Broad-spectrum hydrocarbon-degrading microbes in the global ocean metagenomes

Understanding the diversity and functions of hydrocarbon-degrading microorganisms in marine environments is crucial for both advancing knowledge of biogeochemical processes and improving bioremediation methods. In this study, we leveraged nearly 20,000 metagenome-assembled genomes (MAGs), recovered from a wide array of marine samples across the global oceans, to map the diversity of aerobic hydrocarbon-degrading microorganisms. A broad bacterial diversity was uncovered, with a notable preference for degrading aliphatic hydrocarbons over aromatic ones, primarily within Proteobacteria and Actinobacteriota. Three types of broad-spectrum hydrocarbon-degrading bacteria were identified for their ability to degrade various hydrocarbons and possession of multiple copies of hydrocarbon biodegradation genes. These bacteria demonstrate extensive metabolic versatility, aiding their survival and adaptability in diverse environmental conditions. Evidence of gene duplication and horizontal gene transfer in these microbes suggested a potential enhancement in the diversity of hydrocarbon-degrading bacteria. Positive correlations were observed between the abundances of hydrocarbon-degrading genes and environmental parameters such as temperature (-5 to 35 °C) and salinity (20 to 42 PSU). Overall, our findings offer valuable insights into marine hydrocarbon-degrading microorganisms and suggest considerations for selecting microbial strains for oil pollution remediation.

Synergistic algal/bacterial interaction in membrane bioreactor for detoxification of 1,2-dichloroethane-rich petroleum wastewater

The study addressed the challenge of treating petroleum industry wastewater with high concentrations of 1,2-dichloroethane (1,2-DCA) ranging from 384 to 1654 mg/L, which poses a challenge for bacterial biodegradation and algal photodegradation. To overcome this, a collaborative approach using membrane bioreactors (MBRs) that combine algae and bacteria was employed. This synergistic method effectively mitigated the toxicity of 1,2-DCA and curbed MBR fouling. Two types of MBRs were tested: one (B-MBR) used bacterial cultures and the other (AB-MBR) incorporated a mix of algal and bacterial cultures. The AB-MBR significantly contributed to 1,2-DCA removal, with algae accounting for over 20% and bacteria for approximately 49.5% of the dechlorination process. 1,2-DCA metabolites, including 2-chloroethanol, 2-chloro-acetaldehyde, 2-chloroacetic acid, and acetic acid, were partially consumed as carbon sources by algae. Operational efficiency peaked at a 12-hour hydraulic retention time (HRT) in AB-MBR, enhancing enzyme activities crucial for 1,2-DCA degradation such as dehydrogenase (DH), alcohol dehydrogenase (ADH), and acetaldehyde dehydrogenase (ALDH). The microbial diversity in AB-MBR surpassed that in B-MBR, with a notable increase in Proteobacteria, Bacteroidota, Planctomycetota, and Verrucomicrobiota. Furthermore, AB-MBR showed a significant rise in the dominance of 1,2-DCA-degrading genus such as Pseudomonas and Acinetobacter. Additionally, algal-degrading phyla (e.g., Nematoda, Rotifera, and Streptophyta) were more prevalent in AB-MBR, substantially reducing the issue of membrane fouling.

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.

Risk assessment and biodegradation potential of PAHs originating from Map Ta Phut Industrial Estate, Rayong, Thailand

Petroleum hydrocarbon contamination is a serious concern across the globe. Here, the capability of native bacterial consortium enriched from sediment samples of Map Ta Phut Industrial Estate (MTPIE), Rayong, Thailand was described. The distribution of PAHs was assessed from the sediment samples collected from MTPIE by GC-FID and the toxic unit (TU) was calculated to assess the potential ecological risk to the surrounding biota. This study investigated the degradation potential and determined the PAH-degrading bacterial cultures by enriching collected sediments in PAHs mixtures (naphthalene, phenanthrene, and pyrene). The TPH degradation capacity of each bacterial consortium was validated in a soil microcosm using aged crude oil-contaminated soil. The MTPIE sediments were highly contaminated with PAHs (843.99-3904.39 ng g-1) and posed extremely high ecological risks to benthic biota (TU > 1). The consortium S5-P most significantly removed naphthalene (90.03%) and phenanthrene (88.14%) while the highest removal of pyrene was achieved by the S3-P consortium. Other consortia only partially degraded the PAHs. The dominant microbes in the consortia were determined using PCR-DGGE, it was found that the PAH degrading consortia were known PAH degraders such as Annwoodia, Bacillus, Brevibacillus, Lysinibacillus, Paracoccus, Rhodococcus, Sphingopyxis, Sulfurovum, and Sulfurimonas species and unknown PAH degraders such as Lithuaxuella species. The consortium S5-P showed the highest degradation capacity, removing 74.99% of TPHs in the soil microcosm. Furthermore, the inoculation of PAH-biodegrading bacterial consortia significantly promoted the catechol-2,3-dioxygenase (C23O) and dehydrogenase (DHA) activities which directly correlated with the degradation efficiency of petroleum hydrocarbons (p < 0.05).

Effect of oil contaminants on antioxidant responses and antioxidant properties of Pleurotus florida (P. Kumm)

This research investigated the antioxidant responses of Pleurotus florida at different concentrations of gas oil [0% (control), 2.5%, 5%, and 10% (v:v)] for 30 days. The activities of superoxide dismutase and catalase enzymes decreased in responses to the gas oil presence by an average of 83% and 49%, respectively. In contrast, the activities of the ascorbate peroxidase and glutathione peroxidase enzymes displayed an upward trend in the groups cultured in oil-contaminated media. The gas oil contaminant increased total phenol and flavonoid accumulation, reflecting the variation in secondary metabolism. According to the 1,2-diphenyl-2-picrylhydrazyl radical scavenging, the 2.5% gas oil treatment resulted in the highest antioxidant activity (48 μg mL-1). The highest scavenging activity of nitric oxide radicals (IC50 = 272 μg mL-1) was observed in the treatment with the highest gas oil concentration (10%). Also, this treatment showed an excellent ability to chelate Fe+2 ions (IC50 = 205 μg mL-1). The IC50 values of methanolic extract for nitric oxide scavenging activity and metal chelating ability were significantly reduced by increasing gas oil concentration in the treatments. With increasing the gas oil concentration, malondialdehyde content as a criterion measure of lipid peroxidation level showed significant reduction. These results show that P. florida is resistant to and a compatible mushroom with oil pollutants. Also, the activity of glutathione peroxidase and the ascorbate-glutathione cycle detoxify nitric oxide radicals and products of reactive oxygen species-induced lipid peroxidation in the gas oil treatments.

Evaluating the productivity and bioremediation potential of two tropical marine algae in petroleum hydrocarbon polluted tropical marine water

Bioremediation using tropical marine algae provides cost effective and eco-friendly alternative mean of removing toxic and harmful substances from the environment. Bioremediation is an important tool in sustainable environmental management and protection. This study examined the productivity and bioremediation potential of Nannochloropsis oculata and Porphyridium cruentum in Water Soluble Fraction (WSF) of petroleum fuels by investigating the growth of Nannochloropsis oculata and Porphyridium cruentum at 0%, 10% 20% 30% 40% 50% 75% 100% of WSF of kerosene, diesel, and gasoline. Growth was monitored optically every two days for fourteen days using 721 Visible Spectrophotometer. Productivity was measured using prescribed procedure. Bioremediation potential of test algae were examined using standard method for the GC analysis of diesel range organics in 100% WSFs. The minimum growth for both species was recorded at 100% in all the fuels. The maximum growth of Porphyridium cruentum was obtained at 10% in all fuels, while the maximum growth of Nannochloropsis oculata was obtained at 30% in both kerosene and gasoline and at 50% in diesel. Whereas Porphyridium cruentum was greatly inhibited by all fuels, Nannochloropsis oculata was stimulated at lower concentration of the fuels. Nannochloropsis oculata proved more efficient for bioremediation of the petroleum fuels with 84.58%, 65.51% and 70.77% removal efficiency for kerosene, diesel and gasoline respectively, while Porphyridium cruentum was 58.94%, 46.64% and 56.67% respectively. Nannochloropsis oculata is a very strong and reliable candidate for bioremediation of petroleum hydrocarbons and should be subjected to further examination for sustainable and eco-friendly remediation of petroleum pollution.

