by Shannon Brown, UW CICOES, with support from Sam Setta, UW CICOES, and collaborators from NOAA Ecosystem & Fisheries-Oceanography Coordinated Investigations

When winter arrives in the Arctic, this region transforms into one of the most extreme and inaccessible environments on Earth. Daylight fades away, temperatures plunge below freezing, and the sea surface in both the Chukchi and northern Bering Seas becomes an expanse of ice. Research here is difficult even in summer, when turbulent seas and sparse infrastructure pose challenges, but once the sea surface freezes, vessel-based fieldwork becomes nearly impossible—limited only to rare transits by icebreakers. Yet beneath the frozen expanse, an entire food web continues to flourish, teeming with microorganisms, phytoplankton, zooplankton, fish, and marine mammals.

So how do scientists study a world they can’t access for half the year? How do they detect and monitor the animals living across such an immense and ice-locked region?

CICOES researchers in the Ocean Molecular Ecology (OME) group at NOAA’s Pacific Marine Environmental Laboratory are tackling this challenge with a molecularscale approach. We use environmental DNA (eDNA)—tiny fragments of genetic material shed by organisms—to detect life across the entire tree of life, from bacteria to whales. eDNA acts as a molecular net, revealing which organisms are present and how communities are shifting. When paired with autonomous sampling platforms, eDNA sampling can generate these insights even in regions inaccessible for half the year.

OME uses eDNA to capture species-level and community-level patterns that help fill in information that traditional observing systems are not designed to detect. Rather than replacing traditional approaches such as remote sensing and fisheries surveys, eDNA complements and enhances them—adding a new layer of biological detail to the Arctic research toolbox. This additional resolution enables earlier detection of harmful algal bloom species, and reveals subtle shifts in the food web as sea-ice conditions change.

To study winter dynamics beneath the ice, our group uses autonomous moored water samplers that collect eDNA when most ships cannot access the region. These samplers allow researchers to track how microbial, algal, and zooplankton communities change beneath the ice, and how they respond to environmental shifts. OME also examines the sea ice itself, focusing on ice algae, the microscopic algae that grow inside small water pockets within the ice and along its bottom surface. These algae play an important role in shaping the phytoplankton dynamics below. Together, these efforts contribute an eDNA-based perspective, working in concert with physical, chemical, and biological observations from other researchers, to offer a clearer glimpse into the inner workings of one of the most rapidly changing ecosystems in the ocean.

A molecular window on seasonal shifts

Since 2020, our team has partnered with the Ecosystem & Fisheries-Oceanography Coordinated Investigations (EcoFOCI) team to collect more than 1,000 eDNA samples in the Bering and Chukchi Seas. At each site, we use Niskin bottles—special sampling bottles that close at specific depths—to collect seawater. Back on deck, the seawater is processed for nutrients, oxygen, eDNA, and other oceanographic measurements. Some samples are frozen or chemically preserved, while others, like eDNA, are immediately filtered on board.

Our eDNA filtration process is precise and deliberate. We use a specialized pump to push seawater through an ultrafine, enclosed filter, allowing sterile collection and long-term storage for DNA extraction. After filtration, samples are preserved and frozen at sea to await later extraction and processing at PMEL. To capture the full range of life, OME uses five distinct molecular markers that target specific taxonomic groups. As one of the few research groups applying molecular tools at this scale in the US Arctic, our multimarker approach provides a view of species-level resolution in a region where traditional sampling faces seasonal barriers.

Sequencing from our 2020–2023 collections reveals the remarkable diversity moving through these waters. Fall samples, gathered as sea ice begins to form, and spring samples, collected as sunlight returns and ice retreats, capture the seasonal transitions that shape the Arctic ecosystem. During this sampling window, we detected more than 1,000 species from 39 phyla, including 225 vertebrate species—cod, salmon, lamprey, bowhead whales, walrus, and even Pacific sleeper sharks. The dataset also captured zooplankton that anchor regional food webs, such as copepods, krill, and pteropods, along with ecologically and economically important seafloor species like snow crabs, sea stars, sea cucumbers, and deep-sea corals.

Spring samples also captured the onset of the region’s phytoplankton blooms, events that fuel the entire food web. These blooms can be a signal of healthy productivity or a source of harmful algal species that threaten fish, marine mammals, and coastal communities. Tracking their timing and composition provides early insight into how changes at the base of the food web may shape conditions across the region.

Tracking life beneath winter ice

Complementing seasonal ship-based efforts, we deploy autonomous eDNA samplers to collect data year-round, focusing on the winter months when vessels rarely reach these remote ecosystems. Anchored to the seafloor and suspended ~50 m below the surface, these moorings offer a rare glimpse into biodiversity. OME currently uses the McLane Research Laboratories Particle and Phytoplankton Sampler (PPS), a programmable instrument that can filter and preserve up to 24 eDNA samples in a single deployment. We typically deploy these units for a full year and program them to collect samples every two weeks, with more frequent sampling during the spring bloom when biological activity rapidly changes.

