Research progress in bioremediation of petroleum pollution

Fungal-bacterial consortia: A promising strategy for the removal of petroleum hydrocarbons

Nowadays, petroleum hydrocarbon pollution is one of the most widespread types of contamination that poses a serious threat to both public health and the environment. Among various physicochemical methods, bioremediation is an eco-friendly and cost-effective way to eliminate petroleum hydrocarbon pollutants. The successful degradation of all hydrocarbon components and the achievement of optimal efficiency are necessary for the success of this process. Using potential microbial consortia with rich metabolic networks is a promising strategy for addressing these challenges. Mixed microbial communities, comprising both fungi and bacteria, exhibit diverse synergistic mechanisms to degrade complex hydrocarbon contaminants, including the dissemination of bacteria by fungal hyphae, enhancement of enzyme and secondary metabolites production, and co-metabolism of pollutants. Compared to pure cultures or consortia of either fungi or bacteria, different studies have shown increased bioremediation of particular contaminants when combined fungal-bacterial treatments are applied. However, antagonistic interactions, like microbial competition, and the production of inhibitors or toxins can observed between members. Furthermore, optimizing environmental factors (pH, temperature, moisture, and initial contaminant concentration) is essential for consortium performance. With the advancements in synthetic biology and gene editing tools, it is now feasible to design stable and robust artificial microbial consortia systems. This review presents an overview of using microbial communities for the removal of petroleum pollutants by focusing on microbial degradation pathways, and their interactions. It also highlights the new strategies for constructing optimal microbial consortia, as well as the challenges currently faced and future perspectives of applying fungal-bacterial communities for bioremediation.

Microbial remediation of petroleum-contaminated soil focused on the mechanism and microbial response: a review

The environmental pollution caused by petroleum hydrocarbons has received considerable attention in recent years. Microbial remediation has emerged as the preferred method for the degradation of petroleum hydrocarbons, which is experiencing rapid development driven by advancements in molecular biology. Herein, the capacity of different microorganisms used for crude oil bioremediation was reviewed. Moreover, factors influencing the effectiveness of microbial remediation were discussed. Microbial remediation methods, such as bioaugmentation, biostimulation, and bioventilation, are summarized in this review. Aerobic and anaerobic degradation mechanisms were reviewed to elucidate the metabolic pathways involved. The impacts of petroleum hydrocarbons on microorganisms and the environment were also revealed. A brief overview of synthetic biology and a unique perspective of technique combinations were presented to provide insight into research trends. The challenges and future outlook were also presented to stimulate contemplation of the mechanisms involved and the development of innovative techniques.

In vitro assessment of crude oil degradation by Acinetobacter junii and Alcanivorax xenomutans isolated from the coast of Ghana

This study was aimed at using in vitro microcosm experiments to assess crude oil degradation efficiency of Acinetobacter junii and Alcanivorax xenomutans isolated along Ghana's coast. Uncontaminated seawater from selected locations along the coast was used to isolate bacterial species by employing enrichment culture procedures with crude oil as the only carbon source. The isolates were identified by means of the extended direct colony transfer method of the Matrix Assisted Laser Desorption Ionization Time of Flight Mass Spectroscopy (MALDI-TOF MS), as Acinetobacter junii, and Alcanivorax xenomutans. Remediation tests showed that Acinetobacter junii yielded degradation efficiencies of 27.59 %, 41.38 % and 57.47 %. Whereas efficiencies of 21.14 %, 32.18 % and 43.68 % were recorded by Alcanivorax xenomutans representing 15, 30 and 45 days respectively. Consortia of Acinetobacter junii, and Alcanivorax xenomutans also yielded 32.18 %, 48.28 % and 62.07 % for the selected days respectively. Phylogenetic characterization using ClustalW and BLAST of sequences generated from the Oxford Nanopore Sequencing technique, showed that the Ghanaian isolates clustered with Alcanivorax xenomutans and Acinetobacter junii species respectively. An analysis of the sequenced data for the 1394-bp portion of the 16S rRNA gene of the isolates revealed >99 % sequence identity with the isolates present on the GenBank database. The isolates of closest identity were Alcanivorax xenomutans and Acinetobacter junii with accession numbers, NR_133958.1 and KJ147060.1 respectively. Acinetobacter junii and Alcanivorax xenomutans isolated from Ghana's coast under pristine seawater conditions have therefore demonstrated their capacity to be used for the remediation of crude oil spills.

Laccase-mediated degradation of petroleum hydrocarbons in historically contaminated soil

Laccases (EC1.10.3.2) have attracted growing attention in bioremediation research due to their high reactivity and substrate versatility. In this study, three genes for potential novel laccases were identified in an enrichment culture from contaminated field soil and recombinantly expressed in E. coli. Two of them, designated as PlL and BaL, were biochemically characterized regarding their optimal pH and temperature, kinetic parameters, and substrate versatility. In addition, lacasse PlL from Parvibaculum lavamentivorans was tested on historically contaminated soil. Treatment with PlL led to a significantly higher reduction of total petroleum hydrocarbons (83% w/w) compared to the microbial control (74% w/w). Hereby, PlL was especially effective in degrading hydrocarbons > C17. Their residual concentration was by 43% w/w lower than in the microbial treatment. In comparison to the laccase from Myceliophthora thermophila (MtL), PlL treatment was not significantly different for the fraction > C17 but resulted in a 30% (w/w) lower residual concentration for hydrocarbons < C18. In general, PlL can promote the degradation of petroleum hydrocarbons. As a consequence, it can be applied to reduce remediation time by duly achieving remediation target concentrations needed for site closure.

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.

