Transect Magazine: Charismatic Microfauna

Transect Magazine: Charismatic Microfauna

This story originally appeared in the Winter 2026 edition of Transect.

What do jellyfish, krill, lobsters, and swordfish have in common? They are different sizes with different life cycles and food sources; yet, at some point in their life, they're all classified as zooplankton.

Zooplankton, Latin for "drifting animal," refers to all animals that float in the upper water column. That includes those that are there for one stage of development, such as lobsters, as well as the vast array of microscopic species that spend their entire existence there. Together, they make up the majority of animal life on the planet and are responsible for the world's largest synchronous migration - billions strong moving up and down the water column every day.

"They're extraordinarily beautiful and extremely important to a healthy ecosystem," explained Senior Research Scientist David Fields. "They really are the true charismatic fauna of the sea."

Most zooplankton species never grow out of their drifting habit. The majority are copepods, a crustacean that is among the most abundant and diverse type of animal on the planet and found in every aquatic habitat, from roadside ditches and ephemeral streams to high alpine lakes.

"Zooplankton are so otherworldly and diverse that one never tires of exploring their planet," remarked Senior Research Scientist Nick Record. "From the ghostly skeleton shrimp haunting the dim waters below docks, to the deep-sea Phronima, which inspired the creature in the Alien movies, it's like a never-ending cast of characters from a Halloween universe."

Copepods are also the heart of the marine food web.

"If you take a net tow at the surface at any given time, about 90 percent of what you get are copepods," Fields said. "Almost all of the food at lower trophic levels, at one point, passes through copepods, and then that energy moves up to all of the organisms that feed on them."

Krill, for example, are the most abundant single animal species on the planet, providing the basis of the diet for everything in the Southern Ocean. Meanwhile, in the Northern Hemisphere, Calanus finmarchicus accumulates up to 60 percent body fat, creating a thick layer of buttery energy that stretches across the North Atlantic every winter. As they eat, respire, poop, and die, copepods also play an essential role in the cycling of nutrients like carbon from the atmosphere to the deep ocean.

ZOOPLANKTON-FIRST PERSPECTIVE

Despite their importance, though, most models and satellite tools used for studying the ocean focus on the tiny plants, or phytoplankton, that zooplankton feed on - not the animals themselves.

"It's partly because we have so much more data on phytoplankton, but zooplankton are also harder to study in this context," Record explained. "They occupy a lot of different ecological roles throughout their lives, and, for many of them, their life cycle is more complicated than phytoplankton, so the equations we have don't work as well."

Yet, small changes in the zooplankton population can make a big difference in how much carbon dioxide is recycled back into the atmosphere versus how much is pumped down to the seafloor.

"The focus of global carbon cycles has been on net primary production since that's the base of the food web and phytoplankton production is easier to measure," added Senior Research Scientist Karen Stamieszkin. "Assumptions have been made about the fate of carbon fixed through photosynthesis by these phytoplankton, so research on the fate of carbon has often skipped the nuances of where that carbon goes and how it gets there."

Stamieszkin is leading an interdisciplinary and multi-institutional team that includes Record to change that.

Funded by the Advanced Research Projects Agency-Energy, they're examining the relationship between zooplankton physiology and behavior to develop models of how much carbon zooplankton are actively transporting in their daily migrations. The ultimate goal is to incorporate this nuanced information into regional and global models of biogeochemical cycles.

Those improved models will inform efforts to quantify the effectiveness and impact of marine carbon dioxide removal strategies like ocean iron fertilization. They may also be useful for the shipping, seafood, and aquaculture industries who need to better understand the movement of the fishes and mammals that feed on zooplankton.

To that end, Bigelow Laboratory scientists are working on new tools that center zooplankton in larger animal models to aid shipping, conservation, and management efforts. Because, at the end of the day, whales and the like go where their food is.

Earlier this year, Camille Ross, a former research associate with Record and University of Maine PhD student, published a new modeling approach for tracking North Atlantic right whales that incorporates information on Calanus and other key copepod prey species. By considering where the whales' food is concentrated, as well as their daily energy needs, the approach more accurately predicts right whale movements.

In contrast, most existing whale habitat models account for food by using proxies that are easier to measure. For example, chlorophyll concentration is used to estimate, first, the biomass of phytoplankton and, then, the density of zooplankton that feed on those plants. These indirect measures are easier to collect, but are several steps removed from what scientists are actually interested in.

Senior Research Scientist Catherine Mitchell is also trying to develop ways to detect zooplankton directly with satellites. Some species, including Calanus, produce a reddish tint visible from space when large numbers swarm together. Mitchell and Postdoctoral Scientist Rebekah Shunmugapandi are exploiting that to develop algorithms that translate ocean color data into maps of zooplankton abundance.

The work is adapting methods developed by Cait McCarry, a former postdoc with Mitchell, and refining them for the Gulf of Maine. The team is still working to fully untangle the relationship between the ocean color signal from satellites, zooplankton abundance, and astaxanthin, the pigment that gives these species their red hue. Yet, the work marks significant progress toward applying remote sensing to study zooplankton.

"There are many more phytoplankton than zooplankton, and maybe there was some thought that zooplankton were too large to influence ocean color. Either way, our existing instruments perpetuate the phytoplankton-sized focus view of the ocean color world," Mitchell stated. "But there's so much potential in zooplankton remote sensing, and we've really just scratched the surface with the work we've done so far!"

A CLIMATE CHANGE BELLWETHER

One major challenge to modeling zooplankton is that, as with most marine life, scientists are already seeing shifts in behavior and physiology in response to ocean warming.