Simultaneous removal of crude oil and heavy metals by highly adapted bacterial strain Cutibacterium sp. NL2 isolated from Algerian oilfield

Investigating the ability of bacteria to simultaneously enhance hydrocarbon removal and reduce heavy metals' toxicity is necessary to design more effective bioremediation strategies. A bacterium (NL2 strain) isolated from an Algerian oilfield was cultivated on crude oil as sole carbon and energy sources. Molecular analyses of the 16S rRNA gene sequence placed the strain within the Cutibacterium genera. This isolate was able to tolerate up to 60% of crude oil as sole carbon source. Chemical analyses (GC-MS) evidenced that strain NL2 was able to degrade 92.22% of crude oil (at optimal growing conditions: pH 10, 44 °C, 50 g L-1 NaCl, and 20% of crude oil (v/v) as sole carbon source) in only 7 days. NL2 isolate was also able to produce biosurfactants with reduction of surface tension of growing media (29.4 mN m-1). On the other hand, NL2 strain was able to tolerate high lead (Pb) and copper (Cu) concentrations (up to 60 mM). In fact, NL2 cultivated in the presence of 20% of crude oil, and 0.48 mM of Pb was able to reduce Pb concentration by a 41.36%. In turn, when cultivated on high Pb concentration (15 mM), the strain was able to remove 35.19% of it and 86.25% of crude oil, both in a time frame of 7 days. Our findings suggest that Cutibacterium strain NL2 is able to efficiently use and remove a wide range of crude oil substrates in presence of high Pb concentration. Accordingly, NL2 strain is of extreme interest from a biotechnological standpoint.

Screening biosurfactant-producing actinomycetes: Identification of Streptomyces sp. RP1 as a potent species for bioremediation

This study aimed to isolate biosurfactant-producing and hydrocarbon-degrading actinomycetes from different soils using glycerol-asparagine and starch-casein media with an antifungal agent. The glycerol-asparagine agar exhibited the highest number of actinomycetes, with a white, low-opacity medium supporting pigment production and high growth. Biosurfactant analyses, such as drop collapse, oil displacement, emulsification, tributyrin agar test, and surface tension measurement, were conducted. Out of 25 positive isolates, seven could utilize both olive oil and black oil for biosurfactant production, and only isolate RP1 could produce biosurfactant when grown in constrained conditions with black oil as the sole carbon source and inducer, demonstrating in situ bioremediation potential. Isolate RP1 from oil-spilled garden soil is Gram-staining-positive with a distinct earthy odor, melanin formation, and white filamentous colonies. It has a molecular size of ~621 bp and 100% sequence similarity to many Streptomyces spp. Morphological, biochemical, and 16 S rRNA analysis confirmed it as Streptomyces sp. RP1, showing positive results in all screenings, including high emulsification activity against kerosene (27.2%) and engine oil (95.8%), oil displacement efficiency against crude oil (7.45 cm), and a significant reduction in surface tension (56.7 dynes/cm). Streptomyces sp. RP1 can utilize citrate as a carbon source, tolerate sodium chloride, resist lysozyme, degrade petroleum hydrocarbons, and produce biosurfactant at 37°C in a 15 mL medium culture, indicating great potential for bioremediation and various downstream industrial applications with optimization.

Biogeochemical modelling to assess the effect of bioclogging on multiple electron acceptor-mediated petroleum hydrocarbon bioremediation in vadose zone

Bioremediation is an economically viable and sustainable clean-up strategy. Hydrodynamic, as well as transport characteristics of the porous medium, can evolve over the period as a result of biological clean-up activities. The present study proposes a 2-D numerical framework to simulate the effect of bioclogging on multiple electron acceptor-mediated petroleum hydrocarbon bioremediation in the vadose zone. For modelling, a spill of BTEX (benzene, toluene, ethylbenzene and xylene) is assumed near source zone. The developed model results are validated using three previously published datasets on flow, transport and biodegradation in the vadose zone. Simulations are performed for three types of soil, including clay, sand and loam. The analysis shows that sand has a maximum infiltration rate and clay has a minimum. Hydraulic conductivity and saturation profile peaks reach their minimal value at a shallower depth (around four times) when bioclogging is present compared to when it is absent. The migration depth and concentration of BTEX are observed to be restricted to a shallower depth in aquifers with the presence of microbial clogging. The outcome shows that electron acceptor consumption is more (around sevenfold for oxygen, fourfold for nitrate and threefold for sulphate) in the presence of bioclogging at the shallower zone. Zeroth order spatial moment and sensitivity analyses show that biological clogging, number of electron acceptors and inhibition constant substantially affect BTEX bioremediation in the vadose zone.

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.

Biochar-based materials as remediation strategy in petroleum hydrocarbon-contaminated soil and water: Performances, mechanisms, and environmental impact

Petroleum contamination is considered as a major risk to the health of humans and environment. Biochars as low-cost and eco-friendly carbon materials, have been widely used for the removal of petroleum hydrocarbon in the environment. The purpose of this paper is to review the performance, mechanisms, and potential environmental toxicity of biochar, modified biochar and its integration use with other materials in petroleum contaminated soil and water. Specifically, the use of biochar in oil-contaminated water and soil as well as the factors that could influence the removal ability of biochar were systematically evaluated. In addition, the modification and integrated use of biochar for improving the removal efficiency were summarized from the aspects of sorption, biodegradation, chemical degradation, and reusability. Moreover, the functional impacts and associated ecotoxicity of pristine and modified biochars in various environments were demonstrated. Finally, some shortcoming of current approaches, and future research needs were provided for the future direction and challenges of modified biochar research. Overall, this paper gain insight into biochar application in petroleum remediation from the perspectives of performance enhancement and environmental sustainability.

Performance evaluation of rhamnolipid biosurfactant produced by Pseudomonas aeruginosa and its effect on marine oil-spill remediation

This study aimed to reveal that the effect of biosurfactant on the dispersion and degradation of crude oil. Whole genome analysis showed that Pseudomonas aeruginosa GB-3 contained abundant genes involved in biosurfactant synthesis and metabolic processes and had the potential to degrade oil. The biosurfactant produced by strain GB-3 was screened by various methods. The results showed that the surface tension reduction activity was 28.6 mN·m-1 and emulsification stability was exhibited at different pH, salinity and temperature. The biosurfactant was identified as rhamnolipid by LC-MS and FTIR. The fermentation conditions of strain GB-3 were optimized by response surface methodology, finally the optimal system (carbon source: glucose, nitrogen source: ammonium sulfate, C/N ratio:16:1, pH: 7, temperature: 30-35 °C) was determined. Compared with the initial fermentation, the yield of biosurfactant increased by 4.4 times after optimization. In addition, rhamnolipid biosurfactant as a dispersant could make the dispersion of crude oil reach 38% within seven days, which enhanced the bioavailability of crude oil. As a biostimulant, it could also improve the activity of indigenous microorganism and increase the degradation rate of crude oil by 10-15%. This study suggested that rhamnolipid biosurfactant had application prospect in bioremediation of marine oil-spill.

Petroleum-contaminated soil bioremediation and microbial community succession induced by application of co-pyrolysis biochar amendment: An investigation of performances and mechanisms

This study aimed to remediate petroleum-contaminated soil using co-pyrolysis biochar derived from rice husk and cellulose. Rice husk and cellulose were mixed in various weight ratios (0:1, 1:0, 1:1, 1:3 and 3:1) and pyrolyzed under 500 °C. These biochar variants were labeled as R0C1, R1C0, R1C1, R1C3 and R3C1, respectively. Notably, the specific surface area and carbon content of the co- pyrolysis biochar increased, potentially promoting the growth and colonization of soil microorganisms. On the 60th day, the microbial control group achieved a 46.69% removal of pollutants, while the addition of R0C1, R1C0, R1C3, R1C1 and R3C1 resulted in removals of 70.56%, 67.01%, 67.62%, 68.74% and 67.30%, respectively. In contrast, the highest efficiency observed in the abiotic treatment group was only 24.12%. This suggested that the removal of petroleum pollutants was an outcome of the collaborative influence of co-pyrolysis biochar and soil microorganisms. Furthermore, the abundance of Proteobacteria, renowned for its petroleum degradation capability, obviously increased in the treatment group with the addition of co-pyrolysis biochar. This demonstrated that co-pyrolysis biochar could notably stimulate the growth of functionally associated microorganisms. This research confirmed the promising application of co-pyrolysis biochar in the remediation of petroleum-contaminated soil.