Efficient Bioremediation of Petroleum-Contaminated Soil by Immobilized Bacterial Agent of Gordonia alkanivorans W33

In this article, we report a method for preparing an immobilized bacterial agent of petroleum-degrading bacteria Gordonia alkanivorans W33 by combining high-density fermentation and bacterial immobilization technology and testing its bioremediation effect on petroleum-contaminated soil. After determining the optimal combination of MgCl₂, CaCl₂ concentration, and culture time in the fermentation conditions by conducting a response surface analysis, the cell concentration reached 7.48 × 10⁹ CFU/mL by 5 L fed-batch fermentation. The W33-vermiculite-powder-immobilized bacterial agent mixed with sophorolipids and rhamnolipids in a weight ratio of 9:10 was used for the bioremediation of petroleum-contaminated soil. After 45 days of microbial degradation, 56.3% of the petroleum in the soil with 20,000 mg/kg petroleum content was degraded, and the average degradation rate reached 250.2 mg/kg/d.

Effects of ultraviolet radiation on microorganism and nitrogen metabolism in sewage under plateau background

The experiments were conducted in the Tibetan plateau environment, and the sewage treatment conditions were designed with ultraviolet (UV) irradiation for 5 min, 10 min, 30 min, and 180 min. The Illumina MiSeq high-throughput sequencing technology was used to analyze the microbiological and metabolomic patterns of the plateau sewage treatment at the experimental scale, and then the response mechanisms of microbial and nitrogen metabolism in sewage treatment were explored. The abundance of metabolism at the first level and global and overview maps at the second level were higher in the plateau environment than in other regions. The KEGG pathway shows the effect of UV on nitrogen metabolism and its aptitude to improving or inhibit it. The two main nitrogen removal processes are nitrification and dissimilatory nitrate reduction. This study reveals the response of activated sludge to UV radiation in a plateau environment from microbiological and metabolomic perspectives, providing ideas and perspectives for the study of water treatment system methods, as well as laying a valuable theoretical foundation for the enhancement of plateau sewage treatment capacity.

The role of microorganisms in petroleum degradation: Current development and prospects

Petroleum hydrocarbon compounds are persistent organic pollutants, which can cause permanent damage to ecosystems due to their biomagnification. Bioremediation of oil is currently the main solution for the remediation of petroleum hydrocarbon pollutants in ecosystems. Despite several lab studies on oil microbial biodegradation efficiency, still there are various challenges for microorganisms to perform efficiently in outside environments. Herewith, investigating efficient biodegradation technologies through discovering new microorganisms, biodegradation pathways modification, and new bioremediations technologies are in great demand. The degradation of petroleum pollutants by microorganisms and the remediation of contaminated soils are achieved through their key enzymes and metabolic pathways. Although, several challenges hinder the effective biodegradation processes such as the toxic environment, long chains and versatility of petroleum hydrocarbons and the existence of the full metabolism pathways in a single microorganism. There are several developed oil biodegradation strategies by microorganisms such as synthetic biology, biofilm, recombinant technology and microbial consortia. Herewith, the application of multi-omics technology to discover oil-contaminated environments microbial communities, synthetic biology, microbial consortia, and other technologies would help improve the efficiency of microbial remediation.

Bioengineering for the Microbial Degradation of Petroleum Hydrocarbon Contaminants

Petroleum hydrocarbons are relatively recalcitrant compounds, and as contaminants, they are one of the most serious environmental problems. n-Alkanes are important constituents of petroleum hydrocarbons. Advances in synthetic biology and metabolic engineering strategies have made n-alkane biodegradation more designable and maneuverable for solving environmental pollution problems. In the microbial degradation of n-alkanes, more and more degradation pathways, related genes, microbes, and alkane hydroxylases have been discovered, which provide a theoretical basis for the further construction of degrading strains and microbial communities. In this review, the current advances in the microbial degradation of n-alkanes under aerobic condition are summarized in four aspects, including the biodegradation pathways and related genes, alkane hydroxylases, engineered microbial chassis, and microbial community. Especially, the microbial communities of “Alkane-degrader and Alkane-degrader” and “Alkane-degrader and Helper” provide new ideas for the degradation of petroleum hydrocarbons. Surfactant producers and nitrogen providers as a “Helper” are discussed in depth. This review will be helpful to further achieve bioremediation of oil-polluted environments rapidly.

Petroleum Hydrocarbon Catabolic Pathways as Targets for Metabolic Engineering Strategies for Enhanced Bioremediation of Crude-Oil-Contaminated Environments

Anthropogenic activities and industrial effluents are the major sources of petroleum hydrocarbon contamination in different environments. Microbe-based remediation techniques are known to be effective, inexpensive, and environmentally safe. In this review, the metabolic-target-specific pathway engineering processes used for improving the bioremediation of hydrocarbon-contaminated environments have been described. The microbiomes are characterised using environmental genomics approaches that can provide a means to determine the unique structural, functional, and metabolic pathways used by the microbial community for the degradation of contaminants. The bacterial metabolism of aromatic hydrocarbons has been explained via peripheral pathways by the catabolic actions of enzymes, such as dehydrogenases, hydrolases, oxygenases, and isomerases. We proposed that by using microbiome engineering techniques, specific pathways in an environment can be detected and manipulated as targets. Using the combination of metabolic engineering with synthetic biology, systemic biology, and evolutionary engineering approaches, highly efficient microbial strains may be utilised to facilitate the target-dependent bioprocessing and degradation of petroleum hydrocarbons. Moreover, the use of CRISPR-cas and genetic engineering methods for editing metabolic genes and modifying degradation pathways leads to the selection of recombinants that have improved degradation abilities. The idea of growing metabolically engineered microbial communities, which play a crucial role in breaking down a range of pollutants, has also been explained. However, the limitations of the in-situ implementation of genetically modified organisms pose a challenge that needs to be addressed in future research.