Publications

novel division level bacterial diversity in a yellowstone hot spring.	a culture-independent molecular phylogenetic survey was carried out for the bacterial community in obsidian pool (op), a yellowstone national park hot spring previously shown to contain remarkable archaeal diversity (s. m. barns, r. e. fundyga, m. w. jeffries, and n. r. page, proc. natl. acad. sci. usa 91:1609-1613, 1994). small-subunit rrna genes (rdna) were amplified directly from op sediment dna by pcr with universally conserved or bacteria-specific rdna primers and cloned. unique rdna types ...	1998	9440526
phylogenetic diversity of mesophilic and thermophilic granular sludges determined by 16s rrna gene analysis.	the microbial diversity of two types of methanogenic granular sludge, mesophilic (35 degrees c) and thermophilic (55 degrees c), which had been treating sucrose/propionate/acetate-based artificial wastewater were compared. 16s rdna clone libraries were constructed by pcr with a prokaryote-specific primer set, and partial sequencing of the clonal 16s rdnas was conducted for phylogenetic analysis. of 115 mesophilic granule and 110 thermophilic granule clones sequenced, 19 and 22%, respectively, we ...	1998	9782515
diversity of dissimilatory bisulfite reductase genes of bacteria associated with the deep-sea hydrothermal vent polychaete annelid alvinella pompejana.	a unique community of bacteria colonizes the dorsal integument of the polychaete annelid alvinella pompejana, which inhabits the high-temperature environments of active deep-sea hydrothermal vents along the east pacific rise. the composition of this bacterial community was characterized in previous studies by using a 16s rrna gene clone library and in situ hybridization with oligonucleotide probes. in the present study, a pair of pcr primers (p94-f and p93-r) were used to amplify a segment of th ...	1999	10049872
kinetics of sulfate and hydrogen uptake by the thermophilic sulfate-reducing bacteria thermodesulfobacterium sp. strain jsp and thermodesulfovibrio sp. strain r1ha3	half-saturation constants (km), maximum uptake rates (vmax), and threshold concentrations for sulfate and hydrogen were determined for two thermophilic sulfate-reducing bacteria (srb) in an incubation system without headspace. km values determined for the thermophilic srb were similar to the constants described for mesophilic srb isolated from environments with low sulfate concentrations.	1999	10049897
thermodesulfobacterium hveragerdense sp. nov., and thermodesulfovibrio islandicus sp. nov., two thermophilic sulfate reducing bacteria isolated from a icelandic hot spring.	two thermophilic non-sporeforming sulfate-reducing bacteria (srb) were isolated from microbial mats collected from an icelandic hot spring. strain jsp was a gram negative rod, with an average cell size of 2.8 x 0.5 microm. no flagella were found. growth occurred between 55 and 74 degrees c with an optimum between 70 and 74 degrees c at ph 7.0. the g+c content was 40 mol%. strain r1ha3 was a gram negative vibrio-shaped rod with an average cell size of 1.7 x 0.4 microm. motility was observed media ...	1999	10794144
characterization of a new thermophilic sulfate-reducing bacterium thermodesulfovibrio yellowstonii, gen. nov. and sp. nov.: its phylogenetic relationship to thermodesulfobacterium commune and their origins deep within the bacterial domain.	a thermophilic sulfate-reducing vibrio isolated from thermal vent water in yellowstone lake, wyoming, usa is described. the gram-negative, curved rod-shaped cells averaged 0.3 micrometer wide and 1.5 micrometers long. they were motile by means of a single polar flagellum. growth was observed between 40 degrees and 70 degrees c with optimal growth at 65 degrees c. cultures remained viable for one year at 27 degrees c although spore-formation was not observed. sulfate, thiosulfate and sulfite were ...	1994	11541228
multiple lateral transfers of dissimilatory sulfite reductase genes between major lineages of sulfate-reducing prokaryotes.	a large fragment of the dissimilatory sulfite reductase genes (dsrab) was pcr amplified and fully sequenced from 30 reference strains representing all recognized lineages of sulfate-reducing bacteria. in addition, the sequence of the dsrab gene homologs of the sulfite reducer desulfitobacterium dehalogenans was determined. in contrast to previous reports, comparative analysis of all available dsrab sequences produced a tree topology partially inconsistent with the corresponding 16s rrna phylogen ...	2001	11567003
phylogenetic analysis reveals multiple lateral transfers of adenosine-5'-phosphosulfate reductase genes among sulfate-reducing microorganisms.	lateral gene transfer affects the evolutionary path of key genes involved in ancient metabolic traits, such as sulfate respiration, even more than previously expected. in this study, the phylogeny of the adenosine-5'-phosphosulfate (aps) reductase was analyzed. aps reductase is a key enzyme in sulfate respiration present in all sulfate-respiring prokaryotes. a newly developed pcr assay was used to amplify and sequence a fragment ( approximately 900 bp) of the aps reductase gene, apsa, from a tax ...	2002	11741869
