title: Methane-fed microbial microcosms show differential community dynamics and pinpoint taxa involved in communal response.
abstract: We report observations on the dynamics of bacterial communities in response to methane stimulus in laboratory microcosm incubations prepared with lake sediment samples. We first measured taxonomic compositions of long-term enrichment cultures and determined that, although dominated by Methylococcaceae types, these cultures also contained accompanying types belonging to a limited number of bacterial taxa, methylotrophs and non-methylotrophs. We then followed the short-term community dynamics, in two oxygen tension regimens (150 μM and 15 μM), observing rapid loss of species diversity. In all microcosms, a single type of Methylobacter represented the major methane-oxidizing partner. The accompanying members of the communities revealed different trajectories in response to different oxygen tensions, with Methylotenera species being the early responders to methane stimulus under both conditions. The communities in both conditions were convergent in terms of their assemblage, suggesting selection for specific taxa. Our results support prior observations from metagenomics on distribution of carbon from methane among diverse bacterial populations and further suggest that communities are likely responsible for methane cycling, rather than a single type of microbe.
authors.affiliation: 1] Department of Chemical Engineering, University of Washington, Seattle, WA, USA [2] Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia.
authors.forename: Igor Y
authors.initials: IY
authors.lastname: Oshkin
authors.affiliation: 1] Department of Chemical Engineering, University of Washington, Seattle, WA, USA [2] eScience Institute, University of Washington, Seattle, WA, USA.
authors.forename: David A C
authors.initials: DA
authors.lastname: Beck
authors.affiliation: Department of Chemical Engineering, University of Washington, Seattle, WA, USA.
authors.forename: Andrew E
authors.initials: AE
authors.lastname: Lamb
authors.affiliation: Department of Microbiology, University of Washington, Seattle, WA, USA.
authors.forename: Veronika
authors.initials: V
authors.lastname: Tchesnokova
authors.affiliation: Department of Chemical Engineering, University of Washington, Seattle, WA, USA.
authors.forename: Gabrielle
authors.initials: G
authors.lastname: Benuska
authors.affiliation: Department of Chemical Engineering, University of Washington, Seattle, WA, USA.
authors.forename: Tami L
authors.initials: TL
authors.lastname: McTaggart
authors.affiliation: Department of Microbiology, University of Washington, Seattle, WA, USA.
authors.forename: Marina G
authors.initials: MG
authors.lastname: Kalyuzhnaya
authors.affiliation: Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia.
authors.forename: Svetlana N
authors.initials: SN
authors.lastname: Dedysh
authors.affiliation: 1] Department of Chemical Engineering, University of Washington, Seattle, WA, USA [2] Department of Microbiology, University of Washington, Seattle, WA, USA.
authors.forename: Mary E
authors.initials: ME
authors.lastname: Lidstrom
authors.affiliation: Department of Chemical Engineering, University of Washington, Seattle, WA, USA.
authors.forename: Ludmila
authors.initials: L
authors.lastname: Chistoserdova
mesh_terms: D016680:Genome, Bacterial; D060106:Lakes / Q000382:microbiology*; D056186:Metagenomics; D008697:Methane / Q000737:chemistry*; D008772:Methylococcaceae / Q000235:genetics*; D010100:Oxygen / Q000737:chemistry; D010641:Phenotype; D012336:RNA, Ribosomal, 16S / Q000235:genetics*; D017422:Sequence Analysis, DNA; D014871:Water Microbiology
chemical_list: D012336:RNA, Ribosomal, 16S; D008697:Methane; D010100:Oxygen