A diversified approach to evaluate biostimulation and bioaugmentation strategies for heavy-oil-contaminated soil

Microbial community dynamics and bioremediation strategies for petroleum contamination in an in-service oil Depot, middle-lower Yellow River Basin

This study investigated soil and groundwater contamination at an in-service oil transportation station in the middle-lower Yellow River Basin, China. Spatial analysis combined with 16S rRNA and ITS sequencing revealed localized heavy metal (Cu, Ni, Cd, Pb) and petroleum hydrocarbon (PHs: 15.0 mg/kg) contamination in the oily sewage treatment area, with vertical migration constrained by silty sand layers. Volatile organic compounds (VOCs) primarily originated from oil tank emissions. Groundwater exhibited hydraulic gradient-driven downstream migration of PHs (0.03-0.04 mg/L) and arsenic (1.1-1.5 μg/L). Indigenous microbial communities exhibited redox-stratified functional differentiation: unclassified Comamonadaceae (Proteobacteria) dominated aerobic zones (monitoring well D5), utilizing nitrate for PHs degradation, while Desulfosporosinus (Firmicutes) mediated sulfate-coupled anaerobic alkane degradation and metal immobilization in anoxic zones (D6). Fungal communities featured Trametes (Basidiomycota), facilitating ligninolytic PAH breakdown via peroxidase secretion. Functional prediction (FAPROTAX/FUNGuild) confirmed a synergistic "fungal preprocessing-bacterial mineralization" mechanism. Microbial metabolic plasticity (e.g., nitrogen respiration, photoautotrophy) enabled adaptation to redox fluctuations. Given the site's medium-low risk profile, we proposed a tiered management framework: (1) in situ bioremediation that prioritizes indigenous microbes, (2) hierarchical risk zoning, and (3) dynamic monitoring networks. These strategies align with China's Green Low-Carbon Remediation principles through low-energy microbial technologies. The findings provide a mechanistic basis for balancing industrial operations and ecological health in the Yellow River Basin.

Field application of arbuscular mycorrhizal fungi and Alocasia calidora (Schott) G.Don for effective remediation of heavy metal/metalloid-polluted landfill soil

The research aimed to assess the influence of arbuscular mycorrhizal fungi (AMF) inoculation on the growth, tolerance, and phytoremediation capacity of Alocasia calidora (Schott) G.Don used in heavy metal/metalloid-polluted soil under field conditions. Five new, young A. calidora plants were planted in each treatment and control plot (1 m × 1 m). AMF inoculum was supplemented on days 0, 30, 60, and 90 in the treatment plot, and the experiment was conducted for 120 days. Substantial growth was observed in the roots and shoots of AMF-inoculated A. calidora. In the shoots of treated A. calidora, a high accumulation of Cu, As, Ni, Mn, and Pb was observed. The AMF-treated plant exhibited a higher accumulation of Cu, Fe, and Ni in the roots (P < 0.05). The removal efficiencies in the AMF-treated soil were 84.67, 74.82, 81.61, 80.77, 88.21, 92.26, 92.35, and 67.32% for As, Cr, Cu, Fe, Mn, Ni, Pb, and Zn, correspondingly, while, for control, the corresponding values were 61.24, 52.42, 62.95, 33.46, 57.89, 61.45, 71.19, and 54.98%. AMF-treated A. calidora demonstrated an increased tolerance and metal/metalloid accumulation in response to a variety of compounds, including tryptophan, S-(4-nitrobenzyl) glutathione, 5,7,2',3'-tetrahydroxy flavone, 5,2-dihydroxy flavone, indole-acrylic acid, and various tripeptides. A. calidora proliferation, tolerance, and metal/metalloid accumulation were enhanced by the inoculated AMF. Therefore, treating soil contaminated with heavy metals/metalloids can be accomplished by combining AMF with plants.

Enhanced bioremediation of organically combined contaminated soil by white rot fungal agent: physiological characteristics and contaminants degradation

Microbial remediation of organically combined contaminated sites is currently facing technical challenges. White rot fungi possess broad-spectrum degradation capabilities, but most of the studies are conducted on polluted water bodies, and few research focus on the degradation of combined organically contaminated soils. This study aimed to investigate the physiological changes in Trametes versicolor to enhance its simultaneous degradation ability towards benzo(a)pyrene (BaP) and TPH. The results demonstrated that Trametes versicolor, when subjected to liquid fermentation, achieved an 88.08% degradation of individual BaP within 7 days. However, under the combined contamination conditions of BaP and TPH, the BaP degradation rate decreased to 69.25%, while the TPH degradation rate was only 16.95%. Furthermore, the degradation rate of BaP exhibited a significant correlation with the extracellular protein concentration and laccase activities. Conversely, the TPH degradation rate exhibited a significant and positive correlation with the intracellular protein concentration. Solid-state fermentation utilizing fungal agents proved to be the most effective method for removing BaP and TPH, yielding degradation rates of 56.16% and 15.73% respectively within 60 days. Overall, Trametes versicolor demonstrated a commendable capability for degrading combined PAHs-TPH pollutants, thereby providing theoretical insights and technical support for the remediation of organically combined contaminated sites.

