Scientists discover the secret driver of climate change

The study reveals that the microorganisms, once infected, contain new methane-generating genes.

A recent study reveals that viruses that infect microbes contribute to climate change by playing a key role in cycling methane, a powerful greenhouse gas, through the environment.

By analyzing nearly 1000 metagenomics groups DNA Through data from 15 different habitats, ranging from different lakes to the inside of a cow's stomach, the researchers found that microbial viruses carry special genetic elements to control methane processes, called accessory metabolic genes (AMGs). Depending on where organisms live, the number of these genes can vary, suggesting that the potential impact of viruses on the environment also varies based on their habitat.

This discovery adds a vital piece to better understanding how methane interacts and moves within different ecosystems, said Zhiping Zhong, lead author of the study and a research associate at The Ohio State University Byrd Polar and Climate Research Center.

“It is important to understand how microorganisms drive methane processes,” said Zhong, who is also a microbiologist whose research studies how microbes evolve in diverse environments. “Microbial contributions to methane metabolism have been studied for decades, but research in the viral field remains largely understudied and we want to learn more.”

The study was published in the journal Nature Communications.

The role of viruses in greenhouse gas emissions

Viruses have helped power all ecological, biogeochemical and evolutionary processes on Earth, but scientists have only begun to explore their links to climate change relatively recently. For example, methane is the second largest driver of greenhouse gas emissions after carbon dioxide, but it is produced largely by single-celled organisms called archaea.

“Viruses are the most abundant biological entity on Earth,” said Matthew Sullivan, co-author of the study and professor of microbiology at Ohio State's Center for Microbiome Sciences. “Here, we expand what we know about their effects by adding methane cycle genes to the long list of genes virus– Encoded metabolic genes. Our team sought to answer how much 'microbial metabolism' viruses actually manipulate during infection.

Although the vital role microbes play in accelerating global warming is now well known, little is known about how methane metabolism-related genes encoded by viruses that infect these microbes affect methane production, Zhong said. Solving this mystery is what led Zhong and his colleagues to spend nearly a decade collecting and analyzing microbial and viral DNA samples from unique microbial reservoirs.

One of the most important places the team chose for study is Lake Vrana, which is part of a nature reserve in Croatia. Within the methane-rich lake sediments, researchers found an abundance of microbial genes that influence methane production and oxidation. In addition, they explored diverse viral communities and discovered 13 types of AMGs that help regulate their host's metabolism. However, there is no evidence that these viruses directly encode methane metabolism genes themselves, suggesting that the potential impact of viruses on the methane cycle varies depending on their habitat, Zhong said.

Impacts on livestock and the environment

Overall, the study revealed that a greater number of methane metabolism AMGs are more likely to be found within host-associated environments such as the inside of a cow's stomach, while fewer of these genes are found in environmental habitats, such as lake sediments. Since cows and other livestock are also responsible for generating about 40% of global methane emissions, their work suggests that the complex relationship between viruses, organisms and the environment as a whole may be more intricately linked than scientists previously thought.

“These results indicate that the global impacts caused by viruses are underestimated and deserve more attention,” Zhong said.

Although it is unclear whether human activities have influenced the evolution of these viruses, the team expects that new insights from this work will raise awareness about the power of infectious agents that populate all life on Earth. However, to continue learning more about the internal mechanisms of these viruses, more experiments will be needed to understand more about their contributions to the methane cycle on Earth, Zhong said, especially as scientists work to find ways to mitigate methane emissions caused by microbes.

“This work is a starting step in understanding the viral impacts of climate change,” he said. “We still have a lot to learn.”

Reference: “Viral potential to modulate microbial methane metabolism varies by habitat” by Zhi-Ping Zhong, Jingjie Du, Stephan Köstlbacher, Petra Pjevac, Sandi Orlić, and Matthew B. Sullivan, 29 February 2024, Nature Communications.
doi: 10.1038/s41467-024-46109-x

This work was supported by the National Science Foundation, the Croatian Science Foundation, the Gordon and Betty Moore Foundation, the Hysing-Simons Foundation, the European Union, and the US Department of Energy. Co-authors include Jinji Du of Ohio State, as well as Stefan Kostelbaker and Petra Bejevac of the University of Vienna, and Sandy Orlich of the Ruder Boškovitch Institute.