Desulfotomaculum australicum, sp. nov., a Thermophilic Sulfate-Reducing Bacterium Isolated from the Great Artesian Basin of Australia

A Novel View on the Taxonomy of Sulfate-Reducing Bacterium 'Desulfotomaculum salinum' and a Description of a New Species Desulfofundulus salinus sp. nov

Two thermophilic spore-forming sulfate-reducing strains, 435T and 781, were isolated from oil and gas reservoirs in Western Siberia (Russia) about 50 years ago. Both strains were found to be neutrophilic, chemoorganotrophic, anaerobic bacteria, growing at 45-70 °C (optimum, 55-60 °C) and with 0-4.5% (w/v) NaCl (optimum, 0.5-1% NaCl). The major fatty acids were iso-C15:0, iso-C17:0, C16:0, and C18:0. In sulfate-reducing conditions, the strains utilized H2/CO2, formate, lactate, pyruvate, malate, fumarate, succinate, methanol, ethanol, propanol, butanol, butyrate, valerate, and palmitate. In 2005, based on phenotypic characteristics and a 16S rRNA gene sequence analysis, the strains were described as 'Desulfotomaculum salinum' sp. nov. However, this species was not validly published because the type strain was not deposited in two culture collections. In this study, a genomic analysis of strain 435T was carried out to determine its taxonomic affiliation. The genome size of strain 435T was 2.886 Mb with a 55.1% genomic G + C content. The average nucleotide identity and digital DNA-DNA hybridization values were highest between strain 435T and members of the genus Desulfofundulus, 78.7-93.3% and 25.0-52.2%, respectively; these values were below the species delineation cut-offs (<95-96% and <70%). The cumulative phenotypic and phylogenetic data indicate that two strains represent a novel species within the genus Desulfofundulus, for which the name Desulfofundulus salinus sp. nov. is proposed. The type strain is 435T (=VKM B-1492T = DSM 23196T). A genome analysis of strain 435T revealed the genes for dissimilatory sulfate reduction, autotrophic carbon fixation via the Wood-Ljungdahl pathway, hydrogen utilization, methanol and organic acids metabolism, and sporulation, which were confirmed by cultivation studies.

Alcohol dehydrogenase system acts as the sole pathway for methanol oxidation in Desulfofundulus kuznetsovii strain TPOSR

Desulfofundulus kuznetsovii is a thermophilic, spore-forming sulphate-reducing bacterium in the family Peptococcaceae. In this study, we describe a newly isolated strain of D. kuznetsovii, strain TPOSR, and compare its metabolism to the type strain D. kuznetsovii 17T. Both strains grow on a large variety of alcohols, such as methanol, ethanol and propane-diols, coupled to the reduction of sulphate. Strain 17T metabolizes methanol via two routes, one involving a cobalt-dependent methyl transferase and the other using a cobalt-independent alcohol dehydrogenase. However, strain TPOSR, which shares 97% average nucleotide identity with D. kuznetsovii strain 17T, lacks several genes from the methyl transferase operon found in strain 17T. The gene encoding the catalytically active methyl transferase subunit B is missing, indicating that strain TPOSR utilizes the alcohol dehydrogenase pathway exclusively. Both strains grew with methanol during cobalt starvation, but growth was impaired. Strain 17T was more sensitive to cobalt deficiency, due to the repression of its methyl transferase system. Our findings shed light on the metabolic diversity of D. kuznetsovii and their metabolic differences of encoding one or two routes for the conversion of methanol.

Effect of Sulfate on Carbon Monoxide Conversion by a Thermophilic Syngas-Fermenting Culture Dominated by a Desulfofundulus Species

A syngas-degrading enrichment culture, culture T-Syn, was dominated by a bacterium closely related to Desulfofundulus australicus strain AB33^T (98% 16S rRNA gene sequence identity). Culture T-Syn could convert high CO concentrations (from pCO ≈ 34 kPa to pCO ≈ 170 kPa), both in the absence and in the presence of sulfate as external electron acceptor. The products formed from CO conversion were H₂ and acetate. With sulfate, a lower H₂/acetate ratio was observed in the product profile, but CO conversion rates were similar to those in the absence of sulfate. The ability of D. australicus strain AB33^T to use CO was also investigated. D. australicus strain AB33^T uses up to 40% CO (pCO ≈ 68 kPa) with sulfate and up to 20% CO (pCO ≈ 34 kPa) without sulfate. Comparison of the metagenome-assembled genome (MAG) of the Desulfofundulus sp. from T-Syn culture with the genome of D. australicus strain AB33^T revealed high similarity, with an ANI value of 99% and only 32 unique genes in the genome of the Desulfofundulus sp. T-Syn. So far, only Desulfotomaculum nigrificans strain CO-1-SRB had been described to grow with CO with and without sulfate. This work further shows the carboxydotrophic potential of Desulfofundulus genus for CO conversion, both in sulfate-rich and low-sulfate environments.

Desulfofundulus australicus Wantanabe et al. 2018 is represented by a single deposit is one internationally operating collection

The name Desulfofundulus australicusWantanabe et al. 2018 has appeared in the International Journal of Systematic and Evolutionary Microbiology and is based on the name Desulfotomaculum australicum Love et al. 1993. Consequently, both names are based on the nomenclatural type, strain AB33. At the time of valid publication of the name Desulfotomaculum australicum Love et al. 1993, the strain was also deposited in the Australian Collection of Microorganisms as ACM 3917 and was subsequently accessed to the DSMZ as DSM 11792. The publication of a new combination, Desulfofundulus australicusWantanabe et al. 2018, under Rule 27, and 30 (3b) of the International Code of Nomenclature of Prokaryotes requires that the nomenclatural type be deposited in at least two publicly accessible culture collections in different countries from which subcultures must be available in order that the new combination is validly published. The Australian Collection of Microorganisms no longer appears to operate and therefore the new combination, Desulfofundulus australicusWantanabe et al. 2018 is based on a single deposit in the DSMZ.

