Assessment of bioremediation potential of petroleum-contaminated soils from the shanbei oilfield of China revealed by qPCR and high throughput sequencing

Comprehensive effects of biochar-assisted nitrogen and phosphorus bioremediation on hydrocarbon removal and microecological improvement in petroleum-contaminated soil

Biochar is widely used in agricultural soils, but its effects with nitrogen and phosphorus amendments on petroleum-contaminated soil are unclear. This study investigated biochar-assisted biostimulation in a microcosm experiment, focusing on hydrocarbon degradation, nitrogen cycling, and soil properties. Compared to the biostimulation alone (BS), biochar combined biostimulation (BSC) significantly enhanced the abundances of petroleum hydrocarbon degraders including Lysobacter and Brevundimonas, which led to a 17% increase in total petroleum hydrocarbon (TPH) degradation, with 9% and 39% enhancements in saturated hydrocarbon degradation and aromatic hydrocarbon fraction degradation, respectively. Biochar also promoted ammonia and nitrous oxide oxidation by upregulating AOA, AOB, norB, and nosZ genes, while controlling nitrogen loss by downregulating nirK. Soil moisture, oxidation-reduction potential (ORP), dehydrogenase activity (SDHA), and microbial proliferation were significantly enhanced. Structural equation models (SEM) indicated synergistic interactions between nitrogen cycling and hydrocarbon degradation. Biochar enhances hydrocarbon degradation and nitrogen cycling, offering a promising soil remediation approach.

Microbial adaptation and genetic modifications for enhanced remediation in low-permeability soils

Low-permeability soils, characterized by fine texture and high clay content, pose significant challenges to traditional soil remediation techniques due to limited hydraulic conductivity, restricted nutrient flow, and reduced oxygen availability. These unique properties enable low-permeability soils to function as natural barriers in environmental protection; however, they also trap contaminants, making traditional remediation efforts challenging. This review synthesizes current knowledge on microbial adaptation and genetic engineering approaches that enhance the effectiveness of bioremediation in such environments. Key microbial adaptations, including anaerobic metabolism, extracellular enzyme production, and stress response mechanisms, allow individual microbes to adapt in low-permeability soils. Additionally, community-level strategies like microhabitat creation, biofilm formation, and functional redundancy further support microbial resilience. Advancements in genetic engineering now enable the modification of microbial traits-such as soil adhesion, nutrient utilization, and stress tolerance-to enhance bioremediation efficacy. Synthetic biology techniques further allow for the design of tailored microbial consortia that work cooperatively to degrade contaminants in complex soil matrices. This review highlights the integration of microbial and genetic engineering strategies, offering a comprehensive overview that informs current practices and guides future research in low-permeability soil remediation.

Enhancement of repeated inoculation strategy with a domesticated bacterial consortium on the biodegradation of high-level crude oil in soil

Repeated inoculation of hydrocarbon degrading microbes should be powerful to improve the survival of inoculant, which is vital to achieve efficient remediation of petroleum contaminated soil. This paper aims to study the repeated inoculation (with different inoculum size and time interval) enhanced bioremediation of high-level petroleum contaminated soil with a domesticated bacterial consortium. The copy number of bacterium and alkB gene, soil enzyme activities and microbial community structure during the remediation were systematically analyzed to preliminarily reveal the mechanism of repeated inoculation affecting remediation for the first time. The results revealed that repeated inoculation remarkably improved the total petroleum hydrocarbon (TPH) removal in soil (86.5 % in HC120) compared with a single inoculation (68.9 % in HA120). The TPH removal of repeated inoculation with high inoculum size (HC) on the 60th day was close to that of once inoculation (HA) on the 120th day, suggesting that repeated inoculation led to faster degradation. Interestingly, the effect of inoculation with low dose and more times (LC120, 78.5 %) was equal to that with high dose and less times (HB120, 78.0 %), even much better than that with high dose and once inoculation (HA120). Treatment HC had a significant impact on the soil bacterial diversity and community structure, and the dominant species in the inoculants, such as Stenotrophomonas and Pseudomonas, which was low abundance in the blank group (CK), still maintained high abundance during the remediation process. The soil catalase activities and the number of alkB gene were the highest in HC. Correlation analysis implied that repeated inoculation of hydrocarbon degrading bacteria did improve the survival of inoculant, soil enzyme activities and maintain the number of degrading bacteria, thus promoting the TPH removal. These findings will facilitate the practical application of bioremediation technology to contaminated environment, which has important environmental and economic benefits.

