Bacterial biosurfactant increases ex situ biodiesel bioremediation in clayey soil

The contamination of soils by oily compounds has several environmental impacts, which can be reversed through bioremediation, using biosurfactants as auxiliaries in the biodegradation process. In this study, we aimed to perform ex situ bioremediation of biodiesel-contaminated soil using biosurfactants produced by Bacillus methylotrophicus. A crude biosurfactant was produced in a whey-based culture medium supplemented with nutrients and was later added to biodiesel-contaminated clayey soil. The produced lipopeptide biosurfactant could reduce the surface tension of the fermentation broth to 30.2 mN/m. An increase in the microbial population was observed in the contaminated soil; this finding can be corroborated by the finding of increased CO₂ release over days of bioremediation. Compared with natural attenuation, the addition of a lower concentration of the biosurfactant (0.5% w/w in relation to the mass of diesel oil) to the soil increased biodiesel removal by about 16% after 90 days. The added biosurfactant did not affect the retention of the contaminant in the soil, which is an important factor to be considered when applying in situ bioremediation technologies.

     

On site bioremediation of hydrocarbon-contaminated Arctic tundra soils in inoculated biopiles

There is a need to develop technology to allow the remediation of soil in polar regions that have been contaminated by hydrocarbon fuel spills. Bioremediation is potentially useful for this purpose, but has not been well demonstrated in polar regions. We investigated biopiles for on-site bioremediation of soil contaminated with Arctic diesel fuel in two independent small-scale field experiments at different sites on the Arctic tundra. The results were highly consistent with one another. In biopiles at both sites, extensive hydrocarbon removal occurred after one summer. After 1 year in treatments with optimal conditions, total petroleum hydrocarbons were reduced from 196 to below 10 mg per kg of soil at one site, and from 2,109 to 195 mg per kg of soil at the other site. Addition of ammonium chloride and sodium phosphate greatly stimulated hydrocarbon removal and indicates that biodegradation was the primary mechanism by which this was achieved. Inoculation with cold-adapted, mixed microbial cultures further stimulated hydrocarbon removal during the summer immediately following inoculation. At one site, soil temperature was monitored during the summer season, and a clear plastic cover increased biopile soil temperature, measured as degree-day accumulation, by 30-49%. Our results show that on-site bioremediation of fuel-contaminated soil at Arctic tundra sites is feasible.     

Biodegradation of aged diesel in diverse soil matrixes: impact of environmental conditions and bioavailability on microbial remediation capacity

While bioremediation of total petroleum hydrocarbons (TPH) is in general a robust technique, heterogeneity in terms of contaminant and environmental characteristics can impact the extent of biodegradation. The current study investigates the implications of different soil matrix types (anthropogenic fill layer, peat, clay, and sand) and bioavailability on bioremediation of an aged diesel contamination from a heterogeneous site. In addition to an uncontaminated sample for each soil type, samples representing two levels of contamination (high and low) were also used; initial TPH concentrations varied between 1.6 and 26.6 g TPH/kg and bioavailability between 36 and 100 %. While significant biodegradation occurred during 100 days of incubation under biostimulating conditions (64.4–100 % remediation efficiency), low bioavailability restricted full biodegradation, yielding a residual TPH concentration. Respiration levels, as well as the abundance of alkB, encoding mono-oxygenases pivotal for hydrocarbon metabolism, were positively correlated with TPH degradation, demonstrating their usefulness as a proxy for hydrocarbon biodegradation. However, absolute respiration and alkB presence were dependent on soil matrix type, indicating the sensitivity of results to initial environmental conditions. Through investigating biodegradation potential across a heterogeneous site, this research illuminates the interplay between soil matrix type, bioavailability, and bioremediation and the implications of these parameters for the effectiveness of an in situ treatment.     

