Genus Desulfotomaculum Research Articles

Microbial Diversity of the Produced Waters from the Oilfields in the Republic of Tatarstan (Russian Federation): Participation in Biocorrosion

A variety of microorganisms grow in oil reservoirs, where they participate in the biodegradation of oil and lead to changes in oil quality. Today, our knowledge about microbial processes in oil reservoirs is largely limited, and among the urgent tasks for the oil industry, monitoring and controlling microbial activity (including the activity of microbes responsible for biocorrosion) are important. In this work, we aimed to characterize the bacterial community structure of the produced waters from oilfields in the south of the Republic of Tatarstan (Russian Federation) using cultural and molecular methods of analysis. Bacteria from produced water samples from various oil wells were enriched, and 16S rRNA gene amplicon sequencing was used to assess the phylogenetic diversity of the bacterial communities. Thus, analysis of the bacterial communities revealed the presence of various members within the genera Desulfotomaculum, Clostridium, Acetobacterium, Desulfovibrio, Dethiosulfovibrio, Desulfomicrobium, Fusibacter, Dethiosulfatibacter, Thermovirga, Sphaerochaeta, and Desulfoplanes, but in different produced water samples. The role of the bacterial associations in biocorrosion was separately assessed in experiments on monitoring and stimulating biocorrosion. The bacterial community receiving additional nutrition was shown to have a higher corrosion potential, and scanning electron microscopy analysis confirmed changes in the surface of the metal coupons during immersion testing. The practical value of this research lies in identifying the potential contribution of microbial communities to oil pipeline corrosion.

Anaerobic Degradation of Naphthalene and Pyrene by Sulfate-Reducing Cultures Enriched from Former Manufactured Gas Plant Soil

Biodegradation of polycyclic aromatic hydrocarbons (PAHs) under completely anaerobic sulfate-reducing conditions is an energetically challenging process. To date, anaerobic degradations of only two-ringed naphthalene and three-ringed phenanthrene by sediment-free and enriched sulfate-reducing bacteria have been reported. In this study, sulfate-reducing enrichment cultures capable of degrading naphthalene and four-ringed PAH, pyrene, were enriched from a contaminated former gas plant site soil. Bacterial community composition analysis revealed that a naphthalene-degrading enrichment culture, MMNap, was dominated (84.90%) by a Gram-positive endospore-forming member of the genus Desulfotomaculum with minor contribution (8.60%) from a member of Clostridium. The pyrene-degrading enrichment, MMPyr, was dominated (97.40%) by a species of Desulfotomaculum. The sequences representing the Desulfotomaculum phylotypes shared 98.80% similarity to each other. After 150 days of incubation, MMNap degraded 195 µM naphthalene with simultaneous reduction of sulfate and accumulation of sulfide. Similarly, MMPyr degraded 114 µM pyrene during 180 days of incubation with nearly stochiometric sulfate consumption and sulfide accumulation. In both cases, the addition of sulfate reduction inhibitor, molybdate (20 mM), resulted in complete cessation of the substrate utilization and sulfate reduction that clearly indicated the major role of the sulfate-reducing Desulfotomaculum in biodegradation of the two PAHs. This study is the first report on anaerobic pyrene degradation by a matrix-free, strictly anaerobic, and sulfate-reducing enrichment culture.

Treatment of acid rock drainage using a sulphate-reducing bioreactor with a limestone precolumn

