Enhancement of anaerobic degradation of petroleum hydrocarbons by electron intermediate: Performance and mechanism

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.

Metagenomic analysis reveals the microbial response to petroleum contamination in oilfield soils

The response of the microbes to total petroleum hydrocarbons (TPHs) in three types of oilfield soils was researched using metagenomic analysis. The ranges of TPH concentrations in the grassland, abandoned well, working well soils were 1.16 × 102-3.50 × 102 mg/kg, 1.14 × 103-1.62 × 104 mg/kg, and 5.57 × 103-3.33 × 104 mg/kg, respectively. The highest concentration of n-alkanes and 16 PAHs were found in the working well soil of Shengli (SL) oilfield compared with those in Nanyang (NY) and Yanchang (YC) oilfields. The abandoned well soils showed a greater extent of petroleum biodegradation than the grassland and working well soils. Α-diversity indexes based on metagenomic taxonomy showed higher microbial diversity in grassland soils, whereas petroleum-degrading microbes Actinobacteria and Proteobacteria were more abundant in working and abandoned well soils. RDA demonstrated that low moisture content (MOI) in YC oilfield inhibited the accumulation of the petroleum-degrading microbes. Synergistic networks of functional genes and Spearman's correlation analysis showed that heavy petroleum contamination (over 2.10 × 104 mg/kg) negatively correlated with the abundance of the nitrogen fixation genes nifHK, however, in grassland soils, low petroleum content facilitated the accumulation of nitrogen fixation genes. A positive correlation was observed between the abundance of petroleum-degrading genes and denitrification genes (bphAa vs. nirD, todC vs. nirS, and nahB vs. nosZ), whereas a negative correlation was observed between alkB (alkane- degrading genes) and amo (ammonia oxidation), hao (nitrification). The ecotoxicity of petroleum contamination, coupled with petroleum hydrocarbons (PH) degradation competing with nitrifiers for ammonia inhibited ammonia oxidation and nitrification, whereas PH metabolism promoted the denitrification process. Moreover, positive correlations were observed between the abundance of amo gene and MOI, as well as between the abundance of the dissimilatory nitrate reduction gene nirA and clay content. Thus, improving the soil physicochemical properties is a promising approach for decreasing nitrogen loss and alleviating petroleum contamination in oilfield soils.

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

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

Response mechanism of microbial community during anaerobic biotransformation of marine toxin domoic acid

Domoic acid (DA) is a potent neurotoxin produced by toxigenic Pseudo-nitzschia blooms and quickly transfers to the benthic anaerobic environment by marine snow particles. DA anaerobic biotransformation is driven by microbial interactions, in which trace amounts of DA can cause physiological stress in marine microorganisms. However, the underlying response mechanisms of microbial community to DA stress remain unclear. In this study, we utilized an anaerobic marine DA-degrading consortium GLY (using glycine as co-substrate) to systematically investigate the global response mechanisms of microbial community during DA anaerobic biotransformation.16S rRNA gene sequencing and metatranscriptomic analyses were applied to measure microbial community structure, function and metabolic responses. Results showed that DA stress markedly changed the composition of main species, with increased levels of Firmicutes and decreased levels of Proteobacteria, Cyanobacteria, Bacteroidetes and Actinobacteria. Several genera of tolerated bacteria (Bacillus and Solibacillus) were increased, while, Stenotrophomonas, Sphingomonas and Acinetobacter were decreased. Metatranscriptomic analyses indicated that DA stimulated the expression of quorum sensing, extracellular polymeric substance (EPS) production, sporulation, membrane transporters, bacterial chemotaxis, flagellar assembly and ribosome protection in community, promoting bacterial adaptation ability under DA stress. Moreover, amino acid metabolism, carbohydrate metabolism and lipid metabolism were modulated during DA anaerobic biotransformation to reduce metabolic burden, increase metabolic demands for EPS production and DA degradation. This study provides the new insights into response of microbial community to DA stress and its potential impact on benthic microorganisms in marine environments.

Coupled effect of porous network and water content on the natural attenuation of diesel in unsaturated soils

The natural attenuation potential of a vadose zone against diesel is critical for optimizing remedial actions and determining groundwater vulnerability to contamination. Here, diesel attenuation in unsaturated soils was systematically examined to develop a qualitative relationship between physical soil properties and the natural attenuation capacity of a vadose zone against diesel. The uniformity coefficient (C_u) and water saturation (S_w, %) were considered as the proxies reflecting the degree of effects by porous network and water content in different soils, respectively. These, in turn, are related to the primary diesel attenuation mechanisms of volatilization and biodegradation. The volatilization of diesel was inversely proportional to C_u and S_w, which could be attributed to effective pore channels facilitating gas transport. Conversely, biodegradation was highly proportional to C_u under unsaturated conditions (S_w = 35-71%), owing to nutrients typically associated with fine soil particles. The microbial community in unsaturated soils was affected by S_w rather than C_u. The overall diesel attenuation including volatilization and biodegradation was optimized at S_w = 35% for all tested soils.

