Publications

evolutionary relationships among sulfur- and iron-oxidizing eubacteria.	some 37 reverse transcriptase, partial 16s rrna sequences from sulfur- and/or iron-oxidizing eubacteria, including sequences from species of the genera thiobacillus, thiothrix, thiomicrospira, acidophilium, "leptospirillum," thiovulum, and chlorobium, have been determined. in addition, 16s sequences from a number of unnamed sulfur- and/or iron-oxidizing bacteria from hydrothermal vent sites, from invertebrate-bacterial endosymbioses, and from various mineral recovery operations also have been de ...	1992	1729214
phylogenetic analysis of the genera thiobacillus and thiomicrospira by 5s rrna sequences.	5s rrna nucleotide sequences from thiobacillus neapolitanus, thiobacillus ferrooxidans, thiobacillus thiooxidans, thiobacillus intermedius, thiobacillus perometabolis, thiobacillus thioparus, thiobacillus versutus, thiobacillus novellus, thiobacillus acidophilus, thiomicrospira pelophila, thiomicrospira sp. strain l-12, and acidiphilium cryptum were determined. a phylogenetic tree, based upon comparison of these and other related 5s rrna sequences, is presented. the results place the thiobacilli ...	1985	3924899
thiomicrospira pelophila, gen. n., sp. n., a new obligately chemolithotrophic colourless sulfur bacterium.		1972	4561895
effects of organic compounds on growth of chemostat cultures of thiomicrospira pelophila, thiobacillus thioparus and thiobacillus neapolitanus.		1973	4591719
cell yield and bioenergetics of thiomicrospira denitrificans compared with thiobacillus denitrificans.	from cell yields of thiomicrospira denitrificans grown inthe chemostat at different growth rates under anaerobic conditions a value of 1.4 mm s2o3 = per g dry wt and per h could be calculated for maintenance energy requirements, and of 5.65 dry wt per mole s2o3 = for the true growth yield. cell yields of thiomicrospira denitrificans appeared to be almost half of those of thiobacillus denitrificans. though in thiobacillus denitrificans at d = 0.03 h(-1) under anaerobic conditions a value was foun ...	1981	6791590
physiological characteristics of thiomicrospira sp. strain l-12 isolated from deep-sea hydrothermal vents.	growth of the obligately chemolithotrophic thiomicrospira sp. strain l-12, isolated from a hydrothermal vent at a depth of 2,550 m in the galapagos rift region, was optimal at ph 8 and required 200 mm na+ and divalent ions (ca2+ and mg2+). the organism was microaerophilic and tolerated 300 microm sulfide without a decrease in the rate of co2 incorporation. growth and co2 incorporation occurred within the temperature range of 10 to 35 degrees c, with both optimal at 25 degrees c. at the in situ p ...	1982	7054142
phylogenetic analysis of a highly specific association between ectosymbiotic, sulfur-oxidizing bacteria and a marine nematode.	the phylogenetic relationship of chemoautotrophic, sulfur-oxidizing, ectosymbiotic bacteria growing on a marine nematode, a laxus sp. (formerly a catanema sp.), to known endosymbionts and free-living bacteria was determined. comparative 16s rrna sequencing was used to investigate the unculturable nematode epibionts, and rrna-targeted oligonucleotide hybridization probes were used to identify the ectosymbionts in situ. both analyses revealed a remarkably specific and stable symbiosis. unique hybr ...	1994	7529016
phylogenetic relationships of thiomicrospira species and their identification in deep-sea hydrothermal vent samples by denaturing gradient gel electrophoresis of 16s rdna fragments.	denaturing gradient gel electrophoresis (dgge) of pcr-amplified 16s rdna fragments was used to explore the genetic diversity of hydrothermal vent microbial communities, specifically to determine the importance of sulfur-oxidizing bacteria therein. dgge analysis of two different hydrothermal vent samples revealed one pcr band for one sample and three pcr bands for the other sample, which probably correspond to the dominant bacterial populations in these communities. three of the four 16s rdna fra ...	1995	7545384
characterization of 16s rrna genes from oil field microbial communities indicates the presence of a variety of sulfate-reducing, fermentative, and sulfide-oxidizing bacteria.	oil field bacteria were characterized by cloning and sequencing of pcr-amplified 16s rrna genes. a variety of gram-negative, sulfate-reducing bacteria was detected (16 members of the family desulfovibrionaceae and 8 members of the family desulfobacteriaceae). in contrast, a much more limited number of anaerobic, fermentative, or acetogenic bacteria was found (one clostridium sp., one eubacterium sp., and one synergistes sp.). potential sulfide oxidizers and/or microaerophiles (thiomicrospira, ar ...	1996	8633860
characterization of thiobacillus thioparus lv43 and its distribution in a chemoautotrophically based groundwater ecosystem.	bacterial strain lv43 was previously isolated from a floating microbial mat located in movile cave, the access point to a chemoautotrophically based groundwater ecosystem in southern romania. this gram-negative, rod-shaped organism grows autotrophically through the oxidation of thiosulfate and sulfide, but it does not grow heterotrophically. strain lv43 grows over a ph range of 5.0 to 9.0, with an optimum near 7.5 at 28 degrees c. the ph of the medium decreased from 7.5 to 6.5 during growth on t ...	1997	9251199
increased species diversity and extended habitat range of sulfur-oxidizing thiomicrospira spp.	we combined traditional cultivation methods and new molecular techniques to study the diversity and habitat range of bacteria of the genus thiomicrospira. specific primers were designed and used in the pcr to amplify the 16s ribosomal dna (rdna) of thiomicrospira spp. and thus detect the presence of these bacteria in environmental samples and enrichment cultures. by using this genus-specific pcr, we were able to amplify 722-bp-long 16s rdna fragments from different saltwater habitats as well as ...	1997	9327542