Influence of bioaugmented fungi on tolerance, growth and phytoremediation ability of Prosopis juliflora Sw. DC in heavy metal-polluted landfill soil

The research aimed to determine the influence of endophytic fungi on tolerance, growth and phytoremediation ability of Prosopis juliflora in heavy metal-polluted landfill soil. A consortium of 13 fungal isolates as well as Prosopis juliflora Sw. DC was used to decontaminate heavy metal-polluted landfill soil. Enhanced plant growth (biomass and root and shoot lengths) and production of carotenoids, chlorophyll and amino acids L-phenylalanine and L-leucine that are known to enhance growth were found in the treated P. juliflora. Better accumulations of heavy metals were observed in fungi-treated P. juliflora over the untreated one. An upregulated activity of peroxidase, catalase and ascorbate peroxidase was recorded in fungi-treated P. juliflora. Additionally, other metabolites, such as glutathione, 3,5,7,2',5'-pentahydroxyflavone, 5,2'-dihydroxyflavone and 5,7,2',3'-tetrahydroxyflavone, and small peptides, which include Lys Gln Ile, Ser Arg Ala, Asp Arg Gly, Arg Ser Ser, His His Arg, Arg Thr Glu, Thr Arg Asp and Ser Pro Arg, were also detected. These provide defence supports to P. juliflora against toxic metals. Inoculating the plant with the fungi improved its growth, metal accumulation as well as tolerance against heavy metal toxicity. Such a combination can be used as an effective strategy for the bioremediation of metal-polluted soil.

Effects of soybean oil exposure on the survival, reproduction, biochemical responses, and gut microbiome of the earthworm Eisenia fetida

With increasing production of kitchen waste, cooking oil gradually enters the soil, where it can negatively affect soil fauna. In this study, we explored the effects of soybean oil on the survival, growth, reproduction, tissue structure, biochemical responses, mRNA expression, and gut microbiome of earthworms (Eisenia fetida). The median lethal concentration of soybean oil was found to be 15.59%. Earthworm growth and reproduction were significantly inhibited following exposure to a sublethal concentration of soybean oil (1/3 LC50, 5.2%). The activity of the antioxidant enzymes total superoxide dismutase (T-SOD), peroxidase (POD), and catalase (CAT) were affected under soybean oil exposure. The glutathione (GSH) content decreased significantly, whereas that of the lipid peroxide malondialdehyde (MDA) increased significantly after soybean oil exposure. mRNA expression levels of the SOD, metallothionein (MT), lysenin and lysozyme were significantly upregulated. The abundance of Bacteroides species, which are related to mineral oil repair, and Muribaculaceae species, which are related to immune regulation, increased within the earthworm intestine. These results indicate that soybean oil waste is toxic to earthworms. Thus, earthworms deployed defense mechanisms involving antioxidant system and gut microbiota for protection against soybean oil exposure-induced stress.

Measuring DNA modifications with the comet assay: a compendium of protocols

The comet assay is a versatile method to detect nuclear DNA damage in individual eukaryotic cells, from yeast to human. The types of damage detected encompass DNA strand breaks and alkali-labile sites (e.g., apurinic/apyrimidinic sites), alkylated and oxidized nucleobases, DNA-DNA crosslinks, UV-induced cyclobutane pyrimidine dimers and some chemically induced DNA adducts. Depending on the specimen type, there are important modifications to the comet assay protocol to avoid the formation of additional DNA damage during the processing of samples and to ensure sufficient sensitivity to detect differences in damage levels between sample groups. Various applications of the comet assay have been validated by research groups in academia, industry and regulatory agencies, and its strengths are highlighted by the adoption of the comet assay as an in vivo test for genotoxicity in animal organs by the Organisation for Economic Co-operation and Development. The present document includes a series of consensus protocols that describe the application of the comet assay to a wide variety of cell types, species and types of DNA damage, thereby demonstrating its versatility.

Assessment of Different Spent Mushroom Substrates to Bioremediate Soils Contaminated with Petroleum Hydrocarbons

Bioremediation techniques are being developed as substitutes for physical–chemical methodologies that are expensive and not sustainable. For example, using the agricultural waste spent mushroom substrate (SMS) which contains valuable microbiota for soil bioremediation. In this work, SMSs of four cultivated fungal species, Pleurotus eryngii, Lentinula edodes, Pleurotus ostreatus, and Agaricus bisporus were evaluated for the bioremediation of soils contaminated by petroleum hydrocarbons (TPHs). The bioremediation test was carried out by mixing the four different SMSs with the TPH-contaminated soil in comparison with an unamended soil control to assess its natural attenuation. To determine the most efficient bioremediation strategy, hydrolase, dehydrogenase, and ligninolytic activities, ergosterol content, and percentage of TPHs degradation (total and by chains) were determined at the end of the assay at 40 days. The application of SMS significantly improved the degradation of TPHs with respect to the control. The most effective spent mushroom substrate to degrade TPHs was A. bisporus, followed by L. edodes and P. ostreatus. Similar results were obtained for the removal of aliphatic and aromatic hydrocarbons. The results showed the effectiveness of SMS to remove aliphatic and aromatic hydrocarbons from C10 to C35. This work demonstrates an alternative to valorizing an abundant agricultural waste as SMS to bioremediate contaminated soils.

