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In the summer of 2020,  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. 

Then, in August,  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. 

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." — MJ Farruggia

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 . 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.”

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.”

Global implications

As Earth warms, . 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  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 , 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.

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