Unprecedented 34 S-enrichment of pyrite formed following microbial sulfate reduction in fractured crystalline rocks

In the deep biosphere, microbial sulfate reduction (MSR) is exploited for energy. Here, we show that, in fractured continental crystalline bedrock in three areas in Sweden, this process produced sulfide that reacted with iron to form pyrite extremely enriched in ³⁴ S relative to ³² S. As documented by secondary ion mass spectrometry (SIMS) microanalyses, the δ³⁴ S_pyrite values are up to +132‰V-CDT and with a total range of 186‰. The lightest δ³⁴ S_pyrite values (-54‰) suggest very large fractionation during MSR from an initial sulfate with δ³⁴ S values (δ³⁴ S_sulfate,0 ) of +14 to +28‰. Fractionation of this magnitude requires a slow MSR rate, a feature we attribute to nutrient and electron donor shortage as well as initial sulfate abundance. The superheavy δ³⁴ S_pyrite values were produced by Rayleigh fractionation effects in a diminishing sulfate pool. Large volumes of pyrite with superheavy values (+120 ± 15‰) within single fracture intercepts in the boreholes, associated heavy average values up to +75‰ and heavy minimum δ³⁴ S_pyrite values, suggest isolation of significant amounts of isotopically light sulfide in other parts of the fracture system. Large fracture-specific δ³⁴ S_pyrite variability and overall average δ³⁴ S_pyrite values (+11 to +16‰) lower than the anticipated δ³⁴ S_sulfate,0 support this hypothesis. The superheavy pyrite found locally in the borehole intercepts thus represents a late stage in a much larger fracture system undergoing Rayleigh fractionation. Microscale Rb-Sr dating and U/Th-He dating of cogenetic minerals reveal that most pyrite formed in the early Paleozoic era, but crystal overgrowths may be significantly younger. The δ¹³ C values in cogenetic calcite suggest that the superheavy δ³⁴ S_pyrite values are related to organotrophic MSR, in contrast to findings from marine sediments where superheavy pyrite has been proposed to be linked to anaerobic oxidation of methane. The findings provide new insights into MSR-related S-isotope systematics, particularly regarding formation of large fractions of ³⁴ S-rich pyrite.

Review of Desulfotomaculum species and proposal of the genera Desulfallas gen. nov., Desulfofundulus gen. nov., Desulfofarcimen gen. nov. and Desulfohalotomaculum gen. nov

The genus Desulfotomaculumis a heterogeneous group of spore-forming sulfate-reducing bacteria. The type species of the genus is Desulfotomaculum nigrificans (Approved Lists 1980) emend. Visser et al. 2014. The results of phylogenetic analysis demonstrated that the genus Desulfotomaculum already has lost the clustering monophyly and was segregated into some distinct groups with low sequence similarity. Major features of the type strains in these groups were compared, and four novel genera, Desulfallas gen. nov., Desulfofundulus gen. nov., Desulfofarcimen gen. nov. and Desulfohalotomaculum gen. nov. were proposed to accommodate species transferred from the genus Desulfotomaculum.

Bacterial and archaeal communities in Lake Nyos (Cameroon, Central Africa)

The aim of this study was to assess the microbial diversity associated with Lake Nyos, a lake with an unusual chemistry in Cameroon. Water samples were collected during the dry season on March 2013. Bacterial and archaeal communities were profiled using Polymerase Chain Reaction-Denaturing Gradient Gel Electrophoresis (PCR-DGGE) approach of the 16S rRNA gene. The results indicate a stratification of both communities along the water column. Altogether, the physico-chemical data and microbial sequences suggest a close correspondence of the potential microbial functions to the physico-chemical pattern of the lake. We also obtained evidence of a rich microbial diversity likely to include several novel microorganisms of environmental importance in the large unexplored microbial reservoir of Lake Nyos.

Desulfotomaculum tongense sp. nov., a moderately thermophilic sulfate-reducing bacterium isolated from a hydrothermal vent sediment collected from the Tofua Arc in the Tonga Trench

A novel, strictly anaerobic, moderately thermophilic, endospore-forming, sulfate-reducing bacterium, designated TGB60-1T, was isolated from a hydrothermal sediment vent collected from the Tofua Arc in the Tonga Trench. The strain was characterized phenotypically and phylogenetically. The isolated strain was observed to be Gram-positive, with slightly curved rod-shaped cells and a polar flagellum. Strain TGB60-1T was found to grow anaerobically at 37–60 °C (optimum, 50 °C), at pH 6.0–8.5 (optimum, pH 7.0) and with 1.0–4.0 % (w/v) NaCl (optimum, 3.0 %). The electron acceptors utilised were determined to be sulfate, sulfite, and thiosulfate. Strain TGB60-1T was found to utilise pyruvate and H2 as electron donors. Strain TGB60-1T was determined to be related to representatives of the genus Desulfotomaculum and the closest relatives within this genus were identified as Desulfotomaculum halophilum SEBR 3139T, Desulfotomaculum alkaliphilum S1T and Desulfotomaculum peckii LINDBHT1T (92.7, 92.1, and 91.8 % 16S rRNA gene sequence similarity, respectively). The major fatty acids (>20 %) were identified as C16:0 and C18:1 ω7c. The G+C content of the genomic DNA of this novel bacterium was determined to be 53.9 mol%. Based on this polyphasic taxonomic study, strain TGB60-1T is considered to represent a novel species in the genus Desulfotomaculum, for which the name Desulfotomaculum tongense sp. nov. is proposed. The type strain of D. tongense is strain TGB60-1T (= KTCT 4534T = JCM 18733T).