thermotoga lettingae sp. nov., a novel thermophilic, methanol-degrading bacterium isolated from a thermophilic anaerobic reactor.	a novel, anaerobic, non-spore-forming, mobile, gram-negative, thermophilic bacterium, strain tmot, was isolated from a thermophilic sulfate-reducing bioreactor operated at 65 c with methanol as the sole substrate. the g+c content of the dna of strain tmot was 39.2 mol%. the optimum ph, nacl concentration, and temperature for growth were 7.0, 1.0%, and 65 degrees c, respectively. strain tmot was able to degrade methanol to co2 and h2 in syntrophic culture with methanothermobacter thermautotrophic ...	2002	12148651
phylogenetic diversity of sulfate-reducing prokaryotes in active deep-sea hydrothermal vent chimney structures.	the phylogenetic diversity of sulfate-reducing prokaryotes occurring in active deep-sea hydrothermal vent chimney structures was characterized based on the deduced amino acid sequence analysis of the polymerase chain reaction-amplified dissimilatory sulfite reductase (dsr) gene. the dsr genes were successfully amplified from microbial assemblages of the chimney structures, derived from three geographically and geologically distinct deep-sea hydrothermal systems in the central indian ridge (cir), ...	2004	15033233
microbial community in a geothermal aquifer associated with the subsurface of the great artesian basin, australia.	to investigate the biomass and phylogenetic diversity of the microbial community inhabiting the deep aquifer of the great artesian basin (gab), geothermal groundwater gushing out from the aquifer was sampled and analyzed. microbial cells in the groundwater were stained with acridine orange and directly counted by epifluorescence microscopy. microbial cells were present at a density of 10(8)-10(9) cells per liter of groundwater. archaeal and bacterial small-subunit rrna genes (rdnas) were amplifi ...	2005	15980939
carbon monoxide conversion by thermophilic sulfate-reducing bacteria in pure culture and in co-culture with carboxydothermus hydrogenoformans.	biological sulfate (so(4)) reduction with carbon monoxide (co) as electron donor was investigated. four thermophilic so(4)-reducing bacteria, desulfotomaculum thermoacetoxidans (dsm 5813), thermodesulfovibrio yellowstonii (atcc 51303), desulfotomaculum kuznetsovii (dsm 6115; vkm b-1805), and desulfotomaculum thermobenzoicum subsp. thermosyntrophicum (dsm 14055), were studied in pure culture and in co-culture with the thermophilic carboxydotrophic bacterium carboxydothermus hydrogenoformans (dsm ...	2005	16133342
enrichment and detection of microorganisms involved in direct and indirect methanogenesis from methanol in an anaerobic thermophilic bioreactor.	to gain insight into the microorganisms involved in direct and indirect methane formation from methanol in a laboratory-scale thermophilic (55 degrees c) methanogenic bioreactor, reactor sludge was disrupted and serial dilutions were incubated in specific growth media containing methanol and possible intermediates of methanol degradation as substrates. with methanol, growth was observed up to a dilution of 10(8). however, when methanothermobacter thermoautotrophicus strain z245 was added for h2 ...	2005	16328652
[phylogenetic diversity and activity of anaerobic microorganisms of high-temperature horizons of the dagang oilfield (china)].	the number of microorganisms of major metabolic groups and the rates of sulfate-reducing and methanogenic processes in the formation waters of the high-temperature horizons of dagang oilfield have been determined. using cultural methods, it was shown that the microbial community contained aerobic bacteria oxidizing crude oil, anaerobic fermentative bacteria, sulfate-reducing bacteria, and methanogenic bacteria. using cultural methods, the possibility of methane production from a mixture of hydro ...	2006	16579447
evidence of the activity of dissimilatory sulfate-reducing prokaryotes in nonsulfidogenic tropical mobile muds.	in spite of the nonsulfidic conditions and abundant reactive iron(iii) commonly found in mobile tropical deltaic muds, genes encoding dissimilatory sulfite reductase (dsr) were successfully amplified from the upper approximately 1 m of coastal deposits sampled along french guiana and in the gulf of papua. the dsr sequences retrieved were highly diverse, were generally represented in both study regions and fell into six large phylogenetic groupings: deltaproteobacteria, thermodesulfovibrio groups ...	2006	16867136
identification of acetate-utilizing bacteria and archaea in methanogenic profundal sediments of lake kinneret (israel) by stable isotope probing of rrna.	acetate is an important intermediate in the decomposition of organic matter in anoxic freshwater sediments. here, we identified distinct microorganisms active in its oxidation and transformation to methane in the anoxic methanogenic layers of lake kinneret (israel) profundal sediment by rrna-based stable isotope probing (rna-sip). after 18 days of incubation with amended [u-(13)c]acetate we found that archaeal 16s rrna was (13)c-labelled to a far greater extent than bacterial rrna. we identified ...	2007	17227427