Comparative Mesocosm Study of Biostimulation Efficiency in Two Different Oil-Amended Sub-Antarctic Soils

Biological treatment has become increasingly popular as a remediation method for soils and groundwater contaminated with petroleum hydrocarbon, chlorinated solvents, and pesticides. Bioremediation has been considered for application in cold regions such as Arctic and sub-Arctic climates and Antarctica. Studies to date suggest that indigenous microbes suitable for bioremediation exist in soils in these regions. This paper reports on two case studies at the sub-Antarctic Kerguelen Island in which indigenous bacteria were found that were capable of mineralizing petroleum hydrocarbons in soil contaminated with crude oil and diesel fuel. All results demonstrate a serious influence of the soil properties on the biostimulation efficiency. Both temperature elevation and fertilizer addition have a more significant impact on the microbial assemblages in the mineral soil than in the organic one. Analysis of the hydrocarbons remaining at the end of the experiments confirmed the bacterial observations. Optimum temperature seems to be around 10 degrees C in organic soil, whereas it was higher in mineral soil. The benefit of adding nutrients was much stronger in mineral than in the organic soil. Overall, this study suggests that biostimulation treatments were driven by soil properties and that ex situ bioremediation for treatment of cold contaminated soils will allow greater control over soil temperature, a limiting factor in cold climates.     

Estimating the availability of polycyclic aromatic hydrocarbons for bioremediation of creosote contaminated soils

Bioremediation of soil contaminated by organic compounds can remove the contaminants to a large extent, but residual contamination levels may remain which are not or only slowly biodegraded. Residual levels often exceed existing clean-up guidelines and thereby limit the use of bioremediation in site clean-up. A method for estimating the expected residual levels would be a useful tool in the assessment of the feasability of bioremediation. In this study, three soil types from a creosote-contaminated field site, which had been subjected to 6 months of bioremediation in laboratory column studies, were used to characterize the residual contamination levels and assess their availability for biodegradation. The soils covered a wide range of organic carbon levels and particle size distributions. Results from the biodegradation studies were compared with desorption rate measurements and selective extractability using butanol. Residual levels of polycyclic aromatic hydrocarbons after bioremediation were found to be strongly dependent on soil type. The presence of both soil organic matter and asphaltic compounds in the soil was found to be associated with higher residual levels. Good agreement was found between the biodegradable fraction and the rapidly desorbable fraction in two of the three soils studied. Butanol extraction was found to be a useful method for roughly estimating the biodegradable fraction in the soil samples. The results indicate that both desorption and selective extraction measurements could aid the assessment of the feasability for bioremediation and identifying acceptable end-points. Received: 15 September 1999 / Received revision: 7 February 2000 / Accepted: 13 February 2000     

土壤中高环多环芳烃微生物降解的研究进展

微生物修复是去除土壤中多环芳烃(PAHs)的主要措施。本文以微生物修复PAHs污染土壤的理论基础及其难点为主线,全面综述了土壤中高环PAHs的微生物降解机理。近年来,富集分离得到的以高环PAHs为唯一碳源和能源的优势降解菌逐渐增多,其中,主要是代谢降解四环PAHs的单株降解菌,一些降解菌还能以共代谢方式利用五环PAHs。高环PAHs污染土壤修复的一个难点是其低生物可利用性,微生物通过释放生物表面活性剂、形成生物膜以及分泌胞外多糖提高高环PAHs的生物可利用性,从而加速其降解。真菌和细菌联合作用能增强污染土壤实地修复的效果。因此,通过微生物修复技术来去除土壤中PAHs具有环境友好性、经济适用性以及可持续应用性。     

Fungi as a toolbox for sustainable bioremediation of pesticides in soil and water

Pesticides can help reduce yield losses caused by pests, pathogens, and weeds, but their overuse causes serious environmental pollution. They are persistent in the environment and are biomagnified through the food chain, becoming a serious health hazard for humankind. Bioremediation, where microbes are used to degrade pesticides in situ, is a useful technology. This review summarizes data on the fungi involved in the biodegradation of chemical pesticides and their application in soil and water bioremediation. Indications for future studies in this field are given.     

