Microbial hydrocarbon degradation mediated by natural/modified clay minerals represents an eco-friendly and economically viable remediation strategy for hydrocarbon contamination. However, its effects are not always positive as they depend on multiple factors, including clay mineral types, modification methods, microbial species, and hydrocarbon substrates. This review systematically synthesizes existing fragmented studies concerning the impacts of natural clay minerals, modified clay minerals (acid/alkali/thermal/organic/metal ion), and clay minerals containing composite materials on microbial hydrocarbon biodegradation. Based on current findings, future research should prioritize the following recommendations: (1) avoid using concentrated strong acids in acid activation; (2) exclude metal cations that induce strong adsorption (reducing hydrocarbon bioavailability) or trigger excessive interlayer hydrolysis (some trivalent cations) in metal cation modification; (3) eliminate biologically toxic agents during organic modification; and (4) expand understanding of alkali/thermally modified clay minerals and clay mineral-containing composite materials in this direction. Natural/modified clay mineral-mediated microbial degradation is a highly promising remediation technology for hydrocarbon contamination and poised to advance and achieve breakthroughs through continuous synthesis of knowledge and innovation.

Illite is a widely distributed clay mineral with huge reserves in Earth’s crust, but its effect on heavy oil biodegradation is rarely reported. This study made an investigation of the interactions between illite and a Pseudomonas stutzeri-heavy oil complex (PstHO). Results showed that, although illite exerted a negative effect on P. stutzeri degrading heavy oil by inhibiting the biodegradation of 64 saturated hydrocarbons (SHs) and 50 aromatic hydrocarbons (AHs), it selectively stimulated the biodegradation of 45 AHs with a specific structure, and its biogenic kaolinization at room temperature (35 °C) and pressure (1 atm) was observed in PstHO for the first time. The finding points out for the first time that, in PstHO, illite may change the quasi-sequential of AHs biodegradation of heavy oil, as well as its kaolinization without clay intermediate.

Silicate bacteria, capable of decomposing silicate minerals that are widely distributed in oil reservoirs, have never been applied in microbial enhanced oil recovery (MEOR). This study investigated a typical silicate bacterium (Paenibacillus mucilaginosus) for the first time in a simulation experiment on low-permeability cores. Meanwhile, a biosurfactant-producing bacterium (Pseudomonas aeruginosa) and an acid-producing bacterium (Bacillus licheniformis) that have been widely studied and applied in MEOR were used for comparison. The results show that although P. mucilaginosus is inferior to P. aeruginosa and B. licheniformis in terms of enhancement of oil recovery at the microbial flooding stage, it can maintain efficient dissolution of minerals over extended periods during the subsequent water flooding stage. This is different from the other two bacteria and ultimately leads to a 6.9% enhancement in oil recovery (7.9% for P. aeruginosa and 4.8% for B. licheniformis). P. mucilaginosus improves oil recovery by increasing the porosity (1.4%) and permeability (12.3 mD) of low-permeability cores through biological weathering. The μCT results show that the pore quantity and pore volume across varying pore radii in low-permeability cores are altered after the MEOR simulation experiment by reducing the quantity and volume of pores with radii less than 10 μm and increasing the quantity and volume of pores with radii between 10 and 25 μm. Under MEOR simulation experimental conditions, P. mucilaginosus slightly degrade saturated hydrocarbons (1.9%), mainly the n-alkanes of C11–C20, but cannot degrade aromatic hydrocarbons, resins, and asphaltenes. The enhanced oil recovery by P. mucilaginosus is attributed to its bio-dissolution under neutral pH conditions, which prevents acid sensitivity damage to low-permeability cores. Thus, its MEOR characteristics are significantly different from the biosurfactant-producing bacterium P. aeruginosa and acid-producing bacterium B. licheniformis. Injecting P. mucilaginosus at the early stages of reservoir development or using it together with other microorganisms should maximize its MEOR effect. This study advances the MEOR framework by extending silicate-dissolving bacteria from agricultural microbial fertilizer systems to MEOR in low-permeability reservoirs, revealing the broad prospects of mineral-targeting microbes for both research and industrial applications in MEOR.

