Directional culture of petroleum hydrocarbon degrading bacteria for enhancing crude oil recovery

Biodegradation pathway and mechanism of tri (2-chloropropyl) phosphate by Providencia rettgeri

Tri (2-chloropropyl) phosphate (TCPP) was an emerging contaminant of global concern because of its frequent occurrence, potential toxic effects, and persistence in the environment. Microbial degradation might be an efficient and safe removal method, but limited information was available. In this study, Providencia rettgeri was isolated from contaminated sediment and showed it could use TCPP as unique phosphorus source to promote growth, and decompose 34.7% of TCPP (1 mg/L) within 5 days. The microbial inoculation and the initial concentration of TCPP could affect the biodegradation efficient. Further study results indicated that TCPP decomposition by Providencia rettgeri was mainly via phosphoester bond hydrolysis, evidenced by the production of bis (2-chloropropyl) phosphate (C6H13Cl2PO4) and mono-chloropropyl phosphate (C3H8ClPO4). Both intracellular and extracellular enzymes could degrade TCPP, but intracellular degradation was dominant in the later reaction stage, and the presence of Cu2+ ions had a promoting effect. These findings developed novel insights into the potential mechanism of TCPP microbial degradation.

Enhancing soil petrochemical contaminant remediation through nutrient addition and exogenous bacterial introduction

Biostimulation (providing favorable environmental conditions for microbial growth) and bioaugmentation (introducing exogenous microorganisms) are effective approaches in the bioremediation of petroleum-contaminated soil. However, uncertainty remains in the effectiveness of these two approaches in practical application. In this study, we constructed mesocosms using petroleum hydrocarbon-contaminated soil. We compared the effects of adding nutrients, introducing exogenous bacterial degraders, and their combination on remediating petroleum contamination in the soil. Adding nutrients more effectively accelerated total petroleum hydrocarbon (TPH) degradation than other treatments in the initial 60 days' incubation. Despite both approaches stimulating bacterial richness, the community turnover caused by nutrient addition was gentler than bacterial degrader introduction. As TPH concentrations decreased, we observed a succession in microbial communities characterized by a decline in copiotrophic, fast-growing bacterial r-strategists with high rRNA operon (rrn) copy numbers. Ecological network analysis indicated that both nutrient addition and bacterial degrader introduction enhanced the complexity and stability of bacterial networks. Compared to the other treatment, the bacterial network with nutrient addition had more keystone species and a higher proportion of negative associations, factors that may enhance microbial community stability. Our study demonstrated that nutrient addition effectively regulates community succession and ecological interaction to accelerate the soil TPH degradation.

Response Characteristics of the Community Structure and Metabolic Genes of Oil-Recovery Bacteria after Targeted Activation of Petroleum Hydrocarbon-Degrading Bacteria in Low-Permeability Oil Reservoirs

The microbial enhanced oil recovery (MEOR) process has been identified as a promising alternative to conventional enhanced oil recovery methods because it is eco-friendly and economically advantageous. However, the knowledge about the composition and diversity of microbial communities in artificially regulated reservoirs, especially after activating petroleum hydrocarbon-degrading bacteria (PHDB) by injecting exogenous nutrients, is still insufficient. This study utilized a combination of high-throughput sequencing and metagenomics technology to reveal the structural evolution characteristics of the indigenous microbial community in the reservoir during the PHDB activated for enhanced oil recovery, as well as the response relationship between the expression of its oil production functional genes and crude oil biodegradation. Results showed that Pseudomonas (>75%) gradually evolves into a stable dominant microbial community in the reservoir during the activation of PHDB. Besides, the gene expression and KEGG pathways after crude oil undergoes biodegradation by PHDB show that the number of genes related to petroleum hydrocarbon metabolism dominates the metabolism (21.98%). Meanwhile, a preliminary schematic diagram was drawn to illustrate the evolution mechanism of the EOR metabolic pathway after the targeted activation of PHDB. Additionally, it was found that the abundance of hydrocarbon-degrading enzymes increased significantly, and the activity of alcohol dehydrogenase was higher than that of aldehyde dehydrogenase and monooxygenase after PHDB activation. These research results not only filled in and expanded the theoretical knowledge of MEOR based on artificial interference or regulation of reservoir oil-recovery functional microbial community structure but also provided guidance for the future application of MEOR technology in oil field operations.

