title: Uncultured Desulfobacteraceae and Crenarchaeotal group C3 incorporate 13C-acetate in coastal marine sediment.
abstract: Stable isotope probing (SIP) of deoxyribonucleic acid (DNA) was used to identify microbes incorporating (13) C-labeled acetate in sulfate-reducing sediment from Aarhus Bay, Denmark. Sediment was incubated in medium containing 10 mM sulfate and different (13) C-acetate (10, 1, 0.1 mM) concentrations. The resultant changes in microbial community composition were monitored in total and SIP-fractionated DNA during long-term incubations. Chemical analyses demonstrated metabolic activity in all sediment slurries, with sulfate-reducing activity largely determined by initial acetate concentrations. Sequencing of 16S rRNA gene PCR amplicons showed that the incubations shifted the bacterial but not the archaeal community composition. After 3 months of incubation, only sediment slurries incubated with 10 mM (13) C-acetate showed detectable (13) C-DNA labeling. Based on 16S rRNA and dsrB gene PCR amplicon sequencing, the (13) C-labeled DNA pool was dominated by a single type of sulfate reducer representing a novel genus in the family Desulfobacteraceae. In addition, members of the uncultivated Crenarchaeotal group C3 were enriched in the (13) C-labeled DNA. Our results were reproducible across biological replicate experiments and provide new information about the identities of uncultured acetate-consuming bacteria and archaea in marine sediments.
authors.affiliation: Center for Geomicrobiology, Department of Bioscience, Aarhus University, Ny Munkegade 114, DK-8000, Aarhus, Denmark.
authors.forename: Hyunsoo
authors.initials: H
authors.lastname: Na
authors.affiliation: Center for Geomicrobiology, Department of Bioscience, Aarhus University, Ny Munkegade 114, DK-8000, Aarhus, Denmark.
authors.forename: Mark Alexander
authors.initials: MA
authors.lastname: Lever
authors.affiliation: Center for Geomicrobiology, Department of Bioscience, Aarhus University, Ny Munkegade 114, DK-8000, Aarhus, Denmark.
authors.forename: Kasper Urup
authors.initials: KU
authors.lastname: Kjeldsen
authors.affiliation: Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, University of Vienna, Althanstraße 14, 1090, Vienna, Austria.
authors.forename: Frederik
authors.initials: F
authors.lastname: Schulz
authors.affiliation: Center for Geomicrobiology, Department of Bioscience, Aarhus University, Ny Munkegade 114, DK-8000, Aarhus, Denmark.
authors.forename: Bo Barker
authors.initials: BB
authors.lastname: Jørgensen
mesh_terms: D000085:Acetates / Q000378:metabolism*; D058448:Biota / Q000187:drug effects*; D002244:Carbon / Q000378:metabolism*; D016000:Cluster Analysis; D019615:Crenarchaeota / Q000378:metabolism*; D019641:DNA, Archaeal / Q000737:chemistry / Q000235:genetics; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D020564:Deltaproteobacteria / Q000378:metabolism*; D003718:Denmark; D019015:Geologic Sediments / Q000382:microbiology*; D007553:Isotope Labeling; D010084:Oxidation-Reduction; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA; D013431:Sulfates / Q000378:metabolism
chemical_list: D000085:Acetates; D019641:DNA, Archaeal; D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S; D013431:Sulfates; D002244:Carbon