Thermodynamically favorable reactions shape the archaeal community affecting bacterial community assembly in oil reservoirs

Diversity and Ecological Relevance of Fumarate-Adding Enzymes in Oil Reservoir Microbial Communities

Oil reservoirs are important hydrocarbon-rich environments, where the addition of hydrocarbons to fumarate mediated by fumarate-adding enzymes (FAE) is one of the dominant mechanisms for anaerobic degradation of hydrocarbons. However, the currently available information about FaeA, the catalytic subunit of FAE, in in situ petroleum reservoirs is limited. Here, we investigated the diversity of FaeA and FaeA-harbouring microbes in oil reservoirs and compared them with marine sediments. We obtained 67 FaeA clusters and 46 FaeA-harbouring MAGs from oil reservoirs. Most FaeA sequences and all FaeA-containing microbes were endemic and unique. In oil reservoirs, FaeA sequences were affiliated with Archaeoglobus and 13 bacterial phyla. Fermentative metabolism was a common lifestyle amongst these organisms. Genomes assigned to Desulfobacterota, Caldatribacteriota and Firmicutes_B were the most diverse and prevalent, while Desulfobacterota and Chloroflexota were dominant in marine. Microbial community diversity at the phylum level was strongly related to FaeA in oil reservoirs but not in marine. This suggested that the ability of anaerobic hydrocarbon biodegradation may shape community structure in oil reservoirs. Together, this study provided systematic and comprehensive information regarding the high diversity of FaeA and FaeA-containing anaerobic hydrocarbon degraders in oil reservoirs and underlined the difference between hydrocarbon-rich environments of oil reservoirs and marine.

Phenotypic and Genomic Characterization of a Sulfate-Reducing Bacterium Pseudodesulfovibrio methanolicus sp. nov. Isolated from a Petroleum Reservoir in Russia

The search for the microorganisms responsible for sulfide formation and corrosion of steel equipment in the oil fields of Tatarstan (Russia) resulted in the isolation of a new halotolerant strictly anaerobic sulfate-reducing bacterium, strain 5S69T. The cells were motile curved Gram-negative rods. Optimal growth was observed in the presence of 2.0-4.0% (w/v) NaCl, at pH 6.5, and at 23-28 °C under sulfate-reducing conditions. The isolate was capable of chemoorganotrophic growth with sulfate and other sulfoxides as electron acceptors, resulting in sulfide formation; and of pyruvate fermentation resulting in formation of H2 and acetate. The strain utilized lactate, pyruvate, ethanol, methanol, fumarate, and fructose, as well as H2/CO2/acetate for sulfate reduction. The genome size of the type strain 5S69T was 4.16 Mb with a G + C content of 63.0 mol%. On the basis of unique physiological properties and results of the 16S rRNA gene-based phylogenetic analysis, phylogenomic analysis of the 120 conserved single copy proteins and genomic indexes (ANI, AAI, and dDDH), assigning the type strain 5S69T ((VKM B-3653T = KCTC 25499T) to a new species within the genus Pseudodesulfovibrio, is suggested, with the proposed name Pseudodesulfovibrio methanolicus sp. nov. Genome analysis of the new isolate showed several genes involved in sulfate reduction and its sulfide-producing potential in oil fields with high saline formation water.

Global diversity and ecological functions of viruses inhabiting oil reservoirs

Oil reservoirs, being one of the significant subsurface repositories of energy and carbon, host diverse microbial communities affecting energy production and carbon emissions. Viruses play crucial roles in the ecology of microbiomes, however, their distribution and ecological significance in oil reservoirs remain undetermined. Here, we assemble a catalogue encompassing viral and prokaryotic genomes sourced from oil reservoirs. The catalogue comprises 7229 prokaryotic genomes and 3,886 viral Operational Taxonomic Units (vOTUs) from 182 oil reservoir metagenomes. The results show that viruses are widely distributed in oil reservoirs, and 85% vOTUs in oil reservoir are detected in less than 10% of the samples, highlighting the heterogeneous nature of viral communities within oil reservoirs. Through combined microcosm enrichment experiments and bioinformatics analysis, we validate the ecological roles of viruses in regulating the community structure of sulfate reducing microorganisms, primarily through a virulent lifestyle. Taken together, this study uncovers a rich diversity of viruses and their ecological functions within oil reservoirs, offering a comprehensive understanding of the role of viral communities in the biogeochemical cycles of the deep biosphere.

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

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.