Enrichment of microbial consortia for MEOR in crude oil phase of reservoir-produced liquid and their response to environmental disturbance

Developing microbial consortiums is necessary for microbial enhanced oil recovery (MEOR) in heavy crude oil production. The aqueous phase of produced fluid has long been considered an ideal source of microorganisms for MEOR. However, it is recently found that rich microorganisms (including hydrocarbon-degrading bacteria) are present in the crude oil phase, which is completely different from the aqueous phase of produced fluid. So, in this study, the microbial consortia from the crude oil phase of produced fluids derived from four wells were enriched, respectively. The microbial community structure during passage was dynamically tracked, and the response of enriched consortia to successive disturbance of environmental factors was investigated. The results showed the crude oil phase had high microbial diversity, and the original microbial community structure from four wells was significantly different. After ten generations of consecutive enrichment, different genera were observed in the four enriched microbial consortia, namely, Geobacillus, Bacillus, Brevibacillus, Chelativorans, Ureibacillus, and Ornithinicoccus. In addition, two enriched consortia (eG1614 and eP30) exhibited robustness to temperature and oxygen perturbations. These results further suggested that the crude oil phase of produced fluids can serve as a potential microbial source for MEOR.

Nutrient availability contributes to structural and functional diversity of microbiome in Xinjiang oilfield

Indigenous microbial enhanced oil recovery (IMEOR) is a promising alternative way to promote oil recovery. It activates oil recovery microorganisms in the reservoir by adding nutrients to the injected water, utilizing microbial growth and metabolism to enhance recovery. However, few studies have focused on the impact of injected nutrients on reservoir microbial community composition and potential functions. This limits the further strategic development of IMEOR. In this study, we investigated the effects of nutrition on the composition of the reservoir bacterial community and functions in the Qizhong block of Xinjiang Oilfield, China, by constructing a long core microbial flooding simulation device. The results showed that the microbial community structure of the reservoir changed from aerobic state to anaerobic state after nutrient injection. Reducing the nutrient concentration increased the diversity and network stability of the reservoir bacterial community. At the same time, the nitrogen metabolism function also showed the same change response. Overall, these results indicated that nutrition significantly affected the community structure and function of reservoir microorganisms. Injecting low concentrations of nutrients may be more beneficial to improve oil recovery. This study is of great significance for guiding IMEOR technology and saving costs at the field site.

Study on stabilized mechanism of high internal phase Pickering emulsions based on commercial yeast proteins: Modulating the characteristics of Pickering particle via sonication

The primary significance of this work is that the commercial yeast proteins particles were successfully used to characterize the high internal phase Pickering emulsions (HIPPEs). The different sonication time (0,3,7,11,15 min) was used to modulate the structure and interface characteristics of yeast proteins (YPs) that as Pickering particles. Immediately afterward, the influence of YPs particles prepared at different sonication time on the rheological behavior and coalescence mechanism of HIPPEs was investigated. The results indicate that the YPs sonicated for 7 min exhibited a more relaxed molecular structures and conformation, the smallest particle size, the highest H0 and optimal amphiphilicity (the three-phase contact (θ) was 88.91°). The transition from extended to compact conformations of YPs occurred when the sonication time exceeded 7 min, resulting in an augmentation of size of YPs particles, a reduction in surface hydrophobicity (H0), and an elevation in hydrophilicity. The HIPPEs stabilized by YPs particles sonicated for 7 min exhibited the highest adsorption interface protein percentage and a more homogeneous three-dimensional (3D) protein network, resulting in the smallest droplet size and the highest storage (G'). The HIPPEs sample that stabilized by YPs particles sonicated for 15 min showed the lowest adsorption protein percentage. This caused a reduction in the thickness of its interface protein layer and an enlargement in the droplet diameter (D [3,2]). It was prone to droplet coalescence according to the equation used to evaluate the coalescence probability of droplets (Eq (2)). And the non-adsorbed YPs particles form larger aggregation structures in the continuous phase and act as "structural agents" in 3D protein network. Therefore, mechanistically, the interface protein layer formed by YPs particles sonicated 7 min contributed more to HIPPEs stability. Whereas the "structural agents" contributed more to HIPPEs stability when the sonication time exceeded 7 min. The present results shed important new light on the application of commercial YPs in the functional food fields, acting as an available and effective alternative protein.

