A warming climate could decimate mollusk populations in the Western Atlantic
Mollusks are critical to marine ecosystems, but face risks as their environment experiences the impacts of climate change
Geological Society of America
Contributed by Rudy Molinek, GSA Science Communication Fellow
Boulder, Colo., USA: The consequences of a warming climate are known to be dangerous for marine ecosystems, with environmental changes like ocean acidification and warming, disrupted nutrient supplies, and rising sea levels. For mollusks, important members of marine ecosystems, these changes might spell doom.
According to research presented last week at GSA Connects 2025 in San Antonio, Texas, modelling of environmental change under scenarios of warming climate indicates that mollusks in the western Atlantic Ocean along the coast of North America could face greater than 60% reductions in their range. Surprisingly, the projected losses apply across mollusk species, independent of their physical characteristics or ecological adaptations.
“We’re trying to see if species with specific functional traits might survive or do better than others,” says Dr. Claudia Nuñez-Penichet, a postdoctoral researcher at Virginia Tech’s Department of Fish and Wildlife Conservation. “It didn't matter at all. Everything was very bad for all the species that we looked at in the future, especially under more extreme climatic projections with higher carbon emissions.”
Mollusks, like clams, oysters, and snails, are critical to marine ecosystems. Filter-feeding mollusks like clams and oysters help maintain water quality and control algal blooms. In addition to their biological roles, mollusk shells help shore up the substrate, and features like oyster reefs can provide habitats for many other species. The impacts of a mass loss of mollusks in a region would ripple up and down the food web.
Nuñez-Penichet’s model identifies factors like surface water temperature, acidity, and current velocity in a mollusk species’ modern range, and locates where similar conditions are expected to occur in the future. Then, the researchers explore possible changes of species’ distributions under environmental conditions in different carbon emission scenarios to forecast what might happen to the mollusks in the future.
These types of models don’t capture all the possible factors contributing to species’ survival, like migration, biotic interactions, or sea-level rise, and so the real-world impact of a changing environment might be different than predicted. But this work will help conservationists determine where to direct efforts to promote resilience in coastal marine communities.
“In the case of marine mollusk species, we are showing which areas might be more susceptible” to risk of extinction, says Nuñez-Penichet.
Going forward, Nuñez-Penichet and her collaborators hope to expand their study from 57 mollusk species to more than 200. Additionally, they aim to apply their model to paleontological data to see how past environmental changes shaped current marine ecosystems.
Despite the dire outlook they see in their model, Nuñez-Penichet sees signs of hope. The rates of mollusk loss predicted for the year 2050 in a more extreme carbon emission scenario are similar to those predicted in 2100 under a more moderate scenario. This means that human actions to limit the burning of fossil fuels could prevent the worst impacts on mollusks and the marine ecosystems they support.
“We can make a difference,” Nuñez-Penichet says, “if we actually care.”
Integrating Functional Traits and Ecological Niche Modeling to Assess the Vulnerability of Mollusk Species to Climate Change
Corresponding Author: Claudia Nuñez-Penichet, Virginia Tech, claudianunez@vt.edu
98: T151, Linking Biodiversity Loss to Environmental Stressors Through Integrated Approaches
Geological Society of America
Contributed by Rudy Molinek, GSA Science Communication Fellow
Boulder, Colo., USA: The consequences of a warming climate are known to be dangerous for marine ecosystems, with environmental changes like ocean acidification and warming, disrupted nutrient supplies, and rising sea levels. For mollusks, important members of marine ecosystems, these changes might spell doom.
According to research presented last week at GSA Connects 2025 in San Antonio, Texas, modelling of environmental change under scenarios of warming climate indicates that mollusks in the western Atlantic Ocean along the coast of North America could face greater than 60% reductions in their range. Surprisingly, the projected losses apply across mollusk species, independent of their physical characteristics or ecological adaptations.
“We’re trying to see if species with specific functional traits might survive or do better than others,” says Dr. Claudia Nuñez-Penichet, a postdoctoral researcher at Virginia Tech’s Department of Fish and Wildlife Conservation. “It didn't matter at all. Everything was very bad for all the species that we looked at in the future, especially under more extreme climatic projections with higher carbon emissions.”
Mollusks, like clams, oysters, and snails, are critical to marine ecosystems. Filter-feeding mollusks like clams and oysters help maintain water quality and control algal blooms. In addition to their biological roles, mollusk shells help shore up the substrate, and features like oyster reefs can provide habitats for many other species. The impacts of a mass loss of mollusks in a region would ripple up and down the food web.