ABSTRACT Sulphate reducing bacteria (SRB) offer promise for the treatment of mine waste due to their effectiveness removing toxic heavy metals as highly insoluble metal sulphides and their ability to generate alkalinity. The main objective of this study was to develop a treatment composed of a sulphate-reducing bioreactor with a limestone precolumn for the removal of Cu(II) from a synthetic ARD. The purpose of the limestone column was to increase the pH values and decrease the level of Cu in the effluent to prevent SRB inhibition. The system was fed with a pH-2.7 synthetic ARD containing Cu(II) (10–40 mg/L), sulphate (2000 mg/L) and acetate (2.5 g COD/L) for 150 days. Copper removal efficiencies in the two-stage system were very high (95–99%), with a final concentration of 0.53 mg/L Cu, and almost complete removal occurred in the limestone precolumn. In the same manner, the acidity of the synthetic ARD was effectively reduced in the limestone precolumn to 7.3 and the pH was raised in the bioreactor (7.3–8.0). COD consumption by methanogens was predominant from day 0–118, but SRB dominated at the end of the experiment (day 150) when the average COD removal and sulphide production were 74.8% and 61.7%, respectively. Study of the microbial taxonomic composition in the bioreactor revealed that Methanosarcina and Methanosaeta were the most prevalent methanogens while the genera Desulfotomaculum and Syntrophobacter were the dominant SRB. Among the SRB identified Desulfotomaculum intricatum (99% identity) and Desulfotomaculum acetoxidans (96%) were the most abundant sequences of bacteria capable of using acetate.

The investigation of oil microbocenosis influence on the corrosion process of pipe steel

The paper presents the results of model laboratory experiments carried out to assess the influence of oil microbocenosis bacteria on the corrosion process on the internal surfaces of oil pipelines made of steel 17G1S. It is known that the bacteria of this group most often include hydrocarbon-oxidizing bacteria (HOB), sulfate-reducing bacteria (SRB), sulfur-oxidizing, or thionic (TB) and iron-oxidizing bacteria (IOB). In model experiments with 17G1S steel samples alloyed with 1% manganese we used corrosion-hazardous bacteria of the genera Desulfotomaculum, Paracoccus, Pseudomonas and Sphaerotilus, isolated from a damaged section of an oil pipeline at a field in the northern part of the Samara Region. In the initial phase of the experiment, the titer of the analyzed bacteria was quite high (SRB 10⁴10⁵, TB 1010⁴ cells/cm), but by the end of the experiment, only sulfate-reducing bacteria with quantitative characteristics of 110 cells/cm were isolated from the culture liquid, may be due to the high adhesion capacity of mass cultures of the bacteria. On the surface of the steel samples the method of electron microscopy revealed unevenly distributed loose deposits, but the cells of the bacteria themselves were not visible in them. The morphological features of the revealed corrosion deposits indicated their bacterial origin, which was also confirmed by biochemical analysis of corrosion products suspension, in particular, by revealing a high mass concentration of sulfides, protein, and the dehydrogenase. Aerobic and anaerobic microbiological interactions occurring in the oil microbocenosis on the internal surfaces of pipelines have been experimentally confirmed and are in good agreement with the data of other researchers. It has been established that the main role in the corrosion destruction steel samples belongs to SRB, whose participation can be carried out according to two main mechanisms: hydrogen cracking and anodic dissolution of iron. Pits and through holes are formed on the steel surface, and the local corrosion rate can approaches 7,3 mm/year. The experiments proved the active role of oil microbocenoses, the basis of the microbiont of which consists of four bacteria, in the rapid destruction of oil pipelines in the Samara Region.

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.

The deep-subsurface sulfate reducer Desulfotomaculum kuznetsovii employs two methanol-degrading pathways

Methanol is generally metabolized through a pathway initiated by a cobalamine-containing methanol methyltransferase by anaerobic methylotrophs (such as methanogens and acetogens), or through oxidation to formaldehyde using a methanol dehydrogenase by aerobes. Methanol is an important substrate in deep-subsurface environments, where thermophilic sulfate-reducing bacteria of the genus Desulfotomaculum have key roles. Here, we study the methanol metabolism of Desulfotomaculum kuznetsovii strain 17T, isolated from a 3000-m deep geothermal water reservoir. We use proteomics to analyze cells grown with methanol and sulfate in the presence and absence of cobalt and vitamin B12. The results indicate the presence of two methanol-degrading pathways in D. kuznetsovii, a cobalt-dependent methanol methyltransferase and a cobalt-independent methanol dehydrogenase, which is further confirmed by stable isotope fractionation. This is the first report of a microorganism utilizing two distinct methanol conversion pathways. We hypothesize that this gives D. kuznetsovii a competitive advantage in its natural environment.

Desulfotomaculum aquiferis sp. nov. and Desulfotomaculum profundi sp. nov., isolated from a deep natural gas storage aquifer.