phylogenetic position of an obligately chemoautotrophic, marine hydrogen-oxidizing bacterium, hydrogenovibrio marinus, on the basis of 16s rrna gene sequences and two form i rubisco gene sequences.	two form ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco) genes from the obligately autotrophic, marine hydrogen oxidizer hydrogenovibrio marinus were sequenced. the deduced amino acid sequences of both rubiscos revealed that they are similar to those of sulfur oxidizers (thiobacillus) and a purple sulfur bacterium (chromatium vinosum). according to the 16s rrna gene sequences, h. marinus is also affiliated with these microorganisms, members of thiomicrospira being the closest relatives ...	1998	9531639
comparison of a new thiomicrospira strain from the mid-atlantic ridge with known hydrothermal vent isolates	a new autotrophic thiomicrospira strain, ma-3, was isolated from the surface of a polymetal sulfide deposit collected at a mid-atlantic ridge hydrothermal vent site. the dna homology among three vent isolates, thiomicrospira crunogena, thiomicrospira sp. strain l-12, and thiomicrospira sp. strain ma-3, was 99.3% or higher, grouping them as the same species, t. crunogena (type strain, atcc 35932). the fact that t. crunogena and thiomicrospira sp. strain l-12 were isolated from pacific vent sites ...	1998	9758841
a polyphasic approach to study the diversity and vertical distribution of sulfur-oxidizing thiomicrospira species in coastal sediments of the german wadden sea	recently, four thiomicrospira strains were isolated from a coastal mud flat of the german wadden sea (t. brinkhoff and g. muyzer, appl. environ. microbiol. 63:3789-3796, 1997). here we describe the use of a polyphasic approach to investigate the functional role of these closely related bacteria. microsensor measurements showed that there was oxygen penetration into the sediment to a depth of about 2.0 mm. the ph decreased from 8.15 in the overlaying water to a minimum value of 7.3 at a depth of ...	1998	9835544
thiomicrospira kuenenii sp. nov. and thiomicrospira frisia sp. nov., two mesophilic obligately chemolithoautotrophic sulfur-oxidizing bacteria isolated from an intertidal mud flat.	two new members of the genus thiomicrospira were isolated from an intertidal mud flat sample with thiosulfate as the electron donor and co2 as carbon source. on the basis of differences in genotypic and phenotypic characteristics, it is proposed that strain jb-a1t (= dsm 12350t) and strain jb-a2t (= dsm 12351t) are members of two new species, thiomicrospira kuenenii and thiomicrospira frisia, respectively. the cells were gram-negative vibrios or slightly bent rods. strain jb-a1t was highly motil ...	1999	10319459
thiomicrospira chilensis sp. nov., a mesophilic obligately chemolithoautotrophic sulfuroxidizing bacterium isolated from a thioploca mat.	a new member of the genus thiomicrospira, which utilizes thiosulfate as the electron donor and co2 as the carbon source, was isolated from a sediment sample dominated by the filamentous sulfur bacterium thioploca. although the physiological properties investigated are nearly identical to other described species of the genus, it is proposed that strain ch-1t is a member of a new species, thiomicrospira chilensis sp. nov., on the basis of differences in genotypic characteristics (16s rrna sequence ...	1999	10319513
distribution and diversity of sulfur-oxidizing thiomicrospira spp. at a shallow-water hydrothermal vent in the aegean sea (milos, greece).	a shallow-water hydrothermal vent system in the aegean sea close to the island of milos (greece) was chosen to study the diversity and distribution of the chemolithoautotrophic sulfur-oxidizing bacterium thiomicrospira. cell numbers in samples from different regions around a solitary vent decreased toward the center of the vent (horizontal distribution), as well as with depth (vertical distribution), corresponding to an increase in temperature (from ca. 25 to 60 degrees c) and a decrease in ph ( ...	1999	10473384
isolation and characterization of strains cvo and fwko b, two novel nitrate-reducing, sulfide-oxidizing bacteria isolated from oil field brine.	bacterial strains cvo and fwko b were isolated from produced brine at the coleville oil field in saskatchewan, canada. both strains are obligate chemolithotrophs, with hydrogen, formate, and sulfide serving as the only known energy sources for fwko b, whereas sulfide and elemental sulfur are the only known electron donors for cvo. neither strain uses thiosulfate as an energy source. both strains are microaerophiles (1% o(2)). in addition, cvo grows by denitrification of nitrate or nitrite wherea ...	2000	10831429
molecular characterization of bacterial populations in petroleum-contaminated groundwater discharged from underground crude oil storage cavities.	petroleum-contaminated groundwater discharged from underground crude oil storage cavities (cavity groundwater) harbored more than 10(6) microorganisms ml(-1), a density 100 times higher than the densities in groundwater around the cavities (control groundwater). to characterize bacterial populations growing in the cavity groundwater, 46 pcr-amplified almost full-length 16s ribosomal dna (rdna) fragments were cloned and sequenced, and 28 different sequences were obtained. all of the sequences wer ...	2000	11055927