Dispersal of thermophilic Desulfotomaculum endospores into Baltic Sea sediments over thousands of years

Patterns of microbial biogeography result from a combination of dispersal, speciation and extinction, yet individual contributions exerted by each of these mechanisms are difficult to isolate and distinguish. The influx of endospores of thermophilic microorganisms to cold marine sediments offers a natural model for investigating passive dispersal in the ocean. We investigated the activity, diversity and abundance of thermophilic endospore-forming sulfate-reducing bacteria (SRB) in Aarhus Bay by incubating pasteurized sediment between 28 and 85 °C, and by subsequent molecular diversity analyses of 16S rRNA and of the dissimilatory (bi)sulfite reductase (dsrAB) genes within the endospore-forming SRB genus Desulfotomaculum. The thermophilic Desulfotomaculum community in Aarhus Bay sediments consisted of at least 23 species-level 16S rRNA sequence phylotypes. In two cases, pairs of identical 16S rRNA and dsrAB sequences in Arctic surface sediment 3000 km away showed that the same phylotypes are present in both locations. Radiotracer-enhanced most probable number analysis revealed that the abundance of endospores of thermophilic SRB in Aarhus Bay sediment was ca. 10(4) per cm(3) at the surface and decreased exponentially to 10(0) per cm(3) at 6.5 m depth, corresponding to 4500 years of sediment age. Thus, a half-life of ca. 300 years was estimated for the thermophilic SRB endospores deposited in Aarhus Bay sediments. These endospores were similarly detected in the overlying water column, indicative of passive dispersal in water masses preceding sedimentation. The sources of these thermophiles remain enigmatic, but at least one source may be common to both Aarhus Bay and Arctic sediments.

Desulfotomaculum varum sp. nov., a moderately thermophilic sulfate-reducing bacterium isolated from a microbial mat colonizing a Great Artesian Basin bore well runoff channel

A strictly anaerobic moderately thermophilic bacterium, designated strain RH04-3^T (T = type strain), was isolated from a red colored microbial mat that colonizes a Great Artesian Basin (GAB) bore well (Registered Number 17263) runoff channel at 66 °C. The cells of strain RH04-3^T were straight to slightly curved, sporulating, Gram-positive rods (2.0–5.0 × 1.0 μm) that grew optimally at 50 °C (temperature growth range between 37 and 55 °C) and at pH 7 (pH growth range of 5.0 and 8.5). Growth was inhibited by NaCl concentrations ≥1.5% (w/v), and by chloramphenicol, streptomycin, tetracycline, penicillin and ampicillin. The strain utilized fructose, mannose, glycerol, lactate, pyruvate and H₂ in the presence of sulfate, and fermented pyruvate in the absence of sulfate. Strain RH04-3^T reduced sulfate, sulfite, thiosulfate and elemental sulfur, but not nitrate, nitrite, iron(III), arsenate(V), vanadium(V) or cobalt(III) as terminal electron acceptors. The G + C content of DNA was 52.4 ± 0.8 mol % as determined by the thermal denaturation (Tm) method. 16S rRNA sequence analysis indicated that strain RH04-3^T was a member of the genus Desulfotomaculum and was most closely related to Desulfotomaculum putei (similarity value of 95.2%) and Desulfotomaculum hydrothermale (similarity value of 93.6%). On the basis of phylogenetic and phenotypic characteristics, strain RH04-3^T is considered to represent a novel species of the genus Desulfotomaculum, for which the name Desulfotomaculum varum sp. nov. is proposed. The type strain RH04-3^T = JCM 16158^T = KCTC 5794^T.

Caloramator mitchellensis sp. nov., a thermoanaerobe isolated from the geothermal waters of the Great Artesian Basin of Australia, and emended description of the genus Caloramator

A strictly thermophilic anaerobe, designated strain VF08(T), was isolated from a water sample collected from a Great Artesian Basin bore (registered bore number 22981) situated at Mitchell, QLD, Australia. Cells of isolate VF08(T) were slightly curved, non-sporulating rods (1.5-3.5 x 0.4-0.8 μm), which stained Gram-negative but possessed a Gram-positive cell-wall ultrastructure. The strain grew optimally in tryptone-yeast extract-glucose (TYEG) medium at 55 °C (temperature growth range between 37 and 60 °C) and a pH of 7 (pH growth range, 6.0-9.0). Yeast extract or tryptone was required for growth on glucose, fructose, xylose, maltose, sucrose, raffinose, cellobiose, ribose, pyruvate, tryptone, peptone, Casamino acids, amyl media and serine, but could also support growth as the sole carbon source. End products from glucose fermentation were acetate, ethanol, CO₂ and H₂. The strain reduced vanadium(V), but not iron(III), manganese(IV), elemental sulfur, sulfate, thiosulfate, sulfite, nitrate or nitrite in the presence of 0.2  % yeast extract, peptone, tryptone, glucose, sucrose and Casamino acids, but an increase in the growth rate or cell yield was not observed. Growth was inhibited by chloramphenicol, streptomycin, tetracycline, penicillin, ampicillin and ≥ 2  % NaCl (w/v). The G+C content of the DNA was 38.4 ± 0.8 mol% as determined by the thermal denaturation (T(m)) method. 16S rRNA gene sequence analysis revealed that isolate VF08(T) was a member of the genus Caloramator with Caloramator australicus and Caloramator fervidus (formerly Clostridium fervidus) being the closest relatives with similarity values of 85.0 and 86.1  %, respectively, when helix 6 nucleotides were included in the analysis, and 95.2  % and 94  %, respectively, when these nucleotides were masked from the analysis. Further analysis revealed that strain VF08(T) formed an individual cluster (cluster II) within the genus Caloramator and could be distinguished from other species within the genus Caloramator (clusters I, III and IV) on the basis of signature nucleotides and differences in phenotypic traits. These data suggest that strain VF08(T) is a novel species of the genus Caloramator, for which the name Caloramator mitchellensis sp. nov. is proposed. The type strain is VF08(T) (=JCM 15828(T)=KCTC 5735(T)). An emended description of the genus Caloramator is also provided.