Phytoremediation of soil contaminated with weathered petroleum hydrocarbons by applying mineral fertilization, an anionic surfactant, or hydrocarbonoclastic bacteria

This study evaluated the effect of the application of mineral fertilization (F), the anionic surfactant Triton X-100 (TX100), or the inoculation with a hydrocarbooclastic bacterial consortium (BCons) on the growth of Clitoria ternatea during the phytoremediation of a Gleysol contaminated with weathered petroleum hydrocarbons (39,000 mg kg^-1 WPH) collected from La Venta, Tabasco (Mexico). The experiment consisted of a completely randomized design with seven treatments and four replications each under greenhouse conditions. The application of F (biostimulation) increased plant growth and biomass production; in contrast, TX100 only favored root biomass (11%) but significantly favored WPH degradation. Bioaugmentation with BCons did not show significant effects on plant growth. Nevertheless, the combination of biostimulation with bioaugmentation (BCons + F, BCons + TX100, and BCons + F+TX100) enhanced plant growth, hydrocarbonoclastic bacteria population, and WPH degradation when compared to treatments with the single application of bioaugmentation (BCons) or biostimulation (F).

Remediation of Petroleum-Contaminated Soils with Microbial and Microbial Combined Methods: Advances, Mechanisms, and Challenges

The petroleum industry’s development has been supported by the demand for petroleum and its by-products. During extraction and transportation, however, oil will leak into the soil, destroying the structure and quality of the soil and even harming the health of plants and humans. Scientists are researching and developing remediation techniques to repair and re-control the afflicted environment due to the health risks and social implications of petroleum hydrocarbon contamination. Remediation of soil contamination produced by petroleum hydrocarbons, on the other hand, is a difficult and time-consuming job. Microbial remediation is a focus for soil remediation because of its convenience of use, lack of secondary contamination, and low cost. This review lists the types and capacities of microorganisms that have been investigated to degrade petroleum hydrocarbons. However, investigations have revealed that a single microbial remediation faces difficulties, such as inconsistent remediation effects and substantial environmental consequences. It is necessary to understand the composition and source of pollutants, the metabolic genes and pathways of microbial degradation of petroleum pollutants, and the internal and external aspects that influence remediation in order to select the optimal remediation treatment strategy. This review compares the degradation abilities of microbial–physical, chemical, and other combination remediation methods, and highlights the degradation capabilities and processes of the greatest microbe-biochar, microbe–nutrition, and microbe–plant technologies. This helps in evaluating and forecasting the chemical behavior of contaminants with both short- and long-term consequences. Although there are integrated remediation strategies for the removal of petroleum hydrocarbons, practical remediation remains difficult. The sources and quantities of petroleum pollutants, as well as their impacts on soil, plants, and humans, are discussed in this article. Following that, the focus shifted to the microbiological technique of degrading petroleum pollutants and the mechanism of the combined microbial method. Finally, the limitations of existing integrated microbiological techniques are highlighted.

Worms eat oil: Alcanivorax borkumensis hydrocarbonoclastic bacteria colonise Caenorhabditis elegans nematodes intestines as a first step towards oil spills zooremediation

The environmental hazards of oil spills cannot be underestimated. Bioremediation holds promise among various approaches to tackle oil spills in soils and sediments. In particular, using oil-degrading bacteria is an efficient and self-regulating way to remove oil spills. Using animals for oil spills remediation is in its infancy, mostly due to the lack of efficient oil-degrading capabilities in eukaryotes. Here we show that Caenorhabditis elegans nematodes survive for extended periods (up to 22 days) on pure crude oil diet. Moreover, we report for the first time the use of Alcanivorax borkumensis hydrocarbonoclastic bacteria for colonisation of C. elegans intestines, which allows for effective digestion of crude oil by the nematodes. The worms fed and colonised by A. borkumensis demonstrated the similar or even better longevity, resistance against oxidative and thermal stress and reproductivity as those animals fed with Escherichia coli bacteria (normal food). Importantly, A. borkumensis-carrying nematodes were able to accumulate oil droplet from oil-contaminated soils. Artificial colonisation of soil invertebrates with oil-degrading bacteria will be an efficient way to distribute microorganisms in polluted soil, thus opening new avenues for oil spills zooremediation.

Fungi in PAH-contaminated marine sediments: Cultivable diversity and tolerance capacity towards PAH

The cultivable fungal diversity from PAH-contaminated sediments was examined for the tolerance to polycyclic aromatic hydrocarbon (PAH). The 85 fungal strains, isolated in non-selective media, revealed a large diversity by ribosomal internal transcribed spacer (ITS) sequencing, even including possible new species. Most strains (64%) exhibited PAH-tolerance, indicating that sediments retain diverse cultivable PAH-tolerant fungi. The PAH-tolerance was linked neither to a specific taxon nor to the peroxidase genes (LiP, MnP and Lac). Examining the PAH-removal (degradation and/or sorption), Alternaria destruens F10.81 showed the best capacity with above 80% removal for phenanthrene, pyrene and fluoranthene, and around 65% for benzo[a]pyrene. A. destruens F10.81 internalized pyrene homogenously into the hyphae that contrasted with Fusarium pseudoygamai F5.76 in which PAH-vacuoles were observed but PAH removal was below 20%. Thus, our study paves the way for the exploitation of fungi in remediation strategies to mitigate the effect of PAH in coastal marine sediments.

