Research

Inside the Stable Isotope Lab: unravelling Earth’s mysteries through water, ice and air

Gabe Allen — Wed, 13 May 2026 20:00:00 +0000

Inside the Stable Isotope Lab: unravelling Earth’s mysteries through water, ice and air Gabe Allen Wed, 05/13/2026 - 14:00

Marrissa Grunes

Marissa Grunes is a freelance science writer and Lecturer in the Herbst Program for Engineering, Ethics and Society at CU �鶹ӰԺ. Every semester, she takes first-year Engineering students on a tour of INSTAAR’s Stable Isotope Laboratory to look at ice cores.

Bruce Vaughn gives local middle schoolers a primer on ice core science in the Stable Isotope Lab's walk-in freezer in 2025. (Gabe Allen)

“This would be a warm day in Greenland,” Bruce Vaughn tells us as we crowd into the walk-in freezer at the back of the Stable Isotope Laboratory. Some of the students have heeded warnings to dress warmly. A few brave souls arrived in shorts. All of us discover that -25°C (-13°F) gets cold fast.

Vaughn, one of the lab’s founders, holds a thick cylinder of ice up to the light. It’s about the size of a Nalgene bottle and perfectly clear. Such cores come from deep in the permanent ice sheets of Greenland and Antarctica, where trapped air bubbles are locked in the ice for hundreds of thousands of years. If you popped a chunk in your mouth, the air bubbles would fizz on your tongue as they escaped. You might be breathing the same air as a woolly mammoth or saber-tooth tiger.

Since 1989, the Stable Isotope Laboratory (SIL) has been one of the flagship laboratories for CU’s Institute of Arctic and Alpine Research (INSTAAR), which is celebrating its 75th anniversary this year. The lab supports cutting-edge climate research using custom-made technology, but don’t let its technical-sounding name fool you, the team has a blast doing it. Vaughn’s motto? “No one said it couldn't be fun.”

The chemistry of stable isotopes offers a powerful tool for learning about our world. Carbon dating — used to determine the age of the ancient Dead Sea Scrolls — is probably the most well-known example of isotopes at work. But isotope ratios can record everything from ocean and air temperatures to the sources of greenhouse gases in our atmosphere. Forensic technicians use isotopes, too: isotope ratios can tell them whether olive oil is really from Italy, whether the steroids in an athlete’s blood are natural or synthetic, and even where a person has spent the last three months of their life.

At the SIL, isotopic ratios are used primarily to study two things: ice cores and greenhouse gases. Ice cores tell us about the past atmosphere, while the greenhouse gas research can help establish the sources of warming in our world today. The SIL’s ability to investigate these variables at high levels of precision has made the lab a powerhouse in climate science. “Water and air,” says Vaughn — these are the lab’s bread and butter.

Tracing Water

How do isotopes work? Let’s take a trip back to high school chemistry class. Every element in the universe has a unique number of positively charged protons in its atomic nucleus. However, the number of neutrons can vary. An oxygen atom, for instance, will always have 8 protons, but may have 8 or 10 neutrons. The resulting atoms are the same in all ways but one: the oxygen-16 isotope will weigh slightly less than the oxygen-18 isotope.

Those extra neutrons might seem unimportant. After all, how heavy is an atom, really? But many natural processes filter molecules by their weights. Imagine you’re a “light” oxygen isotope within a drop of seawater in Monterrey Bay, California. It’s a hot day, so you evaporate and become part of a cloud. As you move northwest on jet stream winds, the air gets colder and rain droplets form around you. The heavier isotopes — water whose hydrogen or oxygen atoms have more neutrons — fall to earth first, while you are left in the cloud.

As your cloud hits the Rocky Mountains, even more heavy companions fall away (heavier isotopes have a harder time staying gaseous at higher elevations). By the time you reach �鶹ӰԺ, the population of water molecules in your cloud has undergone a noticeable shift toward lighter isotopes.

When you finally precipitate down to Earth as rain or snow, researchers can use the ratio of O-16 to O-18 isotopes to reconstruct your voyage, all the way back to the temperature of Monterrey Bay when you evaporated.

Valerie Morris loads an ice core sample into a carousel in the stable isotope lab at INSTAAR. The carousel is the front end of a continuous flow analysis system developed by Morris and Bruce Vaughn, which continuously measures isotopic ratios for hydrogen and oxygen as the ice core melts. (Gabe Allen)

Ice cores tell us about the travels of water vapor — like our drop from Monterrey Bay — going back hundreds of thousands of years. As snow falls in Greenland or Antarctica, it presses down older snow beneath it. That pressure creates ice, which becomes denser as more snow and ice pile on top of it. These polar regions have remained frozen for a long time, so their ice preserves a continuous chronological record of ancient snow, and the isotopic ratios within reveal past ocean and air temperatures.

To get the information, though, scientists must melt the ice, destroying a slice of the ice core. It takes several years and millions of dollars to drill these cores — the stakes are high.

