title: Functional and genomic diversity of methylotrophic Rhodocyclaceae: description of Methyloversatilis discipulorum sp. nov.
abstract: Three strains of methylotrophic Rhodocyclaceae (FAM1(T), RZ18-153 and RZ94) isolated from Lake Washington sediment samples were characterized. Based on phylogenetic analysis of 16S rRNA gene sequences the strains should be assigned to the genus Methyloversatilis. Similarly to other members of the family, the strains show broad metabolic capabilities and are able to utilize a number of organic acids, alcohols and aromatic compounds in addition to methanol and methylamine. The main fatty acids were 16:1ω7c (49-59%) and 16:0 (32-29%). Genomes of all isolates were sequenced, assembled and annotated in collaboration with the DOE Joint Genome Institute (JGI). Genome comparison revealed that the strains FAM1T, RZ18-153 and RZ94 are closely related to each other and almost equally distant from two previously described species of the genus Methyloversatilis, Methyloversatilis universalis and Methyloversatilis thermotolerans. Like other methylotrophic species of the genus Methyloversatilis, all three strains possess one-subunit PQQ-dependent ethanol/methanol dehydrogenase (Mdh-2), the N-methylglutamate pathway and the serine cycle (isocitrate lyase/malate synthase, Icl/ms(+) variant). Like M. universalis, strains FAM1(T), RZ18-153 and RZ94 have a quinohemoprotein amine dehydrogenase, a tungsten-containing formaldehyde ferredoxin oxidoreductase, phenol hydroxylase, and the complete Calvin cycle. Similarly to M. thermotolerans, the three strains possess two-subunit methanol dehydrogenase (MxaFI), monoamine oxidase (MAO) and nitrogenase. Based on the phenotypic and genomic data, the strains FAM1(T), RZ18-153 and RZ94 represent a novel species of the genus Methyloversatilis, for which the name Methyloversatilis discipulorum sp. nov. is proposed. The type strain is FAM1(T) ( = JCM 30542(T) = VKM = B-2888(T)).
authors.affiliation: Department of Microbiology, University of Washington, Seattle, WA, 98195, USA.
authors.forename: Nicole E
authors.initials: NE
authors.lastname: Smalley
authors.affiliation: Department of Biological and Environmental Science, University of Jyväskylä, PL 35 (YA), 40014 Jyväskylä, Finland.
authors.forename: Sami
authors.initials: S
authors.lastname: Taipale
authors.affiliation: IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, Portugal.|CESPU, IINFACTS, Gandra PRD, Portugal.
authors.forename: Paolo
authors.initials: P
authors.lastname: De Marco
authors.affiliation: Skryabin G.K. Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Prospect Nauki 5, Pushchino 142290, Moscow Region, Russia.
authors.forename: Nina V
authors.initials: NV
authors.lastname: Doronina
authors.affiliation: US DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA.
authors.forename: Nikos
authors.initials: N
authors.lastname: Kyrpides
authors.affiliation: US DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA.
authors.forename: Nicole
authors.initials: N
authors.lastname: Shapiro
authors.affiliation: US DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA.
authors.forename: Tanja
authors.initials: T
authors.lastname: Woyke
authors.affiliation: Department of Microbiology, University of Washington, Seattle, WA, 98195, USA.|Biology Department, San Diego State University, San Diego, CA, 92182-4614, USA.
authors.forename: Marina G
authors.initials: MG
authors.lastname: Kalyuzhnaya
mesh_terms: D000429:Alcohol Oxidoreductases / Q000737:chemistry; D015373:Bacterial Typing Techniques; D004269:DNA, Bacterial / Q000235:genetics; D005227:Fatty Acids / Q000737:chemistry; D016680:Genome, Bacterial; D023281:Genomics; D019015:Geologic Sediments / Q000382:microbiology*; D060106:Lakes / Q000382:microbiology; D008969:Molecular Sequence Data; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D043362:Rhodocyclaceae / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification; D017422:Sequence Analysis, DNA; D014861:Washington
chemical_list: D004269:DNA, Bacterial; D005227:Fatty Acids; D012336:RNA, Ribosomal, 16S; D000429:Alcohol Oxidoreductases; C019641:alcohol dehydrogenase (acceptor)