thioalkalimicrobium aerophilum gen. nov., sp. nov. and thioalkalimicrobium sibericum sp. nov., and thioalkalivibrio versutus gen. nov., sp. nov., thioalkalivibrio nitratis sp.nov., novel and thioalkalivibrio denitrificancs sp. nov., novel obligately alkaliphilic and obligately chemolithoautotrophic sulfur-oxidizing bacteria from soda lakes.	forty-three strains of obligately chemolithoautotrophic sulfur-oxidizing bacteria were isolated from highly alkaline soda lakes in south-east siberia (russia) and in kenya using a specific enrichment procedure at ph 10. the main difference between the novel isolates and known sulfur bacteria was their potential to grow and oxidize sulfur compounds at ph 10 and higher. the isolates fell into two groups that were substantially different from each other physiologically and genetically. most of the ...	2001	11321103
characterization of a novel biocatalyst system for sulfide oxidation.	it has been demonstrated that an enrichment culture dominated by thiomicrospira sp. cvo may be cultured on h2s(g) as an energy source under sulfide-limiting conditions in suspended culture with nitrate as the electron acceptor. hydrogen sulfide (10,000 ppmv) was completely removed from the feed gas and oxidized to sulfate in <3 s of gas-liquid contacting time. maximum loading of the biomass for sulfide oxidation was observed to be 5.8 mmol h2s/h-g biomass protein, comparable to that reported pre ...	2001	11386863
mechanistic study of microbial control of hydrogen sulfide production in oil reservoirs.	microbial control of biogenic production of hydrogen sulfide in oil fields was studied in a model system consisting of pure cultures of the nitrate-reducing, sulfide-oxidizing bacterium (nr-sob) thiomicrospira sp. strain cvo and the sulfate-reducing bacterium (srb) desulfovibrio sp. strain lac6, as well as in microbial cultures enriched from produced water of a canadian oil reservoir. the presence of nitrate at concentrations up to 20 mm had little effect on the rate of sulfate reduction by a pu ...	2001	11427944
impact of nitrate-mediated microbial control of souring in oil reservoirs on the extent of corrosion.	the effect of microbial control of souring on the extent of corrosion was studied in a model system consisting of pure cultures of the nitrate-reducing, sulfide-oxidizing bacterium (nr-sob) thiomicrospira sp. strain cvo and the sulfate-reducing bacterium (srb) desulfovibrio sp. strain lac6, as well as in an srb consortium enriched from produced water from a canadian oil reservoir. the average corrosion rate induced by the srb consortium (1.4 g x m(-2) x day(-1)) was faster than that observed in ...	2001	11587574
characterization of an autotrophic sulfide-oxidizing marine arcobacter sp. that produces filamentous sulfur.	a coastal marine sulfide-oxidizing autotrophic bacterium produces hydrophilic filamentous sulfur as a novel metabolic end product. phylogenetic analysis placed the organism in the genus arcobacter in the epsilon subdivision of the proteobacteria. this motile vibrioid organism can be considered difficult to grow, preferring to grow under microaerophilic conditions in flowing systems in which a sulfide-oxygen gradient has been established. purified cell cultures were maintained by using this appro ...	2002	11772641
diversity and abundance of bacteria in an underground oil-storage cavity.	microorganisms inhabiting subterranean oil fields have recently attracted much attention. since intact groundwater can easily be obtained from the bottom of underground oil-storage cavities without contamination by surface water, studies on such oil-storage cavities are expected to provide valuable information to understand microbial ecology of subterranean oil fields.	2002	12197947
isolation and characterization of a sulfur-oxidizing chemolithotroph growing on crude oil under anaerobic conditions.	molecular approaches have shown that a group of bacteria (called cluster 1 bacteria) affiliated with the epsilon subclass of the class proteobacteria constituted major populations in underground crude-oil storage cavities. in order to unveil their physiology and ecological niche, this study isolated bacterial strains (exemplified by strain yk-1) affiliated with the cluster 1 bacteria from an oil storage cavity at kuji in iwate, japan. 16s rrna gene sequence analysis indicated that its closest re ...	2003	12513984
nitrite reductase activity of sulphate-reducing bacteria prevents their inhibition by nitrate-reducing, sulphide-oxidizing bacteria.	sulphate-reducing bacteria (srb) can be inhibited by nitrate-reducing, sulphide-oxidizing bacteria (nr-sob), despite the fact that these two groups are interdependent in many anaerobic environments. practical applications of this inhibition include the reduction of sulphide concentrations in oil fields by nitrate injection. the nr-sob thiomicrospira sp. strain cvo was found to oxidize up to 15 mm sulphide, considerably more than three other nr-sob strains that were tested. sulphide oxidation inc ...	2003	12823193
analysis of dissimilatory sulfite reductase and 16s rrna gene fragments from deep-sea hydrothermal sites of the suiyo seamount, izu-bonin arc, western pacific.	this study describes the occurrence of unique dissimilatory sulfite reductase (dsr) genes at a depth of 1,380 m from the deep-sea hydrothermal vent field at the suiyo seamount, izu-bonin arc, western pacific, japan. the dsr genes were obtained from microbes that grew in a catheter-type in situ growth chamber deployed for 3 days on a vent and from the effluent water of drilled holes at 5 degrees c and natural vent fluids at 7 degrees c. dsr clones suiyodsr-a and suiyodsr-b were not closely relate ...	2004	14711668