To make the most of the ice cores examined at the SIL, Vaughn and his longtime colleague Valerie Morris developed a sophisticated system that transformed the way ice is studied. Back in the 1990s, Vaughn explains, researchers looking for oxygen and hydrogen isotopes could only get a single data point every 3-5 centimeters, which might represent hundreds, or even thousands, of years. “You were looking at a blurry vision of the past,” Vaughn says.

When an ice core came back from West Antarctica around 2011, Vaughn and Morris decided to try something new. Working with a Danish team, they overhauled an ice core analysis protocol that was previously considered state-of-the-art. “We took each component in that system, and we were like: How do we optimize this? How do we optimize this? How do we optimize this?” Morris explains.

The new system took several years of trial-and-error, elbow grease, and ingenuity — including finding creative solutions in surprising places, such as “adult” stores. The result was revolutionary. Rather than melting 5-centimeter chunks at a time, Vaughn and Morris’ “continuous flow” system melts the ice slowly, gathering data millimeter by millimeter. With this technological leap, the SIL went from a couple dozen data points per meter to over 2000. The resolution is high enough to see annual summer and winter changes going back thousands of years. “That,” says Vaughn, “was the game changer.”

The “continuous flow” system is such an improvement that the SIL recently secured funding to re-examine an ice core they first studied in the 1990s. According to Brad Markle, a principal investigator at the SIL, the updated technology can enable much finer-grained investigations of temperature and weather patterns over the course of human history. By looking at both oxygen and hydrogen isotope ratios in a core simultaneously, Brad and his colleagues can observe not just overall air temperature, but also temperature differences between the tropics and the poles. Those relationships illuminate how weather patterns change as the planet warms or cools — which can in turn help scientists develop predictive models of global warming.

Counting emissions

Rachel Edie changes gas flasks out on Spock, a mass spectrometer that measures stable isotopes of carbon and oxygen in atmospheric CO2, primarily from the NOAA CMDL Cooperative Air Sampling Network. (Ethan Welty)

A second key to predicting the future of our �鶹ӰԺ climate comes from understanding greenhouse gases. There, too, SIL is a global leader. Since its founding, the SIL has been a go-to lab for one of the largest environmental monitoring programs in the world today: the Global Monitoring Laboratory run by the National Oceanic and Atmospheric Administration (NOAA). Every week, SIL receives air samples collected from over 50 locations on all seven continents. The SIL measures carbon and methane isotope ratios in these samples and provides publicly accessible data to labs around the world — all while making important discoveries of their own.

“We need to understand where these gasses are coming from,” says Sylvia Michel, the SIL’s Laboratory Manager. “Stable isotopes act like a fingerprint.”

In one recent paper, Michel used isotopic ratios to measure the respective contributions of wildfires, fossil fuels, and microbial activity to global methane emissions. As it turns out, the microbes are big contributors.

“The metabolism of these little critters is such that they will take the carbon and spit out methane,” Michel said. Methane traps heat 80 times more efficiently than carbon dioxide over a 20 year period.

As the world warms, microbial activity has been heating up, too. Methane-producing microbes are hard to measure because they’re, well, microscopic. They live wherever oxygen is absent — from melting permafrost to jungles to the intestines of cattle. Supported by the SIL’s data, though, researchers around the world are recognizing microbes’ key role in increasing atmospheric methane concentrations. It’s a new consensus which would not exist without the isotopes.

A few other labs are set up to measure isotope ratios, but, thanks to the NOAA collaboration, the SIL stands out.

“There are probably five labs in the world that measure isotopes of methane,” Michel said. “And we measure by far the most samples.”

The partnership with NOAA also brings stability, which allows the lab to build and retain an impressive roster of researchers with overlapping interests. When people stick around a lab for decades, says postdoctoral fellow Kevin Rozmiarek, “suddenly big things are really possible.”

It helps, adds Markle, that the researchers have “different but related goals.” Ice cores and greenhouse gases can feel distinct, but researchers in both fields benefit from each other’s insight and collaboration. The lab’s founder, Jim White, was passionate about both, and, more than three decades later, the lab still fosters a vibrant and diverse intellectual community.

“I love that about INSTAAR,” Markle said. “Because the point is to bring together people with lots of different interests. [The SIL] is a cool microcosm of what the institute itself is trying to do.”

Alex Rudick, an undergraduate in Aerospace Engineering who traveled to Alaska with the lab, agrees. He joined the team to design and build drone-compatible instruments capable of tracking how water vapor travels over ice sheets.

“The people at SIL are genuinely so passionate about what they do,” he said. “They are people I’d want to be like in the future.”

Science writer Marissa Grunes takes readers on tour through the diverse research and operations of the Stable Isotope Lab. The lab processes samples from all over the world — revealing new details about Earth’s climate.

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Freshly-drilled ice cores are stored in the ice cave, where they await processing and analysis. Photo courtesy of Tyler Jones.