high rates of sulfate reduction in a low-sulfate hot spring microbial mat are driven by a low level of diversity of sulfate-respiring microorganisms.	the importance of sulfate respiration in the microbial mat found in the low-sulfate thermal outflow of mushroom spring in yellowstone national park was evaluated using a combination of molecular, microelectrode, and radiotracer studies. despite very low sulfate concentrations, this mat community was shown to sustain a highly active sulfur cycle. the highest rates of sulfate respiration were measured close to the surface of the mat late in the day when photosynthetic oxygen production ceased and ...	2007	17575000
phylogeny of the alpha and beta subunits of the dissimilatory adenosine-5'-phosphosulfate (aps) reductase from sulfate-reducing prokaryotes--origin and evolution of the dissimilatory sulfate-reduction pathway.	newly developed pcr assays were used to pcr-amplify and sequence fragments of the dissimilatory adenosine-5'-phosphosulfate (aps) reductase genes (aprba) comprising nearly the entire gene locus (2.2-2.4 kb, equal to 92-94 % of the protein coding sequence) from 75 sulfate-reducing prokaryotes (srp) of a taxonomically wide range. comparative phylogenetic analysis included all determined and publicly available aprba sequences from srp and selected homologous sequences of sulfur-oxidizing bacteria ( ...	2007	17600048
thermodesulfovibrio hydrogeniphilus sp. nov., a new thermophilic sulphate-reducing bacterium isolated from a tunisian hot spring.	a new thermophilic sulphate-reducing bacterium (strain hbr5t) was enriched and isolated from a terrestrial tunisian hot spring. it was a non-spore-forming gram-negative curved or vibrio-shaped bacterium. it appeared singly or in long chains and was actively motile by a polar flagellum. it possessed c-type cytochromes and desulfofuscidin. growth occurred between 50 and 70 degrees c, with an optimum of 65 degrees c at ph 7.1. in the presence of sulphate as a terminal electron acceptor, this strain ...	2008	18221850
thermodesulfovibrio aggregans sp. nov. and thermodesulfovibrio thiophilus sp. nov., anaerobic, thermophilic, sulfate-reducing bacteria isolated from thermophilic methanogenic sludge, and emended description of the genus thermodesulfovibrio.	four obligately anaerobic, thermophilic, sulfate-reducing bacterial strains, designated tge-p1(t), tdv(t), tgl-ls1 and tsl-p1, were isolated from thermophilic (operated at 55 degrees c) methanogenic sludges from waste and wastewater treatment. the optimum temperature for growth of all the strains was in the range 55-60 degrees c. the four strains grew by reduction of sulfate with a limited range of electron donors, such as hydrogen, formate, pyruvate and lactate. in co-culture with the hydrogeno ...	2008	18984690
evaluation of the phylogenetic position of the sulfate-reducing bacterium thermodesulfovibrio yellowstonii (phylum nitrospirae) by means of gene order data from completely sequenced genomes.	the phylogenetic placement of thermodesulfovibrio yellowstonii was investigated on the basis of gene order data from completely sequenced bacterial genomes. t. yellowstonii was found to share four gene arrangements characteristic of the proteobacteria, aquificae, planctomycetes, spirochaetes, bacteroidetes, chlorobi, acidobacteria, verrucomicrobia and termite group 1, the presence of which defines superphylum 2. the remaining phyla show sets of alternative gene arrangements and form superphylum ...	2010	19666800
methanol utilization in defined mixed cultures of thermophilic anaerobes in the presence of sulfate.	we studied thermophilic sulfate reduction with methanol as electron donor in continuous cultures. mixed cultures of selected microorganisms were used, representing different methanol degrading pathways followed by various trophic groups of microorganisms. our results show that direct competition for methanol between a homoacetogen, moorella thermoautotrophica, and a sulfate reducer, desulfotomaculum kuznetsovii, is in favour of the sulfate reducer due to its affinity for methanol. methanogenesis ...	2004	19712297
a comparative genomic analysis of energy metabolism in sulfate reducing bacteria and archaea.	the number of sequenced genomes of sulfate reducing organisms (sro) has increased significantly in the recent years, providing an opportunity for a broader perspective into their energy metabolism. in this work we carried out a comparative survey of energy metabolism genes found in 25 available genomes of sro. this analysis revealed a higher diversity of possible energy conserving pathways than classically considered to be present in these organisms, and permitted the identification of new prote ...	2011	21747791