Enhanced bioremediation of nutrient-amended, petroleum hydrocarbon-contaminated soils over a cold-climate winter: The rate and extent of hydrocarbon biodegradation and microbial response in a pilot-scale biopile subjected to natural seasonal freeze-thaw temperatures

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

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

Bioremediation of PAHs-contaminated site in a full-scale biopiling system with immobilized enzymes: Removal efficiency and microbial communities

Bioremediation of PAHs-contaminated soil by immobilized enzymes is a promising technology. Nevertheless, the practical implementation of highly efficient enzymatic remediation remains confined to laboratory settings, with limited experience in full-scale applications. In this study, the extracellular enzymes from white rot fungi are fully applied to treat sites contaminated with PAHs by combining a new hydrogel microenvironment and a biopiling system. The full-scale project was conducted on silty loam soil contaminated with PAHs. In line with China's guidelines for construction land, 7 out of the 12 PAHs identified are considered to be a threat to the soil quality of construction sites, with benzo[a]pyrene levels reaching 1.50 mg kg-1, surpassing the acceptable limit of 0.55 mg kg-1 for the first type of land. After 7 days of remediation, the benzo[a]pyrene level decreased from 1.50 mg kg-1 to 0.51 mg kg-1, reaching the remediation standard of Class I screening values, with a removal rate of 66%. Microbiomes were utilized to assess the microbial biodiversity and structure analyses for PAHs biodegradation. The remediation enhanced the abundance of dominant bacterium (Marinobacter, Pseudomonas, and Truepera) and fugin (Thielavia, Neocosmospora, and Scedosporium). The research offers further insights into the exploration of soil remediation on the full-scale of the immobilized enzyme and biopiling technology.

Simultaneous bioremediation of diesel-contaminated soil and water ecosystems using mixed culture of Acinetobacter baumannii IITG19 and Providencia vermicola IITG20

Diesel degradation and bacterial growth were investigated in soil, marine water, and freshwater ecosystems using Acinetobacter baumannii IITG19, Providencia vermicola IITG20, and their mixed culture. Both bacteria were found to be effective in all three ecosystems, with the best degradation occurring in freshwater. Acinetobacter baumannii IITG19 showed higher degradation (59%, 62%, and 76%) than Providencia vermicola IITG20 (31%, 57%, and 67%) in soil, marine water, and freshwater, respectively. Alkanes showed higher degradation than naphthenes and aromatics for both strains. The mixed culture showed higher diesel degradation efficiency than individual strains in all ecosystems. The overall degradation was similar in soil and marine water (66%), while freshwater showed the highest degradation of 81%. In the presence of the mixed culture, the degradation of alkanes was more than 90%. Bacterial growth was highest in freshwater and lowest in soil for both bacteria and the mixed culture. Metabolite analysis confirmed alcoholic degradation for alkanes and cyclo-alcoholic degradation for naphthenes. The degradation rate for mixed culture was higher than that of both the individual strains. The mixed culture had highest degradation rate constant in freshwater at 0.11 day-1 followed by that in marine ecosystem at 0.078 day-1. The rate constant was lowest for soil ecosystem at 0.066 day-1. Thus the mixed culture showed effectiveness in all three ecosystems, with its highest effectiveness observed in the freshwater ecosystem.

Application of cold-adapted microbial agents in soil contaminate remediation: biodegradation mechanisms, case studies, and safety assessments

The microbial agent technology has made significant progress in remediating nitro-aromatic compounds (NACs), such as p-nitrophenol, 2,4-dinitrophenol, and 2,4,6-Trinitrotoluene, in farmland soil over the past decade. However, there are still gaps in our understanding of the bioavailability and degradation mechanisms of these compounds in low-temperature environments. In this review, we provide a comprehensive summary of the strategies employed by cold-adapted microorganisms and elucidate the degradation pathways of NACs pollutants. To further analyze their metabolic mechanisms, we propose using mass balance to improve our understanding of biochemical processes and refine the degradation pathways through stoichiometry analysis. Additionally, we suggest employing 13C-metabolic flux analysis to track enzyme activity and intermediate products during bio-degradation processes with the aim of accelerating the remediation of nitro-aromatic compounds, particularly in cold regions. Through a comprehensive analysis of pollutant metabolic activities and a commitment to the 'One Health' approach, with an emphasis on selecting non-pathogenic strains, the environmental management strategies for soil remediation could be positioned to develop and implement safe and effective measure.

