A. E. Ivanova

Occurrence and geochemical activity of microorganisms in high‐temperature, water‐flooded oil fields of Kazakhstan and Western Siberia

The distribution of different methanogenic and sulfate‐reducing bacteria and their activity in formation waters of Uzen, Mykhpay, and Talinskoe oil fields, characterized by temperatures of the strata of 50–70°C and higher, were investigated. Injection of surface waters was shown to result in development of biogenic oil transformation. The temperature of injected waters determined the temperature regime and the presence of either mesophilic or thermophilic microorganisms in the microbial community near the bottom zone of injection wells. The number and activity of thermophilic microorganisms in the zone of producing wells were low or absent. Despite the absence of oxygen in the injected water, active microbiological processes occurred in the water‐flooded oil fields. We concluded that the development of biogenic processes in oil fields proceeded not only as an aerobic‐anaerobic microbiological succession but also as anaerobic transformation of organic matter injected with the surface water and of component...

Genome analysis of Desulfotomaculum kuznetsovii strain 17T reveals a physiological similarity with Pelotomaculum thermopropionicum strain SIT

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.

A microbiological study of an underground gas storage in the process of gas extraction

The liquid phase of different units of an underground gas storage (UGS) in the period of gas injection was studied with respect to its hydrochemical composition and characterized microbiologically. The presence of viable aerobic and anaerobic bacteria was revealed in the UGS stratal and associated waters. An important source of microorganisms and biogenic elements in the ecosystem studied is water and various technogenic admixtures contained in trace amounts in the gas entering from the gas main in the period of gas injection into the storage. Owing to this fact, the bacterial functional diversity, number, and activity are maximal in the system of gas treatment and purification and considerably lower in the observation well zone. At the terminal stages, the anaerobic transformation of organic matter in the UGS aqueous media occurs via sulfate reduction and methanogenesis; exceptionally high rates of these processes (up to 4.9 × 105 ng S2− l−1 day−1 and 2.8 × 106 nl CH4 l−1 day−1, respectively) were recorded for above-ground technological equipment.

A hydrocarbon-oxidizing acidophilic thermotolerant bacterial association from sulfur blocks

A stable bacterial association isolated from a sulfur block sample of the Astrakhan gas processing complex was able to utilize n-alkanes as the sole carbon and energy source at low pH. Hydrocarbon-dependent growth occurred at pH 1.6–5.5 (optimum at pH 2.5) and 20–50°C (optimum at 30–35°C). Analysis of the 16S rRNA gene fragments isolated from the total DNA of the enrichment by PCR-DGGE revealed the nucleotide sequences most closely related to extreme acidophilic chemolithotrophs Acidithiobacillus thiooxidans and Sulfobacillus sp. (98–99% similarity) and the sequences exhibiting high similarity to those of slowly growing actinobacteria Mycobacterium europaeum and M. parascrofulaceum (98%). Capacity of any of these organisms for hydrocarbon oxidation has not been reported previously. The taxonomic position of the 16S rRNA gene fragments from the enrichment culture suggests that this bacterial association is a unique microbial community, in which development of acidophilic hydrocarbon-oxidizing bacteria is mediated by a localized pH decrease in the sulfur blocks resulting from elemental sulfur oxidation due to massive development of chemolithotrophic sulfur-oxidizing bacteria.

Hydrocarbon-oxidizing potential and the genes for n-alkane biodegradation in a new acidophilic mycobacterial association from sulfur blocks

The capacity of AGS10, a new aerobic acidophilic (growing within the pH range from 1.3 to 4.5 with the optimum at 2.0–2.5) bacterial association from sulfur blocks of the Astrakhan gas-processing complex (AGC), for oxidation of hydrocarbons of various chemical structure was investigated. A broad spectrum of normal (C10-C21) and iso-alkanes, toluene, naphthalene, and phenanthrene, as well as isoprenoids resistant to microbial degradation, pristane and phytane (components of paraffin oil), and 2,2,4,4,6,8,8,-heptamethylnonane, a branched hydrocarbon, were biodegraded under acidic conditions. Microbiological investigation revealed the dominance of mycobacteria in the AGS10 association, which was confirmed by analysis of the 16S rRNA gene clone library. In the phylogenetic tree, the 16S rRNA sequences formed a branch within the cluster of slow-growing mycobacteria, with 98% homology to the closest species Mycobacterium florentinum. Genomic DNA of AGS10 culture grown on C14-C17n-alkanes at pH 2.5 was found to contain the genes of two hydroxylase families, alkB and Cyp153, indicating their combined involvement in hydrocarbon biodegradation. The high hydrocarbon-oxidizing potential of the AGS10 bacterial association indicated that further search for the genes responsible for degradation of various hydrocarbons in acidophilic mycobacteria could be promising.