Plant biomass extracted eco-friendly natural surfactant enhanced bio-electrokinetic remediation of crude oil contaminated soil

The current work investigates bioremediation (BIO) and electrokinetic (EK) remediation of crude oil hydrocarbons utilizing the biomass-electrokinetic (BIO-EK) approaches. The use of natural surfactants derived from plant biomass may improve remediation capacity by enhancing the solubility of organic pollutants. Sapindus mukorossi, a natural surfactant producer, was extracted from plant biomass in this study. The crude oil biodegradation efficiency was reported to be 98 %. In nature, FTIR confirms that plant biomass is lipopeptide. GCMS revealed that the crude oil (C7 - C23) was efficiently bio-degraded from lower to higher molecular weight. The application of natural surfactants in electokinetic remediation increased the plant biomass degradation of crude oil polluted soil by 98% compared to electrokinetic 55% in 2 days. Natural surfactant improves hydrocarbon solubilization and accelerates hydrocarbon electro migration to the anodic compartment, as confirmed by the presence of greater total organic content than the electrokinetic. This study proves that BIO-EK compared with a natural surfactant derived from plant biomass may be utilized to improve in situ bioremediation of crude oil polluted soils.

Unraveling the mechanisms behind sodium persulphate-induced changes in petroleum-contaminated aquifers' biogeochemical parameters and microbial communities

Sodium persulphate (PS) is a highly effective oxidising agent widely used in groundwater remediation and wastewater treatment. Although numerous studies have examined the impact of PS with respect to the removal efficiency of organic pollutants, the residual effects of PS exposure on the biogeochemical parameters and microbial ecosystems of contaminated aquifers are not well understood. This study investigates the effects of exposure to different concentrations of PS on the biogeochemical parameters of petroleum-contaminated aquifers using microcosm batch experiments. The results demonstrate that PS exposure increases the oxidation-reduction potential (ORP) and electrical conductivity (EC), while decreasing total organic carbon (TOC), dehydrogenase (DE), and polyphenol oxidase (PO) in the aquifer. Three-dimensional excitation-emission matrix (3D-EEM) analysis indicates PS is effective at reducing fulvic acid-like and humic acid-like substances and promoting microbial metabolic activity. In addition, PS exposure reduces the abundance of bacterial community species and the diversity index of evolutionary distance, with a more pronounced effect at high PS concentrations (31.25 mmol/L). Long-term (90 d) PS exposure results in an increase in the abundance of microorganisms with environmental resistance, organic matter degradation, and the ability to promote functional genes related to biological processes such as basal metabolism, transmission of genetic information, and cell motility of microorganisms. Structural equation modeling (SEM) further confirms that ORP and TOC are important drivers of change in the abundance of dominant phyla and functional genes. These results suggest exposure to different concentrations of PS has both direct and indirect effects on the dominant phyla and functional genes by influencing the geochemical parameters and enzymatic activity of the aquifer. This study provides a valuable reference for the application of PS in ecological engineering.

Bioremediation for the recovery of oil polluted marine environment, opportunities and challenges approaching the Blue Growth

The Blue Growth strategy promises a sustainable use of marine resources for the benefit of the society. However, oil pollution in the marine environment is still a serious issue for human, animal, and environmental health; in addition, it deprives citizens of the potential economic and recreational advantages in the affected areas. Bioremediation, that is the use of bio-resources for the degradation of pollutants, is one of the focal themes on which the Blue Growth aims to. A repertoire of marine-derived bio-products, biomaterials, processes, and services useful for efficient, economic, low impact, treatments for the recovery of oil-polluted areas has been demonstrated in many years of research around the world. Nonetheless, although bioremediation technology is routinely applied in soil, this is not still standardized in the marine environment and the potential market is almost underexploited. This review provides a summary of opportunities for the exploiting and addition of value to research products already validated. Moreover, the review discusses challenges that limit bioremediation in marine environment and actions that can facilitate the conveying of valuable products/processes towards the market.

An evaluation model for in-situ bioremediation technology of petroleum hydrocarbon contaminated soil

Considering the interference of the complexity of underground environment to the bioremediation scheme, an evaluation model for bioremediation technology in the soil source area of oil contaminated sites was established. On the basis of traditional CDE model, a compartment model was coupled to express the adsorption and degradation process, and the spatial expression of biodegradation was enriched through environment-dependent factors. The visualization of the model was achieved based on COMSOL Multiphysics software platform. Two sets of indoor sandbox experiments on natural attenuation and bioaugmentation were carried out for 120 days to verify the prediction function of the model. The results showed that bioaugmentation greatly improved the remediation effect. Petroleum hydrocarbons with different occurrence states exhibited different spatial distributions under the influence of environmental factors. The prediction accuracy evaluation results of total petroleum hydrocarbons, bio available hydrocarbons and non extractable hydrocarbons showed excellent fitting degree, and the model had a good prediction function for petroleum hydrocarbon in soil under different bioremediation scenarios. This model can be used to screen bioremediation technical schemes, prevent pollution and assess risk of petroleum hydrocarbon contaminated sites.

Asynchronous application of modified biochar and exogenous fungus Scedosporium sp. ZYY for enhanced degradation of oil-contaminated intertidal mudflat sediment

Intertidal mudflats are susceptible to oil pollution due to their proximity to discharges from industries, accidental spills from marine shipping activities, oil drilling, pipeline seepages, and river outflows. The experimental study was divided into two periods. In the first period, microcosm trials were carried out to examine the effect of chemically modified biochar on biological hydrocarbon removal from sediments. The modified biochar's surface area increased from 2.544 to 25.378 m2/g, followed by a corresponding increase in the hydrogen-carbon and oxygen-carbon ratio, indicating improved stability and polarity. In the second period, the effect of exogenous fungus - Scedoporium sp. ZYY on the bacterial community structure was examined in relation to total petroleum hydrocarbon (TPH) removal. The maximum TPH removal efficiency of 82.4% was achieved in treatments with the modified biochar, followed by a corresponding increase in Fluorescein diacetate hydrolysis activity. Furthermore, high-throughput 16S RNA gene sequencing employed to identify changes in the bacterial community of the original sediment and treatments before and after fungal inoculation revealed Proteobacteria as the dominant phylum. In addition, it was observed that Scedoporium sp. ZYY promoted the proliferation of specific TPH-degraders, particularly, Hyphomonas adhaerens which accounted for 77% of the total degrading populations in treatments where TPH removal was highest. Findings in this study provide valuable insights into the effect of modified biochar and the fundamental role of exogenous fungus towards the effective degradation of oil-contaminated intertidal mudflat sediments.

Exposure of farmed fish to petroleum hydrocarbon pollution and the recovery process: A simulation experiment with tiger puffer Takifugu rubripes

Petroleum hydrocarbon (PH) pollution threatens both wild and farmed marine fish. How this pollution affects the nutrient metabolism in fish and whether this effect can be recovered have not been well-known. The present study aimed to evaluate these effects with a feeding trial on tiger puffer, an important farmed species in Asia. In a 6-week feeding trial conducted in indoor flow-through water, fish were fed a control diet (C) or diets supplemented with diesel oil (0.02 % and 0.2 % of dry matter, named LD and HD, respectively). Following this feeding trial was a 4-week recovery period, during which all fish were fed a same normal commercial feed. At the end of the 6-week feeding trial, dietary PH significantly decreased the fish growth and lipid content. The PH significantly accumulated in fish tissues, in particular the liver, and caused damages in all tissues examined in terms of histology, anti-oxidation status, and serum biochemical changes. Dietary PH also changed the volatile flavor compound profile in the muscle. The hepatic transcriptome assay showed that the HD diet tended to inhibit the DNA replication, cell cycle and lipid synthesis, but to stimulate the transcription of genes related to liver protection/repair and lipid catabolism. The 4-week recovery period to some extent mitigated the damage caused by PH. After the recovery period, the inter-group differences in some parameters disappeared. However, the differences in lipid content, anti-oxidase activity, liver PH concentration, and histological structure still existed. In addition, differences in cellular chemical homeostasis and cytokine-cytokine receptor interaction at the transcriptional level can still be observed, indicated by the hepatic transcriptome assay. In conclusion, 6 weeks of dietary PH exposure significantly impaired the growth performance and health status of farmed tiger puffer, and a short-term recovery period (4 weeks) was not sufficient to completely mitigate this impairment.