For one, species are already moving poleward in search of more favorable conditions. Fields and his colleagues have also shown that some species, including Calanus, are smaller and build up less fat - making them a less nutritious meal - as temperatures rise and their metabolisms ramp up to compensate.

On the behavior front, copepods are known to have a good sense of touch and smell, and many are impressive swimmers.

Former Postdoctoral Scientist Nicole Hellessey worked with Fields and Record to model Antarctic krill's schooling behavior, an ability that makes them unique among invertebrates. The team showed how krill adapt their swimming in response to the scent of food and predators and even slight changes in their environment, like water temperature and flow rate.

"We often assess damage to ecosystems in terms of whether organisms are dying, but behavior changes - if they can't find a mate or they're feeding differently - tell you something about sub-lethal effects of an environmental change," Fields said. "That gives you a finer picture of when ecosystems are starting to be affected."

Of particular concern though, Fields explains, is the growing disconnect between the lifecycle of some copepods and the species that depend on them, a phenomenon that ecologists call a phenological mismatch.

Calanus undergoes diapause, a state of suspended development similar to hibernation, in winter. In spring, millions of them emerge, just in time for a copepod buffet for the newly hatched young of all the animals that eat them. In the subsequent months, Calanus grow in lock step with their predators, providing a steady food source in those early life stages. The Gulf of Maine ecosystem has developed a biological clock over millennia timed precisely with this pulse.

But as waters warm, Calanus appears to be coming out of diapause too early.

"When these cycles become uncoupled for one year, the other species that rely on them can get through it," Fields explains. "But when that uncoupling happens year after year, longer than the organisms that need food for their offspring can survive, entire populations begin to struggle."

Fields has worked with Senior Research Scientist Peter Countway and Research Scientist Robin Sleith, as well as former University of Maine PhD student Alex Ascher, to understand the impacts of this growing mismatch on lobsters.

Despite incredible numbers of lobsters being born in recent years in the Gulf of Maine, scientists have observed that the number of adolescents has actually declined, suggesting that something is affecting the survival rate of lobsters in their first few weeks of life. Earlier this year, the research team published a novel approach for understanding the diet of these newly hatched lobsters using molecular tools that confirms that larval lobsters rely disproportionately on Calanus as a food source. This suggests that the growing mismatch between the Calanus hibernation and the lobster life cycle could be partly to blame for why fewer lobsters are making it to the next life stage.

NEW TOOLS FOR NEW QUESTIONS

Understanding these responses to change - and what impact they could have on how the ocean functions - requires sophisticated tools for counting and characterizing these tiny animals.

Typically, scientists tow a net along the surface, sweeping up lots of different, small organisms that get trapped on a filter, which is then used to estimate overall biomass in that sample. But one has to look at those filters under a microscope and visually identify species to say anything about the individuals in that sample.

Recently, however, Fields's lab acquired a FlowCam, with funding from the Maine Coastal and Marine Climate Action Fund of the Maine Community Foundation, which captures high-resolution images of every particle in a sample. With those images, they can quickly determine the ratio of male to female and the general size distribution of the zooplankton population and identify key species in a sample.

The team is still working to optimize the tool for zooplankton applications. That said, it's already proven invaluable for automating a time-consuming process and standardizing measurements to confidently observe changes over time and between different parts of the ocean. The digital images, he says, also provide a better "long-term storage solution" for the data compared to preserving actual animal samples.

"We take the FlowCam out on the boat with us and process samples as we're collecting them, so by the end of a research cruise, you have reliable information that, in the past, would have taken months to process," Fields said.

Right now, Bigelow Laboratory is the only institution in the state that can process and analyze zooplankton samples with a FlowCam, an analytical service his lab is offering to researchers and resource managers around the world and that he hopes will expand the possibilities of this exciting area of research.

"Because of their sheer number, small changes to copepods matter for the whole ocean," Fields emphasized. "There are questions at a population level that are just hard to get at by poking at individual animals under a microscope. Now, we can start answering those questions."

Photo Captions:

Photo 1: A micrograph of a copepod found offshore of Bermuda (Credit: John Burns).

Video: Micrographs show the unique and complex forms of various zooplankton species, including: an Antarctic krill, various zooplankton collected in the Gulf of Maine, a gravid Euchaeta full of blue eggs, a copepod from a freshwater bog that's stained to make its muscles and cells visible, and a zooplankton from the family Eucalanidae found in the Gulf of California (Credit: David Fields, Billy Hickey, Zachary Wagner, John Burns, Amy Maas)

Photo 2: The right whale nicknamed "Bowtie" is pictured swimming in southern Maine waters in January 2025 during a New England Aquarium survey (Credit: New England Aquarium).

Photo 3: Postdoctoral Scientist Rebekah Shunmugapandi presents at a Café Sci lecture this summer on her work with Senior Research Scientist Catherine Mitchell to develop remote sensing tools to monitor zooplankton from space (Credit: Alex Seise).

Photo 4: Senior Research Scientist David Fields teaches undergraduate students about the ecology and physiology of zooplankton (Credit: Gabe Souza).

Photo 5: Fields and Research Associate Maura Niemisto deploy a CTD, a device for collecting water samples, in the Gulf of Maine while aboard the R/V Bowditch (Credit: Billy Hickey).

Photo 6: The FlowCam provides an image of a zooplankton, one of thousands of images the instrument quickly takes from a single sample of water, helping speed up the process for identifying and counting animals (Credit: David Fields).