Aerobic degradation of adamantanes at highly acidic conditions

Biodegradation of alkyl-substituted adamantane derivatives (1-methyl, 1,3-dimethyl-, and 1,3,5-trimethyladamantane) by slow-growing bacteria Mycobacterium AGS10 was studied. The process was carried out under extremely acidic conditions (pH 2.5). Bacterial strain AGS10 was able to utilize these alicyclic hydrocarbons with a high degree of condensation and diamond-like structure, which are usually resistant to microbial transformation. Efficiency of alkyaldamantane biodegradation by the cells growing with these substrates as the sole carbon and energy sources was affected significantly by their aggregate state, which depended on molecular structure. Compared to the solid 1-methyladamantane, 1,3-dimethyladamantane, which is liquid under normal conditions, was a preferable substrate. Adamantanes in the gas condensate were generally more resistant to bacterial degradation than such markers as normal and isoprenoid alkanes. Moreover, biodegradation had no significant effect on relative distribution of the tested С11–С13 alkyladamantanes.

Hydrocarbon biodegradation and surfactant production by acidophilic mycobacteria

Production of biosurfactants by acidophilic mycobacteria was demonstrated in the course of aerobic degradation of hydrocarbons (n-tridecane, n-tricosane, n-hexacosane, model mixtures of С14–С17, С12‒С19, and С9–С21n-alkanes, 2,2,4,4,6,8,8-heptamethylnonane, squalane, and butylcyclohexane) and their complex mixtures (hydrocarbon gas condensate, kerosene, black oil, and paraffin oil) under extremely acidic conditions (pH 2.5). When grown on hydrocarbons, the studied bacterial culture AGS10 caused a decrease in the surface and interfacial tension of the solutions (to the lowest observed values of 26.0 and 1.3 mN/m, respectively) compared to the bacteria-free control. The rheological characteristics of the culture changed only when mycobacteria were grown on hydrocarbons. Neither the medium nor the cell-free culture liquid had the surfactant activity, which indicated formation of an endotype biosurfactant by mycobacteria. Biodegradation of n-alkanes was accompanied by an increase in cell numbers, surfactant production, and changes in the hydrophobicity of bacterial cell surface and in associated phenomena of adsorption and desorption to the hydrocarbon phase. Research on AGS10 culture liquids containing the raw biosurfactant demonstrated the preservation of its activity within a broad range of pH, temperature, and salinity.

Taxonomic diversity of aerobic organotrophic bacteria from clean vietnamese soils and their capacity for oxidation of petroleum hydrocarbons

The dominant species and abundance of the cultured aerobic organotrophic bacteria were determined in the clean soils of the Republic of Vietnam. The total number of organotrophs varied from 2.0 × 105 to 5.8 × 108 CFU/g soil. A considerable fraction of the bacterial population (1.1 × 105–9.5 × 106 CFU/g soil) was able to utilize petroleum hydrocarbons as the sole carbon and energy source. Most of the organisms obtained in pure cultures were gram-positive bacteria; over 70% were hydrocarbon-oxidizing organisms. Analysis of 16S rRNA gene sequences resulted in tentative determination of the taxonomic position of 22 strains, with 12 belonging to the Firmicutes, 4, to the Proteobacteria, and 6 to the Actinobacteria. The most common bacteria capable of hydrocarbon oxidation belonged to the genera Acinetobacter, Bacillus, Brevibacillus, Chromobacterium, Cupriavidus, Gordonia, Microbacterium, Mycobacterium, and Rhodococcus. Some of the isolated Bacillus and Staphylococcus strains, as well as one Pseudomonas and one Sinomonas strain, did not utilize hydrocarbons. Gram-positive degraders, especially members of the order Actinomycetales, which exhibited high hydrocarbon-oxidizing activity, gained competitive advantage in the presence of hydrocarbons. This microbial group probably plays an important role in hydrocarbon degradation in tropical soils. Thus, Vietnamese soils, which had no history of petroleum contamination, support numerically significant and taxonomically diverse populations of h ydrocarbon-oxidizing bacteria.

Genome analysis of Desulfotomaculum kuznetsovii strain 17T reveals a physiological similarity with Pelotomaculum thermopropionicum SIT

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.