Impact of artisanal refining activities on bacterial diversity in a Niger Delta fallow land

Hydrocarbon pollution is a major ecological problem facing oil-producing countries, especially in the Niger Delta region of Nigeria. In this study, a site that had been previously polluted by artisanal refining activity was investigated using 16S rRNA Illumina high-throughput sequencing technology and bioinformatics tools. These were used to investigate the bacterial diversity in soil with varying degrees of contamination, determined with a gas chromatography-flame ionization detector (GC-FID). Soil samples were collected from a heavily polluted (HP), mildly polluted (MP), and unpolluted (control sample, CS) portion of the study site. DNA was extracted using the Zymo Research (ZR) Fungi/Bacteria DNA MiniPrep kit, followed by PCR amplification and agarose gel electrophoresis. The microbiome was characterized based on the V3 and V4 hypervariable regions of the 16S rRNA gene. QIIME (Quantitative Insights Into Microbial Ecology) 2 software was used to analyse the sequence data. The final data set covered 20,640 demultiplexed high-quality reads and a total of 160 filtered bacterial OTUs. Proteobacteria dominated samples HP and CS, while Actinobacteria dominated sample MP. Denitratisoma, Pseudorhodoplanes, and Spirilospora were the leading genera in samples HP, CS, and MP respectively. Diversity analysis indicated that CS [with 25.98 ppm of total petroleum hydrocarbon (TPH)] is more diverse than HP (with 490,630 ppm of TPH) and MP (with 5398 ppm of TPH). A functional prediction study revealed that six functional modules dominated the dataset, with metabolism covering up to 70%, and 11 metabolic pathways. This study demonstrates that a higher hydrocarbon concentration in soil adversely impacts microbial diversity, creating a narrow bacterial diversity dominated by hydrocarbon-degrading species, in addition to the obvious land and ecosystem degradation caused by artisanal refining activities. Overall, the artisanal refining business is significantly driving ecosystem services losses in the Niger Delta, which calls for urgent intervention, with focus on bioremediation.

Simultaneous removal of aliphatic and aromatic crude oil hydrocarbons by Pantoea agglomerans isolated from petroleum-contaminated soil in the west of Iran

Hydrocarbons are considered as one of the most common and harmful environmental pollutants affecting human health and the environment. Bioremediation as an environmentally friendly, highly efficient, and cost-effective method in remediating oil-contaminated environments has been interesting in recent decades. In this study, hydrocarbon degrader bacterial strains were isolated from the highly petroleum-contaminated soils in the Dehloran oil field in the west of Iran. Out of 37 isolates, 15 can grow on M9 agar medium that contains 1.5 g L-1 of crude oil as the sole carbon source. The morphological, biochemical, and 16SrRNA sequencing analyses were performed for the isolates. The choosing of the isolates as the hydrocarbon degrader was examined by evaluating the efficacy of their crude oil removal at a concentration of 10 g L-1 in an aqueous medium. The results showed that five isolates belonging to Pseudomonas sp., Pseudomonas oryzihabitans, Roseomonas aestuarii, Pantoea agglomerans, and Arthrobacter sp. had a hyper hydrocarbon-degrading activity and they could remove more than 85% of the total petroleum hydrocarbon (TPH) after 96 h. The highest TPH removal of about 95.75% and biodegradation rate of 0.0997 g L-1 h-1 was observed for P. agglomerans. The gas chromatography-mass spectroscopy (GC-MS) analysis was performed during the biodegradation process by P. agglomerans to detect the degradation intermediates and final products. The results confirmed the presence of intermediates such as alcohols and fatty acids in the terminal oxidation pathway of alkanes in this biodegradation process. A promising P. agglomerans NB391 strain can remove aliphatic and aromatic hydrocarbons simultaneously.

Effects of petrogenic pollutants on North Atlantic and Arctic Calanus copepods: From molecular mechanisms to population impacts

Oil and gas industries in the Northern Atlantic Ocean have gradually moved closer to the Arctic areas, a process expected to be further facilitated by sea ice withdrawal caused by global warming. Copepods of the genus Calanus hold a key position in these cold-water food webs, providing an important energetic link between primary production and higher trophic levels. Due to their ecological importance, there is a concern about how accidental oil spills and produced water discharges may impact cold-water copepods. In this review, we summarize the current knowledge of the toxicity of petroleum on North Atlantic and Arctic Calanus copepods. We also review how recent development of high-quality transcriptomes from RNA-sequencing of copepods have identified genes regulating key biological processes, like molting, diapause and reproduction in Calanus copepods, to suggest linkages between exposure, molecular mechanisms and effects on higher levels of biological organization. We found that the available ecotoxicity threshold data for these copepods provide valuable information about their sensitivity to acute petrogenic exposures; however, there is still insufficient knowledge regarding underlying mechanisms of toxicity and the potential for long-term implications of relevance for copepod ecology and phenology. Copepod transcriptomics has expanded our understanding of how key biological processes are regulated in cold-water copepods. These advances can improve our understanding of how pollutants affect biological processes, and thus provide the basis for new knowledge frameworks spanning the effect continuum from molecular initiating events to adverse effects of regulatory relevance. Such efforts, guided by concepts such as adverse outcome pathways (AOPs), enable standardized and transparent characterization and evaluation of knowledge and identifies research gaps and priorities. This review suggests enhancing mechanistic understanding of exposure-effect relationships to better understand and link biomarker responses to adverse effects to improve risk assessments assessing ecological effects of pollutant mixtures, like crude oil, in Arctic areas.

Integrating phytoremediation and mycoremediation with biosurfactant-producing fungi for hydrocarbon removal and the potential production of secondary resources

Treatment of petroleum-contaminated soil to a less toxic medium via physical and chemical treatment is too costly and requires posttreatment. This review focuses on the employment of phytoremediation and mycoremediation technologies in cleaning hydrocarbon-contaminated soil which is currently rare. It is considered environmentally beneficial and possibly cost-effective as it implements the synergistic interaction between plants and biosurfactant producing mycorrhiza to degrade hydrocarbon contaminants. This review also covers possible sources of hydrocarbon pollution in water and soil, toxicity effects, and current technologies for hydrocarbon removal and degradation. In addition to these problems, this review also discusses the challenges and opportunities of transforming the resultant treated sludge and treating plants into potential by-products for a higher quality of life for future generations.

Comparison of two field systems for determination of crude oil biodegradation in cold seawater

Marine oil spills have devastating environmental impacts and extrapolation of experimental fate and impact data from the lab to the field remains challenging due to the lack of comparable field data. In this work we compared two field systems used to study in situ oil depletion with emphasis on biodegradation and associated microbial communities. The systems were based on (i) oil impregnated clay beads and (ii) hydrophobic Fluortex adsorbents coated with thin oil films. The bacterial communities associated with the two systems displayed similar compositions of dominant bacterial taxa. Initial abundances of Oceanospirillales were observed in both systems with later emergences of Flavobacteriales, Alteromonadales and Rhodobacterales. Depletion of oil compounds was significantly faster in the Fluortex system and most likely related to the greater bioavailability of oil compounds as compared to the clay bead system.

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.

Elucidating the significant roles of root exudates in organic pollutant biotransformation within the rhizosphere

Biotransformation of organic pollutants is crucial for the dissipation of environmental pollutants. While the roles of microorganisms have been extensively studied, the significant contribution of various root exudates are still not very well understood. Through plant growth experiment, coupled with gas and liquid chromatography-mass spectrometry methods, this study examined the effect of the presence of M. sativa on microbial-associated biochemical transformation of petroleum hydrocarbons. The results of this study revealed that the concentration of exudates within the soil matrix is a function of proximity to root surfaces. Similarly, biodegradation was found to correlate with distance from roots, ranging from ≥ 90% within the rhizosphere to < 50% in bulk soil and unplanted control soil. Most importantly, for the first time in a study of an entire petroleum distillate, this study revealed a statistically significant negative correlation between root exudate concentration and residual total petroleum hydrocarbons. While not all the compounds that may influence biodegradation are derived from roots, the results of this study show that the presence of plant can significantly influence biodegradation of hydrocarbon pollutants through such root exudation as organic acids, amino acids, soluble sugars and terpenoids. Therefore, root exudates, including secondary metabolites, offer great prospects for biotechnological applications in the remediation of organic pollutants, including recalcitrant ones.

