[Identification of Hydrocarbon-Oxidizing Dietzia Bacteria from Petroleum Reservoirs Based on Phenotypic Properties and Analysis of the 16S rRNA and gyrB Genes].

The taxonomic position of hydrocarbon-oxidizing bacterial strains 263 and 32d isolated from formation water of the Daqing petroleum reservoir (PRC) was determined by polyphasic taxonomy techniques, including analysis of the 16S rRNA and the gyrB genes. The major chemotaxonomic characteristics of both strains, including the IV type cell wall, composition of cell wall fatty acids, mycolic acids, and menaquinones, agreed with those typical of Dietzia strains. The DNA G+C content of strains 263 and 32d were 67.8 and 67.6 mol%, respectively. Phylogenetic analysis of the 16S rRNA gene of strain 32d revealed 99.7% similarity to the gene of D. maris, making it possible to identify strain 32d as belonging to this species. The 16S rRNA gene sequence of strain 263 exhibited 99.7 and 99.9% similarity to those of D. natronolimnaea and D. cercidiphylli YIM65002(T), respectively. Analysis of the gyrB genes of the subterranean isolates and of a number of Dietzia type strains confirmed classiffication of strain 32d as a D. maris strain and of strain 263, as a D. natronolimnaea strain. A conclusion was made concerning higher resolving power of phylogenetic analysis of the gyrB gene compared to the 16S rRNA gene analysis in the case of determination of the species position of Dietzia isolates.

[Microbiological Aspects of Radioactive Waste Storage].

The article gives information about the microorganisms inhabiting in surface storages of solid radioactive waste and deep disposal sites of liquid radioactive waste. It was shown that intensification of microbial processes can lead to significant changes in the chemical composition and physical state of the radioactive waste. It was concluded that the biogeochemical processes can have both a positive effect on the safety of radioactive waste storages (immobilization of RW macrocomponents, a decreased migration ability of radionuclides) and a negative one (biogenic gas production in subterranean formations and destruction of cement matrix).

Inhibitory and bactericidal action of the biocorrosion agents «INCORGAS¼ and «AMDOR¼.

Inhibiting action of A, B and M-X compositions against hydrosulfide corrosion of carbon steel, hydrogen diffusion through the steel membrane has been studied along with their bactericidal effect with respect to sulfate-reducing bacteria of Desulfomicrobium type. Bactericidal properties of the compositions have been studied in the Postgate medium. Corrosion tests have been made in the NACE medium saturated by hydrogen sulfide and carbon dioxide separately and together by methods of gravimetrical measurements and linear polarization resistance (LRP). Potentiodynamic polarization and electrochemical diffusion method have been used. Steel protection is determined in the inhibited solutions by combined action of corrosion products film and inhibitor. Presence of sulfate-reducing bacteria in medium increases hydrogen diffusion flux through the steel membrane by 2-3 times and essentially stimulates effect of the inhibitors. The inhibiting compositions decrease quantity of sulfate-reducing bacteria (SRB) by 95-98%. The obtained results testify about predominately bacteriostatic action of the inhibiting compositions, which has influence on the enzymatic systems of SRB cells responsible directly for the sulfate reduction because of substantially decreasing the biogenic hydrogen sulfide concentration in the system.

[Regulation of geochemical activity of microorganisms in a petroleum reservoir by injection of H2O2 or water-air mixture].