The Effect of Temperature and Aeration Rate on Bioremediation of Diesel-contaminated Soil in Solid-phase Bench-scale Bioreactors

Bioremediation of hydrocarbon (HC) contaminated soils is most effective in aerobic conditions. Despite the fact that mass transfer of oxygen is an important process parameter, the effect of this parameter on solid-phase bioremediation has received limited attention. In this study, the combined effect of temperature and aeration on the bioremediation of low organic content coarse-grained soils, freshly contaminated with diesel, was investigated in solid-phase bench-scale bioreactors. Total HC and carbon range soil concentrations, volatilization, and microbial activity were monitored throughout the six-month experiments at two temperatures (7 and 22°C) and at two aeration rates (13 and 45 mL·s^?1). Total HC removal reached between 48 and 83%. Generally, removal increased proportionally with temperature and aeration rates, and decreased proportionally with HC compounds molecular weight. Both biodegradation and volatilization played important roles in removal in all treatments. The high aeration rate enhanced microbial activity in soil. Enhancement was believed to be due to increased mass transfer of oxygen from the soil gas to the soil solution, where microbial activity occurs. However, high aeration also enhanced volatilization, especially at 22°C where 51% of HCs were lost to volatilization. High aeration rate enhanced biodegradation of compounds > nC15 without promoting their excessive volatilization.     

Incomplete Hydrocarbon Biodegradation in Contaminated Soils: Limitations in Bioavailability or Inherent Recalcitrance?

Bioremediation has been used to treat soils contaminated with complex mixtures of organic compounds such as total petroleum hydrocarbons (TPH), oil and grease (O&G), or polycyclic aromatic hydrocarbons (PAHs). Despite the common use and cost-effectiveness of bioremediation for treating hydrocarbon-contaminated soils, it has been observed that a residual fraction remains undegraded in the soil even when optimal biodegradation conditions have been provided. This paper provides a brief review of the two major conceptual models that have been used to explain why a residual hydrocarbon fraction remains in the soil after bioremediation treatment. The contaminant sequestration model is based on the assumption that a certain fraction of hydrocarbons is “locked up” in small soil pores within soil particles or aggregates. These sorbed hydrocarbons are believed to be inaccessible to soil microorganisms. Consequently, limitations in bioavailability are thought to be the major reason for incomplete hydrocarbon biodegradation, particularly in aged or weathered soils. Alternatively, according to the inherent recalcitrance model, incomplete TPH biodegradation may be caused by the presence of certain hydrocarbons that are inherently recalcitrant to biodegradation or are only extremely slowly degradable even under optimal conditions. Each conceptual model provides different explanations regarding the potential risks of the residual hydrocarbon fraction. If the residual TPH is truly sequestered within the soil pore space, it is unlikely that these compounds will pose any significant risk to human or environmental receptors. By contrast, these risks may be considerably greater if the residual TPH fraction consists of inherently recalcitrant compounds that reside mostly on the surface of soil particles and therefore are much more available to potential receptors. Both conceptual models and their implications for the potential risk of the residual TPH fraction are discussed.     

Isolation and characterisation of polychlorinated biphenyl (PCB) degrading fungi from a historically contaminated soil

Background  

Polychlorinated biphenyls (PCBs) are widespread toxic pollutants. Bioremediation might be an effective, cost competitive and environment-friendly solution for remediating environmental matrices contaminated by PCBs but it is still unsatisfactory, mostly for the limited biodegradation potential of bacteria involved in the processes. Very little is known about mitosporic fungi potential in PCB bioremediation and their occurrence in actual site historically contaminated soils. In the present study, we characterised the native mycoflora of an aged dump site soil contaminated by about 0.9 g kg^-1 of Aroclor 1260 PCBs and its changing after aerobic biotreatment with a commercial complex source of bacteria and fungi. Fungi isolated from the soil resulting from 120 days of treatment were screened for their ability to adsorb or metabolise 3 target PCBs.     

Genotoxicity Assessment of Wood-Preserving Waste-Contaminated Soil Undergoing Bioremediation

