Measurements across 79 lakes show bacteria living on microalgae remove more than 70 percent of the methane in surface waters.

Lakes are quiet giants of the greenhouse gas budget. Collectively they emit about as much methane, the second most important greenhouse gas after carbon dioxide, as agriculture does. A new study from the University of Liège in Belgium suggests the picture is more nuanced than the emissions alone imply, because in many lakes a microbial filter is removing most of the methane before it can escape.

“Methane emissions from a lake result from the balance,” said Alberto Borges, an oceanographer and head of the CO2 Lab at the University of Liège, “between, on the one hand, its production through methanogenesis in the sediments, and, on the other, its loss through microbial oxidation.”

79 lakes, 503 measurements

Borges and colleagues took 503 measurements across 79 African lakes, ranging from clear, low-algae waters to intensely green lakes dominated by phytoplankton. Methane oxidation rose sharply with the abundance of microalgae. In the most productive lakes, it ran tens of thousands of times higher than in the least productive ones.

Overall, microbial oxidation removed more than 70 percent of the methane dissolved in surface waters, far more than the amount that reached the atmosphere.

A partnership on the surface of algae

The work rests on a group of bacteria called methanotrophs. “Methane is, in fact, the preferred substrate of certain bacteria, known as methanotrophs,” Borges said, “which specialise in using it as a source of energy and biomass.”

In these lakes, the methanotrophs live attached to the surfaces of microalgae in a mutually beneficial arrangement. “The methanotrophs supply the algae with carbon dioxide for photosynthesis, whilst the algae produce the oxygen the bacteria need to oxidise methane,” Borges explained. “So the more abundant the microalgae are, the more abundant the methanotrophic bacteria are too, and therefore the more intense the methane oxidation is.”

Lakes bordered by the flooded forests of the Congo Basin also showed high oxidation, driven there by bacteria washed in from submerged forest soils.

Pollution’s double edge

The finding complicates the story of eutrophication, the nutrient pollution that drives algal blooms. The team’s earlier work had shown that more phytoplankton meant more methane production in sediments. “We had previously shown that as phytoplankton biomass increased, so too did methane production in the sediments,” Borges said, “with algal detritus serving as a feedstock for methane-producing microorganisms.”

The new study reveals the other side of the ledger. Eutrophication also multiplies the algae-dwelling methanotrophs, and in the lakes studied the increase in methane consumption can outweigh the increase in production. Without those attached bacteria, the lakes’ methane emissions would be much higher.

“These methanotrophic bacteria thus act as natural and welcome filters,” Borges said, “capable of partially mitigating the effect of lake pollution on global warming.” That is not an argument for nutrient pollution, which causes a host of other harms to water quality and ecosystems, but it does change how scientists model lake emissions.

“This finding enables us to better understand, but also to reassess, methane emissions from lakes,” Borges said. “This is an important piece of the puzzle that was missing and will enable us to better predict the future trend in methane emissions from lakes.”

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Notes

1. “Methane oxidation in African lakes increases with phytoplankton and outweighs photosynthesis-driven oxic methane production.” Nature Communications, 29 September 2026.
2. University of Liège. “In African lakes, microbes living on algae reduce a powerful greenhouse gas.” EurekAlert!, 29 September 2026. https://www.eurekalert.org/news-releases/1145908.

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