A microbial enhanced oil recovery (MEOR) technique was tested at low-temperature heavy oil reservoirs (Russia). The bioaugmentation approach used is based on the introduction of hydrocarbon-oxidizing bacteria into the oilfield in combination with an injection of oxygen as a H₂O₂ solution in order to initiate the first stage of hydrocarbon oxidation and of (NH₄)₂HPO₄ as a source of biogenic elements. Before the pilot trials, the microorganisms of petroleum reservoirs were investigated by high-throughput sequencing, as well as by culture-base and radioisotope techniques. Molecular studies revealed the differences in microbial composition of the carbonate and terrigenous oil reservoirs and the communities of injection and formation water. Aerobic bacteria Rhodococcus erythropolis HO-KS22 and Gordonia amicalis 6-1 isolated from oilfields oxidized oil and produced biosurfactants. Fermentative enrichment and pure cultures produced considerable amounts of low fatty acids and alcohols from sacchariferous substrates. In core-flooding tests, 43.0–53.5% of additional heavy oil was displaced by aerobic bacteria, producing biosurfactants, and 13.4–45.5% of oil was displaced by fermentative bacteria, producing low fatty acids, alcohols, and gas. A total of 1250 t additional oil was recovered as a result of the application of an MEOR technique at the Cheremukhovskoe heavy oil reservoir and Vostochno-Anzirskoe reservoir with light conventional oil.

The development of Arctic regions leads to pollution of marine and coastal environments with oil and petroleum products. The purpose of this work was to determine the diversity of microbial communities in seawater, as well as in littoral and coastal soil, and the potential ability of their members to degrade hydrocarbons degradation and to isolate oil-degrading bacteria. Using high-throughput sequencing of the V4 region of the 16S rRNA gene, the dominance of bacteria in polar communities was shown, the proportion of archaea did not exceed 2% (of the total number of sequences in the libraries). Archaea inhabiting the seawater belonged to the genera Nitrosopumilus and Nitrosoarchaeum and to the Nitrososphaeraceae family. In the polluted samples, members of the Gammaproteobacteria, Alphaproteobacteria, and Actinomycetes classes predominated; bacteria of the classes Bacteroidia, Clostridia, Acidimicrobiia, Planctomycetia, and Deltaproteobacteria were less represented. Using the iVikodak program and KEGG database, the potential functional characteristics of the studied prokaryotic communities were predicted. Bacteria were potentially involved in nitrogen and sulfur cycles, in degradation of benzoate, terephthalate, fatty acids, and alkanes. A total of 19 strains of bacteria of the genera Pseudomonas, Aeromonas, Oceanisphaera, Shewanella, Paeniglutamicibacter, and Rhodococcus were isolated from the studied samples. Among them were psychrotolerant and psychrophilic bacteria growing in seawater and utilizing crude oil, diesel fuel, and motor oils. The data obtained suggest that the studied microbial communities could participate in the removal of hydrocarbons from arctic seawater and coastal soils and suggested the possibility of the application of the isolates for the bioaugmentation of oil-contaminated polar environments.

The reserves of light conditional oil in reservoirs with low-salinity formation water are decreasing worldwide, necessitating the extraction of heavy oil from petroleum reservoirs with high-salinity formation water. As the first stage of defining the microbial-enhanced oil recovery (MEOR) strategies for depleted petroleum reservoirs, microbial community composition was studied for petroleum reservoirs with high-salinity formation water located in Tatarstan (Russia) using metagenomic and culture-based approaches. Bacteria of the phyla Desulfobacterota, Halanaerobiaeota, Sinergistota, Pseudomonadota, and Bacillota were revealed using 16S rRNA-based high-throughput sequencing in halophilic microbial communities. Sulfidogenic bacteria predominated in the studied oil fields. The 75 metagenome-assembled genomes (MAGs) of prokaryotes reconstructed from water samples were assigned to 16 bacterial phyla, including Desulfobacterota, Bacillota, Pseudomonadota, Thermotogota, Actinobacteriota, Spirochaetota, and Patescibacteria, and to archaea of the phylum Halobacteriota (genus Methanohalophilus). Results of metagenomic analyses were supported by the isolation of 20 pure cultures of the genera Desulfoplanes, Halanaerobium, Geotoga, Sphaerochaeta, Tangfeifania, and Bacillus. The isolated halophilic fermentative bacteria produced oil-displacing metabolites (lower fatty acids, alcohols, and gases) from sugar-containing and proteinaceous substrates, which testify their potential for MEOR. However, organic substrates stimulated the growth of sulfidogenic bacteria, in addition to fermenters. Methods for enhanced oil recovery should therefore be developed, combining the production of oil-displacing compounds with fermentative bacteria and the suppression of sulfidogenesis.