Bioremediation represents one of the most cost-effective technologies for treatment of petroleum hydrocarbons in contaminated surface soils. A major concern for regulatory agencies when evaluating bioremediation is how to determine acceptable levels for residual organics in soil. Although guidelines have been developed for some organics in soil, limited information is available to define acceptable levels of the metabolites of biological degradation. The products of oxidative degradation are likely to be more water soluble and may also be more toxic. The purpose of the current study was to monitor changes in compound concentration and genotoxicity in soils undergoing bioremediation. The site selected for this study was a former wood-preserving site in the northwestern United States. Soil samples were collected over a 4-year period from two 6075-m² land treatment units. Conditions for biodegradation were enhanced by the addition of water and nutrients, as well as by frequent tilling to add oxygen. Due to the location of the facility, the temperature was conducive to a more rapid rate of biodegradation for approximately 6 months per year. Soil samples were collected using a grid system and solvent extracted. Polycyclic aromatic hydrocarbons were quantified in soil extracts using gas chromatography-mass spectrometry (GC/MS), and genotoxicity measured using the Salmonella/microsome assay. After 2 years of treatment, concentrations of total and carcinogenic polycyclic aromatic hydrocarbons (PAHs) were reduced to approximately 10% the concentration in the untreated soil. However, the mean weighted activity of the untreated soil was 293 net revertants per g soil, whereas the extracts of soil collected after 2 years induced a mean weighted activity of 325 net revertants per g soil. Thus, although biodegradation clearly reduced the concentration of total and carcinogenic PAHs in the surface soils, the results from the genotoxicity bioassay indicate that there was a lag in the reduction of mutagenicity in treated soils.     

Enhanced crude oil biodegradation in soil via biostimulation

Research on feasible methods for the enhancement of bioremediation in soil contaminated by crude oil is vital in oil-exporting countries such as Kuwait, where crude oil is a major pollutant and the environment is hostile to biodegradation. This study investigated the possibility of enhancing crude oil bioremediation by supplementing soil with cost-effective organic materials derived from two widespread locally grown trees, Conocarpus and Tamarix. Amendments in soils increased the counts of soil microbiota by up to 98% and enhanced their activity by up to 95.5%. The increase in the biodegradation of crude oil (75%) and high levels of alkB expression substantiated the efficiency of the proposed amendment technology for the bioremediation of hydrocarbon-contaminated sites. The identification of crude-oil-degrading bacteria revealed the dominance of the genus Microbacterium (39.6%), Sphingopyxis soli (19.3%), and Bordetella petrii (19.6%) in unamended, Conocarpus-amended, and Tamarix-amended contaminated soils, respectively. Although soil amendments favored the growth of Gram-negative bacteria and reduced bacterial diversity, the structures of bacterial communities were not significantly altered.     

Optimization of environmental parameters for biodegradation of alpha and beta endosulfan in soil slurry by Pseudomonas aeruginosa

Aim: To determine optimal environmental conditions for achieving biodegradation of α‐ and β‐endosulfan in soil slurries following inoculation with an endosulfan degrading strain of Pseudomonas aeruginosa. Methods and Results: Parameters that were investigated included soil texture, soil slurry: water ratios, initial inoculum size, pH, incubation temperature, aeration, and the use of exogenous sources of organic and amino acids. The results showed that endosulfan degradation was most effectively achieved at an initial inoculum size of 600 μl (OD = 0·86), incubation temperature of 30°C, in aerated slurries at pH 8, in loam soil. Under these conditions, the bacterium removed more than 85% of spiked α‐ and β‐endosulfan (100 mg l^?1) after 16 days. Abiotic degradation in noninoculated control medium within same incubation period was about 16%. Biodegradation of endosulfan varied in different textured soils, being more rapid in course textured soil than in fine textured soil. Increasing the soil contents in the slurry above 15% resulted in less biodegradation of endosulfan. Exogenous application of organic acids (citric acid and acetic acid) and amino acids (l ‐methionine and l ‐cystein) had stimulatory and inhibitory effects, respectively, on biodegradation of endosulfan. Conclusion: The results of this study demonstrated that biodegradation of endosulfan by Ps. aeruginosa in soil sediments enhanced significantly under optimized environmental conditions. Significance and Impact of the Study: Endosulfan is a commonly used pesticide that can contaminate soil, wetlands and groundwater. Our study demonstrates that bioaugmentation of contaminated soils with an endosulfan degrading bacterium under optimized conditions provides an effective bioremediation strategy.     