Desulfovibrio fairfieldensis bacteremia associated with choledocholithiasis and endoscopic retrograde cholangiopancreatography

Desulfovibrio fairfieldensis is a gram-negative, curved, motile, anaerobic bacillus. D. fairfieldensis has been isolated only from human specimens and is considered a normal resident of the human gastrointestinal tract. We report the second case of Desulfovibrio bacteremia associated with choledocholithiasis and review the other reported cases of D. fairfieldensis bacteremia.

Identification and Phylogenetic analysis of thermophilic sulfate-reducing bacteria in oil field samples by 16S rDNA gene cloning and sequencing

Thermophilic sulfate-reducing bacteria (SRB) have been recognized as an important source of hydrogen sulfide (H2S) in hydrocarbon reservoirs and in production systems. Four thermophilic SRB enrichment cultures from three different oil field samples (sandstone core, drilling mud, and production water) were investigated using 16S rDNA sequence comparative analysis. In total, 15 different clones were identified. We found spore-forming, low G+C content, thermophilic, sulfate-reducing Desulfotomaculum-related sequences present in all oil field samples, and additionally a clone originating from sandstone core which was assigned to the mesophilic Desulfomicrobium group. Furthermore, three clones related to Gram-positive, non-sulfate-reducing Thermoanaerobacter species and four clones close to Clostridium thermocopriae were found in enrichment cultures from sandstone core and from production water, respectively. In addition, the deeply rooted lineage of two of the clones suggested previously undescribed, Gram-positive, low G+C content, thermophilic, obligately anaerobic bacteria present in production water. Such thermophilic, non-sulfate-reducing microorganisms may play an important ecological role alongside SRB in oil field environments.

Desulfovirgula thermocuniculi gen. nov., sp. nov., a thermophilic sulfate-reducer isolated from a geothermal underground mine in Japan

A thermophilic, Gram-positive, endospore-forming, sulfate-reducing bacterial strain, designated RL80JIVT, was isolated from a geothermally active underground mine in Japan. Cells were rod-shaped and motile. The temperature and pH ranges for growth were 61–80 °C (optimum at 69–72 °C) and pH 6.4–7.9 (optimum at pH 6.8–7.3), and the strain tolerated up to 0.5 % NaCl. Strain RL80JIVT utilized sulfate, sulfite, thiosulfate and elemental sulfur as electron acceptors. Electron donors utilized were H2 in the presence of CO2, and carboxylic acids. Fermentative growth occurred on lactate and pyruvate. The cell wall contained meso-diaminopimelic acid and the major respiratory isoprenoid quinone was menaquinone MK-7. Major whole-cell fatty acids were iso-C15 : 0, iso-C17 : 0 and C16 : 0. Strain RL80JIVT was found to be affiliated with the thiosulfate-reducer Thermanaeromonas toyohensis DSM 14490T (90.9 % 16S rRNA gene sequence similarity) and with the sulfate-reducer Desulfotomaculum thermocisternum DSM 10259T (90.0 % similarity). Strain RL80JIVT is therefore considered to represent a novel species of a new genus, for which the name Desulfovirgula thermocuniculi gen. nov., sp. nov. is proposed. The type strain of Desulfovirgula thermocuniculi is RL80JIVT (=DSM 16036T=JCM 13928T).

Desulfomicrobium thermophilum sp. nov., a novel thermophilic sulphate-reducing bacterium isolated from a terrestrial hot spring in Colombia

A moderately thermophilic, sulphate-reducing bacterium, designated strain P6-2(T), was isolated from a terrestrial hot spring located at a height of 2,500 m in the Andean region, Colombia (5 degrees 43'69''N, 73 degrees 6'10''W). Cells of strain P6-2(T) were rod-shaped, stained Gram-negative and were motile by means of a single polar flagellum. The strain grew lithotrophically with H(2) as the electron donor and organotrophically on lactate, pyruvate, ethanol, malate, fumarate, n-propanol and succinate in the presence of sulphate as the terminal electron acceptor. Fumarate and pyruvate was fermented. Strain P6-2(T) grew optimally at 55 degrees C (range 37-60 degrees C), pH 6.6 (range 5.8-8.8) in the presence of 0.5% NaCl (range 0-4.5%) with lactate and sulphate and produced acetate, CO(2) and H(2)S as the major end-products. Sulphate, sulphite and thiosulphate could be used as electron acceptors but not elemental sulphur or nitrate. The G + C content of the genomic DNA was 58.7 mol%. The 16S rRNA sequence analysis indicated that strain P6-2(T) was a member of the class Deltaproteobacteria, domain Bacteria with Desulfomicrobium baculatum being the closest relative (similarity value of 94%). Phylogeny of genes encoding alpha- and beta-subunits of the dissimilatory sulphite reductase (dsrAB genes) supported its affiliation to members of the genus Desulfomicrobium. On the basis of this evidence, we propose to assign strain P6-2(T) as new species of the genus Desulfomicrobium, D. thermophilum sp. nov., with strain P6-2(T) as the type strain (= DSM 16697(T) = CCUG 49732(T)).

