Impact of bacterial and fungal processes on 14C-hexadecane mineralisation in weathered hydrocarbon contaminated soil

Main Factors Determining the Scale-Up Effectiveness of Mycoremediation for the Decontamination of Aliphatic Hydrocarbons in Soil

Soil contamination constitutes a significant threat to the health of soil ecosystems in terms of complexity, toxicity, and recalcitrance. Among all contaminants, aliphatic petroleum hydrocarbons (APH) are of particular concern due to their abundance and persistence in the environment and the need of remediation technologies to ensure their removal in an environmentally, socially, and economically sustainable way. Soil remediation technologies presently available on the market to tackle soil contamination by petroleum hydrocarbons (PH) include landfilling, physical treatments (e.g., thermal desorption), chemical treatments (e.g., oxidation), and conventional bioremediation. The first two solutions are costly and energy-intensive approaches. Conversely, bioremediation of on-site excavated soil arranged in biopiles is a more sustainable procedure. Biopiles are engineered heaps able to stimulate microbial activity and enhance biodegradation, thus ensuring the removal of organic pollutants. This soil remediation technology is currently the most environmentally friendly solution available on the market, as it is less energy-intensive and has no detrimental impact on biological soil functions. However, its major limitation is its low removal efficiency, especially for long-chain hydrocarbons (LCH), compared to thermal desorption. Nevertheless, the use of fungi for remediation of environmental contaminants retains the benefits of bioremediation treatments, including low economic, social, and environmental costs, while attaining removal efficiencies similar to thermal desorption. Mycoremediation is a widely studied technology at lab scale, but there are few experiences at pilot scale. Several factors may reduce the overall efficiency of on-site mycoremediation biopiles (mycopiles), and the efficiency detected in the bench scale. These factors include the bioavailability of hydrocarbons, the selection of fungal species and bulking agents and their application rate, the interaction between the inoculated fungi and the indigenous microbiota, soil properties and nutrients, and other environmental factors (e.g., humidity, oxygen, and temperature). The identification of these factors at an early stage of biotreatability experiments would allow the application of this on-site technology to be refined and fine-tuned. This review brings together all mycoremediation work applied to aliphatic petroleum hydrocarbons (APH) and identifies the key factors in making mycoremediation effective. It also includes technological advances that reduce the effect of these factors, such as the structure of mycopiles, the application of surfactants, and the control of environmental factors.

Mitigation of arsenic release by calcium peroxide (CaO2) and rice straw biochar in paddy soil

Biochar has a great potential in the stabilization of soil heavy metals; however, the application can actually enhance the mobility of Arsenic (As) in soil. Here, a biochar-coupled calcium peroxide system was proposed to control the increase in As mobility caused by biochar amendment in paddy soil environment. The capability of rice straw biochar pyrolyzed at 500 °C (RB) and CaO₂ to control As mobility was evaluated by incubation for 91 days. CaO₂ encapsulation was performed for pH control of CaO₂, and As mobility was evaluated using a mixture of RB + CaO₂ powder (CaO₂-p), and RB + CaO₂ bead (CaO₂-b), respectively. The control soil solely and RB alone were included for comparison. The combination of RB with CaO₂ exhibited remarkable performance in controlling As mobility in soil, and As mobility decreased by 40.2% (RB + CaO₂-p) and 58.9% (RB + CaO₂-b) compared to RB alone. The result was due to high dissolved oxygen (6 mg L^-1 in RB + CaO₂-p and RB + CaO₂-b) and calcium concentrations (296.3 mg L^-1 in RB + CaO₂-b); oxygen (O₂) and Ca²⁺ derived from CaO₂ is able to prevent the reductive dissolution and chelate-promoted dissolution of As bound to iron (Fe) oxide by biochar. This study revealed that the simultaneous application of CaO₂ and biochar could be a promising way to mitigate the environmental risk of As.

