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Genome Characteristics of Two Novel Type I Methanotrophs Enriched from North Sea Sediments Containing Exclusively a Lanthanide-Dependent XoxF5-Type Methanol Dehydrogenase

Abstract

Microbial methane oxidizers play a crucial role in the oxidation of methane in marine ecosystems, as such preventing the escape of excessive methane to the atmosphere. Despite the important role of methanotrophs in marine ecosystems, only a limited number of isolates are described, with only four genomes available. Here, we report on two genomes of gammaproteobacterial methanotroph cultures, affiliated with the deep-sea cluster 2, obtained from North Sea sediment. Initial enrichments using methane as sole source of carbon and energy and mimicking the in situ conditions followed by serial subcultivations and multiple extinction culturing events over a period of 3 years resulted in a highly enriched culture. The draft genomes of the methane oxidizer in both cultures showed the presence of genes typically found in type I methanotrophs, including genes encoding particulate methane monooxygenase (pmoCAB), genes for tetrahydromethanopterin (H4MPT)- and tetrahydrofolate (H4F)-dependent C1-transfer pathways, and genes of the ribulose monophosphate (RuMP) pathway. The most distinctive feature, when compared to other available gammaproteobacterial genomes, is the absence of a calcium-dependent methanol dehydrogenase. Both genomes reported here only have a xoxF gene encoding a lanthanide-dependent XoxF5-type methanol dehydrogenase. Thus, these genomes offer novel insight in the genomic landscape of uncultured diversity of marine methanotrophs.

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Acknowledgments

This work was funded by Ghent University (BOF09/GOA/005). K. Heylen was funded by the Fund for Scientific Research Flanders for a position as a postdoctoral fellow (FWO11/PDO/084 and FWO15/PDOH1/084). B. Vekeman was supported by a Ph.D. grant (IWT/111108) from the Institute for the Promotion of Innovation through Science and Technology in Flanders (IWT-Vlaanderen). D. Speth was funded by BE-Basic grant fp07.002 and Geert Cremers by SIAM Gravitation grant 24002002 (Netherlands Organization for Scientific Research). H.J.M. Op den Camp gratefully acknowledges funding by ERC grant 669371 (VOLCANO).

Author Contributions

B.V., P.D.V and K.H. designed the research ; B.V., J.W., D.S., and G.C. performed research and analyzed data; B.V., H.O.d.C., and K.H. interpreted the results and wrote the paper.

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Correspondence to Bram Vekeman.

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Vekeman, B., Speth, D., Wille, J. et al. Genome Characteristics of Two Novel Type I Methanotrophs Enriched from North Sea Sediments Containing Exclusively a Lanthanide-Dependent XoxF5-Type Methanol Dehydrogenase. Microb Ecol 72, 503–509 (2016). https://doi.org/10.1007/s00248-016-0808-7

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  • DOI: https://doi.org/10.1007/s00248-016-0808-7

Keywords

  • Methanotrophs
  • Marine
  • Methanol dehydrogenase
  • Draft genome