Autochthonous psychrophilic hydrocarbonoclastic bacteria and its ecological function in contaminated cold environments

Petroleum hydrocarbon (PH) pollution has mostly been caused by oil exploration, extraction, and transportation activities in colder regions, particularly in the Arctic and Antarctic regions, where it serves as a primary source of energy. Due to the resilience feature of nature, such polluted environments become the realized ecological niches for a wide community of psychrophilic hydrocarbonoclastic bacteria (PHcB). In contrast, to other psychrophilic species, PHcB is extremely cold-adapted and has unique characteristics that allow them to thrive in greater parts of the cold environment burdened with PHs. The stated group of bacteria in its ecological niche aids in the breakdown of litter, turnover of nutrients, cycling of carbon and nutrients, and bioremediation. Although such bacteria are the pioneers of harsh colder environments, their growth and distribution remain under the influence of various biotic and abiotic factors of the environment. The review discusses the prevalence of PHcB community in colder habitats, the metabolic processes involved in the biodegradation of PH, and the influence of biotic and abiotic stress factors. The existing understanding of the PH metabolism by PHcB offers confirmation of excellent enzymatic proficiency with high cold stability. The discovery of more flexible PH degrading strategies used by PHcB in colder environments could have a significant beneficial outcome on existing bioremediation technologies. Still, PHcB is least explored for other industrial and biotechnological applications as compared to non-PHcB psychrophiles. The present review highlights the pros and cons of the existing bioremediation technologies as well as the potential of different bioaugmentation processes for the effective removal of PH from the contaminated cold environment. Such research will not only serve to investigate the effects of pollution on the basic functional relationships that form the cold ecosystem but also to assess the efficacy of various remediation solutions for diverse settings and climatic conditions.

Long-term biodegradation of crude oil in high-arctic backshore sediments: The Baffin Island Oil Spill (BIOS) after nearly four decades

With an on-going disproportional warming of the Arctic Ocean and the reduction of the sea ice cover, the risk of an accidental oil spill from ships or future oil exploration is increasing. It is hence important to know how crude oil weathers in this environment and what factors affect oil biodegradation in the Arctic. However, this topic is currently poorly studied. In the 1980s, the Baffin Island Oil Spill (BIOS) project carried out a series of simulated oil spills in the backshore zone of beaches located on Baffin Island in the Canadian High Arctic. In this study two BIOS sites were re-visited, offering the unique opportunity to study the long-term weathering of crude oil under Arctic conditions. Here we show that residual oil remains present at these sites even after almost four decades since the original oiling. Oil at both BIOS sites appears to have attenuated very slowly with estimated loss rates of 1.8-2.7% per year. The presence of residual oil continues to significantly affect sediment microbial communities at the sites as manifested by a significantly decreased diversity, differences in the abundance of microorganisms and an enrichment of putative oil-degrading bacteria in oiled sediments. Reconstructed genomes of putative oil degraders suggest that only a subset is specifically adapted for growth under psychrothermic conditions, further reducing the time for biodegradation during the already short Arctic summers. Altogether, this study shows that crude oil spilled in the Arctic can persist and significantly affect the Arctic ecosystem for a long time, in the order of several decades.

A comprehensive study on diesel oil bioremediation under microcosm conditions using a combined microbiological, enzymatic, mass spectrometry, and metabarcoding approach

This study aims at the application of a marine fungal consortium (Aspergillus sclerotiorum CRM 348 and Cryptococcus laurentii CRM 707) for the bioremediation of diesel oil-contaminated soil under microcosm conditions. The impact of biostimulation (BS) and/or bioaugmentation (BA) treatments on diesel-oil biodegradation, soil quality, and the structure of the microbial community were studied. The use of the fungal consortium together with nutrients (BA/BS) resulted in a TPH (Total Petroleum Hydrocarbon) degradation 42% higher than that obtained by natural attenuation (NA) within 120 days. For the same period, a 72 to 92% removal of short-chain alkanes (C12 to C19) was obtained by BA/BS, while only 3 to 65% removal was achieved by NA. BA/BS also showed high degradation efficiency of long-chain alkanes (C20 to C24) at 120 days, reaching 90 and 92% of degradation of icosane and heneicosane, respectively. In contrast, an increase in the levels of cyclosiloxanes (characterized as bacterial bioemulsifiers and biosurfactants) was observed in the soil treated by the consortium. Conversely, the NA presented a maximum of 37% of degradation of these alkane fractions. The 5-ringed PAH benzo(a)pyrene, was removed significantly better with the BA/BS treatment than with the NA (48 vs. 38 % of biodegradation, respectively). Metabarcoding analysis revealed that BA/BS caused a decrease in the soil microbial diversity with a concomitant increase in the abundance of specific microbial groups, including hydrocarbon-degrading (bacteria and fungi) and also an enhancement in soil microbial activity. Our results highlight the great potential of this consortium for soil treatment after diesel spills, as well as the relevance of the massive sequencing, enzymatic, microbiological and GC-HRMS analyses for a better understanding of diesel bioremediation.