The Influence of Organic Fertilizers on the Abundance of Soil Microorganism Communities, Agrochemical Indicators, and Yield in East Lithuanian Light Soils

Soil microorganisms are one of the main indicators used for assessing the stability of the soil ecosystem, the metabolism in the soil, and its fertility. The most important are the active soil microorganisms and the influence of the fertilizer applied to the soil on the abundance of these microorganisms. We aimed to investigate how the applied organic fertilizers affect the most active soil microorganisms, which determine the soil fertility and stability. Fungi, yeast-like fungi abundance, and abundance of three physiological groups of bacteria were analyzed: non-symbiotic diazotrophic, organotrophic, and mineral nitrogen assimilating. This study is valuable because relatively few similar studies have been performed on infertile Lithuanian soils. The first results of a long-term study were obtained. The results show the effect of fertilizers on trends in the changes of microorganism community diversity; however, more analysis is needed to assess the impact of organic fertilizers on the most active soil microorganisms. Therefore, the investigation was continued. The results of the 2020 quantitative analysis of culturable soil microorganisms show that the highest abundance of organotrophic and non-symbiotic diazotrophic bacteria were recorded during the summer season. Meanwhile, the abundance of bacteria assimilating mineral nitrogen and fungi was higher in autumn. Agrochemical parameters were determined at the beginning of the experiment. The highest concentration of N_min in the soil was determined after fertilizing the plants with the combination of granulated poultry manure (N₁₇₀) + biological substance Azotobacter spp. The yield of barley was calculated. It was found that the highest yield of spring barley in 2020 was obtained by fertilizing the experimental field with organic in combination with mineral fertilizers.

Biological Indicators of Soil Quality under Different Tillage Systems in Retisol

Soil microorganism diversity has a close relation with soil function, and the changes in the composition of the soil microbial population can directly affect it. The aim of this study was to identify the bacterial community composition and determine the main soil chemical and physical properties formed by the different tillage systems. In the experiment, we analyzed the combination of three tillage systems and four organic fertilizers. Soil samples were taken from the two layers of the soil profile: the upper 0–10 cm and the lower 10–20 cm. The composition and diversity of soil bacterial communities were assessed by the sequencing of 16S rRNA genes. Results revealed that the highest biodiversity was found in the soil with shallow ploughless tillage and enriched with farmyard manure. Actinobacteria and Proteobacteria were the dominant bacterial species across all treatments. Their total abundance varied between 26% and 36% in the different analyzed agroecosystems. For the Dystric Bathygleyic Glossic Retisol, shallow ploughless tillage is the most suitable tillage system, as it creates favorable conditions for the accumulation of organic carbon in the soil under the Western Lithuania climate conditions.

Evaluation of pyrene and tetracosane degradation by mixed-cultures of fungi and bacteria

The present study was conducted to compare the efficiency of different microbial mixed-cultures consists of fifteen oil-degrading microorganisms with different combinations. The investigation was targeted toward the removal of 500 mg/l pyrene and 1% w/v tetracosane, as single compounds or mixture. Sequential Fungal-Bacterial Mixed-Culture (SMC) in which bacteria added one week after fungi, recorded 60.76% and 73.48% degradation for pyrene and tetracosane; about 10% more than Traditional Fungal-Bacterial Mixed-Culture (TMC). Co-degradation of pollutants resulted in 24.65% more pyrene degradation and 6.41% less tetracosane degradation. The non-specified external enzymes of fungi are responsible for initial attacks on hydrocarbons. Delayed addition of bacteria and co-contamination would result in higher growth of fungi which increases pyrene degradation. The addition of Rhamnolipid potently increased the extent of pyrene and tetracosane degradation by approximately 16% and 23% and showed twice better performance than Tween-80 in 20 times less concentration. The results indicated the importance of having sufficient knowledge on the characteristics of the contaminated site and its contaminants as well as oil-degrading species. Gaining this knowledge and using it properly, such as the later addition of bacteria (new method of mixed-cultures inoculation) to the contaminated culture, can serve as a promising approach.

Unravelling the process of petroleum hydrocarbon biodegradation in different filter materials of constructed wetlands by stable isotope fractionation and labelling studies

Maintaining and supporting complete biodegradation during remediation of petroleum hydrocarbon contaminated groundwater in constructed wetlands is vital for the final destruction and removal of contaminants. We aimed to compare and gain insight into biodegradation and explore possible limitations in different filter materials (sand, sand amended with biochar, expanded clay). These filters were collected from constructed wetlands after two years of operation and batch experiments were conducted using two stable isotope techniques; (i) carbon isotope labelling of hexadecane and (ii) hydrogen isotope fractionation of decane. Both hydrocarbon compounds hexadecane and decane were biodegraded. The mineralization rate of hexadecane was higher in the sandy filter material (3.6 µg CO2 g-1 day-1) than in the expanded clay (1.0 µg CO2 g-1 day-1). The microbial community of the constructed wetland microcosms was dominated by Gram negative bacteria and fungi and was specific for the different filter materials while hexadecane was primarily anabolized by bacteria. Adsorption / desorption of petroleum hydrocarbons in expanded clay was observed, which might not hinder but delay biodegradation. Very few cases of hydrogen isotope fractionation were recorded in expanded clay and sand & biochar filters during decane biodegradation. In sand filters, decane was biodegraded more slowly and hydrogen isotope fractionation was visible. Still, the range of observed apparent kinetic hydrogen isotope effects (AKIEH = 1.072-1.500) and apparent decane biodegradation rates (k = - 0.017 to - 0.067 day-1) of the sand filter were low. To conclude, low biodegradation rates, small hydrogen isotope fractionation, zero order mineralization kinetics and lack of microbial biomass growth indicated that mass transfer controlled biodegradation.