Desulfotomaculum thermosubterraneum sp. nov., a thermophilic sulfate-reducer isolated from an underground mine located in a geothermally active area

A thermophilic, Gram-positive, endospore-forming, sulfate-reducing bacterium was isolated from an underground mine in a geothermally active area in Japan. Cells of this strain, designated RL50JIIIT, were rod-shaped and motile. The temperature range for growth was 50–72 °C (optimum growth at 61–66 °C) and the pH range was 6.4–7.8 (optimum at pH 7.2–7.4). Strain RL50JIIITtolerated up to 1.5 % NaCl, but optimum growth occurred in the presence of 0–1 % NaCl. Electron acceptors utilized were sulfate, sulfite, thiosulfate and elemental sulfur. Electron donors utilized were H2in the presence of CO2, alanine, various carboxylic acids and alcohols. Fermentative growth occurred on lactate and pyruvate. The cell wall contained mesodiaminopimelic acid and the major respiratory isoprenoid quinone was menaquinone 7 (MK-7). Major whole-cell fatty acids were iso-C15 : 0, iso-C17 : 0DMA (dimethyl acetal), iso-C15 : 0DMA and iso-C17 : 0. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed 98.7 % similarity withDesulfotomaculum solfataricumDSM 14956T. However, DNA–DNA hybridization experiments withDesulfotomaculum kuznetsovii,Desulfotomaculum luciaeandD. solfataricumand the G+C content of the DNA (54.4 mol%) allowed the differentiation of strain RL50JIIITfrom the recognized species of the genusDesulfotomaculum. Strain RL50JIIITtherefore represents a novel species, for which the nameDesulfotomaculum thermosubterraneumsp. nov. is proposed. The type strain is RL50JIIIT(=DSM 16057T=JCM 13837T).

Methanol utilizing Desulfotomaculum species utilizes hydrogen in a methanol-fed sulfate-reducing bioreactor

A sulfate-reducing bacterium, strain WW1, was isolated from a thermophilic bioreactor operated at 65 degrees C with methanol as sole energy source in the presence of sulfate. Growth of strain WW1 on methanol or acetate was inhibited at a sulfide concentration of 200 mg l(-1), while on H2/CO2, no apparent inhibition occurred up to a concentration of 500 mg l(-1). When strain WW1 was co-cultured under the same conditions with the methanol-utilizing, non-sulfate-reducing bacteria, Thermotoga lettingae and Moorella mulderi, both originating from the same bioreactor, growth and sulfide formation were observed up to 430 mg l(-1). These results indicated that in the co-cultures, a major part of the electron flow was directed from methanol via H2/CO2 to the reduction of sulfate to sulfide. Besides methanol, acetate, and hydrogen, strain WW1 was also able to use formate, malate, fumarate, propionate, succinate, butyrate, ethanol, propanol, butanol, isobutanol, with concomitant reduction of sulfate to sulfide. In the absence of sulfate, strain WW1 grew only on pyruvate and lactate. On the basis of 16S rRNA analysis, strain WW1 was most closely related to Desulfotomaculum thermocisternum and Desulfotomaculum australicum. However, physiological properties of strain WW1 differed in some aspects from those of the two related bacteria.

Novel thermophilic sulfate-reducing bacteria from a geothermally active underground mine in Japan

Thermophilic sulfate-reducing bacteria were enriched from samples obtained from a geothermal underground mine in Japan. The enrichment cultures contained bacteria affiliated with the genera Desulfotomaculum, Thermanaeromonas, Thermincola, Thermovenabulum, Moorella, "Natronoanaerobium," and Clostridium. Two novel thermophilic sulfate-reducing strains, RL50JIII and RL80JIV, affiliated with the genera Desulfotomaculum and Thermanaeromonas, respectively, were isolated.

Desulfotomaculum carboxydivorans sp. nov., a novel sulfate-reducing bacterium capable of growth at 100% CO

A moderately thermophilic, anaerobic, chemolithoheterotrophic, sulfate-reducing bacterium, strain CO-1-SRB(T), was isolated from sludge from an anaerobic bioreactor treating paper mill wastewater. Cells were Gram-positive, motile, spore-forming rods. The temperature range for growth was 30-68 degrees C, with an optimum at 55 degrees C. The NaCl concentration range for growth was 0-17 g l(-1); there was no change in growth rate until the NaCl concentration reached 8 g l(-1). The pH range for growth was 6.0-8.0, with an optimum of 6.8-7.2. The bacterium could grow with 100% CO in the gas phase. With sulfate, CO was converted to H(2) and CO(2) and part of the H(2) was used for sulfate reduction; without sulfate, CO was completely converted to H(2) and CO(2). With sulfate, strain CO-1-SRB(T) utilized H(2)/CO(2), pyruvate, glucose, fructose, maltose, lactate, serine, alanine, ethanol and glycerol. The strain fermented pyruvate, lactate, glucose and fructose. Yeast extract was necessary for growth. Sulfate, thiosulfate and sulfite were used as electron acceptors, whereas elemental sulfur and nitrate were not. A phylogenetic analysis of 16S rRNA gene sequences placed strain CO-1-SRB(T) in the genus Desulfotomaculum, closely resembling Desulfotomaculum nigrificans DSM 574(T) and Desulfotomaculum sp. RHT-3 (99 and 100% similarity, respectively). However, the latter strains were completely inhibited above 20 and 50% CO in the gas phase, respectively, and were unable to ferment CO, lactate or glucose in the absence of sulfate. DNA-DNA hybridization of strain CO-1-SRB(T) with D. nigrificans and Desulfotomaculum sp. RHT-3 showed 53 and 60% relatedness, respectively. On the basis of phylogenetic and physiological features, it is suggested that strain CO-1-SRB(T) represents a novel species within the genus Desulfotomaculum, for which the name Desulfotomaculum carboxydivorans is proposed. This is the first description of a sulfate-reducing micro-organism that is capable of growth under an atmosphere of pure CO with and without sulfate. The type strain is CO-1-SRB(T) (=DSM 14880(T)=VKM B-2319(T)).

