A pathway for biological methane production using bacterial iron-only nitrogenase

Abstract

Methane (CH4) is a potent greenhouse gas that is released from fossil fuels and is also produced by microbial activity, with at least one billion tonnes of CH4 being formed and consumed by microorganisms in a single year1. Complex methanogenesis pathways used by archaea are the main route for bioconversion of carbon dioxide (CO2) to CH4 in nature2,3,4. Here, we report that wild-type iron-iron (Fe-only) nitrogenase from the bacterium Rhodopseudomonas palustris reduces CO2 simultaneously with nitrogen gas (N2) and protons to yield CH4, ammonia (NH3) and hydrogen gas (H2) in a single enzymatic step. The amount of CH4 produced by purified Fe-only nitrogenase was low compared to its other products, but CH4 production by this enzyme in R. palustris was sufficient to support the growth of an obligate CH4-utilizing Methylomonas strain when the two microorganisms were grown in co-culture, with oxygen (O2) added at intervals. Other nitrogen-fixing bacteria that we tested also formed CH4 when expressing Fe-only nitrogenase, suggesting that this is a general property of this enzyme. The genomes of 9% of diverse nitrogen-fixing microorganisms from a range of environments encode Fe-only nitrogenase. Our data suggest that active Fe-only nitrogenase, present in diverse microorganisms, contributes CH4 that could shape microbial community interactions.

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Fig. 1: Cells expressing wild-type Fe-only nitrogenase produce CH4
Fig. 2: Fe-only nitrogenase purified from R. palustris reduces CO2 to CH4 in vitro
Fig. 3: Effect of molybdenum on CH4 production by nitrogen-fixing bacteria.
Fig. 4: Co-culture of Methylomonas sp. LW13 and R. palustris

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Acknowledgements

We thank the entire Biological Electron Transfer and Catalysis (BETCy) team for informative discussions. We also thank G. Roberts, Y. Zhang, J. McKinlay and F. Daldal for the generous gifts of R. rubrum and R. capsulatus strains, S. Shaw for assistance with activity assays and M. Tokmina-Lukaszewska for the verification of purified Fe-only nitrogenase by mass spectrometry. This work was supported as part of the BETCy Energy Frontier Research Center (EFRC), an EFRC funded by the US Department of Energy, Office of Science Grant DE-SC0012518.

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Y.Z., D.F.H., Z.Y, K.R.F., E.S.B., M.E.L., L.C.S. and C.S.H. designed the research. Y.Z. performed the in vivo studies of photosynthetic bacteria. Y.Z. and K.R.F. made the R. palustris mutants. Y.Z. grew the R. palustris cells. D.F.H. purified the Fe-only nitrogenase and did the enzyme assays. Z.Y. and Y.F. performed the co-culture experiments. Y.F. carried out the analysis of 13C-labeled metabolites. S.P. completed the taxonomic distribution of nitrogenases; R.N.L. performed the CH4 measurement of A. vinelandii. Z.-Y.Y. performed the GC–MS analysis of CH4. Y.Z., D.F.H., K.R.F., E.S.B., M.E.L., L.C.S. and C.S.H. analysed the data. Y.Z., E.S.B., M.E.L., L.C.S. and C.S.H. wrote the paper. All authors contributed to the revision of the manuscript.

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Correspondence to Caroline S. Harwood.

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Zheng, Y., Harris, D.F., Yu, Z. et al. A pathway for biological methane production using bacterial iron-only nitrogenase. Nat Microbiol 3, 281–286 (2018). https://doi.org/10.1038/s41564-017-0091-5

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