Nuñez-Penichet’s model identifies factors like surface water temperature, acidity, and current velocity in a mollusk species’ modern range, and locates where similar conditions are expected to occur in the future. Then, the researchers explore possible changes of species’ distributions under environmental conditions in different carbon emission scenarios to forecast what might happen to the mollusks in the future.
These types of models don’t capture all the possible factors contributing to species’ survival, like migration, biotic interactions, or sea-level rise, and so the real-world impact of a changing environment might be different than predicted. But this work will help conservationists determine where to direct efforts to promote resilience in coastal marine communities.
“In the case of marine mollusk species, we are showing which areas might be more susceptible” to risk of extinction, says Nuñez-Penichet.
Going forward, Nuñez-Penichet and her collaborators hope to expand their study from 57 mollusk species to more than 200. Additionally, they aim to apply their model to paleontological data to see how past environmental changes shaped current marine ecosystems.
Despite the dire outlook they see in their model, Nuñez-Penichet sees signs of hope. The rates of mollusk loss predicted for the year 2050 in a more extreme carbon emission scenario are similar to those predicted in 2100 under a more moderate scenario. This means that human actions to limit the burning of fossil fuels could prevent the worst impacts on mollusks and the marine ecosystems they support.
“We can make a difference,” Nuñez-Penichet says, “if we actually care.”
Integrating Functional Traits and Ecological Niche Modeling to Assess the Vulnerability of Mollusk Species to Climate Change
Corresponding Author: Claudia Nuñez-Penichet, Virginia Tech, claudianunez@vt.edu
98: T151, Linking Biodiversity Loss to Environmental Stressors Through Integrated Approaches
About the Geological Society of America
The Geological Society of America (GSA) is a global professional society with more than 17,000 members across over 100 countries. As a leading voice for the geosciences, GSA advances the understanding of Earth's dynamic processes and fosters collaboration among scientists, educators, and policymakers. GSA publishes Geology, the top-ranked geoscience journal, along with a diverse portfolio of scholarly journals, books, and conference proceedings—several of which rank among Amazon's top 100 best-selling geology titles.
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The Geological Society of America (GSA) is a global professional society with more than 17,000 members across over 100 countries. As a leading voice for the geosciences, GSA advances the understanding of Earth's dynamic processes and fosters collaboration among scientists, educators, and policymakers. GSA publishes Geology, the top-ranked geoscience journal, along with a diverse portfolio of scholarly journals, books, and conference proceedings—several of which rank among Amazon's top 100 best-selling geology titles.
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DOI
Researchers in Japan discover new jellyfish species deserving of a samurai warrior name
Advanced Institute for Marine Ecosystem Change (AIMEC)
image:
A new species: Physalia mikazuki.
view moreCredit: ©Tohoku University
A student-led research group from Tohoku University has discovered a new species of the venomous Physalia (commonly known as Portuguese man-of-war) that has never been seen before in northeast Japan. This revelation suggests that warming coastal waters and shifting ocean currents are influencing the distribution of marine organisms in northeastern Japan.
The study, published in Frontiers in Marine Science (Marine Molecular Biology and Ecology) on October 30, 2025, presents the first formal description of a Physalia species from Japan.
"I was working on a completely different research project around Sendai Bay in the Tohoku region, when I came across this unique jellyfish I had never seen around here before," remarks second author Yoshiki Ochiai. "So I scooped it up, put it in a ziplock bag, hopped on my scooter, and brought it back to the lab!"
The curiosity sparked by this eye-catching cobalt blue creature is what lead to this remarkable discovery of a new species of Physalia. Professor Cheryl Ames of the Graduate School of Agricultural Science and the Advanced Institute for Marine Ecosystem Change (WPI-AIMEC), stated that the species was named Physalia mikazuki ("crescent helmet man-o-war") in recognition of Sendai's feudal lord Date Masamune, a samurai warrior who is known for the crescent moon adorning his helmet.
"It was a very involved process recording all the unique body structures that distinguish it from the other four species of Physalia," says first author Chanikarn Yongstar, "I looked at each individual part, comparing its appearance to old tomes where scholars drew out the jellyfish anatomy by hand. A real challenge when you look at just how many tangled parts it has."
In Japan, Physalia utriculus is found from Okinawa to Sagami Bay. It was previously assumed this was the only jellyfish of that genus in the area, but through matching DNA sequences to public reference databases, this study revealed that its distribution overlaps with the newly described P. mikazuki. In other words, there were always two species in that area - but no one noticed until it showed up in the Tohoku region.