Nitrogen utilization efficiency assessment during bioremediation of petroleum-contaminated loess soils: insights from metagenomic analysis

Nitrogen addition is commonly used to remediate total petroleum hydrocarbons (TPH) in petroleum-contaminated soils. However, acceptable exogenous nitrogen dosages and their utilization efficiency for the degradation of hydrocarbons in oil-polluted soils are not well understood. This study compared the hydrocarbon bioremediation capacity by applying different doses of NH4Cl as a stimulant in soils contaminated with TPH at 8553 and 17090 mg/kg. The results showed acceptable exogenous nitrogen levels ranging from 60 to 360 mg N/kg soil, and the optimal nitrogen dosage for TPH remediation was 136 mg N/kg in soils with different TPH concentrations. The nitrogen availability efficiency (NAE) and nitrogen polarization factor availability (NPFA) in the 136 mg N/kg addition treatments were 6.69 and 20.47 mg/mg in 8533 mg/kg TPH-polluted soil, and 6.03 and 31.11 mg/mg in 17090 mg/kg TPH-polluted soil, respectively. Metagenomic analysis revealed that the application of 136 mg/kg nitrogen facilitated ammonia oxidation and nitrite reduction to nitric oxide, and induced soil microorganisms to undergo regulatory or adaptive changes in energy supply and metabolic state, which could aid in restoring the ecological functions of petroleum-contaminated soils. These findings underscore that 136 mg/kg of nitrogen dosage application is optimal for remediation of petroleum-contaminated soils irrespective of the TPH concentrations. This exogenous nitrogen application dosage for TPH remediation aligns with the nitrogen requirements for crop growth in agriculture.

Effects of biochar immobilization of Serratia sp. F4 OR414381 on bioremediation of petroleum contamination and bacterial community composition in loess soil

Petroleum hydrocarbons pose a significant threat to human health and the environment. Biochar has increasingly been utilized for soil remediation. This study investigated the potential of biochar immobilization using Serratia sp. F4 OR414381 for the remediation of petroleum-contaminated soil through a pot experiment conducted over 90 days. The treatments in this study, denoted as IMs (maize straw biochar-immobilized Serratia sp. F4), degraded 82.5% of the total petroleum hydrocarbons (TPH), 59.23% of the aromatic, and 90.1% of the saturated hydrocarbon fractions in the loess soils. During remediation, the soil pH values decreased from 8.76 to 7.33, and the oxidation-reduction potential (ORP) increased from 156 to 229 mV. The treatment-maintained soil nutrients of the IMs were 138.94 mg/kg of NO3- -N and 92.47 mg/kg of available phosphorus (AP), as well as 11.29% of moisture content. The activities of soil dehydrogenase (SDHA) and catalase (CAT) respectively increased by 14% and 15 times compared to the CK treatment. Three key petroleum hydrocarbon degradation genes, including CYP450, AJ025, and xylX were upregulated following IMs treatment. Microbial community analysis revealed that a substantial microbial population of 1.01E+ 09 cells/g soil and oil-degrading bacteria such as Salinimicrobium, Saccharibacteria_genera_incertae_sedis, and Brevundimonas were the dominant genera in IMs treatment. This suggests that the biochar immobilized on Serratia sp. F4 OR414381 improves soil physicochemical properties and enhances interactions among microbial populations, presenting a promising and environmentally friendly approach for the stable and efficient remediation of petroleum-contaminated loess soil.

Remediation of crude oil contaminated soil through an integrated biological-chemical-biological strategy

A plausible approach to remediating petroleum contaminated soil is the integration of chemical and biological treatments. Using appropriate chemical oxidation, the integrated remediation can be effectively achieved to stimulate the biodegradation process, consequently bolstering the overall remediation effect. In this study, an integrated biological-chemical-biological strategy was proposed. Both conventional microbial degradation techniques and a modified Fenton method were employed, and the efficacy of this strategy on crude oil contaminated soil, as well as its impact on pollutant composition, soil environment, and soil microorganism, was assessed. The results showed that this integrated remediation realized an overall 68.3 % removal rate, a performance 1.7 times superior to bioremediation alone and 2.1 times more effective than chemical oxidation alone, elucidating that the biodegradation which had become sluggish was invigorated by the judicious application of chemical oxidation. By optimizing the positioning of chemical treatment, the oxidization was allowed to act predominantly on refractory substances like resins, thus effectively enhancing pollutant biodegradability. Concurrently, this oxidating maneuver contributed to a significant increase in concentrations of dissolvable nutrients while maintaining appropriate soil pH levels, thereby generating favorable growth conditions for microorganism. Moreover, attributed to the proliferation and accumulation of degrading bacteria during the initial bioremediation phase, the microbial growth subsequent to oxidation showed rapid resurgence and the relative abundance of typical petroleum-degrading bacteria, particularly Proteobacteria, was substantially increased, which played a significant role in enhancing overall remediation effect. Our research validated the feasibility of biological-chemical-biological strategy and elucidated its correlating mechanisms, presenting a salient reference for the further studies concerning the integrated remediation of petroleum contaminated soil.

