Diagnosing bioremediation of crude oil-contaminated soil and related geochemical processes at the field scale through microbial community and functional genes

Bioremediation of petroleum-contaminated soil based on both toxicity risk control and hydrocarbon removal-progress and prospect

Petroleum contamination remains a worldwide issue requiring cost-effective bioremediation techniques. However, establishing a universal bioremediation strategy for all types of oil-polluted sites is challenging. This difficulty arises from the heterogeneity of soil textures, the complexity of oil products, and the variations in local climate and environment across different oil-contaminated regions. Several factors can impede bioremediation efficacy: (i) differences in bioavailability and biodegradability between aliphatic and aromatic fractions of crude oil; (ii) inconsistencies between hydrocarbon removal efficiency and toxicity attenuation during remediation; (iii) varying adverse effect of aliphatic and aromatic fractions on soil microorganisms. This review examines the ecotoxicity risk of petroleum contamination to soil fauna and flora. It also discusses three primary bioremediation strategies: biostimulation with nutrients, bioaugmentation with petroleum degraders, and phytoremediation with plants. Based on current research and state-of-the-art challenges, we highlighted future research scopes should focus on (i) exploring the ecotoxicity differentiation of aliphatic and aromatic fractions of crude oil, (ii) establishing unified risk factors and indicators for evaluating oil pollution toxicity, (iii) determining the fate and transformation of aliphatic and aromatic fractions of crude oil using advanced analytical techniques, and (iv) developing combined bioremediation techniques that improve petroleum removal and ecotoxicity attenuation.

Incorporating the Soil Gas Gradient Method and Functional Genes to Assess the Natural Source Zone Depletion at a Petroleum-Hydrocarbon-Contaminated Site of a Purification Plant in Northwest China

An increasing number of studies have demonstrated that natural source zone depletion (NSZD) in the vadose zone accounts for the majority (90%~99%) of the natural attenuation of light non-aqueous phase liquid (LNAPL). Until now, 0.05 to 12 kg/a.m² NSZD rates at tens of petroleum LNAPL source zones have been determined in the middle or late evolution stage of LNAPL release, in which limited volatile organic compounds (VOCs) and methane (CH₄) were detected. NSZD rates are normally estimated by the gradient method, yet the associated functional microbial activity remains poorly investigated. Herein, the NSZD at an LNAPL-releasing site was studied using both soil gas gradient methods quantifying the O₂, CO₂, CH₄, and VOCs concentrations and molecular biology methods quantifying the abundance of the pmoA and mcrA genes. The results showed that the methanogenesis rates were around 4 to 40 kg/a.m². The values were greater than the rates calculated by the sum of CH₄ escaping (0.3~1.2 kg/a.m²) and O₂ consuming (3~13 kg/a.m²) or CO₂ generating rates (2~4 kg/a.m²), suggesting that the generated CH₄ was oxidized but not thoroughly to CO₂. The functional gene quantification also supported the indication of this process. Therefore, the NSZD rates at the site roughly equaled the methanogenesis rates (4~40 kg/a.m²), which were greater than most of the previously studied sites with a 90th percentile value of 4 kg/a.m². The study extended the current knowledge of the NSZD and has significant implications for LNAPL remediation management.

Evolution in mitigation approaches for petroleum oil-polluted environment: recent advances and future directions

Increasing petroleum consumption and a rise in incidental oil spillages have become global concerns owing to their aquatic and terrestrial toxicity. Various physicochemical and biological treatment strategies have been studied to tackle them and their impact on environment. One of such approaches in this regard is the use of microbial processes due to their being "green" and also apparent low cost and high effectiveness. This review presents the advancement in the physical and biological remediation methods and their progressive efficacy if employed in combination of hybrid modes. The use of biosurfactants and/or biochar along with microbes seems to be a more effective bioremediation approach as compared to their individual effects. The lacuna in research at community or molecular level has been overcome by the recent introduction of "-omics" technology in hydrocarbon degradation. Thus, the review further focuses on presenting the state-of-art information on the advancement of petroleum bioremediation strategies and identifies the research gaps for achieving total mitigation of petroleum oil.

Microbial Involvement in the Bioremediation of Total Petroleum Hydrocarbon Polluted Soils: Challenges and Perspectives

Nowadays, soil contamination by total petroleum hydrocarbons is still one of the most widespread forms of contamination. Intervention technologies are consolidated; however, full-scale interventions turn out to be not sustainable. Sustainability is essential not only in terms of costs, but also in terms of restoration of the soil resilience. Bioremediation has the possibility to fill the gap of sustainability with proper knowledge. Bioremediation should be optimized by the exploitation of the recent “omic” approaches to the study of hydrocarburoclastic microbiomes. To reach the goal, an extensive and deep knowledge in the study of bacterial and fungal degradative pathways, their interactions within microbiomes and of microbiomes with the soil matrix has to be gained. “Omic” approaches permits to study both the culturable and the unculturable soil microbial communities active in degradation processes, offering the instruments to identify the key organisms responsible for soil contaminant depletion and restoration of soil resilience. Tools for the investigation of both microbial communities, their degradation pathways and their interaction, will be discussed, describing the dedicated genomic and metagenomic approaches, as well as the interpretative tools of the deriving data, that are exploitable for both optimizing bio-based approaches for the treatment of total petroleum hydrocarbon contaminated soils and for the correct scaling up of the technologies at the industrial scale.