Impacts of Arctic diesel contamination on microbial community composition and degradative gene abundance during hydrocarbon biodegradation with and without nutrients: A case study of seven sub-Arctic soils

Although a number of studies have assessed hydrocarbon degradation or microbial responses in petroleum contaminated soils, few have examined both and/or assessed impacts in multiple soils simultaneously. In this study petroleum hydrocarbon biodegradation and microbial activity was monitored in seven sub-Arctic soils at similar levels (∼3500-4000 mg/kg) of Arctic diesel (DSL), amended with moisture and nutrients (70 mg-N/kg, 78 mg-P/kg), and incubated at site-representative summer temperatures (∼7 °C) under water unsaturated conditions. Total petroleum hydrocarbon (TPH) biodegradation extents (42.7-85.4 %) at 50 days were slightly higher in nutrient amended (DSL + N,P) than unamended (DSL) systems in all but one soil. Semi-volatile (C₁₀-C₁₆) hydrocarbons were degraded to a greater extent (40-80 %) than non-volatile (C₁₆-C₂₄) hydrocarbons (20-40 %). However, more significant shifts in microbial diversity and relative abundance of genera belonging to Actinobacteria and Proteobacteria phyla were observed in DSL + N,P than in DSL systems in all soils. Moreover, higher abundance of the alkane degrading gene alkB were observed in DSL + N,P systems than in DSL systems for all soils. The more significant microbial community response in the DSL + N,P systems indicate that addition of nutrients may have influenced the microbial community involved in degradation of carbon sources other than the diesel compounds, such as the soil organic matter or degradation intermediates of diesel compounds. Nocardioides, Arthrobacter, Marmoricola, Pseudomonas, Polaromonas, and Massilia genera were present in high relative abundance in the DSL systems suggesting those genera contained hydrocarbon degraders. Overall, the results suggest that the extents of microbial community shifts or alkB copy number increases may not be closely correlated to the increase in hydrocarbon biodegradation and thus bioremediation performance between various treatments or across different soils.

Current and emerging trends in bioaugmentation of organic contaminated soils: A review

Organic contaminated soils constitute an important environmental problem, whereas field applicability of existing physical-chemical methods has encountered numerous obstacles, such as high chemical cost, large energy consumption, secondary pollution, and soil degradation. Bioaugmentation is an environmentally friendly and potentially economic technology that efficiently removes toxic pollutants from organic contaminated soils by microorganisms or their enzymes and bioremediation additives. This review attempted to explore the recent advances in bioaugmentation of organic contaminated soils and provided a comprehensive summary of various bioaugmentation methods, including bacterial, fungus, enzymes and bioremediation additives. The practical application of bioaugmentation is frequently limited by soil environmental conditions, microbial relationships, enzyme durability and remediation cycles. To tackle these problems, the future of bioaugmentation can be processed from sustainability of broad-spectrum bioremediation carriers, microbial/enzyme agents targeting combined contaminants, desorption of environmentally friendly additives and small molecular biological stimulants. Findings of this research are expected to provide new references for bioaugmentation methods that are practically feasible and economically potential.

Genomic insights revealed the environmental adaptability of Planococcus halotolerans Y50 isolated from petroleum-contaminated soil on the Qinghai-Tibet Plateau

The Tibetan Plateau niche provides unprecedented opportunities to find microbes that are functional and commercial significance. The present study investigated the physiological and genomic characteristics of Planococcus halotolerans Y50 that was isolated from a petroleum-contaminated soil sample from the Qinghai-Tibet Plateau, and it displayed psychrotolerant, antiradiation, and oil-degraded characteristics. Whole genome sequencing indicated that strain Y50 has a 3.52 Mb genome and 44.7% G + C content, and it possesses 3377 CDSs. The presence of a wide range of UV damage repair genes uvrX and uvsE, DNA repair genes radA and recN, superoxide dismutase, peroxiredoxin and dioxygenase genes provided the genomic basis for the adaptation of the plateau environment polluted by petroleum. Related experiments also verified that the Y50 strain could degrade n-alkanes from C₁₁-C₂₃, and approximately 30% of the total petroleum at 25 °C within 7 days. Meanwhile, strain Y50 could withstand 5 × 10³ J/m² UVC and 10 KGy gamma ray radiation, and it had strong antioxidant and high radical scavengers for superoxide anion, hydroxyl radical and DPPH. In addition, pan-genome analysis and horizontal gene transfers revealed that strains with different niches have obtained various genes through horizontal gene transfer in the process of evolution, and the more similar their geographical locations, the more similar their members are genetically and ecologically. In conclusion, P. halotolerans Y50 possesses high potential of applications in the bioremediation of alpine hydrocarbons contaminated environment.

Soil Buffering Capacity Can Be Used To Optimize Biostimulation of Psychrotrophic Hydrocarbon Remediation

Effective bioremediation of hydrocarbons requires innovative approaches to minimize phosphate precipitation in soils of different buffering capacities. Understanding the mechanisms underlying sustained stimulation of bacterial activity remains a key challenge for optimizing bioremediation-particularly in northern regions. Positron emission tomography (PET) can trace microbial activity within the naturally occurring soil structure of intact soils. Here, we use PET to test two hypotheses: (1) optimizing phosphate bioavailability in soil will outperform a generic biostimulatory solution in promoting hydrocarbon remediation and (2) oligotrophic biostimulation will be more effective than eutrophic approaches. In so doing, we highlight the key bacterial taxa that underlie aerobic and anaerobic hydrocarbon degradation in subarctic soils. In particular, we showed that (i) optimized phosphate bioavailability outperformed generic biostimulatory solutions in promoting hydrocarbon degradation, (ii) oligotrophic biostimulation is more effective than eutrophic approaches, and (iii) optimized biostimulatory solutions stimulated specific soil regions and bacterial consortia. The knowledge gleaned from this study will be crucial in developing field-scale biodegradation treatments for sustained stimulation of bacterial activity in northern regions.

