Bacteria in lakes help fight climate change

Methane is a powerful greenhouse gas commonly produced in marine and freshwater environments, with lakes being significant sources of its release into the atmosphere. 

Fortunately, there are microorganisms capable of mitigating this issue by using methane as a source of energy and growth, thereby preventing its escape into the atmosphere. These microorganisms, known as methanotrophs, act as a crucial “biological methane filter.”

Lake bacteria and climate regulation 

Methanotrophs consist of diverse groups of microorganisms, many of which remain understudied. 

A recent study conducted by researchers from the Max Planck Institute for Marine Microbiology in Bremen, Germany, in collaboration with the Swiss research institution Eawag, sheds light on the remarkable capabilities of some of these organisms and their overlooked role in climate regulation. 

Lake bacteria in oxygen-deprived water

In their research, a team led by Sina Schorn and Jana Milucka from the Max Planck Institute explored Lake Zug in Switzerland. This lake, nearly 200 meters deep, is devoid of oxygen below a depth of approximately 120 meters. 

Despite the lack of oxygen, the researchers discovered the presence of aerobic methane-oxidizing bacteria (MOB) in these oxygen-deprived waters. These bacteria, which typically require oxygen to function, posed a mystery: how could they break down methane in an environment devoid of oxygen?

To address this question, the team closely examined the activity of these microorganisms. They introduced methane molecules labeled with “heavy” carbon atoms (13C instead of 12C) into natural lake water samples containing these bacteria. 

Using specialized instruments called NanoSIMS, the researchers traced the path of the heavy carbon within individual cells. 

Results of the study

This technique allowed them to observe how the bacteria convert methane into carbon dioxide, while some of the carbon was also incorporated directly into the bacterial cells. This method revealed the active members of the bacterial community. 

Through advanced techniques like metagenomics and metatranscriptomics, the researchers further explored the metabolic pathways employed by the bacteria.

According to Schorn, now a researcher at the University of Gothenburg, the results of the study show that aerobic methane-oxidizing bacteria remain active also in oxygen-free water.

“However, this only applies to a certain group of MOB, easily recognizable by their distinctive rod-shaped cells. To our surprise, these cells were equally active under oxic and anoxic conditions, i.e., with and without oxygen,” said Schorn. 

“Thus, if we measure lower rates of methane oxidation in anoxic waters, it is probably because there are fewer of these special rod-shaped cells and not because the bacteria are less active.”

Bacteria’s response to low oxygen levels

The researchers were further intrigued by the metabolic versatility of this bacterial group. “Based on the genes present, we were able to determine how the bacteria respond when oxygen becomes scarce,” said Jana Milucka, head of the Greenhouse Gases Research Group at Max Planck. “We found genes that are used for a special type of methane-based fermentation.” 

This process had previously been observed in methane-oxidizing bacteria cultures in the laboratory, but its presence in natural environments had not been confirmed. 

The researchers also identified several genes related to denitrification, which likely enable the bacteria to utilize nitrate instead of oxygen for energy production.

Unexpected methane sinks

The fermentation process is particularly noteworthy. “If the MOB perform fermentation, they likely release substances that other bacteria can use for growth. This means the carbon contained in the methane is retained in the lake for a longer period of time and does not reach the atmosphere,” explained Milucka. 

“This represents a sink for methane carbon in anoxic environments that is typically not accounted for, which we will need to include in our future calculations.”

This study reveals the organisms responsible for methane degradation in oxygen-free habitats and how this process occurs, highlighting the unexpected significance of methane-oxidizing bacteria in controlling methane release from such environments to the atmosphere.

Significance of methane degradation by bacteria

Schorn pointed out that methane is a potent greenhouse gas that is responsible for about a third of the current global rise in temperature.

“Methane oxidation by microorganisms is the only biological sink for methane,” noted Schorn. This means that methane-oxidizing bacteria are crucial for controlling methane emissions and for regulating the global climate. 

“Given the current and predicted increase in anoxic conditions in temperate lakes, the importance of MOB for methane degradation in lakes is expected to grow,” said Schorn.

“Our results suggest that MOB will make a significant contribution to greenhouse gas mitigation and carbon storage in the future.”

The findings are published in the journal Nature Communications.

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