"Our morphological and DNA analyses confirmed that these specimens represent a new species, distinct from its tropical relatives," says Kei Chloe Tan, who did the DNA analysis, "Which is an exciting finding in and of itself, but we still had questions about how it got here."
The sighting in the Tohoku region represents the first record of Physalia being spotted this far north. To answer their questions about how it drifted so far, they ran computer simulations of how objects are carried by ocean surface currents. The results suggest that warm water from the Kuroshio Current, which has recently extended much farther north along with high sea-surface temperature anomalies, may have transported the colonies to Sendai Bay. This finding provides new insight into how marine ecosystem changes can influence the movement of surface-drifting marine organisms.
"I ran a particle simulation - which is like dropping bright red beach balls in the water, then making data-based estimations to track where they will end up days or months later," explains Muhammad Izzat Nugraha, "We were excited to find that in our simulation, all the beach balls essentially made a trail from Sagami Bay up to right where we found the "crescent helmet man-o-war" in the Tohoku region."
The discovery also highlights the importance of coastal observation and public awareness. With tentacles that can extend several metres and cause painful and debilitating stings, continued monitoring can help keep beachgoers safe while also improving our ecological understanding.
"These jellyfish are dangerous and perhaps a bit scary to some, but also beautiful creatures that are deserving of continued research and classification efforts," adds Ayane Totsu.
This research was made possible through funding from WPI-AIMEC (Advanced Institute for Marine Ecosystem Change) and the paper was made open access thanks to the APC Support Project for the Promotion of Open Access at Tohoku University in 2025.
Journal
Frontiers in Marine Science
Article Title
Researchers in Japan Discover New Jellyfish Species Deserving of a Samurai Warrior Name
Article Publication Date
30-Oct-2025
Gamo Beach in Sendai Bay, Miyagi Prefecture, where Physalia mikazuki sp. nov. was first discovered in July 2024. Several colonies of the Portuguese man-of-war were stranded along the shoreline following warm current activity linked to the northward shift of the Kuroshio Current.
Credit
©Tohoku University / Ochiai Yoshiki
Physalia mikazuki sp. nov., a newly described Portuguese man-of-war collected from Gamo Beach, Sendai Bay. The gas-filled float and long trailing tentacles are characteristic of the Portuguese man-of-war. Runner-up names with a similar Sendai-oriented cultural flare included Physalia: zunda shake, blue dragon, and one-eyed dragon.
Credit
© Tohoku University / Cheryl Lewis Ames et al.
Physalia mikazuki sp. nov., a newly described Portuguese man-of-war filmed alive from Sendai Bay, Japan. The footage shows distinct clusters of zooids (feeding, reproductive, and defensive units) arranged beneath the translucent, crescent-shaped float. Their coordinated motion highlights the colony's intricate organization characteristic of the genus Physalia.
Credit
© Tohoku University
National TRAP Program targets ghostly issue with second round of coastal clean up funding
The second round of programmatic funding awarded by William & Mary’s Batten School & VIMS totals $1.8M in support of 13 projects focused on removing derelict fishing gear from U.S. coastal waters.
image:
Crew members recover a ghost trap from the Chesapeake Bay.
view moreCredit: Jordan Salafie, Oyster Recovery Partnership
Lurking in the waters along our shorelines, a haunting presence is luring marine life to their untimely demise and trapping their spirits in an underwater purgatory. This isn’t the plot of a new Halloween blockbuster, it’s the unfortunate impact of derelict fishing equipment commonly known as “ghost traps.”
William & Mary’s Batten School of Coastal & Marine Sciences & VIMS has awarded $1.8 million to 13 organizations throughout the U.S. focused on the removal of derelict fishing gear, which poses a significant threat to the sustainability of coastal and marine environments and the fishing industries from which they originate. This is the second year of subawards distributed through the National Fishing Trap Removal, Assessment and Prevention (TRAP) Program.
A scientific solution for a ghoulish problem
In the United States, commercial trap fisheries generate over $1 billion in annual revenue from seafood sales, referred to as landings. Each year, traps are lost due to vessel-gear interactions, storms and gear degradation. These “ghost traps” become inaccessible to fishermen but continue to function, resulting in mortality of both target and non-target species, habitat damage and reduced fishery landings. A 2016 report found that removing just 10% of derelict crab pots and lobster traps could result in an additional $831 million in global landings annually.