development and application of a real-time pcr approach for quantification of uncultured bacteria in the central baltic sea.	we have developed a highly sensitive approach to assess the abundance of uncultured bacteria in water samples from the central baltic sea by using a noncultured member of the "epsilonproteobacteria" related to thiomicrospira denitrificans as an example. environmental seawater samples and samples enriched for the target taxon provided a unique opportunity to test the approach over a broad range of abundances. the approach is based on a combination of taxon- and domain-specific real-time pcr measu ...	2004	15294837
sulfuricurvum kujiense gen. nov., sp. nov., a facultatively anaerobic, chemolithoautotrophic, sulfur-oxidizing bacterium isolated from an underground crude-oil storage cavity.	a facultatively anaerobic, chemolithoautotrophic, sulfur-oxidizing bacterium, strain yk-1(t), was isolated from an underground crude-oil storage cavity at kuji in iwate, japan. the cells were motile, curved rods and had a single polar flagellum. optimum growth occurred in a low-strength salt medium at ph 7.0 and 25 degrees c. it utilized sulfide, elemental sulfur, thiosulfate and hydrogen as the electron donors and nitrate as the electron acceptor under anaerobic conditions, but it did not use n ...	2004	15545474
thiomicrospira thermophila sp. nov., a novel microaerobic, thermotolerant, sulfur-oxidizing chemolithomixotroph isolated from a deep-sea hydrothermal fumarole in the toto caldera, mariana arc, western pacific.	a novel thermotolerant bacterium, designated strain i78(t), was isolated from a self-temperature-recording in situ colonization system deployed in a hydrothermal diffusing flow (maximal temperature 78 degrees c) at the toto caldera in the mariana arc, western pacific. cells were highly motile curved rods with a single polar flagellum. growth was observed at 15-55 degrees c (optimum 35-40 degrees c; 60 min doubling time) and ph 5.0-8.0 (optimum ph 6.0). the isolate was a microaerobic chemolithomi ...	2004	15545479
thiomicrospira arctica sp. nov. and thiomicrospira psychrophila sp. nov., psychrophilic, obligately chemolithoautotrophic, sulfur-oxidizing bacteria isolated from marine arctic sediments.	two psychrophilic, chemolithoautotrophic, sulfur-oxidizing bacteria were isolated from marine arctic sediments sampled off the coast of svalbard with thiosulfate as the electron donor and co(2) as carbon source. comparative analysis of 16s rrna gene sequences suggested that the novel strains, designated sval-d(t) and sval-e(t), represent members of the genus thiomicrospira. further genotypic (dna-dna relatedness, dna g+c content) and phenotypic characterization revealed that the strains represen ...	2005	15774662
sulfide-oxidizing activity and bacterial community structure in a fluidized bed reactor from a zero-discharge mariculture system.	in the present work we describe a comprehensive analysis of sulfide oxidation in a fluidized bed reactor (fbr) from an environmentally sustainable, zero-discharge mariculture system. the fbr received oxygen-depleted effluent from a digestion basin (db) that is responsible for gasification of organic matter and nitrogen. the fbr is a crucial component in this recirculating system because it safeguards the fish from the toxic sulfide produced in the db. microscale sulfide oxidation potential and b ...	2005	15819240
retrieval of nearly complete 16s rrna gene sequences from environmental dna following 16s rrna-based community fingerprinting.	16s rrna-based fingerprinting techniques allow rapid analyses of overall bacterial community structure but suffer from a lack of phylogenetic information hitherto retrievable from the short 16s rrna gene sequences obtained from excised bands. an approach is presented that allows nearly complete 16s rrna gene sequences to be retrieved for abundant components of the bacterial community as obtained by the community fingerprint, i.e. those reflected by major fingerprint bands. this was achieved by d ...	2005	15819849
evidence for autotrophic co2 fixation via the reductive tricarboxylic acid cycle by members of the epsilon subdivision of proteobacteria.	based on 16s rrna gene surveys, bacteria of the epsilon subdivision of proteobacteria have been identified to be important members of microbial communities in a variety of environments, and quite a few have been demonstrated to grow autotrophically. however, no information exists on what pathway of autotrophic carbon fixation these bacteria might use. in this study, thiomicrospira denitrificans and candidatus arcobacter sulfidicus, two chemolithoautotrophic sulfur oxidizers of the epsilon subdiv ...	2005	15838028
succession of internal sulfur cycles and sulfur-oxidizing bacterial communities in microaerophilic wastewater biofilms.	the succession of sulfur-oxidizing bacterial (sob) community structure and the complex internal sulfur cycle occurring in wastewater biofilms growing under microaerophilic conditions was analyzed by using a polyphasic approach that employed 16s rrna gene-cloning analysis combined with fluorescence in situ hybridization, microelectrode measurements, and standard batch and reactor experiments. a complete sulfur cycle was established via s(0) accumulation within 80 days in the biofilms in replicate ...	2005	15870342
the carbon-concentrating mechanism of the hydrothermal vent chemolithoautotroph thiomicrospira crunogena.		2005	16077123