In the course of pilot trials of biotechnologies for the enhancement of oil recovery in the Gangxi bed of the Dagang oil field (China), microbiological processes were investigated. The biotechnologies were based on injection into the petroleum reservoir of different oxygen sources (H2O2 solution or a water-air mixture) with nitrogen and phosphorus salts. The injection of water-air mixture with nitrogen and phosphorus salts resulted in an increase in the number of aerobic and anaerobic organotrophic bacteria, rates of sulfate reduction and methanogenesis in formation water and also the content of CO2 (from 4.8-12 to 15-23.2%) and methane (from 86-88 to 91.8%) in the gas. The preferential consumption of isotopically light bicarbonate by methanogens resulted in a higher content of the light 12C in methane; the delta13C/CH4 value changed from -45.1...-48.3 to -50.7...-59.3 per thousand). At the same time, mineral carbonates of the formation water became isotopically heavier; the delta13C/Sigmacarbonates value increased from 3.4...4.0 to 5.4...9.6 per thousand. Growth of hydrocarbon-oxidizing bacteria was accompanied by production of biosurfactants and decreased interfacial tension of formation water. Injection of H2O2 solution resulted in the activation of aerobic processes and in suppression of both sulfate reduction and methanogenesis. Methane content in the gas decreased from 86-88 to 75.4-79.8%, probably due to its consumption by methanotrophs. Due to consumption of isotopically light methane, the residual methane carbon became heavier, with the delta13C/CH4 values from -39.0 to -44.3 per thousand. At the same time, mineral carbonates of the formation water became isotopically considerably lighter; the delta13C/Sigmacarbonates value decreased from 5.4... 9.6 to -1.4...2.7 per thousand). The additional amount of oil recovered during the trial of both variants of biotechnological treatment was 3819 t.

[AlkB homologues in thermophilic bacteria of the genus Geobacillus].

Screening of alkane hydroxylase genes (alkB) was performed in the thermophilic aerobic bacteria of the genus Geobacillus. Total DNA was extracted from the biomass of 11 strains grown on the mixture of saturated C10-C20 hydrocarbons, PCR amplification of fragments of alkB genes was performed with degenerate oligonucleotide primers, PCR products were cloned and sequenced. For the first time in the genome of thermophilic bacteria the presence of a set of alkB gene homologues was revealed. The strains each contain three to six homologues among which only two are universal for all of the strains. Comparative phylogenetic analysis of the nucleotide sequences and the inferred amino acid sequences showed close relatedness of six of the revealed variants of geobacilli sequences to the alkB4, alkB3, and alkB2 genes that had previously been revealed by other authors in Rhodococcus erythropolis strains NRRL B-16531 and Q15. The rest two variants of alkB sequences were unique. Analysis of the GC composition of all the Geobacillus alkB homologues revealed closer proximity to the rhodococcal chromosomal DNA than to the chromosomal DNA of geobacilli. This may be an indication of the introduction of the alkB genes into the Geobacillus genome by interspecies horizontal transfer; and rhodococci or other representatives of the Actinobacteria phylum were probably the donors of these genes. Analysis of the codon usage in fragments of alkB genes confirms the suggestion that the pool of these genes is common to the majority of Gram-positive and certain Gram-negative bacteria. Formation of a set of several alkB homologues in a genome of a particular microorganism may result from free gene exchange within this pool.

[Microbiological and production characteristics of the high-temperature Kongdian bed revealed during field trial of biotechnology for the enhancement of oil recovery].

Microbiological technology for the enhancement of oil recovery based on the activation of the stratal microflora was tested in the high-temperature horizons of the Kongdian bed (60 degrees C) of the Dagang oil field (China). This biotechnology consists in the pumping of a water-air mixture and nitrogen and phosphorus mineral salts into the oil stratum through injection wells in order to stimulate the activity of the stratal microflora which produce oil-releasing metabolites. Monitoring of the physicochemical, microbiological, and production characteristics of the test site has revealed large changes in the ecosystem as a result of the application of biotechnology. The cell numbers of thermophilic hydrocarbon-oxidizing, fermentative, sulfate-reducing, and methanogenic microorganisms increased 10-10 000-fold. The rates of methanogenesis and sulfate reduction increased in the near-bottom zone of the injection wells and of some production wells. The microbial oil transformation was accompanied by the accumulation of bicarbonate ions, volatile fatty acids, and biosurfactants in the formation waters, as well as of CH4 and CO2 both in the gas phase and in the oil. Microbial metabolites promoted the additional recovery of oil. As a result of the application of biotechnology, the water content in the production liquid from the test site decreased, and the oil content increased. This allowed the recovery of more than 14000 tons of additional oil over 3.5 years.

[Microbiological investigations of high-temperature horizons of the Kongdian petroleum reservoir in connection with field trial of a biotechnology for enhancement of oil recovery].