The impact of anthropogenic disturbances during reservoir development on the ecological system—encompassing both environmental and microbial components—has long been overlooked. This study pioneers the investigation into the effects of microbially activated water flooding on both reservoir environments and indigenous microbial communities. We conducted a comprehensive analysis of the B9 Reservoir’s parameters before and after field testing, including the pH, redox potential, conductivity, chemical oxygen demand, biochemical oxygen demand, aqueous-phase cell concentration, aqueous-phase deoxyribonucleic acid (DNA) concentration, oil-phase DNA concentration, and microbial population data. The results demonstrate that environmental parameters exhibit high sensitivity to microbially activated water flooding and effectively explain microbial blooms, while microbial blooms reciprocally alter the environmental conditions, forming a mutually influencing dynamic interplay. The 183-day microbially activated water flooding, while causing detectable impacts on the reservoir environment and microorganisms, did not pose a threat to its ecological stability and contributed to enhanced oil production. In contrast, the 60-month pilot test concluded 27 months earlier exhibited potential destabilization risks to the reservoir ecology. By simultaneously monitoring reservoir environments and microbial dynamics, this research not only addresses potential ecological risks associated with human-driven reservoir development but also provides actionable insights to optimize reservoir management strategies.

In the fluid (comprising oil and nutrient solution)–microbe–mineral ternary system of oil reservoirs, current microbial enhanced oil recovery (MEOR) technology lacks investigation into the interactions between the latter two components and their application potential in petroleum production. This may explain why MEOR has achieved only partial success while failing to meet full expectations. This review systematically synthesizes the existing fragmented research on reservoirs regarding rock minerals as direct/indirect microbial substrates in MEOR applications. Currently, microbe–mineral interactions enhance oil recovery primarily through the following mechanisms: clay swelling inhibition, induced mineral precipitation, silicate dissolution, wettability alteration, microbial acids etching, and hydrocarbon degradation modulation. Integrating contemporary findings on microbe–mineral interactions, three strategically prioritized MEOR implementation pathways demonstrate particular promise: microbially mediated weathering processes in silicate/carbonate reservoirs, microbial-induced mineral precipitation/dissolution cycles, and microbial leaching-assisted permeability enhancement. Finally, a total of 20 microorganisms potentially applicable for mineral-targeted MEOR were proposed. If MEOR technology could be re-examined from the perspective of microbe–mineral interactions and thoroughly investigated, integrating the knowledge on fluid–microbe binary systems in oil reservoir, this potentially transformative technology may achieve breakthroughs.

Clay-mediated microbial degradation has been demonstrated as a low-cost, efficient, and eco-friendly strategy for remediating crude oil-contaminated soils. Despite substantial laboratory studies, field tests remain scarce. In this study, montmorillonite treatment was applied to a crude oil production well pad shut down for 753 days. Post-treatment analyses included soil physicochemical parameters (water content, redox potential, pH, elemental analysis, and total organic carbon), crude oil content/composition (gas chromatography–mass spectrometry), microbial biomass (deoxyribonucleic acid concentration), and community structure (high-throughput sequencing), with parallel comparisons to untreated control areas. Results indicated that montmorillonite enhanced the crude oil biodegradation rate (37.27% vs. control 33.00%), increased microbial biomass (83.08% vs. control 35.06%), and enriched biodiversity (7 genera vs. control 0). Specifically, it exhibited the most pronounced promotion effects on saturated hydrocarbon degradation (73.42% vs. control 60.89%) and aromatic hydrocarbon degradation (45.77% vs. control 29.60%). This study not only provides field evidence for clay-mediated microbial remediation but also lays a foundation for developing composite remediation approaches (e.g., nutrient supplements, catalysts, or functional microbial consortia) in future research and practical applications.