Two novel strictly anaerobic bacteria, strains Bs105T and Bs107T, were isolated from a deep aquifer-derived hydrocarbonoclastic community. The cells were rod-shaped, not motile and had terminal spores. Phylogenetic affiliation and physiological properties revealed that these isolates belong to two novel species of the genus Desulfotomaculum. Optimal growth temperatures for strains Bs105T and Bs107T were 42 and 45 °C, respectively. The estimated G+C content of the genomic DNA was 42.9 and 48.7 mol%. For both strains, the major cellular fatty acid was palmitate (C16 : 0). Specific carbon fatty acid signatures of Gram-positive bacteria (iso-C17 : 0) and sulfate-reducing bacteria (C17 : 0cyc) were also detected. An insertion was revealed in one of the two 16S rRNA gene copies harboured by strain Bs107T. Similar insertions have previously been highlighted among moderately thermophilic species of the genus Desulfotomaculum. Both strains shared the ability to oxidize aromatic acids (Bs105T: hydroquinone, acetophenone, para-toluic acid, 2-phenylethanol, trans-cinnamic acid, 4-hydroxybenzaldehyde, benzyl alcohol, benzoic acid 4-hydroxybutyl ester; Bs107T: ortho-toluic acid, benzoic acid 4-hydroxybutyl ester). The names Desulfotomaculum aquiferis sp. nov. and Desulfotomaculum profundi sp. nov. are proposed for the type strains Bs105T (=DSM 24088T=JCM 31386T) and Bs107T (=DSM 24093T=JCM 31387T).

Desulfotomaculum ferrireducens sp. nov., a moderately thermophilic sulfate-reducing and dissimilatory Fe(III)-reducing bacterium isolated from compost.

A novel dissimilatory Fe(III)-reducing bacterium, designated strain GSS09T, was isolated from a compost sample by using a solid medium containing acetate and ferrihydrite as electron donor and electron acceptor, respectively. Cells of strain GSS09T were anaerobic, Gram-stain-positive, motile, endospore-forming and rod-shaped. Growth occurred at 30-55 °C (optimum 50 °C), at pH 6.5-9.0 (optimum pH 7.5) and in the presence of 0-3 % (w/v) NaCl (optimum 1 %). Both sulfur compounds such as sulfate, sulfite and thiosulfate and Fe(III) oxides such as ferrihydrite could be utilized as electron acceptors. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain GSS09T was related closely to Desulfotomaculum hydrothermale Lam5T (94.5 % sequence similarity). The major fatty acids were C16 : 0 and C16 : 1ω7c/C16 : 1ω6c. The G+C content of the genomic DNA was 49.1 mol%. On the basis of phylogenetic analysis, phenotypic characterization and physiological tests, strain GSS09T is considered to represent a novel species of the genus Desulfotomaculum, for which the name Desulfotomaculum ferrireducens sp. nov. is proposed. The type strain is GSS09T (=KCTC 15523T=MCCC 1K01254T).

New Bio-Indicators for Long Term Natural Attenuation of Monoaromatic Compounds in Deep Terrestrial Aquifers.

Deep subsurface aquifers despite difficult access, represent important water resources and, at the same time, are key locations for subsurface engineering activities for the oil and gas industries, geothermal energy, and CO2 or energy storage. Formation water originating from a 760 m-deep geological gas storage aquifer was sampled and microcosms were set up to test the biodegradation potential of BTEX by indigenous microorganisms. The microbial community diversity was studied using molecular approaches based on 16S rRNA genes. After a long incubation period, with several subcultures, a sulfate-reducing consortium composed of only two Desulfotomaculum populations was observed able to degrade benzene, toluene, and ethylbenzene, extending the number of hydrocarbonoclastic–related species among the Desulfotomaculum genus. Furthermore, we were able to couple specific carbon and hydrogen isotopic fractionation during benzene removal and the results obtained by dual compound specific isotope analysis (𝜀C = -2.4‰ ± 0.3‰; 𝜀H = -57‰ ± 0.98‰; AKIEC: 1.0146 ± 0.0009, and AKIEH: 1.5184 ± 0.0283) were close to those obtained previously in sulfate-reducing conditions: this finding could confirm the existence of a common enzymatic reaction involving sulfate-reducers to activate benzene anaerobically. Although we cannot assign the role of each population of Desulfotomaculum in the mono-aromatic hydrocarbon degradation, this study suggests an important role of the genus Desulfotomaculum as potential biodegrader among indigenous populations in subsurface habitats. This community represents the simplest model of benzene-degrading anaerobes originating from the deepest subterranean settings ever described. As Desulfotomaculum species are often encountered in subsurface environments, this study provides some interesting results for assessing the natural response of these specific hydrologic systems in response to BTEX contamination during remediation projects.