The physicochemical conditions and microbiological characteristics of the formation waters of the Kongdian bed of the Dagang oil field (China) were studied. It was demonstrated that this bed is a high-temperature ecosystem with formation waters characterized by low mineralization. The concentrations of nitrogen and phosphorus compounds, as well as of electron acceptors, are low. Oil and oil gas are the main organic matter sources. The bed is exploited with water-flooding. The oil stratum was inhabited mostly by anaerobic thermophilic microorganisms, including fermentative (10(2)-10(5) cells/ml), sulfate-reducing (0-10(2) cells/ml), and methanogenic (0-10(3) cells/ml) microorganisms. Aerobic bacteria were detected mainly in the near-bottom zone of injection wells. The rate of sulfate reduction varied from 0.002 to 18.940 microg S(2-) l(-1) day(-1) and the rate of methanogenesis from 0.012 to 16.235 microg CH4 l(-1) day(-1). Microorganisms with great biotechnological potential inhabited the bed. Aerobic thermophilic bacteria were capable of oxidizing oil with the formation of biomass, the products of partial oxidation of oil (volatile acids), and surfactants. During growth on the culture liquid of oiloxidizing bacteria, methanogenic communities produced methane and carbon dioxide, which also had oil-releasing capabilities. Using various labeled tracers, the primary filtration flows of injected solutions at the testing site were studied. Our comprehensive investigations allowed us to conclude that the tested method for microbial enhancement of oil recovery based on the activation of the stratal microflora can be applied in the Kongdian bed horizons.

[Phylogenetic diversity and activity of anaerobic microorganisms of high-temperature horizons of the Dagang Oilfield (China)].

The number of microorganisms of major metabolic groups and the rates of sulfate-reducing and methanogenic processes in the formation waters of the high-temperature horizons of Dagang oilfield have been determined. Using cultural methods, it was shown that the microbial community contained aerobic bacteria oxidizing crude oil, anaerobic fermentative bacteria, sulfate-reducing bacteria, and methanogenic bacteria. Using cultural methods, the possibility of methane production from a mixture of hydrogen and carbon dioxide (H2 + CO2) and from acetate was established, and this result was confirmed by radioassays involving NaH14CO3 and 14CH3COONa. Analysis of 16S rDNA of enrichment cultures of methanogens demonstrated that these microorganisms belong to Methanothermobacter sp. (M. thermoautotrophicus), which consumes hydrogen and carbon dioxide as basic substrates. The genes of acetate-utilizing bacteria were not identified. Phylotypes of the representatives of Thermococcus spp. were found among 16S rDNAs of archaea. 16S rRNA genes of bacterial clones belong to the orders Thermoanaerobacteriales (Thermoanaerobacter, Thermovenabulum, Thermacetogenium, and Coprothermobacter spp.), Thermotogales, Nitrospirales (Thermodesulfovibrio sp.) and Planctomycetales. 16S rDNA of a bacterium capable of oxidizing acetate in the course of syntrophic growth with H2-utilizing methanogens was found at high-temperature petroleum reservoirs for the first time. These results provide further insight into the composition of microbial communities of high-temperature petroleum reservoirs, indicating that syntrophic processes play an important part in acetate degradation accompanied by methane production.

[Distribution and activity of microorganisms in the deep repository for liquid radioactive waste at the Siberian Chemical Combine].

The physicochemical conditions, composition of microbial communities, and the rates of anaerobic processes in the deep sandy horizons used as a repository for liquid radioactive wastes (LRW) at the Siberian Chemical Combine (Seversk, Tomsk oblast), were studied. Formation waters from the observation wells drilled into the production horizons of the radioactive waste disposal site were found to be inhabited by microorganisms of different physiological groups, including aerobic organotrophs, anaerobic fermentative, denitrifying, sulfate-reducing, and methanogenic bacteria. The density of microbial population, as determined by cultural methods, was low and usually did not exceed 10(4) cells/ml. Enrichment cultures of microorganisms producing gases (hydrogen, methane, carbon dioxide, and hydrogen sulfide) and capable of participation in the precipitation of metal sulfides were obtained from the waters of production horizons. The contemporary processes of sulfate reduction and methanogenesis were assayed; the rates of these terminal processes of organic matter destruction were found to be low. The denitrifying bacteria from the underground repository were capable of reducing the nitrates contained in the wastes, provided sources of energy and biogenic elements were available. Biosorption of radionuclides by the biomass of aerobic bacteria isolated from groundwater was demonstrated. The results obtained give us insight into the functional structure of the microbial community inhabiting the waters of repository production horizons. This study indicates that the numbers and activity of microbial cells are low both inside and outside the zone of radioactive waste dispersion, in spite of the long period of waste discharge.