gene expression analysis of the mechanism of inhibition of desulfovibrio vulgaris hildenborough by nitrate-reducing, sulfide-oxidizing bacteria.	sulfate-reducing bacteria (srb) are inhibited by nitrate-reducing, sulfide-oxidizing bacteria (nr-sob) in the presence of nitrate. this inhibition has been attributed either to an increase in redox potential or to production of nitrite by the nr-sob. nitrite specifically inhibits the final step in the sulfate reduction pathway. when the nr-sob thiomicrospira sp. strain cvo was added to mid-log phase cultures of the srb desulfovibrio vulgaris hildenborough in the presence of nitrate, sulfate redu ...	2005	16104868
identification of bacteria potentially responsible for oxic and anoxic sulfide oxidation in biofilters of a recirculating mariculture system.	bacteria presumably involved in oxygen- or nitrate-dependent sulfide oxidation in the biofilters of a recirculating marine aquaculture system were identified using a new application of reverse transcription-pcr denaturing gradient gel electrophoresis (dgge) analysis termed differential-transcription (dt)-dgge. biofilter samples were incubated in various concentrations of sulfide or thiosulfate (0 to 5 mm) with either oxygen or nitrate as the sole electron acceptor. before and after short-term in ...	2005	16204531
nitrate promotes biological oxidation of sulfide in wastewaters: experiment at plant-scale.	biogenic production of sulfide in wastewater treatment plants involves odors, toxicity and corrosion problems. the production of sulfide is a consequence of bacterial activity, mainly sulfate-reducing bacteria (srb). to prevent this production, the efficiency of nitrate addition to wastewater was tested at plant-scale by dosing concentrated calcium nitrate (nutriox) in the works inlet. nutriox dosing resulted in a sharp decrease of sulfide, both in the air and in the bulk water, reaching maximum ...	2006	16255035
impact of different in vitro electron donor/acceptor conditions on potential chemolithoautotrophic communities from marine pelagic redoxclines.	anaerobic or microaerophilic chemolithoautotrophic bacteria have been considered to be responsible for co2 dark fixation in different pelagic redoxclines worldwide, but their involvement in redox processes is still not fully resolved. we investigated the impact of 17 different electron donor/acceptor combinations in water of pelagic redoxclines from the central baltic sea on the stimulation of bacterial co2 dark fixation as well as on the development of chemolithoautotrophic populations. in situ ...	2005	16269695
morphological survey of microbial mats near deep-sea thermal vents.	a microscopic survey is presented of the most commonly observed and morphologically conspicuous microorganisms found attached to natural surfaces or to artificial materials deposited in the immediate vicinity of thermal submarine vents at the galapagos rift ocean spreading zone at a depth of 2,550 meters. of special interest were the following findings: (i) all surfaces intermittently exposed to h(2)s-containing hydrothermal fluid were covered by layers, ca. 5 to 10 mum thick, of procaryotic, gr ...	1981	16345722
chemolithotrophic sulfur-oxidizing bacteria from the galapagos rift hydrothermal vents.	three distinct physiological types of sulfur-oxidizing bacteria were enriched and isolated from samples collected at several deep-sea hydrothermal vents (2,550 m) of the galapagos rift ocean floor spreading center. twelve strains of the obligately chemolithotrophic genus thiomicrospira were obtained from venting water and from microbial mats covering surfaces in the immediate vicinity of the vents. from these and other sources two types of obligately heterotrophic sulfur oxidizers were repeatedl ...	1981	16345831
fractionation of stable carbon isotopes during chemoautotrophic growth of sulfur-oxidizing bacteria.	laboratory-grown strains of chemoautotrophic thiomicrospira sp. strain l-12 and thiobacillus neapolitanus produced cell carbon that was 24.6 to 25.1 ppt (24.6 to 25.1 mg/g) lower in c isotope abundance than the ambient source of carbon dioxide and bicarbonate. this degree of c isotope depletion was comparable to that found in organic material produced in deep-sea hydrothermal-vent communities.	1987	16347420
identification of a thiomicrospira denitrificans-like epsilonproteobacterium as a catalyst for autotrophic denitrification in the central baltic sea.	identification and functional analysis of key members of bacterial communities in marine and estuarine environments are major challenges for obtaining a mechanistic understanding of biogeochemical processes. in the baltic sea basins, as in many other marine environments with anoxic bodies of water, the oxic-anoxic interface is considered a layer of high bacterial turnover of sulfur, nitrogen, and carbon compounds that has a great impact on matter balances in the whole ecosystem. we focused on au ...	2006	16461688
batch and continuous biooxidation of sulphide by thiomicrospira sp. cvo: reaction kinetics and stoichiometry.	aqueous phase biooxidation of sulphide by the novel sulphide-oxidizing bacterium thiomicrospira sp. cvo was studied in batch and continuous systems. cvo was able to oxidize sulphide at concentrations as high as 19 mm. sulphide biooxidation occurred in two distinct phases, one resulting in the formation of sulphur and possibly other dissolved sulphur compounds rather than sulphate, followed by sulphate formation. the specific growth rate of cvo in the first and second phases were 0.17-0.27 and 0. ...	2006	16730776
occurrence, phylogeny and evolution of ribulose-1,5-bisphosphate carboxylase/oxygenase genes in obligately chemolithoautotrophic sulfur-oxidizing bacteria of the genera thiomicrospira and thioalkalimicrobium.	the occurrence of the different genes encoding ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco), the key enzyme of the calvin-benson-bassham cycle of autotrophic co(2) fixation, was investigated in the members of the genus thiomicrospira and the relative genus thioalkalimicrobium, all obligately chemolithoautotrophic sulfur-oxidizing gammaproteobacteria. the cbbl gene encoding the 'green-like' form i rubisco large subunit was found in all analysed species, while the cbbm gene encoding f ...	2006	16804189