Using prototypes to enable development of commercially viable field scale contaminated site remediation processes

Soil structure was damaged from solvents and localised heating after a large fire which had potential to limit bioremediation of an industrial site. Laboratory prototypes (biopile, bioflushing, bioreactor, slurry reactor) for treating the site contamination were developed. After successful laboratory testing (96% removal of main contaminant, phenol), the bioflushing prototype was then applied in the field. Field prototype removed 95% phenol using a small scale 2000 L bioreactor. Field trial was then scaled to commercial clean-up. Intensive soil grid sampling after 600 days treatment revealed hotspots of solvents remaining as well as the heterogeneity in the subsurface, however overall concentrations were substantially decreased below the initial assessment. The process decreased initial soil phenol concentrations of approximately 500 mg/kg (pre-treatment area average) to 75 mg/kg across the most contaminated areas. Phenol toxicity increased with depth and is linked to increasing oxygen deficit. The study demonstrated the prototyping process enabling site clean-up and scaling for bioremediation at the industrial site, provided certainty for site owner on treatment elements and achieving improved environmental and commercial outcomes.

Innovative Culturomic Approaches and Predictive Functional Metagenomic Analysis: The Isolation of Hydrocarbonoclastic Bacteria with Plant Growth Promoting Capacity

Innovative culturomic approaches were adopted to isolate hydrocarbonoclastic bacteria capable of degrading diesel oil, bitumen and a selection of polycyclic aromatic hydrocarbons (PAH), e.g., pyrene, anthracene, and dibenzothiophene, from a soil historically contaminated by total petroleum hydrocarbons (TPH) (10,347 ± 98 mg TPH/kg). The culturomic approach focussed on the isolation of saprophytic microorganisms and specialist bacteria utilising the contaminants as sole carbon sources. Bacterial isolates belonging to Pseudomonas, Arthrobacter, Achromobacter, Bacillus, Lysinibacillus, Microbacterium sps. were isolated for their capacity to utilise diesel oil, bitumen, pyrene, anthracene, dibenzothiphene, and their mixture as sole carbon sources. Pseudomonas, Arthrobacter, Achromobacter and Microbacterium sps. showed plant growth promoting activity, producing indole-3-acetic acid and expressing 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase activity. In parallel to the culturomic approach, in the microbial community of interest, bacterial community metabarcoding and predictive functional metagenomic analysis were adopted to confirm the potentiality of the isolates in terms of their functional representativeness. The combination of isolation and molecular approaches for the characterisation of a TPH contaminated soil microbial community is proposed as an instrument for the construction of an artificial hydrocarbonoclastic microbiota for environmental restoration.

Sustainable mitigation of heavy metals from effluents: Toxicity and fate with recent technological advancements

Increase in anthropogenic activities due to rapid industrialization had caused an elevation in heavy metal contamination of aquatic and terrestrial ecosystems. These pollutants have detrimental effects on human and environmental health. The majority of these pollutants are carcinogenic, neurotoxic, and are very poisonous even at very low concentrations. Contamination caused by heavy metals has become a global concern for which the traditional treatment approaches lack in providing a cost-effective and eco-friendly solution. Therefore, the use of microorganisms and plants to reduce the free available heavy metal present in the environment has become the most acceptable method by researchers. Also, in microbial- and phyto-remediation the redox reaction shifts the valence which makes these metals less toxic. In addition to this, the use of biochar as a remediation tool has provided a sustainable solution that needs further investigations toward its implementation on a larger scale. Enzymes secreted by microbes and whole microbial cell are considered an eco-efficient biocatalyst for mitigation of heavy metals from contaminated sites. To the best of our knowledge there is very less literature available covering remediation of heavy metals aspect along with the sensors used for detection of heavy metals. Systematic management should be implemented to overcome the technical and practical limitations in the use of these bioremediation techniques. The knowledge gaps have been identified in terms of its limitation and possible future directions have been discussed.

Population dynamics and crude oil degrading ability of bacterial consortia of isolates from oil-contaminated sites in Nigeria

Application of bacterial consortium of hydrocarbon degraders to crude oil-contaminated site can enhance bioremediation. This study evaluated the population dynamics and crude oil degradation abilities of various consortia developed from bacterial strains isolated from crude oil-contaminated sites using crude oil-supplemented Bushnell Haas media. Each consortium consisted of three bacterial strains and was designated as Consortium A (Serratia marcescens strain N4, Pseudomonas aeruginosa strain N3R, Pseudomonas aeruginosa strain W11), B (Pseudomonas aeruginosa strain N3R, Pseudomonas aeruginosa strain W11, Pseudomonas protegens strain P7), C (Serratia marcescens strain N4, Pseudomonas aeruginosa strain W11, Pseudomonas protegens strain P7), and D (Pseudomonas aeruginosa strain W15, Providencia vermicola strain W8, Serratia marcescens strain W13). There was progressive decline in the populations of Serratia marcescens strains in the consortia as the incubation period progressed. This may have led to reduction in their synergistic contribution and, subsequently, total degradation ability of crude oil by the consortia. The gravimetric analyses showed that Consortium D produced the highest % crude oil degradation of 29.66% compared to Consortia A, B, and C with 23.73%, 11.86%, and 19.49% respectively. Based on gas chromatography-mass spectrometry analyses, Consortium D produced the highest percentage total petroleum hydrocarbon degradation of 73.65% compared to 68.24%, 68.94%, and 69.19% produced by Consortia A, B, and C respectively. The biodegradation potential of Consortium D also demonstrates the significance of using isolates from the same isolation site in development of consortium for bioremediation.