Characteristics of microbiota, core sulfate-reducing taxa and corrosion rates in production water from five petroleum reservoirs in China

Microbial diversity and activities in petroleum reservoir systems can be altered by water-flooding operation, but the current understanding of the mechanism for such changes in microbial composition characteristics and community is inadequate. In this study, microbial communities especially functional groups in production water from five petroleum reservoirs in China were investigated by chemical and molecular biological analyses. The dominant and core phyla in the five oil reservoirs were Proteobacteria, Deferribacterota, Firmicutes, Desulfobacterota, Euryarchaeota and Thermoplasmatota. At the genus level, the dominant taxa in each petroleum reservoir were different, and not all of the dominant genera were the core members across the five oil reservoirs. The microbiologically influenced corrosion (MIC) were investigated for the functional groups in each production water. The corrosion rates in production water were higher than controls with a positive correlation to the abundances of sulfate-reducing prokaryotes (SRP). The SRP diversity based on the aprA and dsrA gene analysis showed that obvious differences were evident between onshore (JS, SL, DQ and XJ) and offshore (BS) oilfields. The core SRP taxa in onshore oilfields were Desulfomicrobium and Desulfovibrio, also with Desulfotomaculum in medium/low-temperature oil reservoirs (DQ and XJ), but in high-temperature petroleum reservoirs (JS, BS and SL), Archaeoglobus, Thermodesulfobacterium and Thermodesulfovibrio were the core groups. Statistical analysis indicated that temperature, electron acceptors and donors showed significant influence on the SRP community. This research reveals the characteristics of microbial and functional community as well as their interaction mechanism on corrosion in petroleum reservoir environments, and will improve industrial bio-control and management of MIC in oilfields.

pH and Nitrate Drive Bacterial Diversity in Oil Reservoirs at a Localized Geographic Scale

Oil reservoirs are one of the most important deep subsurface biospheres. They are inhabited by diverse microorganisms including bacteria and archaea with diverse metabolic activities. Although recent studies have investigated the microbial communities in oil reservoirs at large geographic scales, it is still not clear how the microbial communities assemble, as the variation in the environment may be confounded with geographic distance. In this work, the microbial communities in oil reservoirs from the same oil field were identified at a localized geographic scale. We found that although the injected water contained diverse exogenous microorganisms, this had little effect on the microbial composition of the produced water. The Neutral Community Model analysis showed that both bacterial and archaeal communities are dispersal limited even at a localized scale. Further analysis showed that both pH and nitrate concentrations drive the assembly of bacterial communities, of which nitrate negatively correlated with bacterial alpha diversity and pH differences positively correlated with the dissimilarity of bacterial communities. In contrast, the physiochemical parameters had little effect on archaeal communities at the localized scale. Our results suggest that the assembly of microbial communities in oil reservoirs is scale- and taxonomy-dependent. Our work provides a comprehensive analysis of microbial communities in oil reservoirs at a localized geographic scale, which improves the understanding of the assembly of the microbial communities in oil reservoirs.

Growth Inhibition of Sulfate-Reducing Bacteria during Gas and Oil Production Using Novel Schiff Base Diquaternary Biocides: Synthesis, Antimicrobial, and Toxicological Assessment

Upstream crude oil production equipment is always exposed to destruction damagingly which is caused by sulfate-reducing bacterium (SRB) activities that produce H2S gas, which leads to increased metal corrosion (bio-fouling) rates and inflicts effective infrastructure damage. Hence, oil and gas reservoirs must be injected with biocides and inhibitors which still offer the foremost protection against harmful microbial activity. However, because of the economic and environmental risks associated with biocides, the oil and gas sectors improve better methods for their usage. This work describes the synthesis and evaluation of the biological activities as the cytotoxicity and antimicrobial properties of a series of diquaternary cationic biocides that were studied during the inhibition of microbial biofilms. The prepared diquaternary compound was synthesized by coupling vanillin and 4-aminoantipyrene to achieve the corresponding Schiff base, followed by a quaternization reaction using 1,6-bromohexane, 1,8-bromooctane, and 1,12-bromododecane. The increase of their alkyl chain length from 6 to 12 methylene groups increased the obtained antimicrobial activity and cytotoxicity. Antimicrobial efficacies of Q1-3 against various biofilm-forming microorganisms, including bacteria and fungi, were examined utilizing the diameter of inhibition zone procedures. The results revealed that cytotoxic efficacies of Q1-3 were significantly associated mainly with maximum surface excess and interfacial characteristics. The cytotoxic efficiencies of Q1-3 biocides demonstrated promising results due to their comparatively higher efficacies against SRB. Q3 exhibited the highest cytotoxic biocide against the gram +ve, gram -ve, and SRB species according to the inhibition zone diameter test. The toxicity of the studied microorganisms depended on the nature and type of the target microorganism and the hydrophobicity of the biocide molecules. Cytotoxicity assessment and antimicrobial activity displayed increased activity by the increase in their alkyl chain length.