In 2023, the Batten School & VIMS was the recipient of an $8 million, four-year grant from the National Oceanic and Atmospheric Administration’s (NOAA) Marine Debris Program to administer the National TRAP Program. In addition to distributing approximately $1.5 million annually to fund regional cleanup efforts, the program has established a standardized national database to evaluate the environmental and economic benefits of the removal efforts and to inform future policies.
In its first year of funding, the TRAP Program awarded over $1.4 million to fund 11 projects. So far, the efforts have resulted in the removal of over 7,000 derelict traps totaling more than 300,000 pounds of debris. A number of projects are still recovering derelict traps, and removals in Louisiana are set to begin in February. Many other regional success stories have surfaced from these efforts.
“We are thrilled with the initial results from our inaugural TRAP Program recipients. Their success is a testament to the impact that locally-designed solutions can have on global issues,” said Kirk Havens, director of the Batten School & VIMS Center for Coastal Resources Management, which administers the TRAP Program under the direction of co-principal investigators Professor Donna Bilkovic and Associate Professor Andrew Scheld. “Our second round of recipients have demonstrated that same creativity, thoughtfulness and local community engagement in their project proposals, and we are proud to support them as they work for the benefit of their communities and marine ecosystems.”
This year, $1.8 million in grant funding will be distributed across 13 projects in Maine, Massachusetts, Rhode Island, New Jersey, Maryland, South Carolina, Florida, Washington and California. Recipients anticipate the removal of over 8,000 ghost traps and the creation of 195 jobs, mostly for commercial fishers.
Funding recipients will begin their cleanup efforts in January 2026 and will be required to submit standardized data on their progress. The data will be analyzed by the Policy Innovation Lab, a partnership between the Batten School & VIMS and the Carl Vinson Institute of Government at the University of Georgia, to explore drivers of derelict trap abundance, bycatch, and other ecological or economic variables. This information will help inform state and federal policy recommendations to improve derelict trap prevention and mitigation.
Visit the National TRAP Program website for additional information and statistics from first-round projects.
Who you gonna call? Ghost (trap) Busters!
The following projects were selected for funding through a national competitive grant process administered by the Batten School & VIMS:
- Hill Fisheries LTD received $148,622 to remove abandoned and derelict lobster traps in the Cape Ann area and its surrounding islands in Massachusetts. Removal of ghost fishing gear addresses a contributing factor to recent declines in the lobster catch rate. The derelict gear also poses an entanglement risk to marine species, including the endangered North Atlantic right whale.
- University of California, Santa Barbara was awarded $116,433 to identify and remove lost spiny lobster traps from ecologically-sensitive areas in the Channel Islands National Marine Sanctuary. Removal efforts will be undertaken alongside collaborators in the National Park Service and the recreational dive industry. Lost traps will be identified and marked through SCUBA surveys and then removed. Data will be collected to inform fishery management practices and recovered traps will be returned to local fishers.
- A total of $125,493 was awarded to the South Carolina Department of Natural Resources to address ghost traps in four estuarine areas of South Carolina - Calibogue Sound, ACE Basin National Estuarine Research Reserve, and the urbanized watersheds of Charleston and Cape Romain. This effort will comprehensively map 64 square kilometers of major waterways within the estuaries to identify and remove derelict traps.
- Ocean Aid 360 was awarded $150,000 to mobilize commercial fishers alongside dedicated trap data collectors, volunteer coastal residents, and local watershed groups to detect and remove derelict traps. This intervention will include a robust pre-event survey and post-removal monitoring component to measure natural resources and economic benefits of the removal efforts.
- The Commercial Fisheries Research Foundation received $133,172 to remove ghost traps in Narragansett Bay target areas utilizing side-scan sonar equipment. By combining the survey results with those conducted in 2023 and 2025, the project team will estimate the rate and location of reaccumulating derelict traps in the Bay to inform removal activities.
- The Tolowa Dee-ni’ Nation was awarded $140,448 to remove derelict crab traps from the coastal beaches and nearshore waters of Taa-laa-waa-dvn in the Pacific Northwest, restoring marine and intertidal habitats critical to native species. Tolowa Dee-ni’ Nation staff will coordinate on trap removal, repurposing or recycling material when possible.
- Oyster Recovery Partnership was granted $147,571 to remove derelict blue crab traps from Anne Arundel County waters in the Chesapeake Bay using side-scan sonar imagery. The project team will target high-density zones near the mouths of the Severn, South and Rhode Rivers. By engaging local watermen, the project will provide off-season income and opportunities to recycle and reuse commercial gear.