Genome analysis of Desulfotomaculum gibsoniae strain Groll(T) a highly versatile Gram-positive sulfate-reducing bacterium.

Desulfotomaculum gibsoniae is a mesophilic member of the polyphyletic spore-forming genus Desulfotomaculum within the family Peptococcaceae. This bacterium was isolated from a freshwater ditch and is of interest because it can grow with a large variety of organic substrates, in particular several aromatic compounds, short-chain and medium-chain fatty acids, which are degraded completely to carbon dioxide coupled to the reduction of sulfate. It can grow autotrophically with H2 + CO2 and sulfate and slowly acetogenically with H2 + CO2, formate or methoxylated aromatic compounds in the absence of sulfate. It does not require any vitamins for growth. Here, we describe the features of D. gibsoniae strain GrollT together with the genome sequence and annotation. The chromosome has 4,855,529 bp organized in one circular contig and is the largest genome of all sequenced Desulfotomaculum spp. to date. A total of 4,666 candidate protein-encoding genes and 96 RNA genes were identified. Genes of the acetyl-CoA pathway, possibly involved in heterotrophic growth and in CO2 fixation during autotrophic growth, are present. The genome contains a large set of genes for the anaerobic transformation and degradation of aromatic compounds, which are lacking in the other sequenced Desulfotomaculum genomes.

Genome analyses of the carboxydotrophic sulfate-reducers Desulfotomaculum nigrificans and Desulfotomaculum carboxydivorans and reclassification of Desulfotomaculum caboxydivorans as a later synonym of Desulfotomaculum nigrificans.

Desulfotomaculum nigrificans and D. carboxydivorans are moderately thermophilic members of the polyphyletic spore-forming genus Desulfotomaculum in the family Peptococcaceae. They are phylogenetically very closely related and belong to ‘subgroup a’ of the Desulfotomaculum cluster 1. D. nigrificans and D. carboxydivorans have a similar growth substrate spectrum; they can grow with glucose and fructose as electron donors in the presence of sulfate. Additionally, both species are able to ferment fructose, although fermentation of glucose is only reported for D. carboxydivorans. D. nigrificans is able to grow with 20% carbon monoxide (CO) coupled to sulfate reduction, while D. carboxydivorans can grow at 100% CO with and without sulfate. Hydrogen is produced during growth with CO by D. carboxydivorans. Here we present a summary of the features of D. nigrificans and D. carboxydivorans together with the description of the complete genome sequencing and annotation of both strains. Moreover, we compared the genomes of both strains to reveal their differences. This comparison led us to propose a reclassification of D. carboxydivorans as a later heterotypic synonym of D. nigrificans.

Biotic methylation of mercury by intestinal and sulfate-reducing bacteria and their potential role in mercury accumulation in the tissue of the soil-living Eisenia foetida