Metagenomic Insights Into the Mechanisms for Biodegradation of Polycyclic Aromatic Hydrocarbons in the Oil Supply Chain

Petroleum is a very complex and diverse organic mixture. Its composition depends on reservoir location and in situ conditions and changes once crude oil is spilled into the environment, making the characteristics associated with every spill unique. Polycyclic aromatic hydrocarbons (PAHs) are common components of the crude oil and constitute a group of persistent organic pollutants. Due to their highly hydrophobic, and their low solubility tend to accumulate in soil and sediment. The process by which oil is sourced and made available for use is referred to as the oil supply chain and involves three parts: (1) upstream, (2) midstream and (3) downstream activities. As consequence from oil supply chain activities, crude oils are subjected to biodeterioration, acidification and souring, and oil spills are frequently reported affecting not only the environment, but also the economy and human resources. Different bioremediation techniques based on microbial metabolism, such as natural attenuation, bioaugmentation, biostimulation are promising approaches to minimize the environmental impact of oil spills. The rate and efficiency of this process depend on multiple factors, like pH, oxygen content, temperature, availability and concentration of the pollutants and diversity and structure of the microbial community present in the affected (contaminated) area. Emerging approaches, such as (meta-)taxonomics and (meta-)genomics bring new insights into the molecular mechanisms of PAH microbial degradation at both single species and community levels in oil reservoirs and groundwater/seawater spills. We have scrutinized the microbiological aspects of biodegradation of PAHs naturally occurring in oil upstream activities (exploration and production), and crude oil and/or by-products spills in midstream (transport and storage) and downstream (refining and distribution) activities. This work addresses PAH biodegradation in different stages of oil supply chain affecting diverse environments (groundwater, seawater, oil reservoir) focusing on genes and pathways as well as key players involved in this process. In depth understanding of the biodegradation process will provide/improve knowledge for optimizing and monitoring bioremediation in oil spills cases and/or to impair the degradation in reservoirs avoiding deterioration of crude oil quality.

Impact of necrophytoremediation on petroleum hydrocarbon degradation, ecotoxicity and soil bacterial community composition in diesel-contaminated soil

Hydrocarbon degradation is usually measured in laboratories under controlled conditions to establish the likely efficacy of a bioremediation process in the field. The present study used greenhouse-based bioremediation to investigate the effects of natural attenuation (NA) and necrophytoremediation (addition of pea straw (PS)) on hydrocarbon degradation, toxicity and the associated bacterial community structure and composition in diesel-contaminated soil. A significant reduction in total petroleum hydrocarbon (TPH) concentration was detected in both treatments; however, PS-treated soil showed more rapid degradation (87%) after 5 months together with a significant reduction in soil toxicity (EC50 = 91 mg diesel/kg). Quantitative PCR analysis revealed an increase in the number of 16S rRNA and alkB genes in the PS-amended soil. Substantial shifts in soil bacterial community were observed during the bioremediation, including an increased abundance of numerous hydrocarbon-degrading bacteria. The bacterial community shifted from dominance by Alphaproteobacteria and Gammaproteobacteria in the original soil to Actinobacteria during bioremediation. The dominance of two genera of bacteria, Sphingobacteria and Betaproteobacteria, in both NA- and PS-treated soil demonstrated changes occurring within the soil bacterial community through the incubation period. Additionally, pea straw itself was found to harbour a diverse hydrocarbonoclastic community including Luteimonas, Achromobacter, Sphingomonas, Rhodococcus and Microbacterium. At the end of the experiment, PS-amended soil exhibited reduced ecotoxicity and increased bacterial diversity as compared with the NA-treated soil. These findings suggest the rapid growth of species stimulated by the bioremediation treatment and strong selection for bacteria capable of degrading petroleum hydrocarbons during necrophytoremediation. Graphical abstract.