Marine Microbiota Responses to Shipping Scrubber Effluent Assessed at Community Structure and Function Endpoints

The use of novel high-throughput sequencing (HTS) technologies to examine the responses of natural multidomain microbial communities to scrubber effluent discharges to the marine environment is still limited. Thus, we applied metabarcoding sequencing targeting the planktonic unicellular eukaryotic and prokaryotic fraction (phytoplankton, bacterioplankton, and protozooplankton) in mesocosm experiments with natural microbial communities from a polluted and an unpolluted site. Furthermore, metagenomic analysis revealed changes in the taxonomic and functional dominance of multidomain marine microbial communities after scrubber effluent additions. The results indicated a clear shift in the microbial communities after such additions, which favored bacterial taxa with known oil and polycyclic aromatic hydrocarbons (PAHs) biodegradation capacities. These bacteria exhibited high connectedness with planktonic unicellular eukaryotes employing variable trophic strategies, suggesting that environmentally relevant bacteria can influence eukaryotic community structure. Furthermore, Clusters of Orthologous Genes associated with pathways of PAHs and monocyclic hydrocarbon degradation increased in numbers at treatments with high scrubber effluent additions acutely. These genes are known to express enzymes acting at various substrates including PAHs. These indications, in combination with the abrupt decrease in the most abundant PAHs in the scrubber effluent below the limit of detection-much faster than their known half-lives-could point toward a bacterioplankton-initiated rapid ultimate biodegradation of the most abundant toxic contaminants of the scrubber effluent. The implementation of HTS could be a valuable tool to develop multilevel biodiversity indicators of the scrubber effluent impacts on the marine environment, which could lead to improved impact assessment. Environ Toxicol Chem 2024;00:1-18. © 2024 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.

Illegal dumping of oil and gas wastewater alters arid soil microbial communities

The Permian Basin, underlying southeast New Mexico and west Texas, is one of the most productive oil and gas (OG) provinces in the United States. Oil and gas production yields large volumes of wastewater with complex chemistries, and the environmental health risks posed by these OG wastewaters on sensitive desert ecosystems are poorly understood. Starting in November 2017, 39 illegal dumps, as defined by federal and state regulations, of OG wastewater were identified in southeastern New Mexico, releasing ~600,000 L of fluid onto dryland soils. To evaluate the impacts of these releases, we analyzed changes in soil geochemistry and microbial community composition by comparing soils from within OG wastewater dump-affected samples to unaffected zones. We observed significant changes in soil geochemistry for all dump-affected compared with control samples, reflecting the residual salts and hydrocarbons from the OG-wastewater release (e.g., enriched in sodium, chloride, and bromide). Microbial community structure significantly (P < 0.01) differed between dump and control zones, with soils from dump areas having significantly (P < 0.01) lower alpha diversity and differences in phylogenetic composition. Dump-affected soil samples showed an increase in halophilic and halotolerant taxa, including members of the Marinobacteraceae, Halomonadaceae, and Halobacteroidaceae, suggesting that the high salinity of the dumped OG wastewater was exerting a strong selective pressure on microbial community structure. Taxa with high similarity to known hydrocarbon-degrading organisms were also detected in the dump-affected soil samples. Overall, this study demonstrates the potential for OG wastewater exposure to change the geochemistry and microbial community dynamics of arid soils.IMPORTANCEThe long-term environmental health impacts resulting from releases of oil and gas (OG) wastewater, typically brines with varying compositions of ions, hydrocarbons, and other constituents, are understudied. This is especially true for sensitive desert ecosystems, where soil microbes are key primary producers and drivers of nutrient cycling. We found that releases of OG wastewater can lead to shifts in microbial community composition and function toward salt- and hydrocarbon-tolerant taxa that are not typically found in desert soils, thus altering the impacted dryland soil ecosystem. Loss of key microbial taxa, such as those that catalyze organic carbon cycling, increase arid soil fertility, promote plant health, and affect soil moisture retention, could result in cascading effects across the sensitive desert ecosystem. By characterizing environmental changes due to releases of OG wastewater to soils overlying the Permian Basin, we gain further insights into how OG wastewater may alter dryland soil microbial functions and ecosystems.