[Description of Desulfotomaculum nigrificans subsp. salinus as a new species, Desulfotomaculum salinum sp. nov].

This study focused on the physiological, chemotaxonomic, and genotypic characteristics of two thermophilic spore-forming sulfate-reducing bacterial strains, 435T and 781, of which the former has previously been assigned to the subspecies Desulfotomaculum nigrificans subsp. salinus. Both strains reduced sulfate with the resulting production of H2S on media supplemented with H2 + CO2, formate, lactate, pyruvate, malate, fumarate, succinate, methanol, ethanol, propanol, butanol, butyrate, valerate, or palmitate. Lactate oxidation resulted in acetate accumulation; butyrate was oxidized completely, with acetate as an intermediate product. Growth on acetate was slow and weak. Sulfate, sulfite, thiosulfate, and elemental sulfur, but not nitrate, served as electron acceptors for growth with lactate. The bacteria performed dismutation of thiosulfate to sulfate and hydrogen sulfide. In the absence of sulfate, pyruvate but not lactate was fermented. Cytochromes of b and c types were present. The temperature and pH optima for both strains were 60-65 degrees C and pH 7.0. Bacteria grew at 0 to 4.5-6.0% NaCl in the medium, with the optimum being at 0.5-1.0%. Phylogenetic analysis based on a comparison of incomplete 16S rRNA sequences revealed that both strains belonged to the C cluster of the genus Desulfotomaculum, exhibiting 95.5-98.3% homology with the previously described species. The level of DNA-DNA hybridization of strains 435T and 781 with each other was 97%, while that with closely related species D. kuznetsovii 17T was 51-52%. Based on the phenotypic and genotypic properties of strains 435T and 781, it is suggested that they be assigned to a new species: Desulfotomaculum salinum sp. nov., comb. nov. (type strain 435T = VKM B 1492T).

[The phylogenetic diversity of aerobic organotrophic bacteria from the Dagan high-temperature oil field].

The distribution and species diversity of aerobic organotrophic bacteria in the Dagan high-temperature oil field (China), which is exploited via flooding, have been studied. Twenty-two strains of the most characteristic thermophilic and mesophilic aerobic organotrophic bacteria have been isolated from the oil stratum. It has been found that, in a laboratory, the mesophilic and thermophilic isolates grow in the temperature, pH, and salinity ranges characteristic of the injection well near-bottom zones or of the oil stratum, respectively, and assimilate a wide range of hydrocarbons, fatty acids, lower alcohols, and crude oil, thus exhibiting adaptation to the environment. Using comparative phylogenetic 16S rRNA analysis, the taxonomic affiliation of the isolates has been established. The aerobic microbial community includes gram-positive bacteria with a high and low G+C content of DNA, and gamma and beta subclasses of Proteobacteria. The thermophilic bacteria belong to the genera Geobacillus and Thermoactinomyces, and the mesophilic strains belong to the genera Bacillus, Micrococcus, Cellulomonas, Pseudomonas, and Acinetobacter. The microbial community of the oil stratum is dominated by known species of the genus Geobacillus (G. subterraneus, G. stearothermophilus, and G. thermoglucosidasius) and a novel species "Geobacillus jurassicus." A number of novel thermophilic oil-oxidizing bacilli have been isolated.

[Production of oil-processing compounds by microorganisms from the Daqing oil field, China]. / Obrazovanie neftevytesniaiushchikh soedinenii mikroorganizmami iz neftianogo mestorozhdeniia Datsin (KNR).