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Trip report: investigating the biological impact of hurricanes in the Gulf of Mexico

Gabe Allen — Mon, 04 May 2026 17:48:48 +0000

Trip report: investigating the biological impact of hurricanes in the Gulf of Mexico Gabe Allen Mon, 05/04/2026 - 11:48

Gabe Allen

In the spring of 2021, Shaily Rahman embarked from Cocodrie, Louisiana aboard the US Research Vessel Pelican bound for study sites near the Mississippi River Delta in the Gulf of Mexico. Her goal was a one-off trip to collect sediment samples over 2 days at sea. But just two weeks after her return, Hurricane Ida roared into the gulf with such force that it briefly reversed the flow of the Mississippi River.

The storm devastated the Louisiana coastline. For Rahman and her students, it also created a scientific opening. Her sampling effort offered a pre-storm baseline that — if combined with subsequent data — could provide insight into how extreme weather affects the Gulf’s nutrient cycles.

Shaily Rahman takes a much-needed moment of respite aboard the RV Pelican, a boat in the US Academic Research Fleet. (Courtesy)

Rahman quickly secured funding through the National Science Foundation to return to the gulf. Since then, she has returned to the delta seven more times. This week, she is back again from another 10-day cruise aboard the Pelican with samples that will keep her lab busy for months.

Rahman’s focus is silicon, the second most abundant element in the Earth’s crust and an essential nutrient for life. Rivers like the Mississippi transport silicon into the ocean, where much of it is incorporated into the skeletons of single-celled plankton called diatoms. When the diatoms die, they sink to the ocean floor.

While the amount of silicon and other nutrients entering the gulf via the Mississippi River is well-understood, Rahman’s research aims to discern what nutrients are released by the seabed.

“How much of that nutrient flux is being recycled into the water column from the seabed and then available to algae?” Rahman posed.

Extreme weather, like Hurricane Ida, further complicates this question — and makes it more interesting. Heavy storms churn up the seabed and suspend sediment in the water. Rahman and her collaborators aim to discern if this disturbance may release a sudden pulse of nutrients before resettling.

“It’s already a hard question to answer, and when you add in hurricanes and extreme weather — that makes it even harder,” she said.

Crew members pose for a group photo aboard the RV Pelican in April, 2026. (Courtesy)

These processes aren’t just theoretical, they have real-world tangible impacts. Diatoms, which rely on silicon, form the basis of the gulf’s marine food web. That food web, in turn, supports commercial fishing and tourism industries that contribute billions of dollars to regional economies each year. Diatoms are also responsible for more than 15% of Earth’s oxygen production

The right balance of silicon, and other nutrients like nitrogen and phosphorus, can support a thriving marine ecosystem with plentiful fish. Yet, the wrong balance can lead to a proliferation of harmful algae that strip the gulf of oxygen leading to massive fish kills — a scenario that played out off the Texas Gulf Coast in 2023.

Rahman’s research questions are among many others aboard the Pelican. One researcher, for instance, is investigating the overlapping effects of the silicon cycle and the carbon cycle — research that could have major implications for future predictions of greenhouse gas warming.

Rahman will also return to �鶹ӰԺ with a cooler full of preserved sediment samples for use in various graduate student research efforts. Collectively, these inquiries will help to demystify how chemicals move through the sediment, water, and air of the Gulf of Mexico. The results could help regional managers predict and mitigate negative outcomes.

“Developing a baseline is good for predictive models,” Rahman said. “Are the fish going to die, or is your food web going to be more productive?”

If you have questions about this story, or would like to reach out to INSTAAR for further comment, you can contact Senior Communications Specialist Gabe Allen at gabriel.allen@colorado.edu.

INSTAAR fellow Shaily Rahman has just returned from her eighth research cruise in the Mississippi River Delta region of the Gulf of Mexico. Sediment samples from the trip will provide insight into the effects of extreme weather on marine food webs.

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Q&A: 39 days at sea, hunting for clues in seawater’s biological detritus

Gabe Allen — Mon, 27 Apr 2026 14:45:00 +0000

Q&A: 39 days at sea, hunting for clues in seawater’s biological detritus Gabe Allen Mon, 04/27/2026 - 08:45

Gabe Allen

Ten months may seem like an excessive amount of time to prepare for a cruise, but it’s not for a scientist.

Julio Sepúlveda and Edgart Flores got notice that there was a last-minute opening aboard the German Research Vessel Sonne this past December. This presented an opportunity to carry out an ambitious research project that had been indefinitely postponed since the COVID-19 pandemic, but it only left them 10 months to prepare before the ship departed from Antofagasta, Chile in October.

“We had to get ready in a relatively short time, but we managed to do it, in large part because of the efforts by the chief scientists and collaborators in Germany and Chile,” Sepúlveda said.

The cruise, on the whole, was organized around investigations of the extremely arid Atacama Desert and the ocean waters that abut it. The Atacama is the driest nonpolar desert in the world, while the nearby ocean is home to a unique ecosystem that flourishes despite extremely low levels of dissolved oxygen.

