Methane Metabolism in Archaea is Ancient and Widespread

By searching existing metagenomic data to find genes for a key methane metabolism enzyme, researchers identified new and diverse groups of archaea capable of producing or consuming methane. The finding suggests that methane metabolism likely evolved early in the rise of Archaea.

In the oxygen-free parts of lakes, hot springs, and marine environments worldwide, some microbes generate a lot of methane as part of their daily metabolism, while others consume it for energy. Over geological timescales, the interplay of these activities likely had a big impact on Earth’s climate and the global carbon cycle. But despite the importance of methane metabolism, the identities of the microbial species involved is still poorly understood.

DCO Deep Life Community members Yinzhao Wang, Fengping Wang, Xiang Xiao (all at Shanghai JiaoTong University, China), Gunter Wegener (Max Planck Institute for Marine Microbiology and MARUM, Germany), and colleagues expanded the number of groups of archaea believed to use or produce methane. By searching genomic data from environmental samples collected worldwide, the researchers identified a key gene needed for methane metabolism in unexpected and unrelated groups of archaea not known to use methane. The existence of the gene in diverse groups suggests that methane metabolism arose early in archaeal evolution and has long impacted Earth’s carbon cycle. They report their findings in a new paper [1] in Nature Microbiology.

AOM and Nezha
Using genomes assembled from environmental metagenome data, researchers have identified new groups of archaea capable of metabolizing and producing methane. Credit: Image courtesy of Fengping Wang

Wang first began investigating microbes that use or produce methane in 2013, as part of her work studying the South China Sea. She and her colleagues collected sediments from parts of the seafloor leaking methane so that they could sequence the environmental DNA to figure out which organisms were consuming methane in sediments. Many archaea can’t be grown in the lab, but researchers can sequence specific genes from an environmental sample to find out what’s there. Or, they can create a metagenome by sequencing all the DNA in the sample, and even piece together individual microbial genomes from the metagenome. “We kept wondering, how widespread are these methane-metabolizing archaea?” said Wang. “Now, thanks to the vast increase in metagenome sequencing projects, we can access metagenome data from a variety of different environments globally.” 

Archaea are the only organisms known to produce methane or to metabolize it without oxygen, called anaerobic oxidation of methane (AOM). Surprisingly, the two processes both use the same key enzyme, methyl-coenzyme M reductase (MCR). To identify archaeal species capable of either of these activities, the researchers scoured available metagenome data from locations around the world to find genomes carrying the MCR gene. They identified several genomes belonging to archaeal groups previously not known to be capable of methane metabolism.

The Chinese mythological character Nezha inspired the name of a new group of methane-metabolizing archaea, Nezhaarchaeota. According to legend, Nezha flew through the sky on “wind fire wheels” carrying a red sash and a fire-tipped spear. Credit: Photograph from the Ping Sien Si Temple in Perak, Malaysia taken by Anandajoti, via Wikimedia Commons.

The genomes belong to diverse archaeal lineages including two new types of Euryarcheatoa, a lineage that includes other known methane-metabolizing microbes, as well as several genomes from the TACK superphylum, a lineage that includes microbes that may have been the parents of eukaryotic cells, which make up plants, fungi, and animals. The researchers named this new methane-producing group within the TACK superphylum “Nezhaarchaeota” after "Nezha," a Chinese mythological character who flies on wind fire wheels. 

“The fact that we found methane metabolism in diverse archaeal lineages reinforces the idea that it is the most ancient biochemical process in the domain of Archaea, and possibly even one of the earliest life attributes,” said Wang.

The research team also was surprised to discover genomes containing pathways for AOM and sulfate reduction. When coupled, these two pathways can generate energy, but previously, researchers had only observed the metabolisms split between two different cell types, working together symbiotically. This may be the first evidence that a single organism can perform both processes.

Additionally, some of the MCR genes were highly unusual. The researchers think these genes may enable the microbes to oxidize propane and butane.  

“It needs to be pointed out that the metabolic functions of the organisms represented by these genomes must be verified, essentially by isolating and cultivating the organisms in the lab,” said Wang. Next, her team in Shanghai and her collaborators in Germany plan to bring these microbes into the lab. They hope to grow them in culture so that they can learn more about the unusual ways that they generate energy, and how those activities might impact global methane cycling.

Main image: Tengchong hot spring in Yunnan Province, China is one spot where methane-metabolizing archeaa live. Credit: Wenjun Li 

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