Manipulation of Unfrozen Water Retention for Enhancing Petroleum Hydrocarbon Biodegradation in Seasonally Freezing and Frozen Soil

Manipulating the retention of unfrozen water in freezing contaminated soil to achieve prolonged bioremediation in cold climates remains unformulated. This freezing-induced biodegradation experiment shows how nutrient and zeolite amendments affect unfrozen water retention and hydrocarbon biodegradation in field-aged, petroleum-contaminated soils undergoing seasonal freezing. During soil freezing at a site-specific rate (4 to -10 °C and -0.2 °C/d), the effect of nutrients was predominant during early freezing (4 to -5 °C), alleviating the abrupt soil-freezing stress near the freezing-point depressions, elevating alkB1 gene-harboring populations, and enhancing hydrocarbon biodegradation. Subsequently, the effect of increased unfrozen water retention associated with added zeolite surface areas was critical in extending hydrocarbon biodegradation to the frozen phase (-5 to -10 °C). A series of soil-freezing characteristic curves with empirical α-values (soil-freezing index) were constructed for the tested soils and shown alongside representative curves for clays to sands, indicating correlations between α-values and nutrient concentrations (soil electrical conductivity), zeolite addition (surface area), and hydrocarbon biodegradation. Heavier hydrocarbons (F3: C16-C34) notably biodegraded in all treated soils (22-37% removal), as confirmed by biomarker-based analyses (17α(H),21β(H)-hopane), whereas lighter hydrocarbons were not biodegraded. Below 0 °C, finer-grained soils (high α-values) can be biostimulated more readily than coarser-grained soils (low α-values).

Petroleum hydrocarbon rhizoremediation and soil microbial activity improvement via cluster root formation by wild proteaceae plant species

Rhizoremediation potential of different wild plant species for total (aliphatic) petroleum hydrocarbon (TPH)-contaminated soils was investigated. Three-week-old seedlings of Acacia inaequilatera, Acacia pyrifolia, Acacia stellaticeps, Banksia seminuda, Chloris truncata, Hakea prostrata, Hardenbergia violacea, and Triodia wiseana were transplanted in a soil contaminated with diesel and engine oil as TPH at pollution levels of 4,370 (TPH1) and 7,500 (TPH2) mg kg^-1, and an uncontaminated control (TPH0). After 150 days, the presence of TPH negatively affected the plant growth, but the growth inhibition effect varied between the plant species. Plant growth and associated root biomass influenced the activity of rhizo-microbiome. The presence of B. seminuda, C. truncata, and H. prostrata significantly increased the TPH removal rate (up to 30% compared to the unplanted treatment) due to the stimulation of rhizosphere microorganisms. No significant difference was observed between TPH1 and TPH2 regarding the plant tolerance and rhizoremediation potentials of the three plant species. The presence of TPH stimulated cluster root formation in B. seminuda and H. prostrata which was associated with enhanced TPH remediation of these two members of Proteaceae family. These results indicated that B. seminuda, C. truncata, and H. prostrata wild plant species could be suitable candidates for the rhizoremediation of TPH-contaminated soil.

Aplication of Soil Productivity Index after Eight Years of Soil Reclamation with Sewage Sludge Amendments

Remediation methods are gaining acceptance as effective and inexpensive techniques used in the reclamation of degraded areas. The reclamation of post-mining sites has become important for the conservation of soil and vegetation. An assessment of potential productivity of plants based on the depth of their root zone is crucial for the validation of properties of post-mining soils. Our aim was to present soil productivity parameters that would facilitate assessment of various post-mining objects. Soil productivity index (SPI) was calculated to assess soil quality, mainly in areas degraded by hard coal mining. It is based on an equation determining the relationship between the productivity index and the physical, chemical, and hydrological properties of soil. Our study demonstrated the positive effects of enriched sewage sludge with amendments on newly formed soil and plants. The soil productivity index was 0.81, demonstrating the suitable condition of the initial soil resulting from reclamation. This parameter might be important for post-industrial reclamation, such as wasteland intended to be transformed into woodland. Considering the composition of sewage sludge amendments, it can be successfully used as an effective method of restoring and improving both the physical and chemical properties of soils, thus effectively replacing mineral fertilisers. The use of sewage sludge in soil reclamation will be an important method of managing this waste material in post-mining areas.

Bibliometric Analysis of Hydrocarbon Bioremediation in Cold Regions and a Review on Enhanced Soil Bioremediation

Simple Summary

Anthropogenic activities in cold regions require petroleum oils to support various purposes. With the increased demand of petroleum, accidental oil spills are generated during transportation or refuelling processes. Soil is one of the major victims in petroleum pollution, hence studies have been devoted to find solutions to remove these petroleum hydrocarbons. However, the remote and low-temperature conditions in cold regions hindered the implementation of physical and chemical removal treatments. On the other hand, biological treatments in general have been proposed as an innovative approach to attenuate these hydrocarbon pollutants in soils. To understand the relevancy of biological treatments for cold regions specifically, bibliometric analysis has been applied to systematically analyse studies focused on hydrocarbon removal treatment in a biological way. To expedite the understanding of this analysis, we have summarised these biological treatments and suggested other biological applications in the context of cold conditions.

