Methanotrophic microorganisms play a critical role in controlling the flux of methane from natural sediments into the atmosphere. Methanotrophs have been shown to couple the oxidation of methane to the reduction of diverse electron acceptors (e.g., oxygen, sulfate, nitrate, and metal oxides), either independently or in consortia with other microbial partners. Although several studies have reported the phenomenon of methane oxidation linked to selenate reduction, neither the microorganisms involved nor the underlying trophic interaction has been clearly identified. Here, we provide the first detailed evidence for interspecies electron transfer between bacterial populations in a bioreactor community where the reduction of selenate is linked to methane oxidation. Metagenomic and metaproteomic analyses of the community revealed a novel species of Methylocystis as the most abundant methanotroph, which actively expressed proteins for oxygen-dependent methane oxidation and fermentation pathways, but lacked the genetic potential for selenate reduction. Pseudoxanthomonas, Piscinibacter, and Rhodocyclaceae populations appeared to be responsible for the observed selenate reduction using proteins initially annotated as periplasmic nitrate reductases, with fermentation by-products released by the methanotrophs as electron donors. The ability for the annotated nitrate reductases to reduce selenate was confirmed by gene knockout studies in an isolate of Pseudoxanthomonas. Overall, this study provides novel insights into the metabolic flexibility of the aerobic methanotrophs that likely allows them to thrive across natural oxygen gradients, and highlights the potential role for similar microbial consortia in linking methane and other biogeochemical cycles in environments where oxygen is limited.
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All raw Illumina metagenomic sequence data were submitted to the Sequence Read Archive under accession numbers SRP136677, SRP136696, SRP136790, and SRP136859. The 16S rRNA gene sequences generated from the wetland inoculum were submitted under the accession number SRR14328346. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE  partner repository with the dataset identifier PXD011889. Public release of the PRIDE projects will be requested as soon as a citable pre-print is online. The username and password of temporary reviewer account are: email@example.com and Y5JAcO59, respectively.
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The authors greatly thank the “National Natural Science Foundation of China (Grant No. 51878596, 21577123)”, the “Natural Science Funds for Distinguished Young Scholar of Zhejiang Province (LR17B070001)”, and the “National Key Technology R&D Program (2018YFC1802203)” for their financial support. A.K. and M.S. are supported by NSERC, CFI, CFREF and the Government of Alberta. GWT and S.M are supported by Australian Research Council (ARC) Future Fellowships (FT170100070 and FT190100211, respectively). The authors also thank Dr. Erica M. Hartmann for her assistance in manuscript preparation.
The authors declare no competing interests.
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Shi, LD., Lv, PL., McIlroy, S.J. et al. Methane-dependent selenate reduction by a bacterial consortium. ISME J (2021). https://doi.org/10.1038/s41396-021-01044-3