Bacterial and Archaeal Community Distribution in Oilfield Water Re-injection Facilities and the Influences from Microorganisms in Injected Water

Water flooding is widely employed for oil production worldwide. However, there has never been a systematic investigation of the microbial communities occurring in oilfield water re-injection facilities. Here, we investigated the distribution of bacterial and archaeal communities in water re-injection facilities of an oilfield, and illustrated the combined influences of environmental variation and the microorganisms in injected water on the microbial communities. Bacterial communities from the surface injection facilities were dominated by aerobic or facultative anaerobic Betaproteobacteria, Alphaproteobacteria, and Flavobacteria, whereas Clostridia, Deltaproteobacteria, Anaerolineae, and Synergistia predominated in downhole of the injection wells, and Gammaproteobacteria, Betaproteobacteria, and Epsilonproteobacteria predominated in the production wells. Methanosaeta, Methanobacterium, and Methanolinea were dominant archaea in the injection facilities, while Methanosaeta, Methanomethylovorans, and Methanoculleus predominated in the production wells. This study also demonstrated that the microorganisms in injected water could be easily transferred from injection station to wellheads and downhole of injection wells, and environmental variation and diffusion-limited microbial transfer resulted from formation filtration were the main factors determining microbial community assembly in oil-bearing strata. The results provide novel information on the bacterial and archaeal communities and the underlying mechanisms occurring in oilfield water re-injection facilities, and benefit the development of effective microbiologically enhanced oil recovery and microbiologically prevented reservoir souring programs.

Even allocation of benefits stabilizes microbial community engaged in metabolic division of labor

Microbial communities execute metabolic pathways to drive global nutrient cycles. Within a community, functionally specialized strains can perform different yet complementary steps within a linear pathway, a phenomenon termed metabolic division of labor (MDOL). However, little is known about how such metabolic behaviors shape microbial communities. Here, we derive a theoretical framework to define the assembly of a community that degrades an organic compound through MDOL. The framework indicates that to ensure community stability, the strains performing the initial steps should hold a growth advantage (m) over the "private benefit" (n) of the strain performing the last step. The steady-state frequency of the last strain is then determined by the quotient of n and m. Our experiments show that the framework accurately predicts the assembly of our synthetic consortia that degrade naphthalene through MDOL. Our results provide insights for designing and managing stable microbial systems for metabolic pathway optimization.

Bioemulsification and Microbial Community Reconstruction in Thermally Processed Crude Oil

Utilization of low-cost, environmental-friendly microbial enhanced oil recovery (MEOR) techniques in thermal recovery-processed oil reservoirs is potentially feasible. However, how exogenous microbes facilitate crude oil recovery in this deep biosphere, especially under mesophilic conditions, is scarcely investigated. In this study, a thermal treatment and a thermal recurrence were processed on crude oil collected from Daqing Oilfield, and then a 30-day incubation of the pretreated crude oil at 37 °C was operated with the addition of two locally isolated hydrocarbon-degrading bacteria, Amycolicicoccus subflavus DQS3-9A1^T and Dietzia sp. DQ12-45-1b, respectively. The pH, surface tension, hydrocarbon profiles, culture-dependent cell densities and taxonomies, and whole and active microbial community compositions were determined. It was found that both A. subflavus DQS3-9A1^T and Dietzia sp. DQ12-45-1b successfully induced culture acidification, crude oil bioemulsification, and residual oil sub-fraction alteration, no matter whether the crude oil was thermally pretreated or not. Endogenous bacteria which could proliferate on double heated crude oil were very few. Compared with A. subflavus, Dietzia sp. was substantially more effective at inducing the proliferation of varied species in one-time heated crude oil. Meanwhile, the effects of Dietzia sp. on crude oil bioemulsification and hydrocarbon profile alteration were not significantly influenced by the ploidy increasing of NaCl contents (from 5 g/L to 50 g/L), but the reconstructed bacterial communities became very simple, in which the Dietzia genus was predominant. Our study provides useful information to understand MEOR trials on thermally processed oil reservoirs, and proves that this strategy could be operated by using the locally available hydrocarbon-degrading microbes in mesophilic conditions with different salinity degrees.

Genome-Resolved Meta-Analysis of the Microbiome in Oil Reservoirs Worldwide

Microorganisms inhabiting subsurface petroleum reservoirs are key players in biochemical transformations. The interactions of microbial communities in these environments are highly complex and still poorly understood. This work aimed to assess publicly available metagenomes from oil reservoirs and implement a robust pipeline of genome-resolved metagenomics to decipher metabolic and taxonomic profiles of petroleum reservoirs worldwide. Analysis of 301.2 Gb of metagenomic information derived from heavily flooded petroleum reservoirs in China and Alaska to non-flooded petroleum reservoirs in Brazil enabled us to reconstruct 148 metagenome-assembled genomes (MAGs) of high and medium quality. At the phylum level, 74% of MAGs belonged to bacteria and 26% to archaea. The profiles of these MAGs were related to the physicochemical parameters and recovery management applied. The analysis of the potential functional core in the reservoirs showed that the microbiota was specialized for each site, with 31.7% of the total KEGG orthologies annotated as functions (1690 genes) common to all oil fields, while 18% of the functions were site-specific, i.e., present only in one of the oil fields. The oil reservoirs with a lower level of intervention were the most similar to the potential functional core, while the oil fields with a long history of water injection had greater variation in functional profile. These results show how key microorganisms and their functions respond to the distinct physicochemical parameters and interventions of the oil field operations such as water injection and expand the knowledge of biogeochemical transformations in these ecosystems.