Discovery of microbial pathway that may help combat methane emissions

by Beijing Zhongke Journal Publishing Co. Ltd.

The stalactite-like biofilms that hang over the cave ceiling (A) and the star-shaped cell that resides in the biofilm of the wall (B). Credit: Beijing Zhongke Journal Publishing Co. Ltd.

Methane is a potent greenhouse gas that has contributed more than 20% of global warming since pre-industrial times. Anaerobic Oxidation of Methane (AOM) is an important methane sink, reducing methane emissions from various environments to the atmosphere. Methylomirabilota bacterium (Methylomirabilis oxyfera) that can use nitrite as the electron acceptor to drive AOM has recently been reported.

Intriguingly, although M. oxyfera is an anaerobic, it uses the aerobic pathway for methane oxidation, using its own intracellularly formed oxygen via “oxygenic denitrification”. Currently, our understanding of 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 source cave, whose atmosphere was microoxic and thermogenic methane (~3000 ppm) has been investigated. Huge biofilms were discovered covering the cave’s walls and ceilings, creating spectacular stalactite-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 underwater biofilm. In addition, star-shaped cells resembling the morphology of M. oxyfera were directly observed under an electron microscope, suggesting that they are present in the submerged biofilm.

From the metagenome of the submerged biofilm, the authors assembled a MAG (metagenome-assembled genome) of a novel Methylomirabilota bacterium, which they named Candidatus Methylomirabilis jodofontis. In the metagenome, M. iodofontis 16S rRNA reads accounted for 14.3% of the total 16S rRNA reads, suggesting that it is highly present in the biofilm. A complete M. iodofontis 16S rRNA sequence was constructed from these reads and showed a high similarity to that of M. limnetica. However, M. iodofontis MAG had only low identity with the M. iodofontis genome (AAI, 85.8% ANI, 91.3%), suggesting that it may have a different ecophysiology from M. limnetica.

Although there was a high concentration of methane in the cave’s atmosphere, nitrite was undetectable in the well water and the nitrate concentration was low (-1). The authors wondered how this new Methylomirabilota methanotroph, M. iodofontis, thrived in the cave’s biofilm under such geochemical settings. Therefore, they analyzed the M. iodofontis genome and constructed the major respiratory pathways.

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

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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 great similarity to known iodate reductase in other microorganisms. This strongly argues in favor of an ability to reduce iodate in M. iodofontis, and entails its competitiveness in an iodate-rich environment. However, the activity of iodate reduction in combination 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 could potentially drive AOM. The genetic evidence linking 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


Bacterial dynamics of biofilm and changes in inorganic nitrogen density due to the presence of freshwater pearl mussels

More information:
Baoli Zhu et al, A Novel Methylomirabilota Methanotroph May Link Methane Oxidation to Iodate Reduction, mLife (2022). DOI: 10.1002/mlf2.12033

Provided by Beijing Zhongke Journal Publishing Co. Ltd.

Quote: Discovery of Microbial Pathway That May Help Combat Methane Emissions (2022, October 17) retrieved October 17, 2022 from

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