Investigation of biosurfactants produced by three indigenous bacterial strains, their growth kinetics and their anthracene and fluorene tolerance

The study explored the polycyclic aromatic hydrocarbon tolerance of indigenous biosurfactant producing microorganisms. Three bacterial species were isolated from crude oil contaminated sites of Haldia, West Bengal. The three species were screened for biosurfactant production and identified by 16S rRNA sequencing as Brevundimonas sp. IITISM 11, Pseudomonas sp. IITISM 19 and Pseudomonas sp. IITISM 24. The strains showed emulsification activities of 51%, 57% and 63%, respectively. The purified biosurfactants were characterised using FT-IR, GC-MS and NMR spectroscopy and found to have structural similarities to glycolipopeptides, cyclic lipopeptides and glycolipids. The biosurfactants produced were found to be stable under a wide range of temperature (0-100 °C), pH (4-12) and salinity (up to 20% NaCl). Moreover, the strains displayed tolerance to high concentrations (275 mg/L) of anthracene and fluorene and showed a good amount of cell surface hydrophobicity with different hydrocarbons. The study reports the production and characterisation of biosurfactant by Brevundimonas sp. for the first time. Additionally, the kinetic parameters of the bacterial strains grown on up to 300 mg/L concentration of anthracene and fluorene, ranged between 0.0131 and 0.0156 µ_max (h^-1), while the K_s(mg/L) ranged between 59.28 and 102.66 for Monod's Model. For Haldane-Andrew's model, µ_max (h^-1) varied between 0.0168 and 0.0198. The inhibition constant was highest for Pseudomonas sp. IITISM 19 on anthracene and Brevundimonas sp. IITISM 11 on fluorene. The findings of the study suggest that indigenous biosurfactant producing strains have tolerance to high PAH concentrations and can be exploited for bioremediation purposes.

Petroleum hydrocarbon-contaminated soil bioremediation assisted by isolated bacterial consortium and sophorolipid

Pollution in soil by petroleum hydrocarbon has become a global environmental problem. The bioremediation of petroleum hydrocarbon-contaminated soil was enhanced with the combination of an isolated indigenous bacterial consortium and biosurfactant. The biodegradation efficiency of total petroleum hydrocarbon (TPH) was increased from 12.2% in the contaminated soil to 44.5% and 57.7% in isolated consortium and isolated consortium & 1.5 g sophorolipid (SL)/kg dry soil, respectively. The half-life of TPH degradation process was decreased from 32.5 d in the isolated consortium reactor to 20.4 d in the isolated consortium & 1.5 g SL/kg dry soil. The addition of biosurfactant into contaminated soils improved the TPH desorption from solid matrix to the aqueous solution and the subsequent solubilization, which ultimately improved the bioavailability of TPH in contaminated soils. Biosurfactant also served as carbon sources which contributed to the stimulation of cell growth and microbial activity and accelerated the biodegradation process via co-metabolism. The enzyme activities and quantities of functional genes were demonstrated to be incremented in SL reactors. The biosurfactant improved the TPH bioavailability, stimulated the microbial activities and participated in the co-metabolism. The combination of bioaugmentation and SL benefitted the bioremediation of petroleum hydrocarbon-contaminated soil.

Principal component analysis reveals microbial biomass carbon as an effective bioindicator of health status of petroleum-polluted agricultural soil

We investigated a number of microbiological activities in the soil to serve as biomonitoring tools in assessing the ecotoxicity of diesel-contaminated soil samples during the different periods of bioremediation. Sawdust was used as the biostimulant for the biodegradation of artificial diesel-polluted soil samples. Soil microbial population, soil microbial enzymatic activities (catalase, lipase, dehydrogenase, urease, phosphatase and β-glucosidase), soil microbial biomass carbon (MBC), nitrogen (MBN) and phosphorus (MBP), soil microbial respirometric index and total petroleum hydrocarbon (TPH) concentration were monitored to evaluate the efficiency of the bioremediation process. After a period of 56 d, total petroleum hydrocarbon content reduced from 14,221 to 270 mg/kg. The parameter estimation using the nth-order kinetic model revealed that the first-order rate constants (k) for TPH removal were 4.417 d^-1 and 0.2670 d^-1 for sawdust-amended and unamended soil, respectively. This implied that, the sawdust amendment resulted in reaction rate 16.5 times faster than unamended soil. Thus, the biological indicators were generally more pronounced in biostimulated soil than the attenuated soil. However, to evaluate the efficiency of the sawdust-assisted bioremediation, principal component analysis, which was used in selecting the most sensitive bioindicators. It was observed that microbial biomass carbon, catalase, lipase and dehydrogenase were the most responsive bioparameters. A positive relationship between TPH removal and the four most sensitive bioparameters suggests that the use of four biological activities have proven to be effective monitoring tools for evaluating the efficiency of a bioremediation strategy.