Isolation of thermophilic Desulfotomaculum strains with methanol and sulfite from solfataric mud pools, and characterization of Desulfotomaculum solfataricum sp. nov

Four strains of thermophilic, endospore-forming, sulfate-reducing bacteria were enriched and isolated from hot solfataric fields in the Krafla area of north-east Iceland, using methanol and sulfite as substrates. Morphologically, these strains resembled thermophilic Desulfotomaculum species. The strains grew with alcohols, including methanol, with glucose and fructose as electron donors, and with sulfate, sulfite or thiosulfate as electron acceptors. For all four strains, the optimum temperature and pH for growth were 60 degrees C and pH 7.3, respectively; no added NaCl was required. Phylogenetic analysis based on partial 16S rRNA gene sequence comparisons showed high levels of similarity of the novel strains (>92 %) with Desulfotomaculum kuznetsovii and Desulfotomaculum luciae. However, DNA-DNA hybridization studies with D. kuznetsovii revealed that the four strains belonged to one novel species. A representative of this group of isolates, strain V21(T), is proposed as the type strain of a novel species of the spore-forming, sulfate-reducing genus Desulfotomaculum, namely Desulfotomaculum solfataricum (type strain V21(T)=DSM 14956(T)=CIP 107984(T)).

Clostridium caminithermale sp. nov., a slightly halophilic and moderately thermophilic bacterium isolated from an Atlantic deep-sea hydrothermal chimney

A strictly anaerobic, slightly halophilic and moderately thermophilic, sporulating rod designated strain DVird3T was isolated from deep-sea hydrothermal vent samples collected at a depth of approximately 800 m on the Atlantic Ocean Ridge. Strain DVird3T possessed a few laterally inserted flagella, had a DNA G + C content of 33.1 mol% and grew optimally at pH 6.6 and at 45 degrees C. Growth was observed at temperatures between 20 and 58 degrees C and at pH values between 5.8 and 8.2. The optimum NaCl concentration for growth was 3% sea salt (30 g l(-1)); no growth was observed in the presence of 15 or 60 g sea salt l(-1). Strain DVird3T is heterotrophic and utilizes some sugars and various single amino acids. Acetate was the main fatty acid detected from carbohydrate fermentation, together with H2 and CO2. Gelatin was used as an energy source. It performed the Stickland reaction. Phylogenetically, strain DVird3T branched with members of cluster XI of the order Clostridiales, with Clostridium halophilum as its closest relative (similarity of 94.6%). On the basis of its phenotypic, genotypic and phylogenetic characteristics, strain DVird3T (= DSM 15212T = CIP 107654T) is proposed as the type strain of a novel species of the genus Clostridium, Clostridium caminithermale sp. nov.

Microvirga subterranea gen. nov., sp. nov., a moderate thermophile from a deep subsurface Australian thermal aquifer

A strictly aerobic bacterium, strain Fail4T, was isolated from free-flowing geothermal waters of a bore (bore register no. 3768) tapping the Great Artesian Basin of Australia. The non-sporulating, Gram-negative cells of strain Fail4T produced light-pink colonies, were rod-shaped (1 x 1.5-4 microm) and were motile by a single polar flagellum. Strain Fail4T grew optimally at 41 degrees C at a pH of 7.0 and had an absolute requirement for yeast extract. The strain grew on casein hydrolysate, tryptone, gelatin, xylose and acetate in a medium supplemented with 0.06 or 0.006% yeast extract. Weak acid production was detected from glucose and arabinose. Catalase was produced. Nitrite was produced from nitrate. Strain Fail4T was sensitive to antibiotics that inhibit growth of bacteria. The G + C content was 63.5 +/- 0.5 mol%. Strain Fail4T was a member of the class 'Alphaproteobacteria', phylum Proteobacteria, placed almost equidistantly between Methylobacterium species, Chelatococcus asaccharovorans and Bosea thiooxidans (similarity value of 93%) as its nearest phylogenetic relatives. Phylogenetic and phenotypic evidence suggest that strain Fail4T (=ATCC BAA-295T = DSM 14364T) should be placed as the type strain of a species in a newly created genus, for which the name Microvirga subterranea gen. nov., sp. nov. is proposed.

A culture-independent survey of the bacterial community in a radon hot spring

Paralana is an active, radon-containing hot spring situated in a region of South Australia's Flinders Ranges with a long history of hydrothermal activity. Our aim was to determine the bacterial composition of Paralana using a culture-independent, 16S rRNA-based technique. The presence of a diverse bacterial community was strongly suggested by the large number (approximately 180) of different ribotypes obtained upon analysis of nine hot spring samples. DNA sequencing of Paralana 16S rRNA genes corroborated this observation, identifying representatives of seven confirmed and two candidate divisions of the domain Bacteria. These included Cyanobacteria, Proteobacteria (both beta and delta subdivisions), the Cytophaga-Flexibacter-Bacteroides group, Low G + C Gram-positives, Nitrospira, green non-sulfur bacteria, green sulfur bacteria, OP8, and OP12. No known ionizing radiation-resistant Bacteria were identified. Only one Paralana 16S rRNA sequence type (recombinant B5D) was homologous to a sequence previously identified from a radioactive environment.