ghp, a new c-type green heme protein from halochromatium salexigens and other proteobacteria.	we have isolated a minor soluble green-colored heme protein (ghp) from the purple sulfur bacterium, halochromatium salexigens, which contains a c-type heme. a similar protein has also been observed in the purple bacteria allochromatium vinosum and rhodopseudomonas cryptolactis. this protein has wavelength maxima at 355, 420, and 540 nm and remains unchanged upon addition of sodium dithionite or potassium ferricyanide, indicating either an unusually low or high redox potential, respectively. the ...	2006	16817906
molecular signatures (unique proteins and conserved indels) that are specific for the epsilon proteobacteria (campylobacterales).	the epsilon proteobacteria, which include many important human pathogens, are presently recognized solely on the basis of their branching in rrna trees. no unique molecular or biochemical characteristics specific for this group are known.	2006	16817973
sulfurimonas paralvinellae sp. nov., a novel mesophilic, hydrogen- and sulfur-oxidizing chemolithoautotroph within the epsilonproteobacteria isolated from a deep-sea hydrothermal vent polychaete nest, reclassification of thiomicrospira denitrificans as sulfurimonas denitrificans comb. nov. and emended description of the genus sulfurimonas.	a novel mesophilic bacterium, strain go25(t), was isolated from a nest of hydrothermal vent polychaetes, paralvinella sp., at the iheya north field in the mid-okinawa trough. cells were motile short rods with a single polar flagellum. growth was observed between 4 and 35 degrees c (optimum 30 degrees c; 13-16 h doubling time) and between ph 5.4 and 8.6 (optimum ph 6.1). the isolate was a facultatively anaerobic chemolithoautotroph capable of growth using molecular hydrogen, elemental sulfur or t ...	2006	16901999
microbiological and structural aspects of granular sludge from autotrophic denitrifying reactors.	denitrification is applied in the tertiary treatment of wastewater to reduce n-pollutants. fluorescence in situ hybridisation (fish), card (catalyzed reporter deposition)-fish, cloning, and scanning electron microscopy (sem) were applied to follow the evolution of the microbial composition and structure of granular sludge in autotrophic denitrifying bioreactors fed with nitrate and thiosulfate. with this goal, fish oligonucleotide probes for the autotrophic denitrifiers, thiobacillus denitrifica ...	2006	16939078
methane- and sulfur-metabolizing microbial communities dominate the lost city hydrothermal field ecosystem.	hydrothermal venting and the formation of carbonate chimneys in the lost city hydrothermal field (lchf) are driven predominantly by serpentinization reactions and cooling of mantle rocks, resulting in a highly reducing, high-ph environment with abundant dissolved hydrogen and methane. phylogenetic and terminal restriction fragment length polymorphism analyses of 16s rrna genes in fluids and carbonate material from this site indicate the presence of organisms similar to sulfur-oxidizing, sulfate- ...	2006	16957253
diversity of culturable halophilic sulfur-oxidizing bacteria in hypersaline habitats.	unexpectedly high culturable diversity of moderately and extremely halophilic obligately chemolithoautotrophic sulfur-oxidizing bacteria (sob) was discovered in the sediments of various hypersaline habitats, including chloride-sulfate lakes in mongolia, russia and ukraine, a sea saltern in slovenia and a deep-sea salt brine from the mediterranean. six different groups of halophilic sob, including four new genera, all belonging to the gammaproteobacteria, were found. two groups of moderately halo ...	2006	17005982
thiomicrospira halophila sp. nov., a moderately halophilic, obligately chemolithoautotrophic, sulfur-oxidizing bacterium from hypersaline lakes.	enrichments at 2 m nacl and ph 7.5-8, with thiosulfate or sulfide as electron donor, inoculated with sediments from hypersaline chloride-sulfate lakes of the kulunda steppe (altai, russia) resulted in the domination of two different groups of moderately halophilic, chemolithoautotrophic, sulfur-oxidizing bacteria. under fully aerobic conditions with thiosulfate, bacteria belonging to the genus halothiobacillus dominated while, under microaerophilic conditions, a highly motile, short vibrio-shape ...	2006	17012565
the genome of deep-sea vent chemolithoautotroph thiomicrospira crunogena xcl-2.	presented here is the complete genome sequence of thiomicrospira crunogena xcl-2, representative of ubiquitous chemolithoautotrophic sulfur-oxidizing bacteria isolated from deep-sea hydrothermal vents. this gammaproteobacterium has a single chromosome (2,427,734 base pairs), and its genome illustrates many of the adaptations that have enabled it to thrive at vents globally. it has 14 methyl-accepting chemotaxis protein genes, including four that may assist in positioning it in the redoxcline. a ...	2006	17105352
characterization of the prokaryotic diversity in cold saline perennial springs of the canadian high arctic.	the springs at gypsum hill and colour peak on axel heiberg island in the canadian arctic originate from deep salt aquifers and are among the few known examples of cold springs in thick permafrost on earth. the springs discharge cold anoxic brines (7.5 to 15.8% salts), with a mean oxidoreduction potential of -325 mv, and contain high concentrations of sulfate and sulfide. we surveyed the microbial diversity in the sediments of seven springs by denaturing gradient gel electrophoresis (dgge) and an ...	2007	17220254