Abstract

The increased usage of petroleum oils in cold regions has led to widespread oil pollutants in soils. The harsh environmental conditions in cold environments allow the persistence of these oil pollutants in soils for more than 20 years, raising adverse threats to the ecosystem. Microbial bioremediation was proposed and employed as a cost-effective tool to remediate petroleum hydrocarbons present in soils without significantly posing harmful side effects. However, the conventional hydrocarbon bioremediation requires a longer time to achieve the clean-up standard due to various environmental factors in cold regions. Recent biotechnological improvements using biostimulation and/or bioaugmentation strategies are reported and implemented to enhance the hydrocarbon removal efficiency under cold conditions. Thus, this review focuses on the enhanced bioremediation for hydrocarbon-polluted soils in cold regions, highlighting in situ and ex situ approaches and few potential enhancements via the exploitation of molecular and microbial technology in response to the cold condition. The bibliometric analysis of the hydrocarbon bioremediation research in cold regions is also presented.

Petroleum sludge polluted soil remediation: Integrated approach involving novel bacterial consortium and nutrient application

Petroleum sludge has been reported as noteworthy hazardous solid waste generated from industrial activities of petroleum sector. Environment friendly and economically sound treatment of petroleum sludge has attracted global attention worldwide and has become a thrust area of research. Petroleum sludge bioremediation is gaining interest of researchers globally to clean pollutants from soil ecosystems. To date of submission of the work there is no literature available reporting comparing five approaches for remediation of agricultural soil polluted with petroleum sludge employing hydrocarbon utilizing bacterial consortium (HUBC). Further studies on toxicity were performed through pot experiments using Vigna radiata. The aim of this research work was to compare capability of five approaches for remediating petroleum sludge polluted agricultural soil by employing soil microcosms. Best results were obtained when simultaneous application of HUBC and nutrients was performed in microcosm. Highest decrease (93.14 ± 1.75%) of petroleum sludge with sufficient count of hydrocarbon utilizers and decreased nutrients in 42 days was reported. Quality improvement of petroleum sludge contaminated agricultural soil after its bioremediation was performed by pot experiments by checking germination of V. radiata seeds. 85.71% germination of seeds in 5 days was noted for treated soil. Thus, HUBC can be applied as a bioremediating consortium to reclaim petroleum sludge polluted soil.

Microbial Succession under Freeze-Thaw Events and Its Potential for Hydrocarbon Degradation in Nutrient-Amended Antarctic Soil

The polar regions have relatively low richness and diversity of plants and animals, and the basis of the entire ecological chain is supported by microbial diversity. In these regions, understanding the microbial response against environmental factors and anthropogenic disturbances is essential to understand patterns better, prevent isolated events, and apply biotechnology strategies. The Antarctic continent has been increasingly affected by anthropogenic contamination, and its constant temperature fluctuations limit the application of clean recovery strategies, such as bioremediation. We evaluated the bacterial response in oil-contaminated soil through a nutrient-amended microcosm experiment using two temperature regimes: (i) 4 °C and (ii) a freeze–thaw cycle (FTC) alternating between −20 and 4 °C. Bacterial taxa, such as Myxococcales, Chitinophagaceae, and Acidimicrobiales, were strongly related to the FTC. Rhodococcus was positively related to contaminated soils and further stimulated under FTC conditions. Additionally, the nutrient-amended treatment under the FTC regime enhanced bacterial groups with known biodegradation potential and was efficient in removing hydrocarbons of diesel oil. The experimental design, rates of bacterial succession, and level of hydrocarbon transformation can be considered as a baseline for further studies aimed at improving bioremediation strategies in environments affected by FTC regimes.

Bioremediation of oily sludge polluted soil employing a novel strain of Pseudomonas aeruginosa and phytotoxicity of petroleum hydrocarbons for seed germination

Agricultural land pollution is key a problem globally, which is linked with growth of industries. Petroleum industrial sector is one of the major industrial sectors and the activities of petroleum industry lead to the agricultural land pollution. Oily sludge is a type of solid and hazardous waste generated from petroleum industrial activities. Hence, there is an urgent need to find remediation methods of the oily sludge contaminated agricultural land. Thus, the aim of this work was to study bioremediation of oily sludge polluted soil employing a novel strain of Pseudomonas aeruginosa and evaluation of phytotoxicity on germination of Vigna radiata seed in pots. Five different approaches were adopted for the bioremediation studies, which included Bioaugmentation + Biostimulation, bioaugmentation, biostimulation, natural attenuation and abiotic factors. Simultaneous application of P. aeruginosa NCIM 5514 and nutrients in microcosm showed 92.97 ± 0.92% decrease in oily sludge with good hydrocarbon utilizing bacterial count and decreased nutrient level in 56 days. Pot experiments on seed germination of mung beans (Vigna radiata) seeds was performed by pot experiments. 80.95% germination in five days in treated soil. From the results it was concluded that simultaneous use of oily sludge degraders and nutrient supplement could revive seed germination ability of oily sludge polluted soil effectively. This is first report of comparing five techniques to bioremediate oily sludge polluted soil using Pseudomonas aeruginosa, followed by pot study using V. radiata seeds, showing that P. aeruginosa can be an efficient bioremediation agent and can be effectively used for remediation of oily sludge contaminated soil.