Energetics of overall metabolic reactions of thermophilic and hyperthermophilic Archaea and bacteria

Thermophilic and hyperthermophilic Archaea and Bacteria have been isolated from marine hydrothermal systems, heated sediments, continental solfataras, hot springs, water heaters, and industrial waste. They catalyze a tremendous array of widely varying metabolic processes. As determined in the laboratory, electron donors in thermophilic and hyperthermophilic microbial redox reactions include H2, Fe(2+), H2S, S, S2O3(2-), S4O6(2-), sulfide minerals, CH4, various mono-, di-, and hydroxy-carboxylic acids, alcohols, amino acids, and complex organic substrates; electron acceptors include O2, Fe(3+), CO2, CO, NO3(-), NO2(-), NO, N2O, SO4(2-), SO3(2-), S2O3(2-), and S. Although many assimilatory and dissimilatory metabolic reactions have been identified for these groups of microorganisms, little attention has been paid to the energetics of these reactions. In this review, standard molal Gibbs free energies (DeltaGr(0)) as a function of temperature to 200 degrees C are tabulated for 370 organic and inorganic redox, disproportionation, dissociation, hydrolysis, and solubility reactions directly or indirectly involved in microbial metabolism. To calculate values of DeltaGr(0) for these and countless other reactions, the apparent standard molal Gibbs free energies of formation (DeltaG(0)) at temperatures to 200 degrees C are given for 307 solids, liquids, gases, and aqueous solutes. It is shown that values of DeltaGr(0) for many microbially mediated reactions are highly temperature dependent, and that adopting values determined at 25 degrees C for systems at elevated temperatures introduces significant and unnecessary errors. The metabolic processes considered here involve compounds that belong to the following chemical systems: H-O, H-O-N, H-O-S, H-O-N-S, H-O-C(inorganic), H-O-C, H-O-N-C, H-O-S-C, H-O-N-S-C(amino acids), H-O-S-C-metals/minerals, and H-O-P. For four metabolic reactions of particular interest in thermophily and hyperthermophily (knallgas reaction, anaerobic sulfur and nitrate reduction, and autotrophic methanogenesis), values of the overall Gibbs free energy (DeltaGr) as a function of temperature are calculated for a wide range of chemical compositions likely to be present in near-surface and deep hydrothermal and geothermal systems.

Desulfotomaculum genus- and subgenus-specific 16S rRNA hybridization probes for environmental studies

Based on comparative analysis of 16S rRNA sequences and the recently established phylogeny of the genus Desulfotomaculum, a set of phylogenetically nested hybridization probes was developed and characterized. A genus-specific probe targets all known Desulfotomaculum species (with the exception of Desulfotomaculum acetoxidans), and five specific probes target subclusters within the Desulfotomaculum genus. The dissociation temperature of each probe was determined experimentally. Probe specificities were verified through hybridizations with pure culture rRNA isolated from a wide variety of target and non-target organisms and through an evaluation of probe 'nesting' using samples obtained from four different environments. Fixation and hybridization conditions for fluorescence in situ hybridizations were also optimized. The probes were used in quantitative membrane hybridizations to determine the abundance of Desulfotomaculum species in thermophilic anaerobic digesters, in soil, in human faeces and in pig colon samples. Desulfotomaculum rRNA accounted for 0.3-2.1% of the total rRNA in the digesters, 2.6-6.6% in soil, 1.5-3.3% in human faeces and 2.5-6.2% in pig colon samples.

Amylase and 16S rRNA genes from a hyperthermophilic archaebacterium

A hyperthermophilic and amylolytic prokaryote, designated Rt3, was isolated from a thermal spring near Rotorua, New Zealand. The 16S rRNA gene of Rt3 was cloned and sequenced with the aim of determining its phylogenetic affiliations. The phylogenetic analysis of this sequence, which included a selection of archaebacterial and eubacterial 16S rRNA sequences, indicates that Rt3 most likely belongs to the archaebacterial order Thermococcales. An amylase gene (amyA) from Rt3, encoding a highly thermostable amylase activity, was cloned and its DNA sequence determined. Transcriptional signals typical of archaebacteria were evident in this sequence. The sequence is homologous to a broad range of enzymes from the AMY superfamily and contains a typical N-terminal signal peptide. Phylogenetic analysis and comparison of structural features with other AMY superfamily enzymes reveals that, firstly, the closest homologues of the Rt3 amylase are members of the Bacillus and Plant alpha-amylase groups; and secondly, that the Rt3 amylase is closely related to only one other currently known archaebacterial enzyme, i.e. an (AMY superfamily) alpha-amylase from Natronococcus.

Real-time homogeneous assay of rapid cycle polymerase chain reaction product for identification of Leptonema illini

Partial 16S rDNA sequences of eight Leptospira-like field isolates that reacted weakly or not at all to microscope agglutination test were found to be similar to the 16S rDNA sequence of the nonpathogen Leptonema illini-type strain 3055. Comparison of these sequences with those of Leptospira 16S rDNA sequences revealed a Leptonema species signature sequence for which a forward amplification primer was designed. This primer was used in conjunction with a bacterial-specific 16S rDNA universal reverse primer for developing a LightCycler-based rapid PCR protocol in which fluorescence emission due to the binding of SYBR green I dye to the amplified products was continuously monitored. A melting temperature (T(m)) determined from the melting curve of the amplified product immediately after PCR confirmed that the product was of Leptonema. The protocol for 24 samples consisting of 30 PCR cycles and melting curve acquisitions required 30 min to complete and agarose gel electrophoresis of the PCR products was not necessary. The method was specific as PCR products were detected from the seven Leptonema reference strains and the eight field isolates that had been previously verified as Leptonema by 16S rDNA sequencing, but not from the two representative strains from each of the eight Leptospira genospecies tested.

