title: The expanded diversity of methylophilaceae from Lake Washington through cultivation and genomic sequencing of novel ecotypes.
abstract: We describe five novel Methylophilaceae ecotypes from a single ecological niche in Lake Washington, USA, and compare them to three previously described ecotypes, in terms of their phenotype and genome sequence divergence. Two of the ecotypes appear to represent novel genera within the Methylophilaceae. Genome-based metabolic reconstruction highlights metabolic versatility of Methylophilaceae with respect to methylotrophy and nitrogen metabolism, different ecotypes possessing different combinations of primary substrate oxidation systems (MxaFI-type methanol dehydrogenase versus XoxF-type methanol dehydrogenase; methylamine dehydrogenase versus N-methylglutamate pathway) and different potentials for denitrification (assimilatory versus respiratory nitrate reduction). By comparing pairs of closely related genomes, we uncover that site-specific recombination is the main means of genomic evolution and strain divergence, including lateral transfers of genes from both closely- and distantly related taxa. The new ecotypes and the new genomes contribute significantly to our understanding of the extent of genomic and metabolic diversity among organisms of the same family inhabiting the same ecological niche. These organisms also provide novel experimental models for studying the complexity and the function of the microbial communities active in methylotrophy.
authors: Department of Chemical Engineering, University of Washington, Seattle, Washington, United States of America; eScience Institute, University of Washington, Seattle, Washington, United States of America.
authors: David A C
authors: DA
authors: Beck
authors: Department of Chemical Engineering, University of Washington, Seattle, Washington, United States of America.
authors: Tami L
authors: TL
authors: McTaggart
authors: Department of Chemical Engineering, University of Washington, Seattle, Washington, United States of America.
authors: Usanisa
authors: U
authors: Setboonsarng
authors: Department of Chemical Engineering, University of Washington, Seattle, Washington, United States of America.
authors: Alexey
authors: A
authors: Vorobev
authors: Department of Microbiology, University of Washington, Seattle, Washington, United States of America.
authors: Marina G
authors: MG
authors: Kalyuzhnaya
authors: DOE Joint Genome Institute, Walnut Creek, California, United States of America.
authors: Natalia
authors: N
authors: Ivanova
authors: Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America.
authors: Lynne
authors: L
authors: Goodwin
authors: DOE Joint Genome Institute, Walnut Creek, California, United States of America.
authors: Tanja
authors: T
authors: Woyke
authors: Department of Chemical Engineering, University of Washington, Seattle, Washington, United States of America; Department of Microbiology, University of Washington, Seattle, Washington, United States of America.
authors: Mary E
authors: ME
authors: Lidstrom
authors: Department of Chemical Engineering, University of Washington, Seattle, Washington, United States of America.
authors: Ludmila
authors: L
authors: Chistoserdova
mesh_terms: D000429:Alcohol Oxidoreductases / Q000235:genetics / Q000378:metabolism; D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism*; D058440:Denitrification / Q000235:genetics; D060146:Ecotype; D014644:Genetic Variation; D016680:Genome, Bacterial; D005971:Glutamates / Q000378:metabolism; D060106:Lakes / Q000382:microbiology*; D042762:Methylophilaceae / Q000145:classification / Q000235:genetics / Q000378:metabolism*; D009584:Nitrogen / Q000378:metabolism*; D000587:Oxidoreductases Acting on CH-NH Group Donors / Q000235:genetics / Q000378:metabolism; D010802:Phylogeny; D011995:Recombination, Genetic; D014861:Washington
chemical_list: D001426:Bacterial Proteins; D005971:Glutamates; C476559:N-methylglutamate; D000429:Alcohol Oxidoreductases; C019641:alcohol dehydrogenase (acceptor); C021567:methylamine dehydrogenase; D000587:Oxidoreductases Acting on CH-NH Group Donors; D009584:Nitrogen