title: 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.
authors.affiliation: Department of Biochemistry and Microbiology, Laboratory of Microbiology (LM-UGent), Ghent University, Karel Lodewijck Ledeganckstraat 35, 9000, Ghent, Belgium. Bram.Vekeman@ugent.be.
authors.forename: Bram
authors.initials: B
authors.lastname: Vekeman
authors.affiliation: Department of Microbiology, IWWR, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands.
authors.forename: Daan
authors.initials: D
authors.lastname: Speth
authors.affiliation: Department of Biochemistry and Microbiology, Laboratory of Microbiology (LM-UGent), Ghent University, Karel Lodewijck Ledeganckstraat 35, 9000, Ghent, Belgium.
authors.forename: Jasper
authors.initials: J
authors.lastname: Wille
authors.affiliation: Department of Microbiology, IWWR, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands.
authors.forename: Geert
authors.initials: G
authors.lastname: Cremers
authors.affiliation: Department of Biochemistry and Microbiology, Laboratory of Microbiology (LM-UGent), Ghent University, Karel Lodewijck Ledeganckstraat 35, 9000, Ghent, Belgium.
authors.forename: Paul
authors.initials: P
authors.lastname: De Vos
authors.affiliation: Department of Microbiology, IWWR, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands.
authors.forename: Huub J M
authors.initials: HJ
authors.lastname: Op den Camp
authors.affiliation: Department of Biochemistry and Microbiology, Laboratory of Microbiology (LM-UGent), Ghent University, Karel Lodewijck Ledeganckstraat 35, 9000, Ghent, Belgium.
authors.forename: Kim
authors.initials: K
authors.lastname: Heylen
mesh_terms: D000429:Alcohol Oxidoreductases / Q000235:genetics*; D001426:Bacterial Proteins / Q000235:genetics* / Q000378:metabolism; D001482:Base Composition; D002118:Calcium; D004269:DNA, Bacterial / Q000235:genetics; D017753:Ecosystem; D015964:Gene Expression Regulation, Bacterial; D015971:Gene Expression Regulation, Enzymologic; D016680:Genome, Bacterial; D019015:Geologic Sediments / Q000382:microbiology*; D028581:Lanthanoid Series Elements / Q000494:pharmacology*; D053858:Metabolic Networks and Pathways / Q000235:genetics; D008697:Methane / Q000378:metabolism; D008772:Methylococcaceae / Q000145:classification / Q000187:drug effects / Q000201:enzymology* / Q000235:genetics*; D009584:Nitrogen / Q000378:metabolism; D009659:North Sea; D010084:Oxidation-Reduction; D010105:Oxygenases / Q000235:genetics; D010802:Phylogeny; D012623:Seawater / Q000382:microbiology; D013763:Tetrahydrofolates / Q000235:genetics
chemical_list: D001426:Bacterial Proteins; D004269:DNA, Bacterial; D028581:Lanthanoid Series Elements; D013763:Tetrahydrofolates; C030371:5,6,7,8-tetrahydrofolic acid; D000429:Alcohol Oxidoreductases; C019641:alcohol dehydrogenase (acceptor); D010105:Oxygenases; C021555:methane monooxygenase; D009584:Nitrogen; D008697:Methane; D002118:Calcium
keywords: Draft genome; Marine; Methanol dehydrogenase; Methanotrophs