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.

The oil industry in Khuzestan province (Southwest Iran) is one of the main reasons contributing to the pollution of the environment in this area. TPH, including both aromatic and aliphatic compounds, are important parameters in creating pollution. The present study aimed to investigate the source of soil contamination by TPH in the Ahvaz oil field in 2022. The soil samples were collected from four oil centers (an oil exploitation unit, an oil desalination unit, an oil rig, and a pump oil center). An area outside the oil field was determined as a control area. Ten samples with three replicates were taken from each area according to the standard methods. Aromatic and aliphatic compounds were measured by HPLC and GC methods. The positive matrix factorization (PMF) model and isomeric ratios were used to determine the source apportionment of aromatic compounds in soil samples. The effects range low and effects range median indices were also used to assess the level of ecological risk of petroleum compounds in the soil samples. The results showed that Benzo.b.fluoranthene had the highest concentration with an average of 5667.7 ug/kg in soil samples in the Ahvaz oil field. The highest average was found in samples from the pump oil center area at 7329.48 ug/kg, while the lowest was found in control samples at 1919.4 ug/kg-1. The highest level of aliphatic components was also found in the pump oil center, with a total of 3649 (mg. Kg-1). The results of source apportionment of petroleum compounds in soil samples showed that oil activities accounted for 51.5% of the measured PAHs in soil. 38.3% of other measured compounds had anthropogenic origins, and only 10.1% of these compounds were of biotic origin. The results of the isomeric ratios also indicated the local petroleum and pyrogenic origin of PAH compounds, which is consistent with the PMF results. The analysis of ecological risk indices resulting from the release of PAHs in the environment showed that, except for fluoranthene, other PAHs in the oil exploitation unit area were above the effects range median level (ERM) and at high risk. The results of the study showed that soil pollution by total petroleum hydrocarbons (TPH), both aromatic and aliphatic, is at a high level, and is mainly caused by human activities, particularly oil activities.

Reclamation of disturbances from oil sands mining requires effective soil management to ensure successful plant establishment and to promote recovery of native plant communities. In this study we investigated the effects of salvage depths (shallow vs. deep) and placement depths (shallow vs. deep) of forest topsoil on plant establishment, species richness, and soil properties in two substrate types (sand and peat-mineral). Shallow salvage led to greater tree stem densities and higher canopy cover for most plant groups, although there was no significant difference in species richness between shallow and deep salvages. Deep placement generally resulted in greater canopy cover, while its effect on plant density was very small for most plant groups. On peat-mineral substrate, fewer differences were detected between shallow and deep salvage, and multiple treatments resulted in greater cover. Findings suggest that a balance between maximizing the area over which propagules are redistributed and providing sufficient resources for successful plant establishment is necessary. Forest topsoil from shallow salvages and deep placements is recommended when targeting increased site productivity and species diversity. In contrast, deep salvage should be used when the primary objective is to obtain maximum reclamation material volume. Salvage depth effects may be influenced by substrate type, with peat-mineral substrate providing more favourable conditions for plant establishment. Further research is needed to assess the long-term impacts of different salvage and placement depths on plant community development and the potential effects of substrate properties on soil and plant response.

The weathering process can cause the volatilization of light components in crude oil, leading to the accumulation of total petroleum hydrocarbons (TPH) in weathered oil field soils. These TPH compounds are relatively resistant to biodegradation, posing a significant environmental hazard by contributing to soil degradation. TPH represents a complex mixture of petroleum-based hydrocarbons classified as persistent organic pollutants in soil and groundwater. The release of TPH pollutants into the environment poses serious threats to ecosystems and human health. Currently, various methods are available for TPH-contaminated soil remediation, with bioremediation technology recognized as an environmentally friendly and cost-effective approach. While converting TPH to CO2 is a common remediation method, the complex structures and diverse types of petroleum hydrocarbons (PHs) involved can result in excessive CO2 generation, potentially exacerbating the greenhouse effect. Alternatively, transforming TPH into energy forms like methane through bioremediation, followed by collection and reuse, can reduce greenhouse gas emissions and energy consumption. This process relies on the synergistic interaction between Methanogens archaea and syntrophic bacteria, forming a consortium known as the oil-degrading bacterial consortium. Methanogens produce methane through anaerobic digestion (AD), with hydrogenotrophic methanogens (HTMs) utilizing H2 as an electron donor, playing a crucial role in biomethane production. Candidatus Methanoliparia (Ca. Methanoliparia) was found in the petroleum archaeal community of weathered Oil field in northeast China. Ca. Methanoliparia has demonstrated its independent ability to decompose and produce new energy (biomethane) without symbiosis, contribute to transitioning weathered oil fields towards new energy. Therefore, this review focuses on the principles, mechanisms, and developmental pathways of HTMs during new energy production in the degradation of PHs. It also discusses strategies to enhance TPH degradation and recovery methods.

