we had only included one of these aspects [direct or indirect impacts of OA], we would have underestimated the effects of OA on caprellids."

A lab setup with a laptop on the left and a dissecting microscope on the right. There is a hydroid colony under the scope and tweezers and paper towel at the ready to the left of the scope.
The lab set up used to count caprellids on bunches of hydroid colonies

“If we had only included one of these aspects [direct or indirect impacts of OA], we would have underestimated the effects of OA on caprellids,” Em says.

Of course, it is hard to include everything in one study always, Em acknowledges, but these results highlight the need to be cautious when estimating impacts of OA on organisms, and to be mindful of indirect effects.

Em says that one other take-home of their research is the “exceptional” complexity and interconnectedness of marine communities.

“There are so many amazing, breathtaking interactions that happen on a day-to-day basis that shape these communities. It is really astonishing.”

Em continues to explore the complexity of marine ecosystems through their M.Sc. research at SFU. As a non-binary graduate student in marine ecology, Em says that it is important to think about some of the opportunities that not everyone has had to study marine biology, especially when it comes to Indigenous and Black people. To provide more opportunities for students with historically excluded identities, Em has helped the SFU Biology Grad Student EDI Committee launch a fundraiser to endow an Indigenous and Black Graduate Scholarship in Biology. Em hopes such efforts will provide a means of increasing inclusion and diversity within scientific fields such as marine biology.


Read Lim and Harley, 2018 here.

Lim EG, Harley CDG. 2018. Caprellid amphipods (Caprella spp.) are vulnerable to both physiological and habitat-mediated effects of ocean acidification. PeerJ, 6:e5327

To learn more about Em and their research, visit, and follow them on Twitter @sea_en_emily.

Watch Em’s SFU and Regional winning 3MT presentation on their M.Sc. research on animal pee here.

To learn more about the Indigenous and Black Graduate Scholarship in Biology at SFU, visit


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