Sepúlveda and Flores’ mission was at sea. They came to collect biological detritus from vast quantities of seawater in search of a deeper understanding of the ecosystem at a molecular level.

This week, INSTAAR sat down with Sepúlveda to debrief about the cruise, the research, and what comes next.

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One of the projects you were working on during the cruise focused on microbial communities in low-oxygen zones. Can you give us the context?

Yes, so one of the areas we visited, off the coast of northern Chile, right next to the Atacama desert, is characterized by ocean upwelling — water from below is brought up to the surface by local wind and currents. Because of this upwelling, phytoplankton are highly abundant on the surface. When that biomass sinks, it's degraded by microbes, which consume a lot of oxygen. This creates an oxygen-deficient zone. Some people call them dead zones — though that phrase is more often in reference to anthropogenically driven impacts in coastal areas. What we have here occurs naturally in the open ocean.

The problem is that these areas are expanding and becoming more intense because of warming in the ocean. There have been a few studies showing this, and they have also predicted further expansion with global warming. Low oxygen is a big stressor for marine life. So if these areas are becoming larger, that means that the habitat of certain organisms is shrinking.

But these areas are also home to some very unique microbial communities. Unlike other life forms, these organisms don’t rely on oxygen to drive their metabolisms. Instead, they gain energy by breaking down nitrogen-containing compounds into inert nitrogen gas and water. This process removes nitrogen from the ecosystem. So, these microbial communities are very important on a global scale, because they can basically control how much oxygen and nitrogen is available in the ocean.

Julio Sepúlveda logs data at a work station aboard the Sonne. (Courtesy)

What kind of data did you collect on these microbial communities and what questions are you investigating?

We're trying to understand how these communities can adapt to multiple environmental stressors, including ocean warming, ocean acidification, and deoxygenation. How do we do this? We study the fats, or lipids, found in the cell membranes of these organisms. Why? Because organisms are able to change the chemistry of their cell membranes in order to adapt to environmental factors.

Imagine a stick of butter in a cool room, versus a bottle of olive oil. The butter is solid, because it is a saturated fat, while the olive oil is liquid, because it is an unsaturated fat. Organisms that live in warmer waters produce more butter-like fats to keep their cell membranes sturdy, while organisms that live in colder environments produce more olive oil-like fats, to keep their cell membranes flexible. If, all of the sudden, you put an organism that lives in warm waters in the Arctic, it will freeze to death unless it can adjust the ratio of fats it is producing — and the same vice versa.

So, what we do is collect large volumes of sea water at different depths using instruments known as in situ pumps. That allows us to capture a large swath of suspended particles coming from organisms in the ocean. Then we concentrate this material using large filters, freeze it, and bring it to the lab. In the lab, we can study the chemical composition of the entire microbial community at a particular water depth.

This approach is called environmental lipidomics. Basically, we’re able to see all of the fats produced in a given ecosystem. It allows us to do chemical fingerprinting, where we link certain fats back to the organisms that produce them. We also try to figure out which of these chemical signatures are unique to which systems and which signatures represent adaptations to environmental stressors.

Another part of the work we did was to filter smaller volumes of sea water to analyze DNA, which basically allows us to get a better sense of who's there, and look at the genetic potential of certain organisms to produce certain lipids. Finally, we also filtered samples for RNA, which allows us to see which genes are actually being expressed.

So, now we know which lipids are present, which organisms are present, and which genes they are expressing. This allows us to look at how the entire system is adapting to change. Is the makeup of species in the community shifting, or are the existing species genetically equipped to adapt to these changes, for instance? The integration of these genomics techniques with lipidomics is called meta-omics.

Why are these important questions?

If the chemistry of these organisms changes, that influences the quality of the organic matter consumed by all of the organisms in the marine trophic web. If you, for instance, reduce the number of unsaturated fats, that will have huge implications for animals. Animals cannot produce omega-3 and omega-6 fatty acids, we have to get them from eating primary producers like plants and phytoplankton, or from animals that feed on them like fish. So if the composition of phytoplankton changes, that has implications for zooplankton and then fish and eventually all the way up to us. It impacts the nutritional value at the very base of the food web.

This can also have big impacts on fish physiology — fish will struggle if they don't have the right proportion of good fatty acids. It could impact reproduction and potentially even lead to the collapse of some fisheries around the world. Now, this is speculation beyond the current research, obviously, but these are things that we care about, and that's where we study how these ecosystems are changing.

The scientific crew of Expedition SO315 poses aboard the Sonne. (Courtesy)

What’s next?

One of the things that I would love to do in the near future is to team up with some biogeochemical modelers or ecological modelers or climate modelers, people we have in-house, like [INSTAAR director Nicole Lovenduski]. Modelers may be able to put all of this data that we’re parsing into more complex numerical models or statistical analyses that allow us to get a much more quantitative idea of what drives change in these communities —what are the lipids telling us?

