title: XoxF encoding an alternative methanol dehydrogenase is widespread in coastal marine environments.
abstract: The xoxF gene, encoding a pyrroloquinoline quinone-dependent methanol dehydrogenase, is found in all known proteobacterial methylotrophs. In several newly discovered methylotrophs, XoxF is the active methanol dehydrogenase, catalysing the oxidation of methanol to formaldehyde. Apart from that, its potential role in methylotrophy and carbon cycling is unknown. So far, the diversity of xoxF in the environment has received little attention. We designed PCR primer sets targeting clades of the xoxF gene, and used 454 pyrosequencing of PCR amplicons obtained from the DNA of four coastal marine environments for a unique assessment of the diversity of xoxF in these habitats. Phylogenetic analysis of the data obtained revealed a high diversity of xoxF genes from two of the investigated clades, and substantial differences in sequence composition between environments. Sequences were classified as being related to a wide range of both methylotrophs and non-methylotrophs from Alphaproteobacteria, Betaproteobacteria and Gammaproteobacteria. The most prominent sequences detected were related to the family Rhodobacteraceae, the genus Methylotenera and the OM43 clade of Methylophilales, and are thus related to organisms that employ XoxF for methanol oxidation. Furthermore, our analyses revealed a high degree of so far undescribed sequences, suggesting a high number of unknown bacterial species in these habitats.
authors.affiliation: School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.|Department of Aquatic Geomicrobiology, Friedrich Schiller University Jena, Dornburger Str. 159, Jena, 07743, Germany.
authors.forename: Martin
authors.initials: M
authors.lastname: Taubert
authors.affiliation: School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
authors.forename: Carolina
authors.initials: C
authors.lastname: Grob
authors.affiliation: School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
authors.forename: Alexandra M
authors.initials: AM
authors.lastname: Howat
authors.affiliation: School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
authors.forename: Oliver J
authors.initials: OJ
authors.lastname: Burns
authors.affiliation: Plymouth Marine Laboratory, Prospect Place, The Hoe, Plymouth, PL1 3DH, UK.
authors.forename: Joanna L
authors.initials: JL
authors.lastname: Dixon
authors.affiliation: School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK.
authors.forename: Yin
authors.initials: Y
authors.lastname: Chen
authors.affiliation: School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
authors.forename: J Colin
authors.initials: JC
authors.lastname: Murrell
mesh_terms: D000429:Alcohol Oxidoreductases / Q000235:genetics* / Q000378:metabolism*; D020561:Alphaproteobacteria / Q000235:genetics* / Q000378:metabolism; D059001:Aquatic Organisms / Q000235:genetics / Q000378:metabolism; D020562:Betaproteobacteria / Q000235:genetics* / Q000378:metabolism; D057486:Carbon Cycle; D005557:Formaldehyde / Q000378:metabolism; D020563:Gammaproteobacteria / Q000235:genetics* / Q000378:metabolism; D000432:Methanol / Q000378:metabolism; D045542:PQQ Cofactor / Q000378:metabolism; D010802:Phylogeny; D016133:Polymerase Chain Reaction
chemical_list: D005557:Formaldehyde; D045542:PQQ Cofactor; D000429:Alcohol Oxidoreductases; C019641:alcohol dehydrogenase (acceptor); D000432:Methanol