Diverse viromes in polar regions: A retrospective study of metagenomic data from Antarctic animal feces and Arctic frozen soil in 2012–2014

Antarctica and the Arctic are the coldest places, containing a high diversity of microorganisms, including viruses, which are important components of polar ecosystems. However, owing to the difficulties in obtaining access to animal and environmental samples, the current knowledge of viromes in polar regions is still limited. To better understand polar viromes, this study performed a retrospective analysis using metagenomic sequencing data of animal feces from Antarctica and frozen soil from the Arctic collected during 2012–2014. The results reveal diverse communities of DNA and RNA viruses from at least 23 families from Antarctic animal feces and 16 families from Arctic soils. Although the viral communities from Antarctica and the Arctic show a large diversity, they have genetic similarities with known viruses from different ecosystems and organisms with similar viral proteins. Phylogenetic analysis of Microviridae, Parvoviridae, and Larvidaviridae was further performed, and complete genomic sequences of two novel circular replication-associated protein (rep)-encoding single-stranded (CRESS) DNA viruses closely related to Circoviridae were identified. These results reveal the high diversity, complexity, and novelty of viral communities from polar regions, and suggested the genetic similarity and functional correlations of viromes between the Antarctica and Arctic. Variations in viral families in Arctic soils, Arctic freshwater, and Antarctic soils are discussed. These findings improve our understanding of polar viromes and suggest the importance of performing follow-up in-depth investigations of animal and environmental samples from Antarctica and the Arctic, which would reveal the substantial role of these viruses in the global viral community.     

Biostimulation of n-Alkane Degradation in Diesel Fuel-Spiked Soils

Nutrient enhancement of bioremediation with nitrogen, namely biostimulation, increases process performance. Selection of a proper nitrogen source is critical for bioremediation applications. In this study, the effects of different nitrogen sources on biodegradation of C₁₀–C₂₅ n-alkane compounds in diesel fuel-spiked soil were revealed, and the most appropriate nitrogen source for biodegradation of semi- and non-volatile n-alkanes was investigated. Bioremediation of diesel fuel contaminated soil was monitored in lab-scale reactors for 15 days. Ammonium sulfate, potassium nitrate and urea were used as nitrogen sources. Carbon dioxide and oxygen levels in the reactors were recorded to monitor microbiological activity. Contaminant removal process was investigated by pH, heterotrophic plate count, total petroleum hydrocarbons (TPH) and C₁₀–C₂₅ n-alkane analyses. First-order kinetic constants were calculated via respirometric and contaminant concentration data. According to total C₁₀–C₂₅ n-alkane removal levels and degradation rate constants, ammonium sulfate addition resulted in the most efficient contaminant removal followed by potassium nitrate and urea. Simultaneous degradation of individual n-alkanes was observed for all of the nitrogen sources. Urea addition changed the distribution of individual n-alkane concentrations relative to the pre-experimental concentrations. Nitrogen source type had no differential effect on degradation rates of semi- (C₁₀–C₁₆) and non-volatile (C₁₇–C₂₅) fractions.     

A microcosm system and an analytical protocol to assess PAH degradation and metabolite formation in soils

During bioremediation of polycyclic aromatic hydrocarbon (PAH)-polluted soils accumulation of polar metabolites resulting from the biological activity may occur. Since these polar metabolites are potentially more toxic than the parental products, a better understanding of the processes involved in the production and fate of these oxidation products in soil is needed. In the present work we describe the design and set-up of a static soil microcosm system and an analytical methodology for detection of PAHs and their oxidation products in soils. When applied to a soil contaminated with phenanthrene, as a model PAH, and 1-hydroxy-2-naphthoic acid, diphenic acid, and phthalic acid as putative metabolites, the extraction and fractionation procedures resulted in recoveries of 93%, 89%, 100%, and 89%, respectively. The application of the standardized system to study the biodegradation of phenanthrene in an agricultural soil with and without inoculation of the high molecular weight PAH-degrading strain Mycobacterium sp. AP1, demonstrates its suitability for determining the environmental fate of PAHs in polluted soils and for evaluating the effect of bioremediative treatments. In inoculated microcosms 35% of the added phenanthrene was depleted, 19% being recovered as CO₂ and 3% as diphenic acid. The latter, together with other two unidentified metabolites, accumulated in soil.     