The long-term objective is to use some of these chemical signatures as indicators of the status of marine ecosystems. If we can infer which organisms are present, how they are adapting, and which adaptations might occur in response to certain environmental stressors, we might be able to see when and how an ecosystem is experiencing environmental pressure, just from analyzing a water sample.

We may also be able to use these tools to power predictive models of future ecological and chemical changes. It could help us go from models of things like temperature and dissolved oxygen to the future conditions of trophic webs, ocean chemistry, and fisheries. This is really thinking a lot further in time, but I guess those are the kinds of things that get me and others in my group excited about the work we do. We're trying to make stronger connections between what we find and what's really critical for us as humanity to understand.

Lastly, we plan to apply the information gathered from the water column to study changes in microbial processes associated with the expansion of oxygen-deficient zones during glacial-interglacial cycles. Stay tuned.

If you have questions about this story, or would like to reach out to INSTAAR for further comment, you can contact Senior Communications Specialist Gabe Allen at gabriel.allen@colorado.edu.

Julio Sepúlveda and Edgart Flores spent more than a month aboard a German Research Cruise off the coast of Chile last fall. Now, they hope to unlock a new method for inferring ecological health from water samples.

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What does a record-breaking wildfire season mean for life in alpine lakes?

Gabe Allen — Fri, 17 Apr 2026 14:40:35 +0000

What does a record-breaking wildfire season mean for life in alpine lakes? Gabe Allen Fri, 04/17/2026 - 08:40

Gabe Allen

In the summer of 2020, MJ Farruggia embarked on the first field season of her PhD research. With a backpack full of scientific equipment and camping gear, she hiked high into the Emerald Lake Watershed high in the Sierra Nevada Mountains to install environmental sensors and collect water samples from six small lakes and ponds.

A map shows burned areas from the SQF complex fire (2020) and the KNP Complex Fire (2021), as well as the study area for the new investigation from MJ Farruggia and collaborators. (Courtesy)

Then, in August, a dry thunderstorm ignited the forests south of her study area, engulfing the entire region in smoke. At the time, Farruggia was hiking back to the trailhead after a four-day expedition.

“It was one of those apocalyptic-looking days when ash is falling from the sky,” she said.

For months, it was too unsafe to return to the field sites. When the smoke finally lifted, it was clear that Farruggia’s initial research scope would no longer be possible.

“I pulled my sensors at the end of the season and started looking at the data. My first reaction was, ‘whoa, I don’t think we can use this,’” Farruggia said.

Originally, Farruggia planned to investigate how alpine lakes change throughout the year, including how layers of water form and shift. But smoke from the fires had blocked out sunlight, causing an anomalous drop in temperature.

Yet, all was not lost. The unexpected fires created a serendipitous opportunity to study something becoming more and more common in Western alpine ecosystems.

“This study came out of trying to explain what is going on in these little ponds and lakes when the sky is covered in smoke for a really long time,” Farruggia said.

Now, six years later, Farruggia and her collaborators at the University of California, Davis have published the results. The scientists found that, in addition to reducing temperature, smoky skies reduced rates of photosynthesis and respiration. Basically, the ecosystems contained in the lakes and ponds experienced a drop in productivity that rippled throughout the food chain — from single-celled algae to insects and fish.

Though the study was confined to lakes and ponds, these changes may have broader impacts.

“Ponds are considered hotspots for biodiversity — they often support more diversity relative to surrounding terrestrial landscapes,” Farruggia said. “When you change things like how much food is available, or the temperatures that animals are used to thriving at, that could potentially affect biodiversity and carbon cycling across the landscape.”

MJ Farruggia processes water samples at the shore of a pond in Sequoia National Park. (Courtesy Steven Sadro)

An emerging field

Studies investigating the impacts of smoke on aquatic ecosystems are far and few between, and most have been limited to single bodies of water. With data from six different lakes and ponds across multiple fire seasons, Farruggia and her collaborators have produced one of the most robust investigations yet.

But in order to get there, they first needed to devise a method for measuring smoke cover.

The scientists' initial attempts did not bear fruit. A NOAA satellite product proved too coarse to distinguish high-altitude smoke from low-lying smoke, while citizen-mounted particulate sensors were too far from the study sites.

“What ended up working really well was a shortwave radiation sensor on a nearby weather station,” Farruggia explained. “It basically measures incoming light.”

With this problem solved, the researchers could compare smoke cover against water temperature and dissolved oxygen readings from the environmental sensors that Farruggia installed at the beginning of her field campaign.

The trend of dampened productivity and water temperature remained steady across all six lakes, yet there were differences. Ponds experienced more drastic effects than lakes — their larger counterparts.

“The larger lakes, we think, just have more water to buffer the effects,” Farruggia explained.

This point may seem semantic, but it could hint at a broader truth.

“In this paper, we only talk about wildfire smoke, but I suspect it’s true across the board,” Farruggia said. “These ponds, which are the most common aquatic ecosystem worldwide by number, are likely very responsive to environmental change.”

