title: Identifying fermenting bacteria in anoxic tidal-flat sediments by a combination of microcalorimetry and ribosome-based stable-isotope probing.
abstract: A novel approach was developed to follow the successive utilization of organic carbon under anoxic conditions by microcalorimetry, chemical analyses of fermentation products and stable-isotope probing (SIP). The fermentation of (13) C-labeled glucose was monitored over 4 weeks by microcalorimetry in a stimulation experiment with tidal-flat sediments. Based on characteristic heat production phases, time points were selected for quantifying fermentation products and identifying substrate-assimilating bacteria by the isolation of intact ribosomes prior to rRNA-SIP. The preisolation of ribosomes resulted in rRNA with an excellent quality. Glucose was completely consumed within 2 days and was mainly fermented to acetate. Ethanol, formate, and hydrogen were detected intermittently. The amount of propionate that was built within the first 3 days stayed constant. Ribosome-based SIP of fully labeled and unlabeled rRNA was used for fingerprinting the glucose-degrading species and the inactive background community. The most abundant actively degrading bacterium was related to Psychromonas macrocephali (similarity 99%) as identified by DGGE and sequencing. The disappearance of Desulfovibrio-related bands in labeled rRNA after 3 days indicated that this group was active during the first degradation phase only. In summary, ribosome-based SIP in combination with microcalorimetry allows dissecting distinct phases in substrate turnover in a very sensitive manner.
authors.affiliation: Institut für Chemie und Biologie des Meeres, Carl-von-Ossietzky Universität Oldenburg, Oldenburg, Germany.
authors.forename: Jutta
authors.initials: J
authors.lastname: Graue
authors.forename: Sara
authors.initials: S
authors.lastname: Kleindienst
authors.forename: Tillmann
authors.initials: T
authors.lastname: Lueders
authors.forename: Heribert
authors.initials: H
authors.lastname: Cypionka
authors.forename: Bert
authors.initials: B
authors.lastname: Engelen
mesh_terms: D000085:Acetates / Q000378:metabolism; D001419:Bacteria / Q000145:classification / Q000302:isolation & purification* / Q000378:metabolism*; D002151:Calorimetry / Q000379:methods*; D002247:Carbon Isotopes; D058645:Denaturing Gradient Gel Electrophoresis; D003901:Desulfovibrio / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism; D005285:Fermentation; D019015:Geologic Sediments / Q000382:microbiology*; D010802:Phylogeny; D011422:Propionates / Q000378:metabolism; D012329:RNA, Bacterial / Q000032:analysis*; D012335:RNA, Ribosomal / Q000032:analysis*; D012336:RNA, Ribosomal, 16S / Q000235:genetics
chemical_list: D000085:Acetates; D002247:Carbon Isotopes; D011422:Propionates; D012329:RNA, Bacterial; D012335:RNA, Ribosomal; D012336:RNA, Ribosomal, 16S