Characteristic microbiome and synergistic mechanism by engineering agent MAB-1 to evaluate oil-contaminated soil biodegradation in different layer soil

Bioremediation is a sustainable and pollution-free technology for crude oil-contaminated soil. However, most studies are limited to the remediation of shallow crude oil-contaminated soil, while ignoring the deeper soil. Here, a high-efficiency composite microbial agent MAB-1 was provided containing Bacillus (naphthalene and pyrene), Acinetobacter (cyclohexane), and Microbacterium (xylene) to be synergism degradation of crude oil components combined with other treatments. According to the crude oil degradation rate, the up-layer (63.64%), middle-layer (50.84%), and underlying-layer (54.21%) crude oil-contaminated soil are suitable for bioaugmentation (BA), biostimulation (BS), and biostimulation+bioventing (BS+BV), respectively. Combined with GC-MS and carbon number distribution analysis, under the optimal biotreatment, the degradation rates of 2-ring and 3-ring PAHs in layers soil were about 70% and 45%, respectively, and the medium and long-chain alkanes were reduced during the remediation. More importantly, the relative abundance of bacteria associated with crude oil degradation increased in each layer after the optimal treatment, such as Microbacterium (2.10-14%), Bacillus (2.56-12.1%), and Acinetobacter (0.95-12.15%) in the up-layer soil; Rhodococcus (1.5-6.9%) in the middle-layer soil; and Pseudomonas (3-5.4%) and Rhodococcus (1.3-13.2%) in the underlying-layer soil. Our evaluation results demonstrated that crude oil removal can be accelerated by adopting appropriate bioremediation approach for different depths of soil, providing a new perspective for the remediation of actual crude oil-contaminated sites.

Enhanced degradation of petroleum in saline soil by nitrogen stimulation and halophilic emulsifying bacteria Bacillus sp. Z-13

Remediation of petroleum-contaminated soil is a widely concerned challenge. As an ecofriendly method, the performance improvement of indigenous microbial degradation is facing the bottleneck. In this study, a strain with high efficiency of petroleum degradation was isolated from the petroleum-contaminated soil and identified and named as Bacillus sp. Z-13. The strain showed the ability to produce lipopeptide surfactant which could improve 66% more petroleum hydrocarbons eluted. Strain Z-13 and its biosurfactant exhibited broad environmental adaptability to salinity (0-8%), pH (6-9) and temperature (15-45 °C). With the addition of strain Z-13 and the stimulation of NH4Cl, up to 59% of the petroleum in the contaminated soil was removed at the carbon to nitrogen ratio of 10. Microbial community analysis showed that petroleum-degrading bacteria, represented by Bacillus, became the dominant species at genus level and played an important role in the remediation. Additionally, ammonium stimulation facilitated both pathways of ammonium assimilation and nitrification in native microorganisms to achieve efficient degradation of petroleum hydrocarbons. This study could provide a promising approach for stable, environmental-friendly and efficient remediation of petroleum-contaminated soil.

CO2 improves the anaerobic biodegradation intensity and selectivity of heterocyclic hydrocarbons in heavy oil