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Global implications

As Earth warms, wildfires are growing more frequent, larger, and hotter. Farruggia and her collaborators' new investigation is proof that this trend will also impact ecosystems above treeline — beyond the direct reach of flames. In 2024, Farruggia authored a review that found 89% of North American lakes experienced smoke for more than 30 days from 2019 to 2021.

Taken on a global scale, the dampened productivity the scientists observed could impact the Earth’s carbon cycle.

“The contribution of one pond may be small, but the cumulative effect of ponds changing across the country — or across the world — could be really large in terms of how much carbon they store or release,” Farruggia said.

For Farruggia, this reality is motivation to further study these ecosystems. They are an unresolved pixel in a grainy image of a changing planet. With each new investigation, the image sharpens.

Thankfully, the new study also had the benefit of a 43-year-long record of ecological research at Emerald Lake, one of the lakes in Farruggia’s study. What began amidst the acid rain crisis in the 1980s has been sustained by federal grants for four decades.

This record provided a solid foundation for the scientists to build off of.

“Emerald Lake has been studied for 40-plus years, so we understood how at least one of these six systems worked really, really well already,” she said.

Farruggia stresses the importance of keeping these long-running datasets active. It is through these records that scientists can hope to understand the ways that ecosystems are changing beyond the typical three to five-year grant cycle. And, with a little luck, they can capture ephemeral phenomena like wildfires as well.

If you have questions about this story, or would like to reach out to INSTAAR for further comment, you can contact Senior Communications Specialist Gabe Allen at gabriel.allen@colorado.edu.

A new study from INSTAAR postdoc MJ Farruggia investigates the impact of wildfire smoke on aquatic ecosystems in six alpine lakes and ponds in the Sierra Nevada.

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MJ Farruggia looks over one of her study sites in Sequoia National Park. A small yellow buoy marks the spot where an environmental sensor hangs. (Courtesy David Ayers)

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MJ Farruggia looks over one of her study sites in Sequoia National Park. A small yellow buoy marks the spot where an environmental sensor hangs. (Courtesy David Ayers)

New satellite tools track river flows throughout the Lower Mekong Basin

Gabe Allen — Wed, 15 Apr 2026 12:00:00 +0000

New satellite tools track river flows throughout the Lower Mekong Basin Gabe Allen Wed, 04/15/2026 - 06:00

Gabe Allen

Robert Brakenridge is a Senior Research Associate at the Institute of Arctic and Alpine Research (INSTAAR).

After the Mekong River descends from the highlands in China, it flows into Cambodia, Laos, Thailand and Vietnam providing freshwater for farming, fishing, hydropower and transportation. 52 million people rely on the lower Mekong River Basin for their livelihoods, according to the Mekong River Commission.

In the past decade, the Lower Mekong’s flows have dwindled, putting pressure on downstream communities. Until recently, a lack of information on the river’s hydrology has hindered efforts to understand these changes.

A new paper from an international group of researchers, including INSTAAR scientist Robert Brakenridge, takes aim at this knowledge gap. They present a suite of tools capable of precisely monitoring river flows.

The author's techniques rely on satellite-mounted sensors that map “passive microwave radiation” across the Earth’s surface.

“You’re listening to the radiation actually emitted by the Earth,” Brakenridge said. “It turns out that water bodies are much lower emitters than land bodies… we use that difference as a way to track water changes.”

The researchers also pulled data from an extensive network of physical river monitoring stations in the Lower Mekong to double-check the satellite observations and calibrate their model. The alignment was excellent. The satellite-powered data proved accurate even during periods of drought and flood — river stages that often prove challenging for remote sensing.

“These sensors have very precise dynamic range,” Brakenridge said. “Basically you can use each pixel as a gauging station.”

Left: A boat used to measure river discharge is moored at the hydrologic station in Tan Chau, Mekong Delta, Vietnam. Right: The impeller component of a boat-mounted current meter rests on the shop floor. These meters contributed to the in situ data that the authors used to validate their satellite results. (Anna Podkowa)

Trouble on the Mekong

The new investigation is more than just a proof of concept. It also uncovered a nuanced understanding of how the Lower Mekong Basin is changing in the 21st century.

In 2015 and 2016, the Lower Mekong Basin experienced a severe drought. Millions of farmers lost autumn and winter rice harvests and salt water leached upstream into the Mekong River Delta. According to the new investigation, river flows have yet to recover from this historic drought.

The Lower Mekong’s slow recovery after drought may be due, in part, to an increase in damming upstream. Huaneng Power International, a Chinese electricity company, completed two large dams on the upper Mekong in 2010 and 2012 respectively. In addition, two new water diversion projects are planned for the near future in Cambodia and Thailand.

The analysis reveals that the new Chinese dams likely decreased annual flows on the Lower Mekong overall. As the river struggles to recover from the 2015-2016 drought, the diversion projects in the lower basin could further exacerbate the issue.