Investigating the potential of bioremediation in aged oil-polluted hypersaline soils in the south oilfields of Iran

To date, studies for bioremediation of oil-polluted hypersaline soils have been neglected or limited to specific spots. Hence, in this study, ten samples of oil field soils in the Khuzestan province of Iran were collected to evaluate bioremediation's feasibility. These samples were analyzed for their physicochemical properties as well as the most probable number of total and hydrocarbon-degrading bacteria. Thirty-nine hydrocarbon-degrading bacteria were isolated from these soils over a 1-month incubation in an MSM medium enriched with diesel oil as the sole source of carbon. As revealed by 16S-rRNA analysis, the identified strains belonged to the genera Ochrobactrum, Microbacterium, and Bacillus with a high frequency of Ochrobactrum species. Additionally, by using degenerate primers, the third group of alkB gene was detected in Ochrobactrum and Microbacterium isolates through the touchdown nested PCR method for the first time. Ochrobactrum species possessing the alkB gene showed the highest population, and therefore, the highest adaptation to harsh environmental conditions. Most isolates showed outstanding results in the ability to grow with crude and diesel oil and tolerate high salt percentages, biosurfactant production, and emulsification activity, which are considered the most effective factors in bioremediation of such environments. Considering the soil analysis, limiting factors in bioremediation like available phosphorous, and the abundance of bacteria with remediation traits in these soils, these extremely polluted environments can be refined.

Insights into Bacterial Community Involved in Bioremediation of Aged Oil-Contaminated Soil in Arid Environment

Soil contamination by hydrocarbons due to oil spills has become a global concern and it has more implications in oil producing regions. Biostimulation is considered as one of the promising remediation techniques that can be adopted to enhance the rate of degradation of crude oil. The soil microbial consortia play a critical role in governing the biodegradation of total petroleum hydrocarbons (TPHs), in particular polycyclic aromatic hydrocarbons (PAHs). In this study, the degradation pattern of TPHs and PAHs of Kuwait soil biopiles was measured at three-month intervals. Then, the microbial consortium associated with oil degradation at each interval was revealed through 16S rRNA based next generation sequencing. Rapid degradation of TPHs and most of the PAHs was noticed at the first 3 months of biostimulation with a degradation rate of pyrene significantly higher compared to other PAHs counterparts. The taxonomic profiling of individual stages of remediation revealed that, biostimulation of the investigated soil favored the growth of Proteobacteria, Alphaprotobacteria, Chloroflexi, Chlorobi, and Acidobacteria groups. These findings provide a key step towards the restoration of oil-contaminated lands in the arid environment.

Attenuation of petroleum hydrocarbon fractions using rhizobacterial isolates possessing alkB, C23O, and nahR genes for degradation of n-alkane and aromatics

This work assessed the catabolic versatility of functional genes in hydrocarbon-utilizing bacteria obtained from the rhizosphere of plants harvested in aged polluted soil sites in Ogoni and their attenuation efficacy in a bioremediation study. Rhizosphere soil was enumerated for its hydrocarbon-utilizing bacteria. The bacteria were in-vitro screened and selected through the quantification of their total protein and specific intermediate pathway enzyme (catechol 2,3-dioxygenase) activity in the metabolism of hydrocarbon. Thereafter, agarose gel electrophoresis technique was deployed to profile the genome of the selected strains for catechol 2,3-dioxygenase (C23O), 1,2-alkane monooxygenase (alkB), and naphthalene dioxygenase (nahR). Four rhizobacterial isolates namely Pseudomonas fluorescens (A3), Achromobacter agilis (A4), Bacillus thuringiensis (D2), and Staphylococcus lentus (L1) were selected based on the presence of C23O, alkB, and nahR genes. The gel electrophoresis results showed an approximate molecular weight of 200 bp for alkB, 300 bp for C23O, and 400 bp for nahR. The gas chromatogram for residual total petroleum hydrocarbon (TPH) revealed mineralization of fractions C₈-C₁₇, phytane, C₁₈-C₃₀. TPH for in-vitro bioremediation of crude oil-polluted soil was observed to have an optimal reduction/loss of 97% within the 56th day of the investigation. This study has further revealed that the microbiome of plants pre-exposed to crude oil pollution could serve as a reservoir for mining group of bacterial with broad catabolic potentials for eco-recovery and waste treatment purposes.