Biosurfactant and biopolymer producing microorganisms from West Kazakhstan oilfield

Microbiological enhanced oil recovery (MEOR) uses indigenous or exogenous microorganisms and nutrients to enhance oil production through synthesis of metabolites reducing oil viscosity and surface tension. In order to find bacteria suitable for MEOR, we studied 26 isolates from wells in the Akingen oilfield in West Kazakhstan. Six of them were selected for further analysis based on their ability to reduce surface tension to less than 40 mN/m, with the A9 isolate exhibiting tension reduction values of 32.76 ± 0.3 mN/m. Based on the morphological features, biochemical activities, and the 16S rRNA gene, the isolates were classified to the Bacillus subtilis group. In the phylogenetic analysis the isolates grouped into two main clusters. Genes encoding the surfactin synthetase subunits were found in A2, A8, A9, A12, PW2, only the PW2 strain had lchAA encoding lichenysin, while sacB encoding levan was noted in A2, A8, A9, and A12. The expression of srfAB, srfAC, and sacB tested with qPCR varied among strains. Nevertheless, whereas temperature moderately affects the expression level, with the highest level recorded at 40 °C, salinity significantly impacts the expression of the genes encoding biosurfactants. B. subtilis strains isolated in the study, especially A9, are promising for microbial-enhanced oil recovery.

Oleic-acid functionalized mesoporous silica nanoparticles with a hydroxyapatite core enhanced growth of the hydrocarbon degrader Dietzia maris at oil-water interfaces

Rapid biodegradation of poorly water-soluble hydrocarbons as nonaqueous (oil) phases in contaminated aquatic environments is enabled by attachment of hydrocarbon-degrading bacteria to the oil-water interface. Herein, we report the synthesis of nanoparticles comprising a hydroxyapatite (Ca5(PO4)3(OH)) core encapsulated in a mesoporous silica shell and surface-modified with oleic acid (OA-nHAP@MSN) for targeted binding at the oil-water interface and to supply P to bacteria at the interface. P is an essential and often limiting nutrient for bacteria in hydrocarbon-contaminated environments. In microcosm experiments, where the hydrocarbon-degrading bacteria, Dietzia maris strain NWWC4, and OA-nHAP@MSN were inoculated in mineral media in contact with pure liquid hexadecane (sole C source), there was 419.6-fold growth at the hexadecane-water interface, compared to 31.2-fold in identical, but NP-free microcosms. The continuous release of P from the hydroxyapatite core in OA-nHAP@MSN to water was demonstrated in separate experiments in well mixed batch systems and was found to be pH-sensitive. Environmental Scanning Electron Microscopy showed significantly larger cell aggregates and dense biofilms in the OA-nHAP@MSN-amended systems, compared to NP-free systems. Our results demonstrate a strategy for enhancing oil-spill bioremediation using NPs targeting nutrient supply to hydrocarbon-degrading bacteria at oil-water interfaces.

Bentonite addition enhances the biodegradation of petroleum pollutants and bacterial community succession during the aerobic co-composting of waste heavy oil with agricultural wastes

Soil contamination with petroleum significantly threatens the ecological equilibrium and human health. In this context, aerobic co-composting of waste heavy oil with agricultural wastes was performed in the present study to remediate petroleum pollutants through four treatments: CK (control), T1 (petroleum pollutant), T2 (petroleum pollutant with bentonite), and T3 (petroleum pollutant with humic acid-modified bentonite). Comprehensive analyses were conducted to determine the physicochemical parameters, enzymatic activities, removal of petroleum pollutants, microbial community structure, and water-extractable organic matter in different composting systems. Structural equation modeling was employed to identify the key factors influencing the removal of petroleum pollutants. According to the results, petroleum pollutant removal percentages of 44.94%, 79.09%, and 79.67% could be achieved with T1, T2, and T3, respectively. In addition, the activities of polyphenol oxidase (51.21 U/g) and catalase (367.91 U/g), which are the enzymes related to petroleum hydrocarbon degradation, were the highest in T3. Moreover, bentonite addition to the treatment increased the nitrate nitrogen storage in the compost from 10.95 mg/kg in T1 to 18.63 and 17.41 mg/kg in T2 and T3, respectively. Humic acid-modified bentonite could enhance the degree of compost humification, thereby leading to a higher-quality compost product. Collectively, these findings established bentonite addition as an efficient approach to enhance the compost remediation of petroleum pollutants.

Isolation and characterization of Candida tropicalis B: a promising yeast strain for biodegradation of petroleum oil in marine environments

The increasing interest in environmental protection laws has compelled companies to regulate the disposal of waste organic materials. Despite efforts to explore alternative energy sources, the world remains heavily dependent on crude petroleum oil and its derivatives. The expansion of the petroleum industry has significant implications for human and environmental well-being. Bioremediation, employing living microorganisms, presents a promising approach to mitigate the harmful effects of organic hydrocarbons derived from petroleum. This study aimed to isolate and purify local yeast strains from oil-contaminated marine water samples capable of aerobically degrading crude petroleum oils and utilizing them as sole carbon and energy sources. One yeast strain (isolate B) identified as Candida tropicalis demonstrated high potential for biodegrading petroleum oil in seawater. Physiological characterization revealed the strain's ability to thrive across a wide pH range (4-11) with optimal growth at pH 4, as well as tolerate salt concentrations ranging from 1 to 12%. The presence of glucose and yeast extract in the growth medium significantly enhanced the strain's biomass formation and biodegradation capacity. Scanning electron microscopy indicated that the yeast cell diameter varied based on the medium composition, further emphasizing the importance of organic nitrogenous sources for initial growth. Furthermore, the yeast strain exhibited remarkable capabilities in degrading various aliphatic and aromatic hydrocarbons, with a notable preference for naphthalene and phenol at 500 and 1000 mg/l, naphthalene removal reached 97.4% and 98.6%, and phenol removal reached 79.48% and 52.79%, respectively. Optimization experiments using multi-factorial sequential designs highlighted the influential role of oil concentration on the bioremediation efficiency of Candida tropicalis strain B. Moreover, immobilized yeast cells on thin wood chips demonstrated enhanced crude oil degradation compared to thick wood chips, likely due to increased surface area for cell attachment. These findings contribute to our understanding of the potential of Candida tropicalis for petroleum oil bioremediation in marine environments, paving the way for sustainable approaches to address oil pollution.

Bio-augmentation and bio-stimulation with kenaf core enhanced bacterial enzyme activities during bio-degradation of petroleum hydrocarbon in polluted soil

Indigenous micro-organisms often possess the ability to degrade petroleum hydrocarbon (PHC) in polluted soil. However, this process can be improved by supplementing with nutrients or the addition of more potent microbes. In this study, the ability of kenaf-core to stimulate the PHC degradation capability of microbial isolates from PHC polluted soil samples was evaluated. The standard experimental methods used in this study include: the digestion and analysis of the physico-chemical properties of petroleum hydrocarbon contaminated and non-contaminated soil samples; evaluation of petroleum hydrocarbon biodegradation using bio-augmentation and bio-stimulation (with kenaf-core) treatments; and, determination of soil microbial enzyme activities. Results from this study show that K, Na, total nitrogen, organic carbon, exchangeable cations, and heavy metals were found to be significantly (P < 0.05) higher in the polluted soil than in the non-polluted soil. Also, the polluted samples had pH values ranging from 5.5 to 6.0 while the non-polluted samples had a pH of 7.6. The microbial enzyme activities were comparatively lower in the polluted soils as compared to the non-polluted soil. The percentage degradation in the kenaf-core treated samples (AZ1T2-78.38; BN3T2-70.69; OL1T2-71.06; OT1T2-70.10) were significantly (P < 0.05) higher than those of the untreated (AZ1T1-13.50; BN3T1-12.50; OL1T1-10.55; OT1T1-9.50). The degradation of petroleum hydrocarbon in the bio-augmented and bio-stimulated treatments increased with increasing time of incubation, and were higher than that of the untreated sample. Comparatively, the treatment with a combination of kenaf-core and rhamnolipid exhibited a significantly (P < 0.05) higher degradation rate than that of the treatment with only kenaf core or rhamnolipid. While, the bio-stimulated and bio-augmented treatments had appreciable microbial counts that are higher than that of the untreated. In conclusion, the nutrient-supplement with kenaf-core significantly enhanced microbial growth and activities in the soil, thus improving their ability to biodegrade petroleum hydrocarbons in the polluted soils. Thus, supplementing with Kenaf core to encourage microbiological degradation of petroleum hydrocarbon is recommended.