Identification of nitrogen-incorporating bacteria in petroleum-contaminated arctic soils by using [15N]DNA-based stable isotope probing and pyrosequencing

Arctic soils are increasingly susceptible to petroleum hydrocarbon contamination, as exploration and exploitation of the Arctic increase. Bioremediation in these soils is challenging due to logistical constraints and because soil temperatures only rise above 0°C for ∼2 months each year. Nitrogen is often added to contaminated soil in situ to stimulate the existing microbial community, but little is known about how the added nutrients are used by these microorganisms. Microbes vary widely in their ability to metabolize petroleum hydrocarbons, so the question becomes: which hydrocarbon-degrading microorganisms most effectively use this added nitrogen for growth? Using [¹⁵N]DNA-based stable isotope probing, we determined which taxonomic groups most readily incorporated nitrogen from the monoammonium phosphate added to contaminated and uncontaminated soil in Canadian Forces Station-Alert, Nunavut, Canada. Fractions from each sample were amplified with bacterial 16S rRNA and alkane monooxygenase B (alkB) gene-specific primers and then sequenced using lage-scale parallel-pyrosequencing. Sequence data was combined with 16S rRNA and alkB gene C quantitative PCR data to measure the presence of various phylogenetic groups in fractions at different buoyant densities. Several families of Proteobacteria and Actinobacteria that are directly involved in petroleum degradation incorporated the added nitrogen in contaminated soils, but it was the DNA of Sphingomonadaceae that was most enriched in ¹⁵N. Bacterial growth in uncontaminated soils was not stimulated by nutrient amendment. Our results suggest that nitrogen uptake efficiency differs between bacterial groups in contaminated soils. A better understanding of how groups of hydrocarbon-degraders contribute to the catabolism of petroleum will facilitate the design of more targeted bioremediation treatments.     

Aerobic biodegradation of biphenyl and polychlorinated biphenyls by Arctic soil microorganisms.

We examined the degradation of biphenyl and the commercial polychlorinated biphenyl (PCB) mixture Aroclor 1221 by indigenous Arctic soil microorganisms to assess both the response of the soil microflora to PCB pollution and the potential of the microflora for bioremediation. In soil slurries, Arctic soil microflora and temperate-soil microflora had similar potentials to mineralize [14C]biphenyl. Mineralization began sooner and was more extensive in slurries of PCB-contaminated Arctic soils than in slurries of uncontaminated Arctic soils. The maximum mineralization rates at 30 and 7 degrees C were typically 1.2 to 1.4 and 0.52 to 1.0 mg of biphenyl g of dry soil-1 day-1, respectively. Slurries of PCB-contaminated Arctic soils degraded Aroclor 1221 more extensively at 30 degrees C (71 to 76% removal) than at 7 degrees C (14 to 40% removal). We isolated from Arctic soils organisms that were capable of psychrotolerant (growing at 7 to 30 degrees C) or psychrophilic (growing at 7 to 15 degrees C) growth on biphenyl. Two psychrotolerant isolates extensively degraded Aroclor 1221 at 7 degrees C (54 to 60% removal). The soil microflora and psychrotolerant isolates degraded all mono-, most di-, and some trichlorobiphenyl congeners. The results suggest that PCB pollution selected for biphenyl-mineralizing microorganisms in Arctic soils. While low temperatures severely limited Aroclor 1221 removal in slurries of Arctic soils, results with pure cultures suggest that more effective PCB biodegradation is possible under appropriate conditions.     

A suitable model to describe bioremediation of a petroleum-contaminated soil

A critical environmental impact of the petroleum industry is the spillage of oil and related products that causes severe soil contamination. Although biodegradation of petroleum hydrocarbons may be successfully conducted under controlled conditions, the bioremediation of large volumes of contaminated soils still presents some technical challenges, particularly when contamination occurs in soils of high clay content. The main objective of this work is to evaluate the bioremediation of petroleum-contaminated clay-soil by fixed bed experiments. They were conducted in agreement with the full factorial experimental design 2³. The processes employed were shown to be highly effective in decontaminating the soil, achieving removal rates of around 80%. The model chosen to represent the bioremediation process provided satisfactory results. The values calculated by the model were consistent with the experimental results.