Effect of soil organic matter on petroleum hydrocarbon degradation in diesel/fuel oil-contaminated soil

The purpose of this study is to investigate the effect of soil organic matter (SOM) content levels on the biodegradation of total petroleum hydrocarbons (TPH). Batch experiments were conducted with soils with 2% or 10% organic matter that had been contaminated by diesel or fuel oil. In addition to the TPH (diesel or fuel oil) degradation efficiency, a comprehensive investigation was conducted on the TPH-degrading microbial community using molecular tools including oligonucleotide microarray technique and terminal restriction fragment length polymorphism analysis (T-RFLP). TPH was reduced from 10,000 mg/kg to 1849-4352 mg/kg dry weight soil. Higher biodegradation efficiencies and kinetic rate constants were observed in higher SOM contents. Hydrocarbon fractional analyses were conducted to explain the optimal operation with relatively low resin and aromatic fractions detected at the end of the remediation. The bacterial and fungal counts in the 10% SOM were approximately 10 CFU/g to 10² CFU/g above those in the 2% SOM, and the lowest fungal level was found when the least TPH degradability was measured. The internal transcribed spacer microarray identified the microorganisms that were introduced and proved their survival. The associated growth pattern confirmed that different kinds of contamination oils affected the microbial community diversity over time. Both the microarray and T-RFLP profiles indicated that Gordonia alkanivorans, G. desulfuricans, and Rhodococcus erythoropolis were the dominant bacteria, while Fusarium oxysporum and Aspergillus versicolor were the dominant fungi. The T-RFLP-derived nonmetric multidimensional scaling concluded that the dynamics of the microbial communities were impacted by the TPH degradation stages.

Aerobic co-composting degradation of highly PCDD/F-contaminated field soil. A study of bacterial community

This study investigated bacterial communities during aerobic food waste co-composting degradation of highly PCDD/F-contaminated field soil. The total initial toxic equivalent quantity (TEQ) of the soil was 16,004 ng-TEQ kg^-1 dry weight. After 42-day composting and bioactivity-enhanced monitored natural attenuation (MNA), the final compost product's TEQ reduced to 1916 ng-TEQ kg^-1 dry weight (approximately 75% degradation) with a degradation rate of 136.33 ng-TEQ kg^-1 day^-1. Variations in bacterial communities and PCDD/F degraders were identified by next-generation sequencing (NGS). Thermophilic conditions of the co-composting process resulted in fewer observed bacteria and PCDD/F concentrations. Numerous organic compound degraders were identified by NGS, supporting the conclusion that PCDD/Fs were degraded during food waste co-composting. Bacterial communities of the composting process were defined by four phyla (Proteobacteria, Actinobacteria, Bacteroidetes and Firmicutes). At the genus level, Bacillus (Firmicutes) emerged as the most dominant phylotype. Further studies on specific roles of these bacterial strains are needed, especially for the thermophiles which contributed to the high degradation rate of the co-co-composting treatment's first 14 days.

Local fungi, willow and municipal compost effectively remediate petroleum-contaminated soil in the Canadian North

Low energy-input alternatives based on locally available products are needed for treating petroleum-hydrocarbon spills in northern regions. We tested the efficacy of three local biological components (municipal compost, white-rot fungus: Pleurotus ostreatus and willow: Salix planifolia) to remediate diesel-contaminated soils in a subarctic climate (Whitehorse, YT, Canada), and compared their efficacy to natural attenuation and chemical fertilizers (industry standard). After the first growing season, biologically amended treatments (BAT) that contained >2 biological components, had decreased 69-73% of the diesel's F2 fraction (C₁₀-C₁₆), which is more than natural attenuation or fertilizer (48 and 51%). By the third growing season, the BAT dropped below the Canadian Council of Ministers of the Environment's (CCME) Agricultural & Residential/Parkland guideline (<150 mg kg^-1) and 86% of willows had survived and developed extensive roots. MiSeq amplicon sequencing of fungal (ITS) and bacterial (16S) rRNA genes showed the BAT's microbial communities were significantly more abundant and diverse. We found 132 bacterial and 35 fungal genera unique to the BAT. Readily-available local biological components such as municipal compost, fungi and willows may provide an effective alternative to applications of imported chemical fertilizers for the bioremediation and revegetation of diesel-contaminated soil in northern environments.

Influence of rhamnolipid biosurfactant and Brij-35 synthetic surfactant on 14C-Pyrene mineralization in soil

Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous contaminants in soil and are considered priority pollutants due to their carcinogenicity. Bioremediation of PAH-contaminated soils is often limited by the low solubility and strong sorption of PAHs in soil. Synthetic surfactants and biosurfactants have been used to enhance the bioavailability of PAHs and to accelerate microbial degradation. However, few studies have compared synthetic and biosurfactants in their efficiency in promoting PAH biodegradation in either native or bioaugmented soils. In this study, we evaluated mineralization of ¹⁴C-pyrene in soils with or without the augmentation of Mycobacterium vanbaalenii PYR-1, and characterized the effect of Brij-35 (synthetic) and rhamnolipid biosurfactant at different amendment rates. Treatment of rhamnolipid biosurfactant at 140 or 1400 μg surfactant g-dry soil^-1 rates resulted in a significantly longer lag period in ¹⁴C-pyrene mineralization in both native and bioaugmented soils. In contrast, amendment of Brij-35 generally increased ¹⁴C-pyrene degradation, and the greatest enhancement occurred at 21.6 or 216 μg surfactant g-dry soil^-1 rates, which may be attributed to increased bioavailability. Brij-35 and rhamnolipid biosurfactant were found to be non-toxic to M. vanbaalenii PYR-1 at 10X CMC, thus indicating rhamnolipid biosurfactant likely served as a preferential carbon source to the degrading bacteria in place of ¹⁴C-pyrene, leading to delayed and inhibited ¹⁴C-pyrene degradation. Mineralization of ¹⁴C-pyrene by M. vanbaalenii PYR-1 was rapid in the unamended soils, and up to 60% of pyrene was mineralized to ¹⁴CO₂ after 10 d in the unamended or Brij-35 surfactant-amended soils. Findings of this study suggest that application of surfactants may not always lead to enhanced PAH biodegradation or removal. If the surfactant is preferentially used as an easier carbon substrate than PAHs for soil microorganisms, it may actually inhibit PAH biodegradation. Selection of surfactant types is therefore crucial for the effectiveness of surfactant-aided bioremediation of PAH-contaminated soils.