characterization of a sulfide-oxidizing biofilm developed in a packed-column reactor.	the potential of microbial mats to develop sulfide-oxidizing biofims was explored. a bioreactor specially designed for the treatment of sulfide-containing effluents was inoculated with a microbial-mat sample, and a complex microbial biofilm with sulfide-oxidation activity developed. the microbial composition of the biofilm was studied by pigment, microscopy, and 16s rrna gene analyses. purple sulfur bacteria and diatoms were observed by microscopy, chlorophyll a and bacteriochlorophyll a were de ...	2007	17407058
bacterial diversity associated with blood falls, a subglacial outflow from the taylor glacier, antarctica.	blood falls is the surface manifestation of brine released from below the taylor glacier, mcmurdo dry valleys, antarctica. geochemical analyses of blood falls show that this brine is of a marine origin. the discovery that 74% of clones and isolates from blood falls share high 16s rrna gene sequence homology with phylotypes from marine systems supports this contention. the bacterial 16s rrna gene clone library was dominated by a phylotype that had 99% sequence identity with thiomicrospira arctica ...	2007	17468282
microbial co(2) fixation and sulfur cycling associated with low-temperature emissions at the lilliput hydrothermal field, southern mid-atlantic ridge (9 degrees s).	lilliput was discovered in 2005 as the southernmost known hydrothermal field along the mid-atlantic ridge. it is exceptional in that it lacks high-temperature venting probably because of a thickened crust. the absence of thermophilic and hyperthermophilic prokaryotes in emissions supports the argument against the presence of a hot subsurface at lilliput, as is typically suggested for diffuse emissions from areas of high-temperature venting. the high phylogenetic diversity and novelty of bacteria ...	2007	17472634
nitrate stimulation of indigenous nitrate-reducing, sulfide-oxidising bacterial community in wastewater anaerobic biofilms.	the role of the nitrate-reducing, sulfide-oxidising bacteria (nr-sob) in the nitrate-mediated inhibition of sulfide net production by anaerobic wastewater biofilms was analyzed in two experimental bioreactors, continuously fed with the primary effluent of a wastewater treatment plant, one used as control (brc) and the other one supplemented with nitrate (brn). this study integrated information from h(2)s and ph microelectrodes, rna-based molecular techniques, and the time course of biofilm growt ...	2007	17524444
population dynamics of marine magnetotactic bacteria in a meromictic salt pond described with qpcr.	magnetotactic bacteria (mtb) contain membrane-bound magnetic iron minerals and are globally abundant in the suboxic/anoxic portions of chemically stratified marine and freshwater environments. however, their population dynamics and potential quantitative contribution to the biogeochemical cycles that they influence (iron, sulfur, carbon) have not been previously considered. here we report the first quantitative description of the distribution of individual species of magnetite- and greigite-prod ...	2007	17686015
microbial community dynamics in a chemolithotrophic denitrification reactor inoculated with methanogenic granular sludge.	denitrification is applied in the tertiary treatment of wastewater to reduce nitrogen pollution. fluorescence in situ hybridization (fish), catalyzed reporter deposition (card)-fish, cloning, and scanning electron microscopy (sem) were applied to follow the evolution of the microbial composition and structure of granular sludge in chemolithotrophic denitrifying bioreactors fed with nitrate and thiosulfate. fish oligonucleotide probes for the chemolitoautotrophic denitrifiers thiobacillus denitri ...	2008	17689587
culture-dependent and -independent characterization of microbial communities associated with a shallow submarine hydrothermal system occurring within a coral reef off taketomi island, japan.	microbial communities in a shallow submarine hydrothermal system near taketomi island, japan, were investigated using cultivation-based and molecular techniques. the main hydrothermal activity occurred in a craterlike basin (depth, approximately 23 m) on the coral reef seafloor. the vent fluid (maximum temperature, >52 degrees c) contained 175 microm h2s and gas bubbles mainly composed of ch4 (69%) and n2 (29%). a liquid serial dilution cultivation technique targeting a variety of metabolism typ ...	2007	17921273
assessment of the addition of thiobacillus denitrificans and thiomicrospira denitrificans to chemolithoautotrophic denitrifying bioreactors.	the aim of the present study was to assess the impact of adding cultures of thiobacillus denitrificans and thiomicrospira denitrificans to two upflow anaerobic sludge bed (uasb) reactors: one inoculated with granular sludge and the other filled only with activated carbon (ac). the performances of the bioreactors and the changes in biomass were compared with a non-bioaugmented control uasb reactor inoculated with granular sludge. the reactors inoculated with granular sludge achieved efficiencies ...	2008	18843596
novel sulfur-oxidizing streamers thriving in perennial cold saline springs of the canadian high arctic.	the perennial springs at gypsum hill (gh) and colour peak (cp), situated at nearly 80 degrees n on axel heiberg island in the canadian high arctic, are one of the few known examples of cold springs in thick permafrost on earth. the springs emanate from deep saline aquifers and discharge cold anoxic brines rich in both sulfide and sulfate. grey-coloured microbial streamers form during the winter months in snow-covered regions of the gh spring run-off channels (-1.3 degrees c to 6.9 degrees c, app ...	2009	19278448