- A total of $149,168 was awarded to Rutgers University to remove derelict crab traps and pilot recycling and prevention strategies from New Jersey waters within the Delaware Bay and in partnership with Stockton University. Side-scan sonar will be used to locate derelict traps in three focus areas and in collaboration with commercial crabbers. Funds generated from the recycling of recovered traps will be reinvested to further support prevention strategies.
- The Northwest Straits Foundation was awarded $150,000 to conduct a crab trap removal and prevention project in the Olympic Peninsula’s Port Angeles Harbor and Sequim Bay. Removal operations intend to clear approximately 3,980 acres of marine debris. Results of the project will be presented to the community and used to inform the outreach activities of local organizations.
- OceansWide received $135,751 to locate, characterize, and remove abandoned, lost, or otherwise discarded fishing gear in Midcoast Maine. They will focus on large aggregations of lobster traps known colloquially as “gear balls,” using a specialized grapple that will be fabricated for the project. OceansWide will work with lobster fishermen to locate high-priority gear balls that pose the biggest risk to fishing and navigation in the Midcoast Maine region.
- The City of Beverly, Massachusetts received $124,700 to support the removal of derelict lobster traps from Beverly Harbor using SCUBA-based recovery methods. Operations will be led by the Beverly Harbormaster Department in partnership with a coalition of regional stakeholders, including commercial fishermen, environmental organizations, and local dive professionals.
- The National Marine Sanctuary Foundation was awarded $146,553 to remove derelict traps from the coastal waterways of the Florida Keys National Marine Sanctuary. Surveys will be conducted to locate and remove traps using SCUBA-based methods that allow for the extraction of traps otherwise inaccessible from the surface. Data collected will support informed decision-making of critical marine habitat.
- The Gulf of Maine Lobster Foundation received $149,980 to utilize experiential knowledge and existing resources of rural Maine fishermen to target, remove, document and synthesize data surrounding the loss and impacts of derelict fishery gear in rural Maine waterways. Mapping of qualitative and quantitative data will highlight the cost and time efficiency of gear removal by active fishermen.
Blue crabs recovered from a ghost trap in the Chesapeake Bay.
Credit
John Wallace, William & Mary’s Batten School & VIMS
Divers utilize lift bags to extract ghost traps from the Florida Keys National Marine Sanctuary that are otherwise inaccessible from the surface.
Credit
National Marine Sanctuary Foundation
Global call to “Help the Kelp” with US $14 billion conservation target
An international team is calling for a US $14 billion investment to protect and restore one of the planet’s most valuable and overlooked marine ecosystems, kelp forests.
University of New South Wales
Published by UNSW researchers and the Kelp Forest Alliance, the research establishes a clear financial benchmark for global kelp conservation.
The funding is needed to achieve the Kelp Forest Challenge, a global mission to protect three million hectares and restore one million hectares of kelp forests by 2040.
Kelp forests fringe nearly a third of the world’s coastlines, sheltering fisheries, absorbing carbon, and supporting biodiversity worth an estimated US $500 billion per year.
Yet as much 60% of global kelp forests have declined over the past half-century due to ocean warming, pollution, and overgrazing by sea urchins.
The $14 billion target was developed through expert consultation workshops, a review of the costs of marine conservation, and benchmarks kelp forests alongside initiatives in global mangrove and coral reef conservation.
The target represents a middle-ground scenario — “ambitious but achievable” — and helps align kelp conservation with the UN Climate Champion’s “Ocean Breakthrough’s Initiative.
Lead author Dr Aaron Eger says establishing a tangible funding goal is essential for mobilising action and tracking progress.
“Kelp forests are truly the fabric of our cold-water seas, but they’ve long been invisible in national and global conservation finance.
“It varies year to year but for every dollar invested in kelp conservation in Australia, our country invests 10-100 dollars for coral reefs. This mismatch is despite the fact that 2/3rds of Australians live right next door to a kelp forest.
“Setting a clear target sets the agenda and really stresses the fact that we cannot do this alone. We need everyone in society to pitch in and meet this goal.”
If realised, the investment would secure kelp forests for future generations—protecting biodiversity, stabilising coastlines, and sustaining livelihoods from Tasmania to Norway to California.