Mechanisms for rhamnolipids-mediated biodegradation of hydrophobic organic compounds

The widespread existence of hydrophobic organic compounds (HOCs) in soil and water poses a potential health hazard to human, such as skin diseases, heart diseases, carcinogenesis, etc. Surfactant-enhanced bioremediation has been regarded as one of the most viable technologies to treat HOCs contaminated soil and groundwater. As a biosurfactant that has been intensively studied, rhamnolipids have shown to enhance biodegradation of HOCs in the environment, however, the underlying mechanisms are not fully disclosed. In this paper, properties and production of rhamnolipids are summarized. Then effects of rhamnolipids on the biodegradation of HOCs, including solubilization, altering cell affinity to HOCs, and facilitating microbial uptake are reviewed in detail. Special attention is paid to how rhamnolipids change the bioavailability of HOCs, which are crucial for understanding the mechanism of rhamnolipids-mediated biodegradation. The biodegradation and toxicity of rhamnolipids are also discussed. Finally, perspectives and future research directions are proposed. This review adds insight to rhamnolipids-enhanced biodegradation process, and helps in application of rhamnolipids in bioremediation.

Strengthening detoxication impacts of Coprinus comatus on nickel and fluoranthene co-contaminated soil by bacterial inoculation

To develop an efficient and environmental-friendly approach to detoxicate nickel (Ni) and fluoranthene co-contaminated soil, the combined application of Coprinus comatus (C. comatus) with Serratia sp. FFC5 and/or Enterobacter sp. E2 was investigated. The pot experiment tested the influences of bacterial inoculation on the growth of C. comatus, content of Ni in C. comatus, Ni speciation in soil, fluoranthene dissipation, soil enzymatic activities, bacterial population and community structure. With the inoculation of bacteria, the fresh weights of C. comatus, concentration of Ni in C. comatus and the dissipation rates of fluoranthene were increased by 17.73-29.38%, 68.97-204.97% and 34.84-60.90%, respectively. Notably, results illustrated that the co-inoculation of FFC5 and E2 showed better effect in biomass enhancement, Ni accumulation and fluoranthene dissipation than solitary inoculation. Simultaneously, higher soil enzymatic and microbiological activities suggested that the integrated detoxication method of bacteria and C. comatus could improve soil quality. Therefore, we can infer that bacterial inoculation strengthened detoxication effect of C. comatus in Ni-fluoranthene co-contaminated soil, indicating that the combined application of C. comatus and bacteria can be an efficient alternative for detoxicating Ni and fluoranthene co-contaminated soil.

A comparative study to evaluate natural attenuation, mycoaugmentation, phytoremediation, and microbial-assisted phytoremediation strategies for the bioremediation of an aged PAH-polluted soil

Biological treatments are considered an environmentally option to clean-up polluted soil with polycyclic aromatic hydrocarbons (PAHs). A pot experiment was conducted to comparatively evaluate four different strategies, including natural attenuation (NA), mycoaugmentation (M) by using Crucibulum leave, phytoremediation (P) using maize plants, and microbial-assisted phytoremediation (MAP) for the bioremediation of an aged PAH-polluted soil at 180 days. The P treatment had higher affinity degrading 2-3 and 4 ring compounds than NA and M treatments, respectively. However, M and P treatments were more efficient in regards to naphthalene, indeno[l,2,3-c,d]pyrene and benzo[g,h,i]perylene degradation respect to NA. However, 4, 5-6 rings undergo a strong decline during the microbe-assisted phytoremediation, being the treatment which determined the highest rates of PAHs degradation. Sixteen PAH compounds, except fluorene and dibenzo[a,h]anthracene, were found in maize roots, whereas the naphthalene, phenanthrene, anthracene, fluoranthene, and pyrene were accumulated in the shoots, in both P and MAP treatments. However, higher PAH content in maize biomass was achieved during the MAP treatment respect to P treatment. The bioconversion and translocation factors were less than 1, indicating that phystabilization/phytodegradation processes occurred rather than phytoextraction. The microbial biomass, activity and ergosterol content were significantly boosted in the MAP treatment respect to the other treatments at 180 days. Ours results demonstrated that maize-C. laeve association was the most profitable technique for the treatment of an aged PAH-polluted soil when compared to other bioremediation approaches.