Microbial community evolution during the aerobic biodegradation of petroleum hydrocarbons in marine sediment microcosms: Effect of biostimulation and seasonal variations

Evolution of the microbial community structure in crude oil contaminated marine sediments was assessed under aerobic biodegradation during wet (18 °C) and dry (28 °C) seasons experiments, to account for seasonal variations in nutrients and temperature, under biostimulation and natural attenuation conditions. NMDS showed significant variation in the microbial communities between the wet and the dry season experiments, and between the biostimulation and the natural attenuation treatments in the dry season microcosms. No significant variation in the microbial community and oil biodegradation was observed during the wet season experiments due to high background nitrogen levels eliminating the effect of biostimulation. Larger variations were observed in the dry season experiments and were correlated to enhanced alkanes removal in the biostimulated microcosms, where Alphaproteobacteria dominated the total microbial community by the end of biodegradation (54%). Many hydrocarbonoclastic bacterial genera showed successive dominance during the operation affecting the ultimate performance of the microcosms.

Material flow analysis and heavy hydrocarbon removal in a full-scale biopile and soil washing plant in northern Italy

This study aimed to assess the mass fluxes and removal efficiencies of heavy hydrocarbons in a full-scale plant located in northern Italy. This plant receives and treats contaminated soil, soils and rocks from construction and demolition activities, incineration slags and street cleaning residues. The plant has three sections, consisting of bioremediation using biopile, a soil washing stage and a stabilization/solidification unit, which can perform independently or together with the others. The material flow analysis showed how the crisis in the construction industry changed the final destination of waste after the treatment: as the market demand for coarse material decreased, waste was sent directly to landfills for inert waste, instead of being recovered. Hydrocarbon mass fluxes showed that a considerable amount of pollutants was removed. In the period 2009-2014, the removal efficiencies of the bioremediation, the soil washing section and the entire plant were respectively 73%, 58% and 62%. The percentages of removal attained at the facility in study were sufficient to ensure the possibility of recovering the waste or disposing of it in different landfill categories, according to the national regulations.

Natural attenuation of spilled crude oil by cold-adapted soil bacterial communities at a decommissioned High Arctic oil well site

Romulus C-42 is a decommissioned oil well on Ellesmere Island in the Canadian High Arctic, and is the northernmost well to have produced oil and gas anywhere in the world. The remote site has been untouched since a crude oil spill in 1972, offering a rare opportunity to examine natural attenuation in Arctic soils >40 years after a pollution event. Bacterial community composition in crude oil contaminated soils was significantly different from adjacent background soils. Two members of the genus Rhodanobacter (Alphaproteobacteria) were found consistently in contaminated soils, whereas two members of the genus Sphingomonas (Gammaproteobacteria) appeared opposite to each other, one consistently within the oil contaminated soil and the other consistently in non-oil contaminated soils. GC of soil hydrocarbon extracts revealed moderate levels of biodegradation relative to the original oil produced in 1972. Despite conditions permissive for bacterial activity (>0 °C) being limited to only a few months each year, natural attenuation by cold adapted soil microbial communities has taken place since the oil spill over 40 years ago. Rhodanobacter and Sphingomonas lineages are associated with contaminated and baseline conditions in this extreme environment, revealing the utility of bacterial diversity measurements for assessing long-term responses of Arctic soils to pollution. ORIGINALITY-SIGNIFICANCE STATEMENT: Romulus C-42, the northernmost onshore drilling well in the world, was decommissioned following a small crude oil spill in 1972. Soil bacterial diversity profiles obtained >40 years later revealed significant differences in oil contaminated soils relative to adjacent non-oil contaminated background soils, consistent with evidence for moderate biodegradation of spilled crude oil having taken place since 1972. The results indicate that microbial diversity profiling is an effective tool for assessing natural attenuation in remote High Arctic soils with a history of oil pollution.