Twenty pure cultures isolated from formation waters of the Daqing oil field were studied with respect to their capacity to produce surface-active compounds in media with individual hydrocarbons, lower alcohols, and fatty acids. Aerobic saprotrophic bacteria belonging to the genera Bacillus, Brevibacillus, Rhodococcus, Dietzia, Kocuria, Gordonia, Cellulomonas, Clavibacter, Pseudomonas, and Acinetobacter decreased the surface tension of cultivation media from 55-63 to 28-44 mN/m. Strains of Bacillus cereus, Rhodococcus ruber, and Bacillus licheniformis produced biosurfactants most actively. Bacteria of the genera Rhodococcus, Dietzia, Kocuria, and Gordonia produced exopolysaccharides in media with hydrocarbons. Culture liquids of the strains of R. ruber and B. licheniformis exhibited oil-releasing effect. Thus, the Daqing oil field is inhabited by aerobic bacteria capable of producing effective oil-releasing agents.

[Phylogenetic diversity of aerobic saprotrophic bacteria isolated from the Daqing oil field]. / Filogeneticheskoe raznoobrazie aérobnykh saprotrofnykh bakterii iz neftianogo mestorozhdeniia Datsin.

A diverse and active microbial community in the stratal waters of the Daqing oil field (China), which is exploited with the use of water-flooding, was found to contain aerobic chemoheterotrophic bacteria (including hydrocarbon-oxidizing ones) and anaerobic fermentative, sulfate-reducing, and methanogenic bacteria. The aerobic bacteria were most abundant in the near-bottom zones of injection wells. Twenty pure cultures of aerobic saprotrophic bacteria were isolated from the stratal waters. Under laboratory conditions, they grew at temperatures, pH, and salinity values typical of the stratal water from which they were isolated. These isolates were found to be able to utilize crude oil and a wide range of hydrocarbons, fatty acids, and alcohols. Phylogenetic analysis carried out with the use of complete 16S rRNA sequences showed that the isolates could be divided into three major groups: gram-positive bacteria with a high and a low G + C content of DNA and gram-negative bacteria of the gamma-subclass of the Proteobacteria. Gram-positive isolates belonged to the genera Bacillus, Brevibacillus, Rhodococcus, Dietzia, Kocuria, Gordonia, Cellulomonas, and Clavibacter. Gram-negative isolates belonged to the genera Pseudomonas and Acinetobacter. In their 16S rRNA sequences, many isolates were similar to the known microbial species and some probably represented new species.

Isolation and characterization of Thermococcus sibiricus sp. nov. from a Western Siberia high-temperature oil reservoir.

Anaerobic organotrophic hyperthermophilic Archaea were isolated from five of eight samples from oil wells of the Samotlor oil reservoir (depth, 1,799-2,287 m; temperature, 60 degrees-84 degrees C). Three strains were isolated in pure cultures and characterized phylogenetically on the basis of comparison of the 16S rRNA gene sequences. All strains belonged to a new species of the genus Thermococcus, with Thermococcus litoralis, Thermococcus aggregans, Thermococcus fumicolans, and Thermococcus alcaliphilus being the nearest relatives (range of sequence similarity, 97.2%-98.8%). Strain MM 739 was studied in detail. The new isolate grew on peptides but not on carbohydrates. Elemental sulfur had a stimulatory effect on growth. The temperature range for growth was between 40 degrees and 88 degrees C, with the optimum at 78 degrees C; the pH range was 5.8 to 9.0, with the optimum around 7.3; and the salinity range was 0.5% to 7.0%, with the optimum at 1.8%-2.0%. The doubling time at optimal growth conditions was about 43 min. The G+C content of the DNA was 38.4 mol%. The DNA-DNA relatedness between strain MM 739 and T. litoralis was 27%; between strain MM 739 and T. aggregans, it was 22%. Based on the phenotypic and genomic differences with known Thermococcus species, the new species Thermococcus sibiricus is proposed. The isolation of a hyperthermophilic archaeum from a deep subsurface environment, significantly remote from shallow or abyssal marine hot vents, indicates the existence of a subterranean biosphere inhabited by indigenous hyperthermophilic biota.