The effects of fluoride based fire-fighting foams on soil microbiota activity and plant growth during natural attenuation of perfluorinated compounds

The use of fluoride based foams increases the effectiveness of fire-fighting operations, but they are also accompanied by major drawbacks regarding environmental safety of perfluorinated compounds (PFCs). The main concern with PFCs release is due to their well-known persistence and bioaccumulative potential, as they have been detected in many environmental samples. There is a significant knowledge gap on PFC toxicity to plants, even though such data could be useful towards bioremediation procedures. It is consensus that a realistic assessment of fire-fighting foam toxicity should cover as many test organisms as possible, however, few studies combine the performance of ecotoxicological tests with a detailed study of microbial communities in soil contaminated with firefighting foams. Our research evaluated the effects of natural attenuation of PFCs on the development of arugula and lettuce seeds. The effects of variable PFCs amounts were also observed in soil microbiota using the 2,6 dichlorophenol-indophenol redox dye as microbial metabolism indicator. We aimed to determine whether aqueous film forming foams toxicity increased or decreased over time in a simulated contamination scenario. We argued that the long-term biotransformation of fire-fighting foams should be taken in to account when evaluating toxicity, focusing on a time-based monitoring analysis, since potentially toxic intermediates may be formed though biodegradation. The phyto-toxicity of PFCs to lettuce and arugula was high, increasing as a function of the concentration and decreasing as a function of exposure time to the environment. However, very specific concentrations throughout biodegradation result in the formation of non-inhibiting intermediates. Therefore, variable biodegradation-dependent germination rates may be misleading on non-time-based monitoring approaches. Also, the low phyto-toxicity after 240days does not exclude the potential for PFC bioaccumulation in plants. We also proposed that the colorimetric data modelling could also establish a novel toxicity parameter to evaluate the release impacts to soil and biota. The combined assays allowed the monitoring of PFCs during long-term exposition to plants as well as their immediate effects on the same soil microbiota.

Bioremediation of hydrocarbon degradation in a petroleum-contaminated soil and microbial population and activity determination

Bioremediation of hydrocarbon degradation in petroleum-polluted soil is carried out by various microorganisms. However, little information is available for the relationships between hydrocarbon degradation rates in petroleum-contaminated soil and microbial population and activity in laboratory assay. In a microcosm study, degradation rate and efficiency of total petroleum hydrocarbons (TPH), alkanes, and polycyclic aromatic hydrocarbons (PAH) in a petroleum-contaminated soil were determined using an infrared photometer oil content analyzer and a gas chromatography mass spectrometry (GC-MS). Also, the populations of TPH, alkane, and PAH degraders were enumerated by a modified most probable number (MPN) procedure, and the hydrocarbon degrading activities of these degraders were determined by the Biolog (MT2) MicroPlates assay. Results showed linear correlations between the TPH and alkane degradation rates and the population and activity increases of TPH and alkane degraders, but no correlation was observed between the PAH degradation rates and the PAH population and activity increases. Petroleum hydrocarbon degrading microbial population measured by MPN was significantly correlated with metabolic activity in the Biolog assay. The results suggest that the MPN procedure and the Biolog assay are efficient methods for assessing the rates of TPH and alkane, but not PAH, bioremediation in oil-contaminated soil in laboratory.

Surfactant-induced bacterial community changes correlated with increased polycyclic aromatic hydrocarbon degradation in contaminated soil

Bioremediation as a method for removing polycyclic aromatic hydrocarbons (PAHs) from contaminated environments has been criticized for poor removal of potentially carcinogenic but less bioavailable high molecular weight (HMW) compounds. As a partial remedy to this constraint, we studied surfactant addition at sub-micellar concentrations to contaminated soil to enhance the biodegradation of PAHs remaining after conventional aerobic bioremediation. We demonstrated increased removal of four- and five-ring PAHs using two nonionic surfactants, polyoxyethylene(4)lauryl ether (Brij 30) and polyoxyethylene sorbitol hexaoleate (POESH), and analyzed bacterial community shifts associated with those conditions. Eight groups of abundant bacteria were implicated as potentially being involved in increased HMW PAH removal. A group of unclassified Alphaproteobacteria and members of the Phenylobacterium genus in particular showed significantly increased relative abundance in the two conditions exhibiting increased PAH removal. Other implicated groups included members of the Sediminibacterium, Terrimonas, Acidovorax, and Luteimonas genera, as well as uncharacterized organisms within the families Chitinophagaceae and Bradyrhizobiaceae. Targeted isolation identified a subset of the community likely using the surfactants as a growth substrate, but few of the isolates exhibited PAH-degradation capability. Isolates recovered from the Acidovorax and uncharacterized Bradyrhizobiaceae groups suggest the abundance of those groups may have been attributable to growth on surfactants. Understanding the specific bacteria responsible for HMW PAH removal in natural and engineered systems and their response to stimuli such as surfactant amendment may improve bioremediation efficacy during treatment of contaminated environmental media.

Use of sugarcane filter cake and nitrogen, phosphorus and potassium fertilization in the process of bioremediation of soil contaminated with diesel

This study evaluated the use of sugarcane filter cake and nitrogen, phosphorus and potassium (NPK) fertilization in the bioremediation of a soil contaminated with diesel fuel using a completely randomized design. Five treatments (uncontaminated soil, T1; soil contaminated with diesel, T2; soil contaminated with diesel and treated with 15 % (wt) filter cake, T3; soil contaminated with diesel and treated with NPK fertilizer, T4; and soil contaminated with diesel and treated with 15 % (wt) filter cake and NPK fertilizer, T5) and four evaluation periods (1, 60, 120, and 180 days after the beginning of the experiment) were used according to a 4 × 5 factorial design to analyze CO2 release. The variables total organic carbon (TOC) and total petroleum hydrocarbons (TPH) remaining in the soil were analyzed using a 5 × 2 factorial design, with the same treatments described above and two evaluation periods (1 and 180 days after the beginning of the experiment). In T3 and T5, CO2 release was significantly higher, compared with the other treatments. Significant TPH removal was observed on day 180, when percent removal values were 61.9, 70.1, 68.2, and 75.9 in treatments T2, T3, T4, and T5, respectively, compared with the initial value (T1).