Application of seawater for secondary oil recovery stimulates the development of sulfidogenic bacteria in the oil field leading to microbially influenced corrosion of steel equipment, oil souring, and environmental issues. The aim of this work was to investigate potential sulfide producers in the high-temperature Uzen oil field (Republic of Kazakhstan) exploited with seawater flooding and the possibility of suppressing growth of sulfidogens in both planktonic and biofilm forms. Approaches used in the study included 16S rRNA and dsrAB gene sequencing, scanning electron microscopy, and culture-based techniques. Thermophilic hydrogenotrophic methanogens of the genus Methanothermococcus (phylum Euryarchaeota) predominated in water from the zone not affected by seawater flooding. Methanogens were accompanied by fermentative bacteria of the genera Thermovirga, Defliviitoga, Geotoga, and Thermosipho (phylum Thermotogae), which are potential thiosulfate- or/and sulfur-reducers. In the sulfate- and sulfide-rich formation water, the share of Desulfonauticus sulfate-reducing bacteria (SRB) increased. Thermodesulforhabdus, Thermodesulfobacterium, Desulfotomaculum, Desulfovibrio, and Desulfoglaeba were also detected. Mesophilic denitrifying bacteria of the genera Marinobacter, Halomonas, and Pelobacter inhabited the near-bottom zone of injection wells. Nitrate did not suppress sulfidogenesis in mesophilic enrichments because denitrifiers reduced nitrate to dinitrogen; however, thermophilic denitrifiers produced nitrite, an inhibitor of SRB. Enrichments and a pure culture Desulfovibrio alaskensis Kaz19 formed biofilms highly resistant to biocides. Our results suggest that seawater injection and temperature of the environment determine the composition and functional activity of prokaryotes in the Uzen oil field.

The current work deals with genomic analysis, possible ecological functions, and biotechnological potential of two bacterial strains, HO-A22^T and SHC 2-14, isolated from unique subsurface environments, the Cheremukhovskoe oil field (Tatarstan, Russia) and nitrate- and radionuclide-contaminated groundwater (Tomsk region, Russia), respectively. New isolates were characterized using polyphasic taxonomy approaches and genomic analysis. The genomes of the strains HO-A22^T and SHC 2-14 contain the genes involved in nitrate reduction, hydrocarbon degradation, extracellular polysaccharide synthesis, and heavy metal detoxification, confirming the potential for their application in various environmental biotechnologies. Genomic data were confirmed by cultivation studies. Both strains were found to be neutrophilic, chemoorganotrophic, facultatively anaerobic bacteria, growing at 15–33 °C and 0–1.6% NaCl (w/v). The 16S rRNA gene sequences of the strains were similar to those of the type strains of the genus Ensifer (99.0–100.0%). Nevertheless, genomic characteristics of strain HO-A22^T were below the thresholds for species delineation: the calculated average nucleotide identity (ANI) values were 83.7–92.4% (<95%), and digital DNA–DNA hybridization (dDDH) values were within the range of 25.4–45.9% (<70%), which supported our conclusion that HO-A22^T (=VKM B-3646^T = KCTC 92427^T) represented a novel species of the genus Ensifer, with the proposed name Ensifer oleiphilus sp. nov. Strain SHC 2-14 was assigned to the species ‘Ensifer canadensis’, which has not been validly published. This study expanded the knowledge about the phenotypic diversity among members of the genus Ensifer and its potential for the biotechnologies of oil recovery and radionuclide pollution treatment.

The cytosolic calcium concentration ([Ca²⁺]_cyt) in yeast cells is maintained at a low level via the action of different transporters sequestrating these cations in the vacuole. Among them, the vacuolar Ca²⁺ ATPase Pmc1 crucially contributes to this process. Its inactivation in Ogataea yeasts was shown to cause sodium dodecyl sulfate (SDS) hypersensitivity that can be alleviated by the inactivation of the plasma membrane high-affinity Ca²⁺ channel Cch1. Here, we show that SDS at low concentrations induces a rapid influx of external Ca²⁺ into cells, while the plasma membrane remains impermeable for propidium iodide. The inactivation of Pmc1 disturbs efficient adaptation to this activity of SDS. The inactivation of Cch1 partially restores the ability of pmc1 mutant cells to cope with an increased [Ca²⁺]_cyt that correlates with the suppression of SDS hypersensitivity. At the same time, Cch1 is unlikely to be directly involved in SDS-induced Ca²⁺ influx, since its inactivation does not decrease the amplitude of the rapid [Ca²⁺]_cyt elevation in the pmc1-Δ mutant. The obtained data suggest that the effects of CCH1 inactivation on SDS sensitivity and coping with increased [Ca²⁺]_cyt are related to an additional Cch1 function beyond its direct involvement in Ca²⁺ transport.