Process affected water and other industrial wastewaters are a major environmental concern. During oil sands mining, large amounts of oil sands process affected water (OSPW) are generated and stored in ponds until reclaimed and ready for surface water discharge. While much research has focused on organics in process waters, trace metals at high concentrations may also pose environmental risks. Phytoremediation is a cost effective and sustainable approach that employs plants to extract and reduce contaminants in water. The research was undertaken in mesocosm scale constructed wetlands with plants exposed to OSPW for 60 days. The objective was to screen seven native emergent wetland species for their ability to tolerate high metal concentrations (arsenic, cadmium, copper, chromium, copper, nickel, selenium, zinc), and then to evaluate the best performing species for OSPW phytoremediation. All native plant species, except Glyceria grandis, tolerated and grew in OSPW. Carex aquatilis (water sedge), Juncus balticus (baltic rush), and Typha latifolia (cattail) had highest survival and growth, and had high metal removal efficiencies for arsenic (81-87 %), chromium (78-86 %), and cadmium (74-84 %), relative to other metals; and greater than 91 % of the dissolved portions were removed. The native plant species were efficient accumulators of all metals, as demonstrated by high root and shoot bioaccumulation factors; root accumulation was greater than shoot accumulation. Translocation factor values were greater than one for Juncus balticus (chromium, zinc) and Carex aquatilis (cadmium, chromium, cobalt, nickel). The results demonstrate the potential suitability of these species for phytoremediation of a number of metals of concern and could provide an effective and environmentally sound remediation approach for wastewaters.

The extraction and processing of bitumen from the oil sands in northern Alberta, Canada generates large volumes of oil sands process-affected water (OSPW). OSPW contains a complex mixture of inorganic and organic compounds, including naphthenic acid fraction compounds (NAFCs) that are of particular concern due to their toxicity to aquatic organisms. Phytoremediation is a cost-effective, scalable approach that has the potential to remove NAFCs from OSPW and reduce OSPW toxicity. Environmental pH influences the chemical form and bioavailability of NAFCs. However, little is known about the influence of pH on the uptake of NAFCs in plant systems. This study sought to elucidate the impact of rhizosphere pH on the uptake of NAFCs using a sandbar willow (Salix interior) hydroponic system. To mimic and maintain the naturally low pH conditions of the root, OSPW solutions in these systems were adjusted to a low pH level (pH 5.0) and their NAFC uptake from solution was compared to that of OSPW at native pH (pH 8.0). Our findings revealed that the lower pH hydroponic systems demonstrated enhanced NAFC removal from solution as determined by LC-MS analysis, where up to 26% of NAFCs were removed from OSPW over 72 h at pH 5.0 compared to 8% removed at pH 8.0. Similarly, analysis of spike-in 13C-labeled NAs demonstrated that the OSPW hydroponic system rapidly removed a relatively labile NA (13C-cyclohexane carboxylic acid) from solution at both pH levels, whereas near complete removal of a recalcitrant NA (13C-1-adamantane carboxylic acid) was observed in pH 5.0 solutions only. These results provide insight into the importance of rhizosphere pH on efficient NAFC uptake by plant root systems. Further research will determine whether OSPW phytoremediation efficiency can be enhanced using field treatment conditions that promote low rhizosphere pH levels.

BACKGROUND: The Atribacterota are widely distributed in the subsurface biosphere. Recently, the first Atribacterota isolate was described and the number of Atribacterota genome sequences retrieved from environmental samples has increased significantly; however, their diversity, physiology, ecology, and evolution remain poorly understood.
RESULTS: We report the isolation of the second member of Atribacterota, Thermatribacter velox gen. nov., sp. nov., within a new family Thermatribacteraceae fam. nov., and the short-term laboratory cultivation of a member of the JS1 lineage, Phoenicimicrobium oleiphilum HX-OS.bin.34TS, both from a terrestrial oil reservoir. Physiological and metatranscriptomics analyses showed that Thermatribacter velox B11T and Phoenicimicrobium oleiphilum HX-OS.bin.34TS ferment sugars and n-alkanes, respectively, producing H2, CO2, and acetate as common products. Comparative genomics showed that all members of the Atribacterota lack a complete Wood-Ljungdahl Pathway (WLP), but that the Reductive Glycine Pathway (RGP) is widespread, indicating that the RGP, rather than WLP, is a central hub in Atribacterota metabolism. Ancestral character state reconstructions and phylogenetic analyses showed that key genes encoding the RGP (fdhA, fhs, folD, glyA, gcvT, gcvPAB, pdhD) and other central functions were gained independently in the two classes, Atribacteria (OP9) and Phoenicimicrobiia (JS1), after which they were inherited vertically; these genes included fumarate-adding enzymes (faeA; Phoenicimicrobiia only), the CODH/ACS complex (acsABCDE), and diverse hydrogenases (NiFe group 3b, 4b and FeFe group A3, C). Finally, we present genome-resolved community metabolic models showing the central roles of Atribacteria (OP9) and Phoenicimicrobiia (JS1) in acetate- and hydrocarbon-rich environments.
CONCLUSIONS: Our findings expand the knowledge of the diversity, physiology, ecology, and evolution of the phylum Atribacterota. This study is a starting point for promoting more incisive studies of their syntrophic biology and may guide the rational design of strategies to cultivate them in the laboratory. Video Abstract.