While new construction proliferates on the Mekong, climate change is causing precipitation to become more erratic in the region. As such, it is hard to parse out which factor — climate change or human infrastructure — is the driving force behind recent water shortages.

Brakenridge is careful to hedge on this point. There are conflicting results in the literature, and more research is needed to resolve the issue.

“It becomes very political very fast,” he said. “Our conclusions are pretty conservative. They mainly describe the observations we made.”

A new wavelength

A map of the Lower Mekong Basin shows "satellite gauging reaches" — focus sites of Brakenridge and his collaborator's recent investigation. (Courtesy)

While the new investigation stops short of naming a leading culprit of the Mekong’s dwindling water supply, it does suggest a way forward. The results show the power of passive microwave radiation to monitor the river into the past, present, and future.

Brakenridge has honed these techniques for decades. In the early 2000s, he was one of the first to demonstrate the ability of “Ka band” radiation for river monitoring. In recent years, he has joined a new generation of researchers leveraging “L band” radiation data from NASA’s Soil Moisture Active Passive mission, colloquially known as SMAP, for the same purpose.

“With the L band microwave you see through the vegetation much better,” he said. “So if you’re looking at a floodplain with a forest canopy, it doesn’t matter so much.”

The new investigation employs both types of radiation.

“The two seem to counterbalance each other,” he explained.

Though L band data is only available for the past decade, Ka records extend to the late 1990s and other passive microwave records extend back to the late 1970s. By combining all three, the scientists compiled a record of river flows spanning nearly half a century, adding weight to the trends they observed.

Planned NASA missions will also extend L band data into the future — at least to the 2040s. Brakenridge hopes that one day water managers may use this data to monitor the river in near real time. But for this to happen, NASA or another entity would need to build a system to translate and transmit data to end-users on a daily basis.

“All that needs to happen now is a daily refresh of the data that’s already being gathered,” Brakenridge said. “It may sound easy, but it’s not yet clear who might have the capacity to take on such a role. It could be an in-country agency, or an international organization such as the Mekong River Commission.”

For now, data from the new investigation is already being put to good use. Several years ago, Brakenridge attended a meeting of the Mekong River Commission in Laos and shared preliminary data from the project. Now that it’s completed, the researchers have shared their results with the commission.

“The short term goal is to improve their technical capabilities,” Brakenridge said. “Long-term, they may be able to avoid bad outcomes and be more prosperous and water-resilient overall.”

If you have questions about this story, or would like to reach out to INSTAAR for further comment, you can contact Senior Communications Specialist Gabe Allen at gabriel.allen@colorado.edu.

An investigation by INSTAAR scientist Robert Brakenridge and collaborators unveils a new method for monitoring water throughout the most important river basin in Southeast Asia.

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A new map of ecological hotspots makes waves in Antarctica

Gabe Allen — Tue, 07 Apr 2026 20:52:15 +0000

A new map of ecological hotspots makes waves in Antarctica Gabe Allen Tue, 04/07/2026 - 14:52

Gabe Allen

The ocean surrounding Antarctica is one of the most austere habitats on Earth. But, amidst the frozen, windswept landscape, an incredible diversity of life thrives. Each spring, phytoplankton harness the energy of the southern sun and, in turn, give rise to other microorganisms, fish and marine predators like penguins and seals.

Cassandra Brooks (left) and Zephyr Sylvester present at the 44th annual meeting of the Commission for the Conservation of Antarctic Marine Living Resources in October 2025. The researchers shared a new mapping tool with an audience of global leaders. (Courtesy, Cassandra Brooks)

In a new paper, a team of scientists led by The National Science Foundation Center for Atmospheric Research’s Alice DuVivier and INSTAAR’s Cassandra Brooks have designed a tool capable of mapping the relative importance of specific areas to the overall Antarctic ecosystem. The tool, called the Antarctic Ecosystem Value Index, captures life throughout the food web — from phytoplankton to penguins.

Even before the paper was published, their findings were already making waves. Last fall, Brooks and postdoctoral scholar Zephyr Sylvester traveled to Australia to present the Antarctic Ecosystem Value to the international governing body in charge of creating Marine Protected Areas in Antarctica.

“They are the ones that actually make the decisions about what to protect,” Brooks said. “They’re required to make decisions based on the best available science with the whole ecosystem in mind, so they really are our target audience.”

The researchers didn’t stop with policy makers. In partnership with ocean and climate communication nonprofit OnlyOne, the team developed a public-facing web campaign where users can explore ecosystem values via an interactive map. John Weller, a photographer, filmmaker and senior fellow at OnlyOne, also produced a 5-minute documentary about the project.

“We wanted to be able to show these areas we could consider protecting through stories,” Brooks said.

Oases in the ice

The ocean surrounding Antarctica is dominated by sea ice. It forms sprawling plains, towering walls and buckling glaciers. Every so often though, natural forces create a stretch of open water. These breaks in the ice are known as polynyas, and they are oases for marine life. The sunlight allows phytoplankton to get a head start each spring, and marine animals flock to the areas in search of food.