Microbe combined with Fe2+-heat activated persulfate to decompose phenanthrene in red soil: comparison of acid-resistant degrading microflora and indigenous bacteria

This work is designed to counteract the deficiency of targeted research on the PAHs polluted specific soil, especially when the chemicals extremely denatured it. Phenanthrene-contaminated red soil was treated through two-stage process: persulfate oxidation (on dosages of 3.48%, 5.21%, and 6.94%, combined with Fe2+ and β-cyclodextrin, then heated) followed by biodegradation (indigenous bacteria vs. acid-resistant PAHs-degrading microflora (named ADM)) for 90 days. The dosage of oxidant greatly affected the removal efficiencies, which ranged from 46.78 to 85.34% under different treatment. After undergoing oxidation, the soil pH dropped below 3.0 synchronously and retained relatively strong oxidation state. The indigenous bacteria in red soil showed considerable degradation potential that will not vanish upon the sudden change of soil properties, whose average combined removal reached 95.43%, even higher than subgroups of bioaugmentation, but the population structure showed extremely simplex (Proteobacteria as superior occupied proportion of 91.77% after 90-day rehabilitation). The ADM screened from the coking wastewater was dominated by Klebsiella (75.4%) and Pseudomonas (23.6%), whose cooperation with 6.94% persulfate made the residual PHE reduced to less than 50 mg·kg-1 in about 28 days. High-throughput sequencing analysis showed that the microbial community composition of the ADM applied-group was more abundant in the later stage of remediation. ADM inoculation has the advantages of shortening the restoration period and having a positive impact on the soil micro-ecology.

Phenanthrene removal from a spent sediment washing solution in a continuous-flow stirred-tank reactor

The issue of polycyclic aromatic hydrocarbons (PAHs) is widespread in marine sediments involving ecological systems and human health. Sediment washing (SW) has proven to be the most effective remediation approach for sediments polluted by PAHs, such as phenanthrene (PHE). However, SW still raises waste handling concerns due to a considerable amount of effluents generated downstream. In this context, the biological treatment of a PHE- and ethanol-containing spent SW solution can represent a highly efficient and environmentally-friendly strategy, but its knowledge is still scarce in scientific literature and no studies have so far been conducted in continuous mode. Therefore, a synthetic PHE-polluted SW solution was biologically treated in a 1 L aerated continuous-flow stirred-tank reactor for 129 days by evaluating the effect of different pH values, aeration flowrates and hydraulic retention times as operating parameters over five successive phases. A PHE removal efficiency of up to 75-94% was achieved by an acclimated PHE-degrading consortium mainly composed of Proteobacteria, Bacteroidota and Firmicutes phyla through biodegradation following the adsorption mechanism. PHE biodegradation, mainly occurring via the benzoate route due to the presence of PAH-related-degrading functional genes and a phthalate accumulation up to 46 mg/L, was also accompanied by a reduction of dissolved organic carbon and ammonia nitrogen above 99% in the treated SW solution.

Bioremediation of polycyclic aromatic hydrocarbons: An updated microbiological review

A class of organic priority pollutants known as PAHs is of critical public health and environmental concern due to its carcinogenic properties as well as its genotoxic, mutagenic, and cytotoxic properties. Research to eliminate PAHs from the environment has increased significantly due to awareness about their negative effects on the environment and human health. Various environmental factors, including nutrients, microorganisms present and their abundance, and the nature and chemical properties of the PAH affect the biodegradation of PAHs. A large spectrum of bacteria, fungi, and algae have ability to degrade PAHs with the biodegradation capacity of bacteria and fungi receiving the most attention. A considerable amount of research has been conducted in the last few decades on analyzing microbial communities for their genomic organization, enzymatic and biochemical properties capable of degrading PAH. While it is true that PAH degrading microorganisms offer potential for recovering damaged ecosystems in a cost-efficient way, new advances are needed to make these microbes more robust and successful at eliminating toxic chemicals. By optimizing some factors like adsorption, bioavailability and mass transfer of PAHs, microorganisms in their natural habitat could be greatly improved to biodegrade PAHs. This review aims to comprehensively discuss the latest findings and address the current wealth of knowledge in the microbial bioremediation of PAHs. Additionally, recent breakthroughs in PAH degradation are discussed in order to facilitate a broader understanding of the bioremediation of PAHs in the environment.

New insights into the bioremediation of petroleum contaminants: A systematic review

Petroleum product is an essential resource for energy, that has been exploited by wide range of industries and regular life. A carbonaceous contamination of marine and terrestrial environments caused by errant runoffs of consequential petroleum-derived contaminants. Additionally, petroleum hydrocarbons can have adverse effects on human health and global ecosystems and also have negative demographic consequences in petroleum industries. Key contaminants of petroleum products, primarily includes aliphatic hydrocarbons, benzene, toluene, ethylbenzene, and xylene (BTEX), polycyclic aromatic hydrocarbons (PAHs), resins, and asphaltenes. On environmental interaction, these pollutants result in ecotoxicity as well as human toxicity. Oxidative stress, mitochondrial damage, DNA mutations, and protein dysfunction are a few key causative mechanisms behind the toxic impacts. Henceforth, it becomes very evident to have certain remedial strategies which could help on eliminating these xenobiotics from the environment. This brings the efficacious application of bioremediation to remove or degrade pollutants from the ecosystems. In the recent scenario, extensive research and experimentation have been implemented towards bio-benign remediation of these petroleum-based pollutants, aiming to reduce the load of these toxic molecules in the environment. This review gives a detailed overview of petroleum pollutants, and their toxicity. Methods used for degrading them in the environment using microbes, periphytes, phyto-microbial interactions, genetically modified organisms, and nano-microbial remediation. All of these methods could have a significant impact on environmental management.