Heterocyclic hydrocarbons pollution generated by oil spills and oilfield wastewater discharges threatens the ecological environment and human health. Here we described a strategy that combines the greenhouse gas CO₂ reduction with microbial remediation. In the presence of nitrate, CO₂ can improve the biodegradation efficiency of the resins and asphaltenes in heavy oil, particularly the biodegradation selectivity of the polar heterocyclic compounds by the newly isolated Klebsiella michiganensis. This strain encoded 80 genes for the xenobiotic biodegradation and metabolism, and can efficiently utilize CO₂ when degrading heavy oil. The total abundance of resins and asphaltenes decreased significantly with CO₂, from 40.816% to 26.909%, to 28.873% with O₂, and to 36.985% with N₂. The transcripts per million (TPM) value of accA gene was 57.81 under CO₂ condition, while respectively 8.86 and 21.23 under O₂ and N₂ conditions. Under CO₂ condition, the total relative percentage of N1-type heterocyclic compounds was selectively decreased from 32.25% to 22.78%, resulting in the heavy oil viscosity decreased by 46.29%. These results demonstrated a novel anaerobic degradation mechanism that CO₂ can promote the anaerobic biodegradation of heterocyclic hydrocarbons in heavy oil, which provides a promising biotreatment technology for the oil-contaminated water.

Construction of microbial consortia for microbial degradation of complex compounds

Increasingly complex synthetic environmental pollutants are prompting further research into bioremediation, which is one of the most economical and safest means of environmental restoration. From the current research, using microbial consortia to degrade complex compounds is more advantageous compared to using isolated bacteria, as the former is more adaptable and stable within the growth environment and can provide a suitable catalytic environment for each enzyme required by the biodegradation pathway. With the development of synthetic biology and gene-editing tools, artificial microbial consortia systems can be designed to be more efficient, stable, and robust, and they can be used to produce high-value-added products with their strong degradation ability. Furthermore, microbial consortia systems are shown to be promising in the degradation of complex compounds. In this review, the strategies for constructing stable and robust microbial consortia are discussed. The current advances in the degradation of complex compounds by microbial consortia are also classified and detailed, including plastics, petroleum, antibiotics, azo dyes, and some pollutants present in sewage. Thus, this paper aims to support some helps to those who focus on the degradation of complex compounds by microbial consortia.

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.

A review on anaerobic microorganisms isolated from oil reservoirs

The Role of microorganisms in the petroleum industry is wide-ranging. To understand the role of microorganisms in hydrocarbon transformation, identification of such microorganisms is vital, especially the ones capable of in situ degradation. Microorganisms play a pivotal role in the degradation of hydrocarbons and remediation of heavy metals. Anaerobic microorganisms such as Sulphate Reducing Bacteria (SRB), responsible for the production of hydrogen sulphide (H₂S) within the reservoir, reduces the oil quality by causing reservoir souring and reduction in oil viscosity. This paper reviews the diversity of SRB, methanogens, Nitrogen Reducing Bacteria (NRB), and fermentative bacteria present in oil reservoirs. It also reviews the extensive diversity of these microorganisms, their applications in petroleum industries, characteristics and adaptability to survive in different conditions, the potential to alter the petroleum hydrocarbons properties, the propensity to petroleum hydrocarbon degradation, and remediation of metals.

Succession of microbial communities and synergetic effects during bioremediation of petroleum hydrocarbon-contaminated soil enhanced by chemical oxidation

Biotechnologies integrated with chemical techniques are promising in treating the soils contaminated by petroleum hydrocarbons. Experiments by applying the degrading consortium and the modified Fenton (MF) with the chelator sodium citrate simultaneously were carried out to investigate the effects of the MF reagents on the degradation of total petroleum hydrocarbons (TPHs), changes in enzyme activities and the succession of microbial communities at the 0, 20, 100 and 500 mmol/kg hydrogen peroxide concentration levels. The ratio between hydrogen peroxide, ferrous sulfate and sodium citrate in the MF reagents was 100:1:1. The results indicated that the degradation of TPHs conformed to first-order kinetics and MF treatments increased the total removal rates of TPHs (4.73-24.26%) and activated dehydrogenase and polyphenol oxidase activities. A shift in microbial communities from Proteobacteria to Bacteroidetes was observed during the enhanced bioremediation, and the predominant genus shifted from Pseudomonas with an average relative abundance (ARAs) of 76.61% at the beginning to Sphingobacterium with ARAs of 52.06% at the later stage. The MF reagents at the proper level could simplify the relationship among the community populations, alleviate their competition and strengthen their associations, which would optimize the removal efficiency.