Discovery of microbial pathway that may help combat methane emissions

by Beijing Zhongke Journal Publising Co. Ltd.

A new microbial pathway discovered can potentially contribute to combat methane emissions
The stalactites-like biofilms hanging over cave ceiling (A) and the star-shaped cell residing in the wall biofilm (B). Credit: Beijing Zhongke Journal Publising Co. Ltd.

Methane is a powerful greenhouse gas, contributing more than 20% of global warming since preindustrial times. Anaerobic oxidation of methane (AOM) is an important methane sink, reducing methane emission from various environments to the atmosphere. Methylomirabilota bacterium (Methylomirabilis oxyfera) that can use nitrite as the electron acceptor to drive AOM has been recently reported.

Intriguingly, although M. oxyfera is an anaerobe, it employs the aerobic pathway for methane oxidation, using its own intracellularly formed oxygen via “oxygenic denitrification.” Currently, our understanding towards the ecophysiology and ecology of Methylomirabilota methanotrophs is limited.

In the study led by Dr. Baoli Zhu (Institute of Subtropical Agriculture, Chinese Academy of Sciences) and Dr. Tillmann Lueders (University of Bayreuth, Germany), an iodine-rich spring cave, whose atmosphere was microoxic and contained high-level thermogenic methane (~3000 ppm) has been investigated. Massive biofilms were discovered covering the cavern walls and ceilings, forming spectacular stalactites-like views.

16S rRNA amplicon sequencing revealed that aerobic methanotrophs and methylotrophs were present in all biofilms, but Methylomirabilota bacteria were exceptionally abundant in the submersed wall biofilm. Additionally, star-shaped cells resembling the morphology of M. oxyfera were directly observed under electron microscope, suggesting its presence in the submersed biofilm.

From the metagenome of the submersed biofilm, the authors assembled a MAG (metagenome-assembled genome) of a novel Methylomirabilota bacterium, which they named Candidatus Methylomirabilis iodofontis. In the metagenome, M. iodofontis 16S rRNA reads accounted up to 14.3% of the total 16S rRNA reads, suggesting its high abundance in the biofilm. A complete M. iodofontis 16S rRNA sequence was built from these reads, and it showed high similarity to that of M. limnetica. However, M. iodofontis MAG only had low identity to M. iodofontis genome (AAI, 85.8%´╝ŤANI, 91.3%), suggesting it may have a different ecophysiology from M. limnetica.

Although there was high concentration of methane in the cave atmosphere, nitrite was undetectable in the spring water, and nitrate concentration was low (-1). The authors were wondering how this novel Methylomirabilota methanotroph, M. iodofontis, was thriving in the cave biofilm under such geochemical settings. Therefore, they analyzed the M. iodofontis genome and constructed its key respiration pathways.

Surprisingly, in addition to the aerobic methane oxidation and “oxygenic denitrification” pathways as in other Methylomirabilota methanotrophs, including M. oxyfera and M. limnetica, there was a gene cluster (IdrP2,P1,B,A) encoding iodate reductase.

The organization of these genes in the cluster is the same as in Pseudomonas sp. SCT and Denitromons sp. IR-12, and the sequence of the catalyzing subunit IdrA also showed high similarity to known iodate reductase in other microorganisms. This strongly argues for an iodate reduction capability in M. iodofontis, and entails its competitiveness in an iodate-rich environment. However, the activity of iodate reduction coupled with methane oxidation needs further validation.

These new exciting results expand the versatility of Methylomirabilota methanotrophs, and add to the list of electron acceptors that can potentially drive AOM. The genetic evidence for coupling iodine and carbon cycles in M. iodofontis suggests that such microbes could play an important role in controlling methane emissions, especially in iodate-rich marine ecosystems.

The research was published in mLife.

Biofilm bacterial dynamics and changes in inorganic nitrogen density due to the presence of freshwater pearl mussels

More information:
Baoli Zhu et al, A novel Methylomirabilota methanotroph potentially couples methane oxidation to iodate reduction, mLife (2022). DOI: 10.1002/mlf2.12033

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Discovery of microbial pathway that may help combat methane emissions (2022, October 17)
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