Soil Microbial Community Response Differently to the Frequency and Strength of Freeze-Thaw Events in a Larix gmelinii Forest in the Daxing'an Mountains, China

Sustained climate warming increases the frequency and strength of soil freeze-thaw (FT) events, which strongly affect the properties of soil microbial communities. To explore the responses and mechanisms of the frequency and strength of freeze-thaw events on soil microbial communities, a lab-scale FT test was conducted on forest soil in permafrost region from the Daxing'an Mountains, China. The number of FT cycles (FTN) had a greater effect on microbial communities than FT temperature fluctuation (FTF). The FTN and FTF explained 20.9 and 10.8% of the variation in microbial community structure, respectively, and 22.9 and 11.6% of the variation in enzyme activities, respectively. The total and subgroup microbial biomass, the ratio of fungi to bacteria (F/B), and C- and N-hydrolyzing enzyme activities all decreased with an increase in FTN. Among microbial groups, arbuscular mycorrhizal fungi (AMF) were the most sensitive to FT events. Based on the changes of F/B and AMF, the reduction in soil carbon sequestration caused by frequent FT events can be explained from a perspective of microorganisms. Based on redundancy analysis and Mental Test, soil moisture, total organic carbon, and total nitrogen were the major factors affecting microorganisms in FT events. In the forest ecosystem, soil water and fertilizer were important factors to resist the damage of FT to microorganism, and sufficient water and fertilizer can lighten the damage of FT events to microorganisms. As a result of this study, the understanding of the responses of soil microorganisms to the variation in FT patterns caused by climate changes has increased, which will lead to better predictions of the effects of likely climate change on soil microorganisms.

Digital PCR as an Emerging Tool for Monitoring of Microbial Biodegradation

Biodegradation of contaminants is extremely complicated due to unpredictable microbial behaviors. Monitoring of microbial biodegradation drives us to determine (1) the amounts of specific degrading microbes, (2) the abundance, and (3) expression level of relevant functional genes. To this endeavor, the cultivation independent polymerase chain reaction (PCR)-based monitoring technique develops from endpoint PCR, real-time quantitative PCR, and then into novel digital PCR. In this review, we introduce these three categories of PCR techniques and summarize the timely applications of digital PCR and its superiorities than qPCR for biodegradation monitoring. Digital PCR technique, emerging as the most accurately absolute quantification method, can serve as the most promising and robust tool for monitoring of microbial biodegradation.

Advancing soil ecological risk assessments for petroleum hydrocarbon contaminated soils in Canada: Persistence, organic carbon normalization and relevance of species assemblages

Sediment toxicity studies and ecological risk assessments on organic contaminants routinely apply organic carbon normalization to toxicity data; however, no studies examine its potential for use in soils with petroleum hydrocarbon (PHC) contamination. Limited studies in soil ecotoxicology assess the influence of species assemblages used in species sensitivity distribution construction on the resulting guideline designated to of soil dwelling organisms. Canadian regulations utilize more conservative approaches to deriving guidelines with soil ecotoxicology data compared to the rest of the world, so we investigated the impact of these on soil invertebrates in a variety of field soils. In addition to toxicity, the persistence of a medium PHC mixture was also assessed in the field soils to determine the duration of toxic effects. We found organic matter influenced PHC toxicity to soil invertebrates, but persistence was influenced more by soil cation exchange capacity. Incorporating organic carbon normalization into species sensitivity distribution curves provided a higher level of protection to soil dwelling receptors in low organic matter soils as well as reduce the variability of PHC soil toxicity data. Soil remediation guidelines derived for protection of soil dwelling organisms using a diverse species assemblage provided similar levels of protection as guidelines developed with test species specific for remote, forested land uses in Canada. We conclude that: (i) Canadian hazard concentration values for PHC contamination of soils should be revisited as they may not be protective and (ii) that soil PHC guidelines for protection of soil dwelling organisms should be expressed as carbon normalized values.

Modified soil respiration model (URESP) extended to sub-zero temperatures for biostimulated petroleum hydrocarbon-contaminated sub-Arctic soils

It has been increasingly reported that aerobic soil respiration activity (CO₂ production and O₂ consumption) is measurable in frozen cold-climate soils. This study modifies the Generalized Respiration (GRESP) model, a function of soil temperature (T) and unfrozen water content (M), to cover the frozen, partially frozen and unfrozen phases of successfully bioremediated, petroleum hydrocarbon-contaminated, sandy sub-Arctic soils. The Michaelis-Menten equation was modified to express the observable change in unfrozen water content near 0 °C, which is related to soil respiration activity during soil phase changes and at temperatures below the effective endpoint of detectable unfrozen water at -2 °C. The modified Michaelis-Menten equation was further combined with a Q₁₀ temperature term, and was then incorporated into the GRESP equation to produce a new URESP model for the engineered soil bioremediation system at sub-zero temperatures. The URESP model was applied to published input data measured from the biostimulated site soils of a pilot-scale soil tank experiment conducted between -5 and 15 °C. The model fit well with the experimental data for CO₂ production (R² = 0.96) and O₂ consumption (R² = 0.92). A numerical soil thermal model (TEMP/W model) of the thawing biotreated soils in the tank was also used in this study to produce valid alternative (predictive) input T and M data for the URESP model. The URESP-derived respiration quotients (RQ; 0.695 to 0.698), or the ratios of CO₂ production to O₂ consumption, aligned with the experimental RQ values from the soil tank experiment (0.69) and fell within the theoretical RQ range for aerobic hydrocarbon degradation (0.63-0.80). The URESP model combined with the TEMP/W simulation approximated changes in soil respiration during thawing and characterized the computed soil respiration outputs as related to hydrocarbon utilization, based on their RQ values.