Taxonomic study of aerobic thermophilic bacilli: descriptions of Geobacillus subterraneus gen. nov., sp. nov. and Geobacillus uzenensis sp. nov. from petroleum reservoirs and transfer of Bacillus stearothermophilus, Bacillus thermocatenulatus, Bacillus thermoleovorans, Bacillus kaustophilus, Bacillus thermodenitrificans to Geobacillus as the new combinations G. stearothermophilus, G. th.

Five hydrocarbon-oxidizing strains were isolated from formation waters of oilfields in Russia, Kazakhstan and China. These strains were moderately thermophilic, neutrophilic, motile, spore-forming rods, aerobic or facultatively anaerobic. The G+C content of their DNA ranged from 49.7 to 52.3 mol%. The major isoprenoid quinone was menaquinone-7; cellular fatty acid profiles consisted of significant amounts of iso-15:0, iso-16:0 and iso-17:0 fatty acids (61.7-86.8% of the total). Based on data from 16S rDNA analysis and DNA-DNA hybridization, the subsurface isolates could be divided into two groups, one of which consisted of strains UT and X and the other of which consisted of strains K, Sam and 34T. The new strains exhibited a close phylogenetic relationship to thermophilic bacilli of 'Group 5' of Ash et al. [Ash, C., Farrow, J. A. E., Wallbanks, S. & Collins, M. D. (1991). Lett Appl Microbiol 13, 202-206] and a set of corresponding signature positions of 16S rRNA. Comparative analysis of the 16S rDNA sequences and fatty acid compositions of the novel isolates and established species of thermophilic bacilli indicated that the subsurface strains represent two new species within a new genus, for which the names Geobacillus subterraneus gen. nov., sp. nov., and Geobacillus uzenensis sp. nov. are proposed. It is also proposed that Bacillus stearothermophilus, Bacillus thermoleovorans, Bacillus thermocatenulatus, Bacillus kaustophilus, Bacillus thermoglucosidasius and Bacillus thermodenitrificans be transferred to this new genus, with Geobacillus stearothermophilus (formerly Bacillus stearothermophilus) as the type species.

[Heterogeneity of nucleotide sequences of 16S ribosomal RNA genes from the Desulfotomaculum kuznetsovii type strain]. / Geterogennost' nukleotidnykh posledovatel'nostei genov 16S ribosomnoi RNK tipovogo shtamma Desulfotomaculum kuznetsovii.

Two copies of the 16S rRNA gene, rrnA and rrnB, of the type strain 17T of the thermophilic sulfate-reducing bacterium Desulfotomaculum kuznetsovii were cloned and completely sequenced. The comparison of the determined sequences revealed considerable heterogeneity (8.3%) of the two genes, rrnA and rrnB. The main differences were associated with superlong inserts located at the variable 5'- and 3'-terminal regions of the 16S rRNA genes. Comparative analysis that involved analogous genes from the phylogenetically closest representatives of the genus Desulfotomaculum showed that disregard of the heterogeneity of the two gene copies distorts the position of the bacterium studied in the phylogenetic tree.

[Physico-chemical and microbiological characteristics of groundwater from observation boreholes of a deep radioactive liquid waste repository]. / Fiziko-khimicheskaia i mikrobiologicheskaia kharakteristika podzemnykh vod iz nabliudatel'nykh skvazhin glubinnogo khranilishcha zhidkikh radioaktivnykh otkhodov.

A radioactive liquid waste repository was found to be a habitat of the rich microbial community with a high catabolic potential. Groundwater from a depth of 162-189 m contained aerobic saprotrophic and anaerobic fermentative, sulfate-reducing, and denitrifying bacteria. Nitrate-reducing bacteria residing in this groundwater were isolated in pure cultures. Based on the results of their physiological studies, 16S rRNA sequencing, and phylogenetic analysis, the microorganisms isolated were ascribed to one phylogenetic branch, the gamma-subclass of gram-negative bacteria. Among six isolates, four belonged to the genus Acinetobacter, whereas two others belonged to the genera Comamonas and Aeromonas. The data obtained indicate that the microflora of the repository can exert a certain effect on the chemical composition of the formation fluids and bearing rocks, as well as on the migration of radionuclides.