Journal
Biological Conservation
Method of Research
Content analysis
Subject of Research
Animals
Article Title
Creating a global kelp forest conservation fundraising target: A 14-billion-dollar investment to “help the kelp”
Article Publication Date
26-Oct-2025
Expansion microscopy helps chart the planktonic universe
A new study provides unprecedented insights into the cellular architecture of over 200 species of plankton, using a technique called ultrastructure expansion microscopy
European Molecular Biology Laboratory
image:
Expansion microscopy image of Lacrymaria, a ciliated eukaryotic microorganism, collected from environmental samples in Tokyo. Highlighted in green is tubulin, the major protein component of microtubules, a cytoskeletal filament (scale bar represents 5 microns).
view moreCredit: Felix Mikus/EMBL
Plankton are the invisible engines of life on Earth, producing much of the planet’s oxygen and forming the foundation of the oceanic food chain. They are also incredibly diverse, with tens of thousands of species described so far, and many more waiting to be discovered. Among them, protists, tiny, single-celled organisms, stand out for their extraordinary diversity and evolutionary significance, yet for decades, scientists could study them only through genomic data, as reliable imaging methods were lacking.
During the COVID-19 pandemic, EMBL Group Leader Gautam Dey received a Zoom call from his collaborator Omaya Dudin, then leading a group at EPFL. Dudin had just adapted a new technique to visualise the internal architecture of Ichthyosporea — a marine protist closely related to animals and fungi — overcoming the long-standing barrier of its impermeable cell walls. The new technique called expansion microscopy, first developed by scientists at MIT, USA, and further optimised into ultrastructure expansion microscopy (U-ExM) for exploring sub-cellular ultrastructure by Paul Guichard and Virginie Hamel at the University of Geneva, had made the cell wall permeable, and the protist's inner structures could now be clearly visualised and studied.
Determined to study more marine organisms with this method, Dudin, Dey, Guichard and Hamel started a cooperation that, three years later, has succeeded in generating almost encyclopedic knowledge of hundreds of protist species and is on its path to creating a planetary atlas of plankton.
The EMBL-led Traversing European Coastlines (TREC) expedition was a great opportunity for the researchers to dive deeper into the internal structures of different marine microbes. Recently published in Cell, their collaboration has yielded unprecedented and in-depth insights into the cellular architecture of over 200 plankton species, in particular eukaryotes – organisms that have a cell nucleus enclosed by a membrane. This was the first step in PlanExM, a TREC plug-in project which aims to reveal the world of planktonic ultrastructural diversity with expansion microscopy.
Unveiling cellular secrets with ultrastructure expansion microscopy
At Roscoff, France, one of the TREC expedition's first prominent sampling stops, the Station Biologique hosts one of the most complete culture collections of marine microorganisms in Europe. The team asked Ian Probert, the facility's manager, how many samples they might receive to run an expansion microscopy pilot – expecting about 20 species – only to find the doors of the full facility, with over 200 species, being opened to them.
"We spent three days and nights just fixing those samples. This was a treasure trove we could not let go of," said co-first author Felix Mikus, who completed his PhD from the Dey Group and is now a postdoc in Dudin’s current lab at the University of Geneva.
Expansion microscopy, a relatively young technique only turning 10 years old this year, works by physically 'expanding' biological samples. The sample – which can contain single-celled organisms, cells, or tissues – is first embedded in a clear gel. Then, the gel is allowed to expand by absorbing water. Marvellously, many of the cell's internal structures remain intact during the process and expand more or less proportionally, allowing scientists to 'magnify' the sample four or even 16 times without needing to resort to lenses.
“When combined with regular light microscopy methods, expansion microscopy allows scientists to bypass the standard wavelength barriers which limit how small a structure can be resolved using light microscopy,” said Guichard and Hamel.
Using the Roscoff samples, as well as a second culture collection from Bilbao, Spain, the researchers went on to perform one of the most extensive investigations to date of diversity of the cytoskeleton – the filamentous network that forms the underlying structure of eukaryotic cells. In particular, researchers looked at microtubules – hollow, tubular filaments that help the cell maintain its structure, divide, and move, and centrins – a family of proteins found in the structures that organise microtubules inside cells.
“We were able to map features of microtubule and centrin organisation across many different eukaryotic groups,” said Hiral Shah, EIPOD Postdoctoral Fellow in EMBL's Dey and Schwab groups and co-first author of the study. “The scale of the study, with many species characterised in each group, opens up the possibility to make evolutionary predictions. For instance, dinoflagellates, one of the most diverse groups found in oceans across the planet, are well-represented in our study. We were able to map the presence of tubulin and centrin structures associated with the cell cortex or the flagella in these species.”