Orca Whales gather at a polynya in the Ross Sea. (John B. Weller)

In the new paper, Brooks and her collaborators confirmed a theory that scientists have long suspected — polynyas play an outsized role in the Antarctic ecosystem. According to the Antarctic Ecosystem Value Index, they are 31 to 72 percent more important than surrounding areas.

“People are always saying that polynyas are really important,” Brooks said. “But, as far as I know, we are the first ones to quantify what that actually means.”

To arrive at these values, the researchers combined ecological models that predict productivity at every level of the food web. Specifically, they focused on phytoplankton, krill, bottom-feeding fish and penguins — each group being key to the functioning of the ecosystem.

The next step was to project these values through time. Antarctica is warming nearly twice as fast as the global average, a reality that will permanently alter marine ecosystems. If the researchers could predict ecological value in the future, it could reveal which areas will remain important candidates for conservation.

To accomplish this, DuVivier combined the Antarctic Ecological Value with computer-simulated Earth system models. The results were clear, despite future losses in sea ice, polynyas will remain vital ecological hotspots at least to the end of the century. Protecting these areas now could safeguard Antarctic ecosystems for years to come.

“With careful management of protected areas, policy makers can ensure we conserve Antarctic biodiversity ,” DuVivier said. “You give the ecosystem the best chance at adapting to change.”

Cassandra Brooks captures photos of Emperor Penguins in the Ross Sea. (Christina Riesslman)

Safeguarding the future

Aside from global warming, the largest human impacts on marine ecosystems in Antarctica are commercial fishing and tourism. But, according to the scientists, more informed conservation can help, not just ecosystems, but industry too. For instance, placing restrictions on the right areas can help commercial vessels get a good catch for years to come.

“It can be a really good fisheries management tool,” DuVivier said.

There are limitations to the data, for instance it does not capture the effect of short-term events like marine heat waves. But, it’s the best tool yet for weighing potential impacts of conservation around the continent. And, though Antarctica is distant from the rest of the world, it is critical to the functioning of global earth systems. It stores the majority of the world’s freshwater, drives global ocean circulation and regulates our climate, storing disproportionate amounts of carbon and heat.

“What happens in Antarctica does not stay in Antarctica,” Brooks said. “By safeguarding Antarctica, we actually help safeguard our own future.”

If you have questions about this story, or would like to reach out to INSTAAR for further comment, you can contact Senior Communications Specialist Gabe Allen at gabriel.allen@colorado.edu.

Cassandra Brooks, Zephyr Sylvester and Alice DuVivier have published a new tool for evaluating ecological value in the Antarctic ocean. Now they are launching a campaign in support of Antarctic ecosystems.

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A pair of emperor penguins stand near the ice edge at a polynya in the Ross Sea in Antarctica. The new paper predicts a sharp decline in emperor penguin populations across the continent by the end of the century, while Adélie penguin populations will remain relatively stable. (John B. Weller)

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How do you measure snow from space? First, climb a mountain (New York Times)

Gabe Allen — Tue, 24 Mar 2026 14:59:08 +0000

How do you measure snow from space? First, climb a mountain (New York Times) Gabe Allen Tue, 03/24/2026 - 08:59

New York Times journalists followed the mountain hydrology lab on recent a winter excursion to Niwot Ridge. The researchers were measuring snow on the landscape in real time in order to calibrate data from an overhead satellite.

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Why pristine mountain lakes are suddenly turning green (Scientific American)

Gabe Allen — Tue, 17 Mar 2026 21:14:20 +0000

Why pristine mountain lakes are suddenly turning green (Scientific American) Gabe Allen Tue, 03/17/2026 - 15:14

Journalist Cody Cottier tells the story of the Oleksy lab's summer expedition to an alpine lake in the San Juan range. The scientists are investigating the source of a mysterious algal bloom that was first spotted by a ranger in 2021.

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Garrett Boudinot and the Many Paths to Entrepreneurship (Leeds School of Business)

Gabe Allen — Thu, 12 Mar 2026 22:30:34 +0000

Garrett Boudinot and the Many Paths to Entrepreneurship (Leeds School of Business) Gabe Allen Thu, 03/12/2026 - 16:30

A recent alum of INSTAAR's organic chemistry lab is the founder of a new climate tech startup called Vycarb. The company amplifies natural processes in the ocean to remove carbon dioxide from the atmosphere.

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What Colorado’s mountain lakes can tell scientists about climate change (Aspen Times)

Gabe Allen — Wed, 11 Mar 2026 22:40:22 +0000

What Colorado’s mountain lakes can tell scientists about climate change (Aspen Times) Gabe Allen Wed, 03/11/2026 - 16:40

Mountain lakes are the "canary in the coal mine" for how ecosystems are responding to climate change. That's according to the Mountain Liminology Lab's Mary Jade Farruggia, who was featured in an article from the Aspen Times this week.

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