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.

RNA-sequencing analysis reveals the co-biodegradation performance of crude oil by marine Chlorella vulgaris under norfloxacin stress

In this study, the microalgal growth and crude oil (CRO) biodegradation by marine Chlorella vulgaris (C. vulgaris) were assessed under norfloxacin (NFX) stress. The presence of NFX negatively affected the bio-removal of CRO within 5 days, as the NFX concentration increased from 100 to 1600 μg/L, due to its toxicity as an antibiotic. However, its negative impact on the final degradation capabilities of C. vulgaris was less significant (P-value <0.05). After 9 days of cultivation, CRO bio-removal efficiencies still exceeded 90 %, while NFX bio-removal efficiencies maintained over 47 %. RNA-seq analysis revealed that the degradation of CRO and NFX was attributed to the combined action of functional genes involved in scavenging reactive oxygen species. The production of pigments and the bio-removal performance of C. vulgaris in CRO, NFX, and CRO & NFX coexistence media were consistent with the changes in the number of differentially expressed genes in these samples.

Biodegradation of naphthalene - Ecofriendly approach for soil pollution mitigation

Naphthalene (NPT), a widely used household pest repellent and insecticide obtained from crude oil, serves as a toxic pollutant to non-target living matter. The stable and resistant nature of NPT makes it difficult to degrade through the physiochemical processes. The present study investigated the bacterial degradation of NPT isolated from crude oil-contaminated soil. Initially, the potent bacteria, Bacillus sp. GN 3.4, were isolated by enrichment culture method and subsequently assessed for NPT biodegradation. The optimum conditions for NPT biodegradation were pH 7.0 at 37 °C, 80 mg/L (initial NPT), 3% v/v (inoculum dose), and 7 days of treatment which showed 100% biodegradation. Furthermore, GC-MS analysis revealed the presence of degradation metabolites, namely, salicylate and hydroquinone indicating potential metabolic pathways. Considering the water-solubility and non-toxic nature of these metabolites, the results imply that Bacillus sp. GN 3.4. could potentially play a role in bioremediation by aiding in eliminating NPT from the soil.

Potential biodegradation of polycyclic aromatic hydrocarbons (PAHs) and petroleum hydrocarbons by indigenous fungi recovered from crude oil-contaminated soil in Iran

A total of 265 fungal individuals were isolated from soils exposed to heavy oil spills in the Yadavaran oil field in Iran to discover indigenous fungal species with a high potential to biodegrade petroleum hydrocarbon pollutants. Morphological and molecular identification of obtained fungal species led to their assignment into 16 genera and 25 species. Alternaria spp. (78%), Fusarium spp. (5%), and Cladosporium spp. (4%) were the most common genera, along with Penicillium spp., Neocamarosporium spp., Epicoccum sp., Kotlabaea sp., Aspergillus sp., Mortierella sp., and Pleurotus sp. A preliminary screening using the DCPIP indicator revealed that approximately 35% of isolates from Alternaria, Epicoccum, Neocamarosporium, Cladosporium, Fusarium, Stachybotrys, Penicillium, and Stemphylium demonstrated promising tolerance to crude oil. The best-performing isolates (12 fungal individuals) were further investigated for their capacity to mineralize a mixture of four polycyclic aromatic hydrocarbons (PAH) for 47 days, quantified by GC-MS. Eventually, two top-performing isolates, namely 5c-12 (Alternaria tenuissima) and 3b-1 (Epicoccum nigrum), were applied to petroleum-contaminated soil. The GC-MS analysis showed that 60 days after inoculation, these isolates successfully degraded more than 70% of the long-chain hydrocarbons in the soil, including C8-C16 n-alkanes, C36 n-alkane, and Pristane. This study introduces two fungal species (5c-12 and 3b-1) with high potential for biodegrading petroleum compounds and PAHs, offering promising prospects for the decontamination of oil-contaminated soil.

Degradation of polycyclic aromatic hydrocarbons in aquatic environments by a symbiotic system consisting of algae and bacteria: green and sustainable technology

Polycyclic aromatic hydrocarbons (PAHs) are genotoxic, carcinogenic, and persistent in the environment and are therefore of great concern in the environmental protection field. Due to the inherent recalcitrance, persistence and nonreactivity of PAHs, they are difficult to remediate via traditional water treatment methods. In recent years, microbial remediation has been widely used as an economical and environmentally friendly degradation technology for the treatment of PAH-contaminated water. Various bacterial and microalgal strains are capable of potentially degrading or transforming PAHs through intrinsic metabolic pathways. However, their biodegradation potential is limited by the cytotoxic effects of petroleum hydrocarbons, unfavourable environmental conditions, and biometabolic limitations. To address this limitation, microbial communities, biochemical pathways, enzyme systems, gene organization, and genetic regulation related to PAH degradation have been intensively investigated. The advantages of algal-bacterial cocultivation have been explored, and the limitations of PAHs degradation by monocultures of algae or bacteria have been overcome by algal-bacterial interactions. Therefore, a new model consisting of a "microalgal-bacterial consortium" is becoming a new management strategy for the effective degradation and removal of PAHs. This review first describes PAH pollution control technologies (physical remediation, chemical remediation, bioremediation, etc.) and proposes an algal-bacterial symbiotic system for the degradation of PAHs by analysing the advantages, disadvantages, and PAH degradation performance in this system to fill existing research gaps. Additionally, an algal-bacterial system is systematically developed, and the effects of environmental conditions are explored to optimize the degradation process and improve its technical feasibility. The aim of this paper is to provide readers with an effective green and sustainable remediation technology for removing PAHs from aquatic environments.

Functional response of microbial communities in lab-controlled oil-contaminated marine sediment

Crude oil contamination is one of the biggest problems in modern society. As oil enters into contact with the environment, especially if the point of contact is a body of water, it begins a weathering process by mixing and spreading. This is dangerous to local living organisms' communities and can impact diversity. However, despite unfavorable conditions, some microorganisms in these environments can survive using hydrocarbons as a nutrient source. Thus, understanding the local community dynamics of contaminated areas is essential. In this work, we analyzed the 16S rRNA amplicon sequencing and metatranscriptomic data of uncontaminated versus contaminated shallow marine sediment from publicly available datasets. We investigated the local population's taxonomic composition, species diversity, and fluctuations over time. Co-expression analysis coupled with functional enrichment showed us a prevalence of hydrocarbon-degrading functionality while keeping a distinct transcriptional profile between the late stages of oil contamination and the uncontaminated control. Processes related to the degradation of aromatic compounds and the metabolism of propanoate and butanoate were coupled with evidence of enhanced activity such as flagellar assembly and two-component system. Many enzymes of the anaerobic toluene degradation pathways were also enriched in our results. Furthermore, our diversity and taxonomical analyses showed a prevalence of the class Desulfobacteria, indicating interesting targets for bioremediation applications on marine sediment.

