Metagenomic and Culture-Based Analyses of Microbial Communities from Petroleum Reservoirs with High-Salinity Formation Water, and Their Biotechnological Potential

Simple Summary A significant amount of residual oil is located in oil reservoirs with high-salinity formation water levels. Microorganisms are capable of producing a number of oil-displacing metabolites, such as volatile acids, alcohols, biosurfactants, biopolymers, and others. The application of microbial-enhanced oil recovery (MEOR) methods is possible after a detailed study of the microbial community of the oil reservoir. The aim of this study was to elucidate the biodiversity of microorganisms in oil reservoirs of Tatarstan (Russia) with high saline formation water in order to select suitable MEOR technologies for these reservoirs. Using metagenomic and cultural methods, it was shown that fermentative and sulfate-reducing bacteria predominate in reservoirs with high-sulfate formation water, whereas in oil reservoirs with low-sulfate water, in the community of Methanohalophilus methanogens predominated. A total of 20 pure bacterial cultures were isolated from oil reservoirs. The isolated fermentative bacteria were able to produce oil-displacing metabolites from sugar-containing and protein substrates. However, fermentation products stimulate the growth of sulfidogenic bacteria that form sulfide, which reduces the quality of oil and causes the corrosion of steel equipment. Thus, when choosing MEOR technology, it is necessary to take into account the possibility of activation of fermentative prokaryotes with simultaneous suppression of the growth of sulfidogens in the oil reservoir.Abstract 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.