Enrichment of the soil microbial community in the bioremediation of a petroleum-contaminated soil amended with rice straw or sawdust

Two common organic wastes from agriculture (rice straw) and forestry (sawdust) were applied to a petroleum-contaminated soil to estimate their effectiveness in the removal of total petroleum hydrocarbons (TPHs) and polycyclic aromatic hydrocarbons (PAHs). Rice straw was the more effective amendment than the other treatments in reducing TPH contents and addition of sawdust resulted in a significant decrease in PAH removal, particularly high-molecular-weight (5-6 ring) PAHs. Principal coordinates analysis (PCoA) indicates that rice straw treatment separated only the bacterial community but sawdust greatly affected both the soil bacterial and fungal communities. Moreover, the abundance of some petroleum degraders such as the bacteria Sphingomonas, Idiomarina and Phenylobacterium and the fungi Humicola, Wallemia and Graphium was promoted by inputs of the two agricultural and forestry wastes. These results highlight the potential of waste applications in accelerating hydrocarbon biodegradation which may be attributed to the enrichment of keystone taxa that show strong positive associations with hydrocarbon degradation.

Application of an emulsified polycolloid substrate biobarrier to remediate petroleum-hydrocarbon contaminated groundwater

Emulsified polycolloid substrate (EPS) was developed and applied in situ to form a biobarrier for the containment and enhanced bioremediation of a petroleum-hydrocarbon plume. EPS had a negative zeta potential (-35.7 mv), which promoted its even distribution after injection. Batch and column experiments were performed to evaluate the effectiveness of EPS on toluene containment and biodegradation. The EPS-to-water partition coefficient for toluene (target compound) was 943. Thus, toluene had a significant sorption affinity to EPS, which caused reduced toluene concentration in water phase in the EPS/water system. Groundwater containing toluene (18 mg/L) was pumped into the three-column system at a flow rate of 0.28 mL/min, while EPS was injected into the second column to form a biobarrier. A significant reduction of toluene concentration to 0.1 mg/L was observed immediately after EPS injection. This indicates that EPS could effectively contain toluene plume and prevent its further migration to farther downgradient zone. Approximately 99% of toluene was removed after 296 PVs of operation via sorption, natural attenuation, and EPS-enhanced biodegradation. Increase in total organic carbon and bacteria were also observed after EPS supplement. Supplement of EPS resulted in a growth of petroleum-hydrocarbon degrading bacteria, which enhanced the toluene biodegradation.

Degradation of crude oil by mixed cultures of bacteria isolated from the Qinghai-Tibet plateau and comparative analysis of metabolic mechanisms

This study investigates the biodegradation of crude oil by a mixed culture of bacteria isolated from the Qinghai-Tibet plateau using gas chromatography-mass spectrometer (GC-MS) and the gravimetric method. The results showed that a mixed culture has a stronger ability to degrade hydrocarbon than pure cultures. Once both Nocardia soli Y48 and Rhodococcus erythropolis YF28-1 (8) were present in a culture, the culture demonstrated the highest crude oil removal efficiency of almost 100% after 10 days of incubation at 20 °C. Moreover, further analysis of the degradation mechanisms used by the above strains, which revealed utilization of different n-alkane substrates, indicated the diversity of evolution and variations in different strains, as well as the importance of multiple metabolic mechanisms for alkane degradation. Therefore, it is concluded that a mixed culture of Y48 and YF28-1 (8) strains can provide a more effective method for bioremediation of hydrocarbon-contaminated soil in permafrost regions.

Insights into microbial communities mediating the bioremediation of hydrocarbon-contaminated soil from an Alpine former military site

The study of microbial communities involved in soil bioremediation is important to identify the specific microbial characteristics that determine improved decontamination rates. Here, we characterized bacterial, archaeal, and fungal communities in terms of (i) abundance (using quantitative PCR) and (ii) taxonomic diversity and structure (using Illumina amplicon sequencing) during the bioremediation of long-term hydrocarbon-contaminated soil from an Alpine former military site during 15 weeks comparing biostimulation (inorganic NPK fertilization) vs. natural attenuation and considering the effect of temperature (10 vs. 20 °C). Although a considerable amount of total petroleum hydrocarbon (TPH) loss could be attributed to natural attenuation, significantly higher TPH removal rates were obtained with NPK fertilization and at increased temperature, which were related to the stimulation of the activities of indigenous soil microorganisms. Changing structures of bacterial and fungal communities significantly explained shifts in TPH contents in both natural attenuation and biostimulation treatments at 10 and 20 °C. However, archaeal communities, in general, and changing abundances and diversities in bacterial and fungal communities did not play a decisive role on the effectiveness of soil bioremediation. Gammaproteobacteria and Bacteroidia classes, within bacterial community, and undescribed/novel groups, within fungal community, proved to be actively involved in TPH removal in natural attenuation and biostimulation at both temperatures.