Since launching this autonomous program, we have completed five deployments across the Bering and Chukchi Seas. I have personally overseen the careful preparation and deployment of a majority of these units, often in tight shipboard labs or rough conditions. Each unit must be cleaned, primed, and made bubblefree before deployment, when it will be inaccessible for months while sampling eDNA.

In fall 2025, two units were deployed in the Bering Sea, programmed to monitor the winter-to-spring transition. By the time the samplers are recovered in fall 2026, they will have captured a continuous record of the Arctic’s hidden seasonal rhythms, allowing us to reconstruct entire communities of life, from microscopic bacteria and phytoplankton to zooplankton and fish…all from microscopic traces of DNA.

Sampling sea ice in a warming Arctic

As winter ice melts and spring floes break apart, the ice algae communities living within the ice, often dominated by diatoms, face dramatic changes. Ice algae serve as primary producers at the base of the food web, supporting organisms from tiny invertebrates to marine mammals. Despite their crucial role, these biological communities within the sea ice remain far less studied than their subsurface counterparts in the water column.

When sea ice melts, algal cells are released into the water column, where our autonomous samplers can detect them. But directly sampling the ice itself offers a much clearer picture of the organisms living within it. For decades, Arctic researchers have collected blocks of ice, allowed them to melt slowly, and filtered the meltwater to assess community dynamics. Unfortunately, relatively few sea-ice biological studies have taken place in the US Arctic since 2019, due to reduced ice presence and logistical constraints.

Aboard the NOAA ship Oscar Dyson in spring 2025, OME scientist Han Weinrich led our group’s first sea-ice sampling effort. When weather and sea conditions allowed the vessel to maneuver close to small, isolated floes, Weinrich worked with the crew to collect ice chunks using a net. Each piece was transferred into sterile containers and left to melt under natural outdoor conditions for up to 30 hours, slow enough to maintain the integrity of the embedded microbial communities. Once fully melted, the water was filtered and preserved for DNA extraction and sequencing. Nine ice-derived samples provide a rare and valuable snapshot of Bering Sea ice-algae communities at the seasonal turning point.

This work is especially timely. The Arctic has experienced unprecedented warming—the ten warmest years on record have all occurred since 2011—making it increasingly important to understand how sea-iceassociated ecosystems are shifting. OME can track species overlap by integrating these ice-derived samples with our autonomous water-column eDNA datasets to understand the interplay between ice-algae and spring phytoplankton blooms in the water column, which play an important role at the base of the Arctic food web.

Shifting phytoplankton communities

The Arctic is warming nearly four times faster than the global average, reshaping the foundation of its marine ecosystems. OME postdoctoral researcher Sam Setta specializes in using molecular tools to understand how phytoplankton communities respond to shifting ocean conditions. Her work bridges the gap between molecular data and real-world ecological change, helping us determine how the smallest organisms shape the Arctic ecosystems.

As sea ice retreats earlier each year, the timing and composition of phytoplankton blooms change, creating opportunities for new species, including harmful species that can result in harmful algal blooms (HABs), to flourish. One example is Alexandrium catenella, a dinoflagellate that forms dormant cysts on the seafloor. These cysts remain inactive until warmer, more stable conditions trigger their transition into toxin-producing cells. Large cyst beds of this species have accumulated in waters in the US Arctic, raising concern that continued warming and changes in ocean circulation could lead to more frequent or widespread HAB events. While there are ongoing monitoring efforts of HAB species, Alaska lacks a robust, well-funded monitoring system comparable to the mainland US West Coast. This makes molecular approaches like Setta’s especially valuable, complementing traditional tools.

Using eDNA, OME has detected dozens of HABassociated taxa, including A. catenella, just north of the Bering Strait above known cyst beds, and several toxinproducing Pseudo-nitzschia species across the US Arctic. These Pseudo-nitzschia species have been observed in the region and produce the potent neurotoxin “domoic acid,” known to affect mammals (including humans) who consume it when eating shellfish. “Although these species can cause many harmful impacts to both ecosystems and humans, we still have a long way to go toward understanding how harmful algal blooms will change with shifting ocean conditions,” Setta notes. By pairing ship-based eDNA sampling with autonomous sensors that track the spring transition, OME is working to determine where HAB species occur, how they respond to warming waters, and what environmental thresholds trigger bloom formation.

Conclusion

eDNA is emerging as an important complement to traditional Arctic observing tools, providing species-level insights into biodiversity, community shifts, and harmful algal blooms throughout the year. By combining ship-based sampling, autonomous samplers, and sea-ice studies, we address three interconnected lines of research: mapping biodiversity and community dynamics, understanding under-ice winter ecosystems, and investigating how ice algal communities influence spring phytoplankton blooms. This integrated, yearround approach provides a high-resolution view of the Arctic, helping scientists anticipate which species may persist or decline, understand how warming waters reshape ecosystem structure, and deliver early warnings of emerging HAB events. Working alongside other research groups, OME is building the predictive tools needed to study, manage, and protect one of the fastest-changing marine ecosystems on Earth.