A biodegradable chitosan-based polymer for sustained nutrient release to stimulate groundwater hydrocarbon-degrading microflora

Petroleum hydrocarbon-contaminated groundwater often has a low indigenous microorganism population and lacks the necessary nutrient substrates for biodegradation reaction, resulting in a weak natural remediation ability within the groundwater ecosystem. In this paper, we utilized the principle of petroleum hydrocarbon degradation by microorganisms to identify effective nutrients (NaH2PO4, K2HPO4, NH4NO3, CaCl2, MgSO4·7H2O, FeSO4·7H2O, and VB12) and optimize nutrient substrate allocation through a combination of actual surveys of petroleum hydrocarbon-contaminated sites and microcosm experiments. Building on this, combining biostimulation and controlled-release technology, we developed a biodegradable chitosan-based encapsulated targeted biostimulant (i.e., YZ-1) characterized by easy uptake, good stability, controllable slow-release migration, and longevity to stimulate indigenous microflora in groundwater to efficiently degrade petroleum hydrocarbon. Results showed that YZ-1 extended the active duration of nutrient components by 5-6 times, with a sustainable release time exceeding 2 months. Under YZ-1 stimulation, microorganisms grew rapidly, increasing the degradation rate of petroleum hydrocarbon (10 mg L-1) by indigenous microorganisms from 43.03% to 79.80% within 7 d. YZ-1 can easily adapt to varying concentrations of petroleum hydrocarbon-contaminated groundwater. Specifically, in the range of 2-20 mg L-1 of petroleum hydrocarbon, the indigenous microflora was able to degrade 71.73-80.54% of the petroleum hydrocarbon within a mere 7 d. YZ-1 injection facilitated the delivery of nutrient components into the underground environment, improved the conversion ability of inorganic electron donors/receptors in the indigenous microbial community system, and strengthened the co-metabolism mechanism among microorganisms, achieving the goal of efficient petroleum hydrocarbon degradation.

Genome features of a novel hydrocarbonoclastic Chryseobacterium oranimense strain and its comparison to bacterial oil-degraders and to other C. oranimense strains

For the first time, we report the whole genome sequence of a hydrocarbonoclastic Chryseobacterium oranimense strain isolated from Trinidad and Tobago (COTT) and its genes involved in the biotransformation of hydrocarbons and xenobiotics through functional annotation. The assembly consisted of 11 contigs with 2,794 predicted protein-coding genes which included a diverse group of gene families involved in aliphatic and polycyclic hydrocarbon degradation. Comparative genomic analyses with 18 crude-oil degrading bacteria in addition to two C. oranimense strains not associated with oil were carried out. The data revealed important differences in terms of annotated genes involved in the hydrocarbon degradation process that may explain the molecular mechanisms of hydrocarbon and xenobiotic biotransformation. Notably, many gene families were expanded to explain COTT's competitive ability to manage habitat-specific stressors. Gene-based evidence of the metabolic potential of COTT supports the application of indigenous microbes for the remediation of polluted terrestrial environments and provides a genomic resource for improving our understanding of how to optimize these characteristics for more effective bioremediation.

HADEG: A curated hydrocarbon aerobic degradation enzymes and genes database

Databases of genes and enzymes involved in hydrocarbon degradation have been previously reported. However, these databases specialize on only a specific group of hydrocarbons and/or are constructed partly based on enzyme sequences with putative functions indicated by in silico research, with no experimental evidence. Here, we present a curated database of Hydrocarbon Aerobic Degradation Enzymes and Genes (HADEG) containing proteins and genes involved in alkane, alkene, aromatic, and plastic aerobic degradation and biosurfactant production based solely on experimental evidence, which are present in bacteria, and fungi. HADEG includes 259 proteins for petroleum hydrocarbon degradation, 160 for plastic degradation, and 32 for biosurfactant production. This database will help identify and predict hydrocarbon degradation genes/pathways and biosurfactant production in genomes.

Methylated cycloalkanes fuel a novel genus in the Porticoccaceae family (Ca. Reddybacter gen. nov)

Cycloalkanes are abundant and toxic compounds in subsurface petroleum reservoirs and their fate is important to ecosystems impacted by natural oil seeps and spills. This study focuses on the microbial metabolism of methylcyclohexane (MCH) and methylcyclopentane (MCP) in the deep Gulf of Mexico. MCH and MCP are often abundant cycloalkanes observed in petroleum and will dissolve into the water column when introduced at the seafloor via a spill or natural seep. We conducted incubations with deep Gulf of Mexico (GOM) seawater amended with MCH and MCP at four stations. Within incubations with active respiration of MCH and MCP, we found that a novel genus of bacteria belonging to the Porticoccaceae family (Candidatus Reddybacter) dominated the microbial community. Using metagenome-assembled genomes, we reconstructed the central metabolism of Candidatus Reddybacter, identifying a novel clade of the particulate hydrocarbon monooxygenase (pmo) that may play a central role in MCH and MCP metabolism. Through comparative analysis of 174 genomes, we parsed the taxonomy of the Porticoccaceae family and found evidence suggesting the acquisition of pmo and other genes related to the degradation of cyclic and branched hydrophobic compounds were likely key events in the ecology and evolution of this group of organisms.

Remediation of hydrocarbons and metals by hydrocarbon utilizing Pseudomonas taiwanensis YSA-17 isolated from soil contaminated with petroleum

Careless handling of petroleum in petrochemical industries releases toxic hydrocarbons and metals to soil and water. The aim of the present study was to isolate hydrocarbon-utilizing and metal-tolerant bacteria. Hydrocarbon-utilizing bacteria from petroleum-contaminated soils were isolated on the Bushnell Hass medium. Hydrocarbon degradation by Pseudomonas taiwanensis strain YSA-17 was observed by gas chromatography-mass spectrometry. Bioaccumulation of metals by strain YSA-17 was assessed in nutrient broth. Among different strains, YSA-17 showed the highest potential for hydrocarbon utilization. After 20 days of incubation, YSA-17 completely degraded one compound and during its degradation, there was the formation of 13 new compounds which were absent in uninoculated control. Results of scanning electron microscope and Fourier transmission infrared (FTIR) indicated degradation of hydrocarbons. FTIR showed the formation of new functional groups in YSA-17 inoculated medium. Expression of the total quantity of hydrocarbon-degrading gene (AlkB and NehAc) in petroleum-amended nutrient broth inoculated with strain YSA-17 enhanced significantly during 20 days of incubation compared to control. YSA-17 also significantly removed metals. This study concluded that bioinoculant can be utilized for the bioremediation of pollutants cocontaminated with hydrocarbons and metals. Petroleum-contaminated soil will be remediated for pollutants.

Development of a highly tolerant bacterial consortium for asphaltene biodegradation in soils

Asphaltenes are the most polar and heavy fraction of petroleum, and their complex structure and toxicity make them resistant to biodegradation. The ability to tolerate high asphaltene concentrations is crucial to reducing the toxicity-related inhibition of microbial growth and improving their capacity for adaptation, survival, and biodegradation in soils highly contaminated with asphaltenes. This study developed a highly tolerant consortium for efficient asphaltene biodegradation in soils from 22 bacterial isolates obtained from heavy-crude oil-contaminated soils. Isolates corresponded to the Rhodococcus, Bacillus, Stutzerimonas, Cellulosimicrobium, Pseudomonas, and Paenibacillus genera, among others, and used pure asphaltenes and heavy crude oil as the only carbon sources. Surface plate assays were used to evaluate the tolerance of individual isolates to asphaltenes, and the results showed variations in the extension and inhibition rates with maximum tolerance levels at 60,000 mg asphaltenes l-1. Inhibition assays were used to select non-antagonistic bacterial isolates among those showing the highest tolerance levels to asphaltenes. A consortium made up of the five most tolerant and non-antagonistic bacterial isolates was able to degrade up to 83 wt.% out of 10,000 mg asphaltenes kg-1 in the soil after 52 days. Due to its biological compatibility, high asphaltene tolerance, and ability to utilise it as a source of energy, the degrading consortium developed in this work has shown a high potential for soil bioremediation and is a promising candidate for the treatment of aged soil areas contaminated with heavy and extra-heavy crude oil. This would be the first research to assess and consider extreme bacterial tolerance and microbial antagonism between individual degrading microbes, leading to the development of an improved consortium capable of efficiently degrading high amounts of asphaltenes in soil.

Investigation of the transport and metabolic patterns of oil-displacing bacterium FY-07-G in the microcosm model using X-CT technology

AIMS

Microbial enhanced oil recovery (MEOR) is dedicated to enhancing oil recovery by harnessing microbial metabolic activities and their byproducts within reservoir rocks and fluids. Therefore, the investigation of microbial mobility and their extensive distribution within crude oil is of paramount importance in MEOR. While microscale models have been valuable for studying bacterial strain behavior in reservoirs, they are typically limited to 2D representations of porous media, making them inadequate for simulating actual reservoir conditions. Consequently, there is a critical need for 3D models and dependable visualization methods to observe bacterial transport and metabolism within these complex reservoir environments.

