Abstract
Despite its toxicity to many organisms, including most prokaryotes, carbon monoxide (CO) is utilized by some aerobic and anaerobic prokaryotes. Hydrogenogenic CO utilizers employ carbon monoxide dehydrogenase (CODH) and energy-converting hydrogenase (ECH) to oxidize CO and reduce protons to produce H2. Those prokaryotes constitute a rare biosphere and are difficult to detect even with PCR amplification and with metagenomic analyses. In this study, anaerobic CO-enrichment cultures followed by construction of metagenome assembled genomes (MAGs) detected high-quality MAGs from potential hydrogenogenic CO utilizers. Of 32 MAGs constructed, 5 were potential CO utilizer harboring CODH genes. Of the five MAGs, two were classified into the genus Thermolithobacter on the basis of 16S rRNA sequence identity, related to Carboxydocella tharmautotrophica 41, with an average nucleotide identity (ANI) of approximately 72%. Additionally, two were related to Geoglobus acetivorans with ANI values ranging from 75 to 77% to G. acetivorans SBH6, and one MAG was identified as Desulfotomaculum kuznetsovii with an ANI > 96% to D. kuznetsovii DSM 6115. The two Thermolithobacter MAGs identified in this study contained CODH-ECH gene clusters, and were therefore identified as potential hydrogenogenic CO utilizers. However, these MAGs harbored three CODH gene clusters that showed distinct physiological functions in addition to CODH-ECH gene clusters. In total, the five potential CO utilizer MAGs contained sixteen CODH genes. Among those CODHs, four sets did not cluster with any known CODH protein sequences (with an identity of > 90%), and the CODH database was expanded.
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Acknowledgements
This work was supported by JSPS KAKENHI Grant number JP16H06381 (to Y.S.), the Institute for Fermentation, Osaka Grant number L-2021-1-002 (to T.Y.) and by JST SPRING, Grant number JPMJSP2110. Computation time was provided by Super Computer System, Institute for Chemical Research, Kyoto University.
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Funding was supported by JST SPRING (JPMJSP2110), Japan Society for the Promotion of Science (JP16H06381), Institute for Fermentation, Osaka (L-2021-1-002).
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T.Y., R.K. and Y.S. conceived this research. K.O. prepared the samples. S.N. performed metagenomic sequence and analyzed the metagenomic data. M.I. supported the molecular analyses. S.N. wrote the draft manuscript and all authors commented on it. And all authors approved the final version of the manuscript.
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Communicated by Yusuf Akhter.
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Nishida, S., Omae, K., Inoue, M. et al. Construction of multiple metagenome assembled genomes containing carbon monoxide dehydrogenases from anaerobic carbon monoxide enrichment cultures. Arch Microbiol 205, 292 (2023). https://doi.org/10.1007/s00203-023-03635-4
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DOI: https://doi.org/10.1007/s00203-023-03635-4