Soil microbial ecological effect of shale gas oil-based drilling cuttings pyrolysis residue used as soil covering material

The residue derived from oil-based drilling cutting pyrolysis could be used as paving materials. Some petroleum hydrocarbons remain in the residue after pyrolysis and cause severe environmental pollution. In this study, the soil column leaching experiments were carried out under different leaching amounts, and the vertical migration characteristics of petroleum hydrocarbons in soil and the dynamic response mechanism of microorganisms to petroleum hydrocarbons were analyzed. The result showed that the soil pH value and water content with different leaching amounts did not differ significantly, but the vertical migration ability of each petroleum hydrocarbon component was different. In petroleum hydrocarbon contaminated soil, the relative abundance of Proteobacteria maintained a high level (23.6%-60.7%). At the genus level, the relative abundance of Massilia decreased with the leaching amount increased. According to PICRUSt, Monooxygenase [EC: 1.14.13.-] played a significant role in petroleum hydrocarbon degradation. While Long-chain-fatty-acid-CoA ligase [EC: 6.2.1.3] had the highest relative abundance. By studying the influence of shale gas oil-based drilling cuttings pyrolysis residue on soil physical and chemical properties and soil microorganisms, this work provides scientific ecological assessment for the resource application of pyrolysis residue.

Different performance of pyrene biodegradation on metal-modified montmorillonite: Role of surface metal ions from a bioelectrochemical perspective

Microbial extracellular electron transfer (EET) at microbe-mineral interface has been reported to play a significant role in pollutant biotransformation. Different metals often co-exist with organic pollutants and are immobilized on mineral surfaces. However, little is known about the influence of mineral surface metal ions on organic pollutant biodegradation and the involved electron transfer mechanism. To address this knowledge gap, pyrene was used as a model compound to investigate the biodegradation of polycyclic aromatic hydrocarbon on montmorillonite mineral saturated with metal ions (Na(I), Ni(II), Co(II), Cu(II) and Fe(III)) by Mycobacteria strain NJS-1. Further, the possible underlying electron transfer mechanism by electrochemical approaches was investigated. The results show that pyrene biodegradation on montmorillonite was markedly influenced by surface metal ions, with degradation efficiency following the order Fe(III) > Na(I) ≈ Co(II) > Ni(II) ≈ Cu(II). Bioelectrochemical analysis showed that electron transfer activities (i.e., electron donating capacity and electron transport system activity) varied in different metal-modified montmorillonites and were closely related to pyrene biodegradation. Fe(III) modification greatly stimulated degrading enzyme activities (i.e., peroxidase and dioxygenase) and electron transfer activities resulting in enhanced pyrene biodegradation, which highlights its potential as a technique for pollutant bioremediation. The bacterial extracellular protein and humic substances played important roles in EET processes. Membrane-bound cytochrome C protein and extracellular riboflavin were identified as the electron shuttles responsible for transmembrane and cross extracellular matrix electron transfer, respectively. Additions of exogenetic electron mediators of riboflavin, humic acid and potassium ferricyanide accelerated pyrene biodegradation which further verified the critical role of EET in PAH transformation at bacteria-mineral interfaces. These results support the development of clay mineral based advanced bioremediation techniques through regulating the electron transfer processes at the microbe-mineral interfaces by mineral surface modification.

Hydrocarbon transformation pathways and soil organic carbon stability in the biostimulation of oil-contaminated soil: Implications of 13C natural abundance

Mineralization, assimilation, and humification are key processes to detoxify oil-contaminated soil by biostimulation remediation strategies, and these processes are affected by stimulants. In this study, we investigated the effects of either inorganic salts or organic stimulants (organic compost and sawdust) on hydrocarbon transformation. Total petroleum hydrocarbons (TPH) and hydrocarbon components were determined by gravimetry and gas chromatography, and the ¹³C of CO₂, microbial biomass carbon (MBC), and humus were measured by stable isotope mass spectrometry. The results showed that organic compost was the most beneficial for the dissipation of hydrocarbons. After 60 days of remediation, the removal rates of TPH, saturates, aromatics, C7-C30 n-alkanes, and 16 PAHs were 35.7%, 39.6%, 15.9%, 80.5%, and 8.8%, respectively. A total of 84.7%-88.5% of the removed hydrocarbons were mineralized in all the treatments. The hydrocarbon degradation pathway in the control soil (without stimulant addition) was "assimilation → humification → mineralization". The hydrocarbon transformation pathways in the biostimulation treatments were "assimilation → mineralization → humification". The soil organic carbon (SOC) stability decreased during remediation, which was attributed to the enhanced microbial activity and the removal of recalcitrant hydrocarbons.