“U-ExM is transforming how we explore protist ultrastructure,” said Armando Rubio Ramos, co-first author of the study and Postdoctoral Fellow at Hamel & Guichard’s research group at the University of Geneva. “By combining this technique with high-throughput imaging and comparative analyses, we can begin to decode how cellular architecture has diversified across evolution. It’s a bridge between molecular data and the physical organisation of life at the microscopic scale.”
According to the researchers, this analysis not only helps us understand the fundamental principles that underlie the organisation of a eukaryotic cell, it also offers clues to the evolutionary history of the cytoskeleton architecture in these species. Moreover, it demonstrates the potential of expansion microscopy as a powerful tool for studying complex samples, including those collected directly from marine ecosystems.
“Our adventures with expansion microscopy are only beginning,” said Dey. “This is perhaps the first high-resolution microscopy technique that has the potential to match the scale and ambition of large biodiversity genomics projects, enabling us in the near future to associate new multiomics data with cellular physiology at scale across the tree of life.”
With Thomas Richards from Oxford University joining the team, Dey and Dudin were also successful in obtaining a prestigious Moore Foundation Grant worth CHF 2 million to continue this project.
“The next step is to selectively look deeper into certain species within this broad collection to answer specific questions, such as understanding how mitosis and multicellularity evolved and the phenotypic diversity that underlie major evolutionary transitions,” Dudin said.
Journal
Cell
Method of Research
Experimental study
Subject of Research
Cells
Article Title
Charting the landscape of cytoskeletal diversity in microbial eukaryotes.
Article Publication Date
31-Oct-2025
How climate-damaging nitrous oxide forms in the ocean
University of Basel
image:
To investigate the conversion of nitrate into nitrous oxide in the ocean, hundreds of water samples were taken from various depths using a probe and water samplers. (Photo: Claudia Frey)
view moreCredit: Photo: Claudia Frey
To many people, nitrous oxide, or laughing gas, is only known as a party drug or from the dentist. However, the nitrogenous substance also contributes significantly to global warming. As a greenhouse gas, its effect in the atmosphere is almost three hundred times more powerful than that of CO2, and it also attacks the ozone layer. “The emission of this almost forgotten greenhouse gas is decisive for the global climate,” says Dr. Claudia Frey from the Department of Environmental Sciences at the University of Basel. The biogeochemist has now investigated the conditions under which microorganisms produce nitrous oxide in the ocean.
Since the 19th century, nitrous oxide concentrations in the atmosphere have been steadily increasing, mainly due to human activities, such as the use of fossil fuels and the intensification of agriculture. For example, fertilizer contains a lot of nitrogen, which then ends up in rivers, lakes and oceans in the form of nitrate. There, bacteria convert the nitrogenous substances into food and energy. This process also produces nitrous oxide, which then escapes into the atmosphere.
Focus on hypoxic zones
The processes involved in the production of nitrous oxide in the ocean are complex and only partially understood so far. However, it is known that a particularly high amount of it is released in hypoxic, or low-oxygen, water. This is home to special microbial communities that convert nitrate into nitrous oxide to generate energy. Frey has therefore taken a closer look at the processes that take place in these zones.
The researcher spent six weeks on a research vessel along the coasts of California and Mexico. This is where the largest hypoxic areas of the Pacific are located. She collected hundreds of water samples at different depths and carried out some analyses and experiments while still on board. “Since time on the boat is so precious, we practically worked day and night,” she recalls. In order to preserve the samples in their original condition, they had to be examined without oxygen and in cold rooms – all while the vessel was moving through tropical waters.
Bacterial metabolism works differently than expected
The investigations yielded several surprising results. Until now, it had been assumed that the conversion of nitrate into nitrous oxide only worked at extremely low oxygen concentrations. In her water samples, however, Frey was able to provide proof that the microbes can also do this at much higher oxygen concentrations – namely when a lot of organic material is present in the hypoxic zones in the form of small dead algae, for example.
Another unexpected finding: the bacteria always preferred to go through the entire multi-stage metabolic pathway from nitrate to nitrous oxide. Research had previously thought that the bacteria would switch to a shorter pathway if an intermediate product required for this was provided in the water. The assumption was that the shortcut required less energy. The experiments showed that this is not true.