Monomethylmercury as one of the most toxic mercury species influences the health and development of higher organisms and tends to accumulate in the tissue of animals and humans. The aim of this study was to explore the mercury methylating capability of (1) intestinal microbiota of the soil-living earthworm Eisenia foetida (E. foetida) and (2) intestinal sulfate reducing-bacteria in pure cultures. After exposing animals to inorganic mercury chloride (4 mg kg−1 Hg2+) in soil and sterile soil for ten days, the amount of methylmercury in tissue was measured. Despite sterilization of soil, the accumulation of the organic mercury species in tissue was 51 ng g−1. To elucidate the potential of mercury methylation by the intestinal bacterial community, the methylation of inorganic mercury (0.1 mg L−1 Hg2+) in growth media inoculated with soil, gut content and gut epithelia was compared. The media with microorganisms of gut content and gut epithelia reached 710–980 pg mL−1 methylmercury while the methylmercury amount in samples inoculated with soil was below the detection limit. This lead to the assumption that, in this experiment, the soil microbiota is not the main source for methylmercury. Furthermore, we investigated the distribution of mercury in tissue thin-sections of worms kept in soil containing mercury chloride using laser ablation inductively coupled plasma mass spectrometry. Thereby, a mercury gradient with highest signal intensities in the intestines and lowest intensities in the epidermis was measured. These results indicated that the biotic production of methylmercury in the gut of the soil-living earthworm E. foetida is mainly related to the intestinal and, to a much lesser extent, to the soil microbiota in their habitat. Moreover, we demonstrated the capability of intestinal sulfate-reducing bacteria in pure cultures to be a source for methylmercury. Ten of 14 intestinal sulfate-reducing bacteria were found to be able to produce methylmercury in growth medium. In the presence of 0.1 mg L−1 inorganic HgCl2 bacterial cultures produced 100–1200 pg mL−1 methylmercury in 12 h. The mercury methylating species were Desulfovibrio spp., Desulfovibrio piger, Desulfovibrio giganteus, Desulfovibrio termitidis, Desulfotomaculum ruminis and Desulfobulbus propionicus, and two enrichment cultures, Zy1 and EF4, originating from the gut of a damselfly and E. foetida, respectively. To the best of our knowledge, this is the first study concerning biotic methylation including several pure and enrichment strains of intestinal microorganisms and it is a new insight that mercury methylating capability was found within the genus Desulfotomaculum.

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).

Genome analysis of Desulfotomaculum kuznetsovii strain 17(T) reveals a physiological similarity with Pelotomaculum thermopropionicum strain SI(T).

Desulfotomaculum kuznetsovii is a moderately thermophilic member of the polyphyletic spore-forming genus Desulfotomaculum in the family Peptococcaceae. This species is of interest because it originates from deep subsurface thermal mineral water at a depth of about 3,000 m. D. kuznetsovii is a rather versatile bacterium as it can grow with a large variety of organic substrates, including short-chain and long-chain fatty acids, which are degraded completely to carbon dioxide coupled to the reduction of sulfate. It can grow methylotrophically with methanol and sulfate and autotrophically with H2 + CO2 and sulfate. For growth it does not require any vitamins. Here, we describe the features of D. kuznetsovii together with the genome sequence and annotation. The chromosome has 3,601,386 bp organized in one contig. A total of 3,567 candidate protein-encoding genes and 58 RNA genes were identified. Genes of the acetyl-CoA pathway, possibly involved in heterotrophic growth with acetate and methanol, and in CO2 fixation during autotrophic growth are present. Genomic comparison revealed that D. kuznetsovii shows a high similarity with Pelotomaculum thermopropionicum. Genes involved in propionate metabolism of these two strains show a strong similarity. However, main differences are found in genes involved in the electron acceptor metabolism.

Desulfotomaculum spp. and related gram-positive sulfate-reducing bacteria in deep subsurface environments.

Gram-positive spore-forming sulfate reducers and particularly members of the genus Desulfotomaculum are commonly found in the subsurface biosphere by culture based and molecular approaches. Due to their metabolic versatility and their ability to persist as endospores. Desulfotomaculum spp. are well-adapted for colonizing environments through a slow sedimentation process. Because of their ability to grow autotrophically (H2/CO2) and produce sulfide or acetate, these microorganisms may play key roles in deep lithoautotrophic microbial communities. Available data about Desulfotomaculum spp. and related species from studies carried out from deep freshwater lakes, marine sediments, oligotrophic and organic rich deep geological settings are discussed in this review.