Anaerobic degradation of xenobiotic organic contaminants (XOCs): The role of electron flow and potential enhancing strategies

In groundwater, deep soil layer, sediment, the widespread of xenobiotic organic contaminants (XOCs) have been leading to the concern of human health and eco-environment safety, which calls for a better understanding on the fate and remediation of XOCs in anoxic matrices. In the absence of oxygen, bacteria utilize various oxidized substances, e.g. nitrate, sulphate, metallic (hydr)oxides, humic substance, as terminal electron acceptors (TEAs) to fuel anaerobic XOCs degradation. Although there have been increasing anaerobic biodegradation studies focusing on species identification, degrading pathways, community dynamics, systematic reviews on the underlying mechanism of anaerobic contaminants removal from the perspective of electron flow are limited. In this review, we provide the insight on anaerobic biodegradation from electrons aspect - electron production, transport, and consumption. The mechanism of the coupling between TEAs reduction and pollutants degradation is deconstructed in the level of community, pure culture, and cellular biochemistry. Hereby, relevant strategies to promote anaerobic biodegradation are proposed for guiding to an efficient XOCs bioremediation.

The investigation of bioremediation potential of Bacillus subtilis and B. thuringiensis isolates under controlled conditions in freshwater

Bioremediation is widely used to remove water pollution as environmentally friendly smart solutions. In this study, Bacillus isolates were investigated in terms of the effectiveness of single and multiple cultures in eliminating aquatic pollution related to aquaculture activities. In the established experimental setups, the environments where Bacillus isolates were inoculated with single and multiple cultures at 1 × 10⁷ CFU/mL were evaluated comparatively with control groups without these isolates, and total aerobic mesophilic bacterial counts were performed in the petri dish by inoculation method. At the end of the 6 days of the experiment, in the environment in which single and multiple cultures of Bacillus isolates were presented with 17-20 ± 0.05 °C temperature and 5.1-8.1 pH 2-4.6 mg/l dissolved oxygen values (O₂), 2% increase in total phosphorus (TP) value was observed. On the other hand, 4% removal of Ammonia-nitrogen (NH₃-N), 80% removal of Nitrite-nitrogen (NO₂-N), and 100% removal of Nitrate-nitrogen (NO₃-N) were observed. In the changes in heavy metal concentrations, the removal of Ni, Cr, Se, Al, Cd, Mn, Fe, and B was observed from highest to lowest as 57%, 50%, 50%, 43%, 40%, 23%, 5%, and 2%, respectively. It also has been seen that B. thuringiensis isolate was observed to be more effective than B. subtilis in metal removal.

The Role of Dactylis Glomerata and Diesel Oil in the Formation of Microbiome and Soil Enzyme Activity

The global demand for petroleum contributes to a significant increase in soil pollution with petroleum-based products that pose a severe risk not only to humans but also to plants and the soil microbiome. The increasing pollution of the natural environment urges the search for effective remediation methods. Considering the above, the objective of this study was to determine the usability of Dactylis glomerata for the degradation of hydrocarbons contained in diesel oil (DO), as well as the effects of both the plant tested and DO on the biochemical functionality and changes in the soil microbiome. The experiment was conducted in a greenhouse with non-polluted soil as well as soil polluted with DO and phytoremediated with Dactylis glomerata. Soil pollution with DO increased the numbers of microorganisms and soil enzymes and decreased the value of the ecophysiological diversity index of microorganisms. Besides, it contributed to changes in the bacterial structure at all taxonomic levels. DO was found to increase the abundance of Proteobacteria and to decrease that of Actinobacteria, Acidobacteria, Chloroflexi, Gemmatimonadetes and Firmicutes. In the non-polluted soil, the core microbiome was represented by Kaistobacter and Rhodoplanes, whereas in the DO-polluted soil, it was represented by Parvibaculum and Rhodococcus. In soil sown with Dactylis glomerata, gasoline fraction (C₆–C₁₂) degradation was higher by 17%; mineral oil (C₁₂–C₃₅), by 9%; benzene, by 31%; anthracene, by 12%; chrysene, by 38%; benzo(a)anthracene, by 19%; benzo(a)pyrene, by 17%; benzo(b)fluoranthene, by 15%; and benzo(k)fluoranthene, by 18% than in non-sowed soil. To conclude, Dactylis glomerata proved useful in degrading DO hydrocarbons and, therefore, may be recommended for the phytoremediation of soils polluted with petroleum-based products. It has been shown that the microbiological, biochemical and chemical tests are fast and sensitive in the diagnosis of soil contamination with petroleum products, and a combination of all these tests gives a reliable assessment of the state of soils.