Frey used the new findings to close gaps in a model for the ecosystem in hypoxic zones. This now takes into account, for example, that the presence of organic material increases the oxygen tolerance of the bacteria. This also increases the number of regions in which nitrous oxide production is possible.
“When it comes to climate predictions, it is crucial to understand what happens in these peripheral zones,” says Frey. Especially as people continue to add more and more nitrogen to water bodies. “What happens in the oceans is relevant to us, because they cover two-thirds of our planet.”
Journal
Nature Communications
Subject of Research
Not applicable
Article Title
Mechanistic understanding of nitrate reduction as the dominant production pathway of nitrous oxide in marine oxygen minimum zones
Article Publication Date
27-Oct-2025
Unprecedented decline in marine viruses in the western Mediterranean linked to climate change revealed
Details are included in a recently published scientific article, based on the Blanes Bay Observatory time series, the longest known record of marine viruses
Spanish National Research Council (CSIC)
image:
The results show that since 2011 the abundance of viruses in seawater has continuously decreased
view moreCredit: ICM-CSIC.
A team led by the Institut de Ciències del Mar (ICM-CSIC) has described a sustained and unprecedented decrease in the abundance of marine viruses in the northwestern Mediterranean over the last two decades. The finding, published in the journal ISME Communications, is based on the longest-known time series data on marine viruses to date, from the Blanes Bay Microbial Observatory (BBMO) in Girona.
The results show that since 2011, the abundance of viruses in seawater has continuously decreased, coinciding with a progressive increase in water temperature and transparency, along with a significant reduction in nutrients and phytoplankton biomass. These changes reflect an oligotrophication process – meaning an impoverishment in nutrients – which transforms the marine ecosystem into a more pristine and less altered environment.
“What we observe is a clear signal that global change, and especially climate change, is reconfiguring even the most minute microbial communities—those invisible to the human eye but essential for the functioning of the oceans,” explains Xabier López-Alforja, lead author of the study. “Marine viruses fulfill critical roles in ecosystems: they regulate microbial populations, recycle nutrients, and can favor the transport of carbon to the ocean floor, a key process in global climate regulation.”
A unique observatory
The work relies on the data series generated by the Blanes Bay Microbial Observatory, where monthly surface water samples have been collected since 2001. This continuous effort spanning over two decades makes the BBMO a unique observatory worldwide for studying long-term microbial dynamics.
The research utilized advanced statistical tools, such as Generalized Additive Mixed Models (GAMMs), which allowed the team to model and understand the marked seasonal variability of both microorganisms and different environmental variables in this part of the Mediterranean. Additionally, the scientific team applied artificial intelligence techniques—specifically, neural network models—to unravel the complex interactions between viruses and their environment.
“Thanks to the combination of advanced statistics and machine learning, we’ve been able to see beyond immediate variability and recognize hidden patterns that indicate how viruses respond to warming and nutrient loss,” details López-Alforja.
Ecological and social implications
The decline in the abundance of marine viruses could have significant consequences for ecosystems and for society. By altering the control of microbial populations and the efficiency of nutrient recycling, these changes can accelerate the decrease in marine productivity and affect the stability of the food web.
“If viruses decrease, the way nutrients circulate in the ocean is also modified,” adds Dolors Vaqué, an ICM researcher. “That can affect not only the balance of coastal ecosystems but also human activities like fishing, upon which entire societies in the Mediterranean depend.”
Until now, most studies on marine viruses were conducted along spatial gradients or in very short time series, usually less than two years. The lack of long-term data made it difficult to clearly evaluate the effects of global change on these organisms.
“Our research raises questions about how this effect on viral communities translates to those of other microorganisms and to biogeochemical cycles,” comments Felipe Coutinho. “Only with long time series can we distinguish natural fluctuations from trends induced by climate change. And in this case, the signal is unequivocal: viruses are decreasing in parallel with the oligotrophication of the Mediterranean.”
Towards new research avenues
The study is the result of a collective effort among various ICM-CSIC researchers who keep the Blanes Bay Observatory operational. The research team is now working on sequencing and analyzing the genetic material of the viruses collected over these years to determine if the loss of abundance is also reflected in changes in the genetic diversity of viral communities.
They also assert that the consistency with analyses from other studies based on shorter time series in the region confirms a generalized trend across the entire Mediterranean basin.
CSIC Comunicación
comunicacion@csic.es
Journal
ISME Communications
Method of Research
News article
Subject of Research
Not applicable
Article Title
Long-term decline of marine viruses associated with warming and oligotrophication at a NW Mediterranean coastal site
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