Complete genome sequence of the sulfate-reducing firmicute Desulfotomaculum ruminis type strain (DLT)

Desulfotomaculum ruminis Campbell and Postgate 1965 is a member of the large genus Desulfotomaculum which contains 30 species and is contained in the family Peptococcaceae. This species is of interest because it represents one of the few sulfate-reducing bacteria that have been isolated from the rumen. Here we describe the features of D. ruminis together with the complete genome sequence and annotation. The 3,969,014 bp long chromosome with a total of 3,901 protein-coding and 85 RNA genes is the second completed genome sequence of a type strain of the genus Desulfotomaculum to be published, and was sequenced as part of the DOE Joint Genome Institute Community Sequencing Program 2009.

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 RH04-3T (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 RH04-3T 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 RH04-3T 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 RH04-3T 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 RH04-3T is considered to represent a novel species of the genus Desulfotomaculum, for which the name Desulfotomaculum varum sp. nov. is proposed. The type strain RH04-3T = JCM 16158T = KCTC 5794T.

Characterization of bacterial diversity to a depth of 1500 m in the Outokumpu deep borehole, Fennoscandian Shield

This paper demonstrates the first microbiological sampling of the Outokumpu deep borehole (2516 m deep) aiming at characterizing the bacterial community composition and diversity of sulphate-reducing bacteria (SRB) in Finnish crystalline bedrock aquifers. Sampling was performed using a 1500-m-long pressure-tight tube that provided 15 subsamples, each corresponding to a 100-m section down the borehole. Microbial density measurements, as well as community fingerprinting with 16S rRNA gene-based denaturing gradient gel electrophoresis, demonstrated that microbial communities in the borehole water varied as a function of sampling depth. In the upper part of the borehole, bacteria affiliated to the family Comamonadaceae dominated the bacterial community. Further down the borehole, bacteria affiliated to the class Firmicutes became more prominent and, according to 16S rRNA gene clone libraries, dominated the bacterial community at 1400-1500 m. In addition, the largest number of bacterial classes was observed at 1400-1500 m. The dsrB genes detected in the upper part of the borehole were more similar to the dsrB genes of cultured SRBs, such as the genus Desulfotomaculum, whereas in the deeper parts of the borehole, the dsrB genes were more closely related to the uncultured bacteria that have been detected earlier in deep earth crust aquifers.

Capture of Planktonic Microbial Diversity in Fractures by Long-Term Monitoring of Flowing Boreholes, Evander Basin, South Africa

The diversity of planktonic microorganisms in fluids from a group of flowing subterranean boreholes was monitored from the day they were drilled to as long as three and a half months after drilling as they drained into Evander Au mine. Geochemical analyses of the water, characterization of microbial communities by phospholipids fatty acid (PLFA) and DNA sequence analyses, and calculations of free energy flux indicated that mine-introduced microbial contaminants, dominated by β and γ Proteobacteria, Cenarchaeaceae and Candidatus Nitrososphaera, were flushed from the boreholes and replaced by fracture water derived microbial communities dominated by Firmicutes, Methanosarcinalesand Thermoproteaceaea. The fracture water was a mixture of paleometeoric water and 2.0 Ga old, diagenetically altered, hydrothermal fluid. The C and H isotopic data for C1−4 indicated that the CH4 was primarily abiogenic in origin although ∼35–50% of it might have originated from microbial methanogenesis. Noble gas analyses yielded estimated residence times of some 10 million years for the fracture water, which is estimated to represent a capture cross-section of 0.25–0.50 km2. The 16S rRNA and dsrAB gene sequences indicated that the indigenous bacterial communities were predominantly comprised of sulfate reducers belonging to the genera Desulfotomaculum, Candiditus Desulforudis and Desulfofustis. The sulfur isotopic analyses of sulfate and sulfide yielded fractionation Δ34S values ranging from 16 to 22% consistent with microbial sulfate reduction. Thermodynamic analyses indicate that methanogenic reactions are inhibited by the high partial pressure of abiogenic CH4 and that sulfate-reducing reactions are more favorable, which is consistent with the abundance of 16S rRNA genes belonging to known sulfate reducing bacteria. Supplemental materials are available for this article. Go to the publisher's online edition of Geomicrobiology Journal to view the free supplemental files.