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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

(2016) MICROBIAL ECOLOGY. 72(3). p.503-509
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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.
Keywords
Methanotrophs, Marine, Methanol dehydrogenase, Draft genome, GEN. NOV., NITROGEN-FIXATION, OXIDIZING BACTERIUM, MARINE-SEDIMENTS, OCEAN, MONOOXYGENASE, METABOLISM, SEQUENCES, OXIDATION, AMMONIUM

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MLA
Vekeman, Bram, et al. “Genome Characteristics of Two Novel Type I Methanotrophs Enriched from North Sea Sediments Containing Exclusively a Lanthanide-Dependent XoxF5-Type Methanol Dehydrogenase.” MICROBIAL ECOLOGY, vol. 72, no. 3, 2016, pp. 503–09, doi:10.1007/s00248-016-0808-7.
APA
Vekeman, B., Speth, D., Wille, J., Cremers, G., De Vos, P., Op den Camp, H. J. M., & Heylen, K. (2016). Genome characteristics of two novel type I methanotrophs enriched from North Sea sediments containing exclusively a lanthanide-dependent XoxF5-type methanol dehydrogenase. MICROBIAL ECOLOGY, 72(3), 503–509. https://doi.org/10.1007/s00248-016-0808-7
Chicago author-date
Vekeman, Bram, Daan Speth, Jasper Wille, Geert Cremers, Paul De Vos, Huub J. M. Op den Camp, and Kim Heylen. 2016. “Genome Characteristics of Two Novel Type I Methanotrophs Enriched from North Sea Sediments Containing Exclusively a Lanthanide-Dependent XoxF5-Type Methanol Dehydrogenase.” MICROBIAL ECOLOGY 72 (3): 503–9. https://doi.org/10.1007/s00248-016-0808-7.
Chicago author-date (all authors)
Vekeman, Bram, Daan Speth, Jasper Wille, Geert Cremers, Paul De Vos, Huub J. M. Op den Camp, and Kim Heylen. 2016. “Genome Characteristics of Two Novel Type I Methanotrophs Enriched from North Sea Sediments Containing Exclusively a Lanthanide-Dependent XoxF5-Type Methanol Dehydrogenase.” MICROBIAL ECOLOGY 72 (3): 503–509. doi:10.1007/s00248-016-0808-7.
Vancouver
1.
Vekeman B, Speth D, Wille J, Cremers G, De Vos P, Op den Camp HJM, et al. Genome characteristics of two novel type I methanotrophs enriched from North Sea sediments containing exclusively a lanthanide-dependent XoxF5-type methanol dehydrogenase. MICROBIAL ECOLOGY. 2016;72(3):503–9.
IEEE
[1]
B. Vekeman et al., “Genome characteristics of two novel type I methanotrophs enriched from North Sea sediments containing exclusively a lanthanide-dependent XoxF5-type methanol dehydrogenase,” MICROBIAL ECOLOGY, vol. 72, no. 3, pp. 503–509, 2016.
@article{8689190,
  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.}},
  author       = {{Vekeman, Bram and Speth, Daan and Wille, Jasper and Cremers, Geert and De Vos, Paul and Op den Camp, Huub J. M. and Heylen, Kim}},
  issn         = {{0095-3628}},
  journal      = {{MICROBIAL ECOLOGY}},
  keywords     = {{Methanotrophs,Marine,Methanol dehydrogenase,Draft genome,GEN. NOV.,NITROGEN-FIXATION,OXIDIZING BACTERIUM,MARINE-SEDIMENTS,OCEAN,MONOOXYGENASE,METABOLISM,SEQUENCES,OXIDATION,AMMONIUM}},
  language     = {{eng}},
  number       = {{3}},
  pages        = {{503--509}},
  title        = {{Genome characteristics of two novel type I methanotrophs enriched from North Sea sediments containing exclusively a lanthanide-dependent XoxF5-type methanol dehydrogenase}},
  url          = {{http://dx.doi.org/10.1007/s00248-016-0808-7}},
  volume       = {{72}},
  year         = {{2016}},
}

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