Identification of Leptospira inadai by continuous monitoring of fluorescence during rapid cycle PCR

Seven new Leptospira isolates from rats, a buffalo, and contaminated media showed either reactive serology against more than 1 serogroup or no reactive serology against a reference panel of 22 serovars in the microscopic agglutination test (MAT). Because of these inconclusive results, the 16S rDNA sequences of these isolates were determined and found to resemble that of the type strain of Leptospira inadai (L. inadai), serovar lyme strain 10, which is considered to be nonpathogenic for humans. Comparative analyses of other Leptospira 16S rDNA sequences from databases revealed a L. inadai-specific signature sequence, against which an amplification primer was designed. This primer when used in conjunction with an universal primer enabled the trial of a rapid PCR protocol in which fluorescence emissions due to binding of SYBR Green I dye to PCR products were continuously monitored during rapid thermal cycling. A melting curve acquired immediately after PCR was used to distinguish the intended product. The thermal cycling and continuous monitoring of fluorescence emission were accomplished by the LightCycler; the whole procedure of 30 PCR cycles and melting curve acquisition required only 20 minutes. The primer achieved the required specificity, as the intended PCR product resulted only from 6 confirmed L. inadai reference strains and 7 field isolates that had been verified as L. inadai by the 16S rDNA sequencing, but not from 16 reference strains of Leptospira belonging to 7 other genospecies. Furthermore, these experiments showed that the PCR protocol was robust because target DNA of different conditions, which were extracted by either 1 of the 4 methods used, could be detected.

Comparison of two PCR methods for rapid identification of Leptospira genospecies interrogans

Based on (i) an analysis of Leptospira 16S rDNA sequences determined by us and of those from databases and (ii) a previously published finding that restriction fragment length polymorphisms (RFLPs) within the Leptospira 16S and 23S rDNA were detected by nine restriction enzymes and these RFLPs allowed categorisation of Leptospira into eight genospecies, we predicted that one particular DdeI restriction site polymorphism within 16S rDNA could be independently used for identifications of Leptospira strains belonging to the genospecies interrogans. Two PCR-based methods, namely allele-specific amplification (ASA) and PCR-RFLP, were tested for the rapid detection of the DdeI restriction site polymorphism. One or two representative strains from each of nine genospecies were tested by ASA, whereas 73 strains from nine genospecies and two field isolates were tested by PCR-RFLP. Our experiments showed that the ASA method was not as specific as intended, but the PCR-RFLP method was useful for rapid identifications of the genospecies interrogans. We have not only confirmed a previous finding and extended the number of samples particularly from the genospecies biflexa, weilii, and inadai, but also simplified a previous PCR-RFLP protocol.

Reevaluating the classification of Halobacteroides and Haloanaerobacter species based on sequence comparisons of the 16S ribosomal RNA gene

The 16S rRNA gene (rDNA) sequence analysis of four halophilic anaerobes: Halobacteroides halobius, H. lacunaris. Haloanaerobacter (Hb.) chitinovorans and H. acetoethylicus confirmed that they were all members of the family Haloanaerobiaceae. H. lacunaris and H. halobius were found to be more closely related to each other and were distantly related to Sporohalobacter lortetti and the members of the genera Haloanaerobium and Halothermothrix. These data are in agreement with their assignment to the genus Halobacteroides. Further analysis indicated that Hb. chitinovorans was closely affiliated to members of the genus Halobacteroides, and therefore we propose to transfer it to the genus Halobacteroides as H. chitinovorans comb. nov. This transfer would invalidate the genus Haloanaerobacter, as Hb. chitinovorans is the only member of this genus. The 16S rDNA sequence analysis of H. acetoethylicum indicated that it was very closely related to members of the genus Haloanaerobium, viz. Haloanaerobium (Ha.) praevalens, Ha. salsugo, and Ha. alcaliphilum, and hence we propose to transfer it to the genus Haloanaerobium as Ha. acetoethylicus comb. nov.

Desulfovibrio longreachii sp. nov., a sulfate-reducing bacterium isolated from the Great Artesian Basin of Australia

A new mesophilic, thermotolerant sulfate-reducing bacterium, was isolated from the flowing bore waters of a deep aquifer, the Great Artesian Basin, Australia. The strain, designated isolate AB16910a, is a curved rod and resembled members of the genus Desulfovibrio. However, the isolate can be differentiated from other members of the Desulfovibrio species because of the high G+C content of 69 +/- 0.25% the 16S rRNA sequence data and other physiological characteristics. The name Desulfovibrio longreachii is proposed for the new isolate.

Phylogenetic analysis of Desulfotomaculum thermobenzoicum using polymerase chain reaction-amplified 16S rRNA-specific DNA

The 16S rRNA gene of the thermophilic sulfate-reducing bacterium Desulfotomaculum thermobenzoicum was amplified by polymerase chain reaction using two eubacterial consensus oligodeoxynucleotide primers flanking the majority of the 16S rRNA gene, cloned, and sequenced. Phylogenetic analysis revealed that D. thermobenzoicum belongs to the Gram-positive (low G + C content) branch and is more related to the thermophilic sulfate-reducing bacterium, D. australicum than the moderate thermophile D. nigrificans, or the mesophiles D. orientis, and D. ruminis. This relationship is further strengthened by the presence of an unusual idiosyncrasy in helix 6 of the 16S rRNA gene of D. thermobenzoicum resembling that of D. australicum but not found in other desulfotomacula species and in any other bacteria sequenced to date.