Appropriate characterization of reservoir properties and investigation of the effect of these properties on microbial metabolism and oil recovery under simulated reservoir conditions can aid in development of a sustainable microbial enhanced oil recovery (MEOR) process. Our present study has unveiled the promising potential of the hyperthermophilic archaeon, identified as Thermococcus petroboostus sp. nov. 101C5, to positively influence the microenvironment within simulated oil reservoirs, by producing significant amounts of metabolites, such as biosurfactants, biopolymers, biomass, acids, solvents, gases. These MEOR desired metabolites were found to cause a series of desirable changes in the physicochemical properties of crude oil and reservoir rocks, thereby enhancing oil recovery. Furthermore, our study demonstrated that the microbial activity of 101C5 led to the mobilization of crude oil, consequently resulting in enhanced production rates and increased efficiency in simulated sand pack trials. 101C5 exhibited considerable potential as a versatile microorganism for MEOR applications across diverse reservoir conditions, mediating significant light as well as heavy oil recovery from Berea/carbonaceous nature of rock bearing intergranular/vugular/fracture porosity at extreme reservoir conditions characterized by high temperature (80-101 °C) and high pressure (700-1300 psi). Core flood study, which truly mimicked the reservoir conditions demonstrated 29.5% incremental oil recovery by 101C5 action from Berea sandstone at 900 psi and 96 °C, underscoring the potential of strain 101C5 for application in the depleted high temperature oil wells.

The rate of mass transfer of lower molecular weight hydrocarbons (naphtha) from bitumen drops in mature fine tailings of oil sand tailings ponds (OSTPs) may control their bioavailability and the associated rate of GHG production. Experiments were conducted using bitumen drops spiked with o-xylene and 1-methylnaphthalene to determine the mass transfer rate of these naphtha components from bitumen drops. The results were compared to simulations using a multi-component numerical model that accounted for transport in the drop and across the oil-water interface. The results demonstrate rate-limited mass transfer, with aqueous concentrations after 60 days of dissolution that were different than those in equilibrium with the initial drop composition (less for o-xylene and greater for 1-methylnaphthalene). The simulations suggest that mole fractions were unchanged at the center of the drop, resulting in concentration gradients out to the oil-water interface. Numerical simulations conducted using different drop sizes and bitumen viscosities also suggest the potential for persistent naphtha dissolution, where the time required to deplete 80% of the o-xylene and 1-methylnaphthalene mass from an oil drop was estimated to be on the order of months to years for mm-sized drops, and years to decades for cm-sized drops assuming instantaneous biodegradation in the aqueous phase surrounding the bitumen.

Bitumen extraction in Alberta\'s oil sands region uses large volumes of water, leading to an abundance of oil sands process-affected water (OSPW). OSPW contains naphthenic acid fraction compounds (NAFCs) which have been found to contribute to OSPW toxicity. This study utilized a multistep treatment, coupling biological degradation with UV photocatalytic oxidation, and nutrient addition to boost the native microbial community\'s degradation capacity. OSPW initially contained 40-42 mg/L NAFCs with a toxicity of 3.8-3.9 TU. Initial biodegradation (Step 1) was used to remove the easily biodegradable NAFCs (11-25% removal), followed by a light or heavy dose of oxidation (Step 2) to breakdown the recalcitrant NAFCs (66-82% removal). Lastly, post-oxidation biodegradation with nutrients (Step 3) removed the residual bioavailable NAFCs (16-31% removal). By the end of the multistep treatment, the final NAFC concentrations and toxicity ranged from 5.3 to 6.8 mg/L and 1.1-1.2 TU. Analysis showed that OPSW was limited in phosphorus (below detection limit), and the addition of nutrients improved the degradation of NAFCs. Two treatments throughout the multistep treatment never received nutrients and showed minimal NAFC degradation post-oxidation. The native microbial community survived the stress from UV photocatalytic oxidation as seen by the post-oxidation NAFC biodegradation. Microbial community diversity was reduced considerably following oxidation, but increased with nutrient addition. The microbial community consisted predominately of Proteobacteria (Gammaproteobacteria and Alphaproteobacteria), and the composition shifted depending on the level of oxidation received. Possible NAFC-degrading microbes identified after a light oxidation dose included Pseudomonas, Acinetobacter and Xanthomonadales, while Xanthobacteracea and Rhodococcus were the dominant microbes after heavy oxidation. This experiment confirms that the microbial community is capable of degrading NAFCs and withstanding oxidative stress, and that degradation is further enhanced with the addition of nutrients.