Enriching acid rock drainage related microbial communities from surface-deposited oil sands tailings

Little is known about the microbial communities native to surface-deposited pyritic oil sands tailings, an environment where acid rock drainage (ARD) could occur. The goal of this study was to enrich sulfur-oxidizing organisms from these tailings and determine whether different populations exist at pH levels 7, 4.5, and 2.5. Using growth-based methods provides model organisms for use in the future to predict potential activities and limitations of these organisms and to develop possible control methods. Thiosulfate-fed enrichment cultures were monitored for approximately 1 year. The results showed that the enrichments at pH 4.5 and 7 were established quicker than at pH 2.5. Different microbial community structures were found among the 3 pH environments. The sulfur-oxidizing microorganisms identified were most closely related to Halothiobacillus neapolitanus, Achromobacter spp., and Curtobacterium spp. While microorganisms related to Chitinophagaceae and Acidocella spp. were identified as the only possible iron-oxidizing and -reducing microbes. These results contribute to the general knowledge of the relatively understudied microbial communities that exist in pyritic oil sands tailings and indicate these communities may have a potential role in ARD generation, which may have implications for future tailings management.

Ecotoxicity monitoring and bioindicator screening of oil-contaminated soil during bioremediation

A series of toxicity bioassays was conducted to monitor the ecotoxicity of soils in the different phases of bioremediation. Artificially oil-contaminated soil was inoculated with a petroleum hydrocarbon-degrading bacterial consortium containing Burkholderia cepacia GS3C, Sphingomonas GY2B and Pandoraea pnomenusa GP3B strains adapted to crude oil. Soil ecotoxicity in different phases of bioremediation was examined by monitoring total petroleum hydrocarbons, soil enzyme activities, phytotoxicity (inhibition of seed germination and plant growth), malonaldehyde content, superoxide dismutase activity and bacterial luminescence. Although the total petroleum hydrocarbon (TPH) concentration in soil was reduced by 64.4%, forty days after bioremediation, the phytotoxicity and Photobacterium phosphoreum ecotoxicity test results indicated an initial increase in ecotoxicity, suggesting the formation of intermediate metabolites characterized by high toxicity and low bioavailability during bioremediation. The ecotoxicity values are a more valid indicator for evaluating the effectiveness of bioremediation techniques compared with only using the total petroleum hydrocarbon concentrations. Among all of the potential indicators that could be used to evaluate the effectiveness of bioremediation techniques, soil enzyme activities, phytotoxicity (inhibition of plant height, shoot weight and root fresh weight), malonaldehyde content, superoxide dismutase activity and luminescence of P. phosphoreum were the most sensitive.

Inoculation of bacteria for the bioremediation of heavy metals contaminated soil by Agrocybe aegerita

The combination of mushrooms and bacteria was used as a novel technique to remediate soils polluted by heavy metals.

Enhanced Bioremediation of Soil Artificially Contaminated with Petroleum Hydrocarbons after Amendment with Capra aegagrus hircus (Goat) Manure

This study was carried out to evaluate the biostimulant potentials of Capra aegagrus hircus manure for bioremediation of crude oil contaminated soil (COCS) under tropical conditions. 1 kg of COCS sample was amended with 0.02 kg of C. a. hircus manure and monitored at 14-day intervals for total petroleum hydrocarbon (TPH), nutrient content, and changes in microbial counts. At the end of the study period, there was 62.08% decrease in the concentration of TPH in the amended sample compared to 8.15% decrease in the unamended sample, with significant differences (P < 0.05) in TPH concentrations for both samples at different time intervals. Similarly, there was a gradual decrease in the concentrations of total organic carbon, nitrogen, phosphorus, and potassium in both samples. The culturable hydrocarbon-utilizing bacteria (CHUB) increased steadily from 8.5 × 10⁵ cfu/g to 2.70 × 10⁶ cfu/g and from 8.0 × 10⁵ cfu/g to 1.78 × 10⁶ cfu/g for both samples. Acinetobacter, Achromobacter, Bacillus, Flavobacterium, Klebsiella, Micrococcus, Pseudomonas, and Staphylococcus were isolated from amended sample with Pseudomonas being the predominant isolated bacterial genus. This study demonstrated that C. a. hircus manure is a good biostimulant, which enhanced the activities of indigenous hydrocarbonoclastic bacteria resulting in significant decrease in TPH concentration of COCS.

Effect of biodiesel addition on microbial community structure in a simulated fuel storage system

Understanding changes in microbial structure due to biodiesel storage is important both for protecting integrity of storage systems and fuel quality management. In this work a simulated storage system was used to study the effect of biodiesel (0%, 25%, 50%, 75% and 100%) on a microbial population, which was followed by community level physiological profiling (CLPP), 16s rDNA analysis and plating in selective media. Results proved that structure and functionality were affected by biodiesel. CLPP showed at least three populations: one corresponding to diesel, one to biodiesel and one to blends of diesel and biodiesel. Analysis of 16s rDNA revealed that microbial composition was different for populations growing in diesel and biodiesel. Genera identified are known for degradation of hydrocarbons and emulsifier production. Maximum growth was obtained in biodiesel; however, microbial counts in standard media were lower for this samples. Acidification of culture media was observed at high biodiesel concentration.