METHODS AND RESULTS

Bacterial cellulose (bc) is a water-insoluble polysaccharide produced by bacteria that exhibits biocompatibility and biodegradability. It holds significant potential for applications in the field of MEOR as an effective means for selective plugging and spill prevention during oil displacement processes. Conditionally cellulose-producing strain, FY-07-G, with green fluorescent labeling, was engineered for enhanced oil recovery. 3D micro-visualization model was constructed to directly observe the metabolic activities of the target bacterial strain within porous media and to assess the plugging interactions between cellulose and the medium. Additionally, X-ray computed tomography (X-CT) technology was employed for a comprehensive analysis of the transport patterns of the target strain in oil reservoirs with varying permeabilities. The results indicated that FY-07-G, as a microorganism employing biopolymer-based plugging principles to enhance oil recovery, selectively targets and seals regions characterized by lower permeability and smaller pore spaces.

CONCLUSIONS

This work provided valuable insights into the transport and metabolic behavior of MEOR strains and tackled the limitation of 2D models in faithfully replicating oil reservoir conditions, offering essential theoretical guidance and insights for the further application of oil-displacing bacterial strains in MEOR processes.

Taxonomic and Predictive Functional Profile of Hydrocarbonoclastic Bacterial Consortia Developed at Three Different Temperatures

Microbial community exhibit shift in composition in response to temperature variation. We report crude oil-degrading activity and high-throughput 16S rRNA gene sequencing (metagenome) profiles of four bacterial consortia enriched at three different temperatures in crude oil-amended Bushnell-Hass Medium from an oily sludge sediment. The consortia were referred to as O (4 ± 2 ℃ in 3% w/v crude oil), A (25 ± 2 ℃ in 1% w/v crude oil), H (25 ± 2 ℃ in 3% w/v crude oil), and X (45 ± 2 ℃ in 3% w/v crude oil). The hydrocarbon-degrading activity was highest for consortium A and H and lowest for consortium O. The metagenome profile revealed the predominance of Proteobacteria (62.12-1.25%) in each consortium, followed by Bacteroidota (18.94-37.77%) in the consortium O, A, and H. Contrarily, consortium X comprised 7.38% Actinomycetota, which was essentially low (< 0.09%) in other consortia, and only 0.41% Bacteroidota. The PICRUSt-based functional analysis predicted major functions associated with the metabolism and 5060 common KEGG Orthology (KOs). A total of 296 KOs were predicted exclusively in consortium X. Additionally, 247 KOs were predicted from xenobiotic biodegradation pathways. This study found that temperature had a stronger influence on the composition and function of the bacterial community than crude oil concentration.

Elucidating response mechanisms at the metabolic scale of Eisenia fetida in typical oil pollution sites: A native driver in influencing carbon flow

Previous investigations on the stress response patterns of earthworms (Eisenia fetida) in practical petroleum hydrocarbon (PH) contamination systems were less focused. Therefore, this study investigated the ecotoxicological effect of PH contamination on earthworms based on metabonomics and histological observation, followed by correlation analysis between the earthworm metabolism, PH types and concentrations, soil physicochemical characteristics, and the microbial community structures (i.e., diversity and abundance) and functions. The results showed that due to the abundant PH organics, the cell metabolism of earthworms shifts under PH contamination conditions, leading them to use organic acids as alternative energy sources (i.e., gluconeogenesis pathway). Simultaneously, biomarker metabolites related to cellular uptake, stress response, and membrane disturbance were identified. In addition, when compared to the controls, considerable epicuticle and cuticle layer disruption was observed, along with PH internalization. It was demonstrated that PH pollution preferentially influences the physiological homeostasis of earthworms through indirect (i.e., microbial metabolism regulation) than direct (i.e., direct interaction with earthworms) mechanisms. Moreover, the varied CO2 releasement was verified, which highlights the potential role of earthworms in influencing carbon transformation and corresponds with the considerably enriched energy metabolism-related pathway. This study indicated that PH contamination can induce a strong stress response in earthworms through both direct and indirect mechanisms, which in turn, substantially influences carbon transformation in PH contamination sites.

Transcriptome analysis of a springtail, Folsomia candida, reveals energy constraint and oxidative stress during petroleum hydrocarbon exposure

Petroleum hydrocarbon (PHC) contamination in soil is ubiquitous and poses harmful consequences to many organisms. The toxicity of PHC-impacted soil is difficult to predict due to variations in mixture composition and the impacts of natural weathering processes. Hence, high-throughput methods to assess PHC-impacted soils is required to expedite land management decisions. Next-generation sequencing is a robust tool that allows researchers to investigate the effects of contaminants on the transcriptome of organisms and identify molecular biomarkers. In this study, the effects of PHCs on conventional endpoints (i.e., survival and reproduction) and gene expression rates of a model springtail species, Folsomia candida were investigated. Age-synchronized F. candida were exposed to ecologically-relevant concentrations of soils spiked with fresh crude oil to calculate the reproductive EC25 and EC50 values using conventional toxicity testing. Soils spiked to these concentrations were then used to evaluate effects on the F. candida transcriptome over a 7-day exposure period. RNA-seq analysis found 98 and 132 differentially expressed genes when compared to the control for the EC25 and EC50 treatment groups, respectively. The majority of up-regulated genes were related to xenobiotic biotransformation reactions and oxidative stress response, while down-regulated genes coded for carbohydrate and peptide metabolic processes. Promotion of the pentose phosphate pathway was also found. Results suggest that the decreased reproduction rates of F. candida exposed to PHCs is due to energy constraints caused by inhibition of carbohydrate metabolic processes and allocation of remaining energy to detoxify xenobiotics. These findings provide insights into the molecular effects in F. candida following exposure to crude oil for seven days and highlight their potential to be used as a high-throughput screening test for PHC-contaminated sites. Adverse molecular effects can be measured as early as 24 h following exposure, whereas conventional toxicity tests may require a minimum of four weeks.

Potential for natural attenuation of crude oil hydrocarbons in benthic microbiomes near coastal communities in Kivalliq, Nunavut, Canada

Oil spilled in marine environments can settle to the seafloor through aggregation and sedimentation processes. This has been predicted to be especially relevant in the Arctic due to plankton blooms initiated by melting sea ice. These conditions exist in the Kivalliq region in Nunavut, Canada, where elevated shipping traffic has increased the risk of accidental spills. Experimental microcosms combining surface sediment and crude oil were incubated at 4 °C over 21 weeks to evaluate the biodegradation potential of seabed microbiomes. Sediments sampled near the communities of Arviat and Chesterfield Inlet were assessed for biodegradation capabilities by combining hydrocarbon geochemistry with 16S rRNA gene and metagenomic sequencing, revealing decreased microbial diversity but enrichment of oil-degrading taxa. Alkane and aromatic hydrocarbon losses corresponded to detection of genes and genomes that encode enzymes for aerobic biodegradation of these compounds, pointing to the utility of marine microbiome surveys for predicting the fate of oil released into Arctic marine environments.

Ribosomal RNA gene operon copy number, a functional trait indicating the hydrocarbon degradation level of bacterial communities

The lack of universal indicators for predicting microbial biodegradation potential and assessing remediation effects limits the generalization of bioremediation. The community-level ribosomal RNA gene operon (rrn) copy number, an important functional trait, has the potential to serve as a key indicator of the bioremediation of organic pollutants. A meta-analysis based on 1275 samples from 26 hydrocarbon-related studies revealed a positive relationship between the microbial hydrocarbon biodegradation level and the community-level rrn copy number in soil, seawater and culture. Subsequently, a microcosm experiment was performed to decipher the community-level rrn copy number response mechanism during total petroleum hydrocarbon (TPH) biodegradation. The treatment combining straw with resuscitation-promoting factor (Rpf) exhibited the highest community-level rrn copy number and the most effective biodegradation compared with other treatments, and the initial TPH content (20,000 mg kg-1) was reduced by 67.67% after 77 days of incubation. TPH biodegradation rate was positively correlated with the average community-level rrn copy number (p = 0.001, R2 = 0.5781). Both meta and community analyses showed that rrn copy number may reflect the potential of hydrocarbon degradation and microbial dormancy. Our findings provide insight into the applicability of the community-level rrn copy number to assess bacterial biodegradation for pollution remediation.