bacterial communities in a crude oil gathering and transferring system (china).	bacterial communities in crude oil and oil field production water samples from an oil gathering and transferring system in changqing oil field in china were investigated by 16s rrna denaturing gradient gel electrophoresis (dgge) analysis followed by gene cloning and sequencing. dgge profiles showed that bacterial communities are far more rich in the water samples than that in the crude oil samples, and that bacteria related to ochrobactrum sp. and stenotrophomonas sp. were detected in all crude ...	2009	19351561
autotrophic denitrification in nitrate-induced marine sediment remediation and sulfurimonas denitrificans-like bacteria.	a group of autotrophic sulfide-oxidizing denitrifying bacteria was identified from an aged anthropogenic marine sediment treated by nitrate for the removal of recalcitrant organic residues. based on 16s rdna similarity, they were most closely related to sulfurimonas denitrificans which oxidizes sulfide to sulfate using nitrate as electron acceptor. this group of bacteria was one of the eleven operational taxonomy units (otus) identified using a universal primer set for eubacteria, but it was acc ...	2009	19406451
biochemistry and molecular biology of lithotrophic sulfur oxidation by taxonomically and ecologically diverse bacteria and archaea.	lithotrophic sulfur oxidation is an ancient metabolic process. ecologically and taxonomically diverged prokaryotes have differential abilities to utilize different reduced sulfur compounds as lithotrophic substrates. different phototrophic or chemotrophic species use different enzymes, pathways and mechanisms of electron transport and energy conservation for the oxidation of any given substrate. while the mechanisms of sulfur oxidation in obligately chemolithotrophic bacteria, predominantly belo ...	2009	19645821
abundance of zetaproteobacteria within crustal fluids in back-arc hydrothermal fields of the southern mariana trough.	to extend knowledge of subseafloor microbial communities within the oceanic crust, the abundance, diversity and composition of microbial communities in crustal fluids at back-arc hydrothermal fields of the southern mariana trough (smt) were investigated using culture-independent molecular techniques based on 16s rrna gene sequences. seafloor drilling was carried out at two hydrothermal fields, on- and off-ridge of the back-arc spreading centre of the smt. 16s rrna gene clone libraries for bacter ...	2009	19691504
expression and function of four carbonic anhydrase homologs in the deep-sea chemolithoautotroph thiomicrospira crunogena.	the hydrothermal vent chemolithoautotroph thiomicrospira crunogena grows rapidly in the presence of low concentrations of dissolved inorganic carbon (dic) (= co(2) + hco(3)(-) + co(3)(-2)). its genome encodes alpha-carbonic anhydrase (alpha-ca), beta-ca, carboxysomal beta-like ca (csosca), and a protein distantly related to gamma-ca. the purposes of this work were to characterize the gene products, determine whether they were differentially expressed, and identify those that are necessary for di ...	2010	20400567
metagenomic comparison of two thiomicrospira lineages inhabiting contrasting deep-sea hydrothermal environments.	the most widespread bacteria in oxic zones of carbonate chimneys at the serpentinite-hosted lost city hydrothermal field, mid-atlantic ridge, belong to the thiomicrospira group of sulfur-oxidizing chemolithoautotrophs. it is unclear why thiomicrospira-like organisms thrive in these chimneys considering that lost city hydrothermal fluids are notably lacking in hydrogen sulfide and carbon dioxide.	2010	20975831
diversity of rubisco and atp citrate lyase genes in soda lake sediments.	sediments from six soda lakes of the kulunda steppe (altai, russia) and from hypersaline alkaline lakes of wadi natrun (egypt) were analyzed for the presence of cbb and aclb genes encoding key enzymes ci assimilation (rubisco in calvin-benson and atp citrate lyase in rtca cycles, respectively). the cbbl gene (rubisco form i) was found in all samples and was most diverse, while the cbbm (rubisco form ii) and aclb were detected only in few samples and with a much lower diversity. the cbbl librarie ...	2010	21073490
metagenomic assessment of a sulfur-oxidizing enrichment culture derived from marine sediment.	the biological oxidation of reduced sulfur compounds is a critically important process in global sulfur biogeochemistry. in this study, we enriched from marine sediments under denitrifying conditions, chemolithotrophic sulfur oxidizers that could oxidize a variety of reduced sulfur compounds: thiosulfate, tetrathionate, sulfide, and polysulfide. two major phylotypes of 16s rrna gene (>99% identity in each phylotype) were detected in this enrichment culture. in order to characterize sulfide oxida ...	2010	21221928
low temperature s(0) biomineralization at a supraglacial spring system in the canadian high arctic.	elemental sulfur (s(0) ) is deposited each summer onto surface ice at borup fiord pass on ellesmere island, canada, when high concentrations of aqueous h(2) s are discharged from a supraglacial spring system. 16s rrna gene clone libraries generated from sulfur deposits were dominated by β-proteobacteria, particularly ralstonia sp. sulfur-cycling micro-organisms such as thiomicrospira sp., and ε-proteobacteria such as sulfuricurvales and sulfurovumales spp. were also abundant. concurrent cultivat ...	2011	21592302