Enhanced biodegradation of n-Hexadecane in solid-phase of soil by employing immobilized Pseudomonas Aeruginosa on size-optimized coconut fibers

In this research, biodegradation of hexadecane as a model contaminant in solid soil using both free and immobilized Pseudomonas Aeruginosa, capable of producing biosurfactant, was investigated. Coconut fibers in three mesh sizes were used as a cellulosic biocarrier for immobilization procedure. Bioremediation experiments were monitored for 60 days after incubation at 27 °C in small columns, containing contaminated solid soil, with the capability of aeration from bottom to top. The difference in the number of immobilized bacteria cells on the fibers with different particle sizes, emphasizes the importance of choosing an optimized carrier size. Enhancement in hexadecane degradation up to 50 % at the end of experiments was achieved by immobilized Pseudomonas Aeruginosa on the fibers with a mesh size between 8 and 16 compared to inoculation of free bacteria cells into the soil. Effect of mixing the pretreated fibers with soil and inoculating free cells into this mixture was also investigated compared to free cell experiments without fiber, which led to 28 % decrease in hexadecane degradation. Obtained kinetic equations for experiments confirm the impact of immobilization of bacteria on the enhancement of biodegradation rate and reduction of the half-life of the contaminant is soil.

Hydrocarbon Removal by Two Differently Developed Microbial Inoculants and Comparing Their Actions with Biostimulation Treatment

Bioremediation of soils polluted with petroleum compounds is a widely accepted environmental technology. We compared the effects of biostimulation and bioaugmentation of soil historically contaminated with aliphatic and polycyclic aromatic hydrocarbons. The studied bioaugmentation treatments comprised of the introduction of differently developed microbial inoculants, namely: an isolated hydrocarbon-degrading community C1 (undefined-consisting of randomly chosen degraders) and a mixed culture C2 (consisting of seven strains with well-characterized enhanced hydrocarbon-degrading capabilities). Sixty days of remedial treatments resulted in a substantial decrease in total aliphatic hydrocarbon content; however, the action of both inoculants gave a significantly better effect than nutrient amendments (a 69.7% decrease for C1 and 86.8% for C2 vs. 34.9% for biostimulation). The bioaugmentation resulted also in PAH removal, and, again, C2 degraded contaminants more efficiently than C1 (reductions of 85.2% and 64.5%, respectively), while biostimulation itself gave no significant results. Various bioassays applying different organisms (the bacterium Vibrio fischeri, the plants Sorghum saccharatum, Lepidium sativum, and Sinapis alba, and the ostracod Heterocypris incongruens) and Ames test were used to assess, respectively, potential toxicity and mutagenicity risk after bioremediation. Each treatment improved soil quality, however only bioaugmentation with the C2 treatment decreased both toxicity and mutagenicity most efficiently. Illumina high-throughput sequencing revealed the lack of (C1) or limited (C2) ability of the introduced degraders to sustain competition from indigenous microbiota after a 60-day bioremediation process. Thus, bioaugmentation with the bacterial mixed culture C2, made up of identified, hydrocarbon-degrading strains, is clearly a better option for bioremediation purposes when compared to other treatments.

Evaluation of heavy petroleum degradation using bacterial-fungal mixed cultures

The use of potent microbial mixed cultures is a promising method for the bioremediation of recalcitrant compounds. In this study, eight molds, three yeasts, and four bacterial isolates were screened from an aged oil-polluted area. An oil degradation assay with various combinations including Bacterial Mixed Culture (BMC), Fungal Mixed Culture (FMC), Fungal-Bacterial Mixed Culture (TMC), and Sequential Fungal-Bacterial Mixed Culture (SMC) was investigated. The results indicated that the SMC culture had the highest yield of degradation (65.96%) in comparison with the degradation yields of TMC, FMC and BMC, which were 59.04%, 56.64%, and 47.56%, respectively. The degradation of saturates, aromatics, resins, and asphaltenes in the crude oil found using the Iatroscan system were, as follows: 64.21%, and 67.63% for aromatics, 72.90%, and 73.59% for saturates, and 53.88% and 58.25% for resins with respect to the TMC and SMC cultures as the superior mixed cultures. The growth rates of yeasts, molds, and bacteria in the TMC and SMC cultures were compared for further evaluation of the role of each microorganism in the degradation. Our findings support the use of mixed cultures in the bioremediation of recalcitrant petroleum pollution.

Enhanced biodegradation of sediment-bound heavily weathered crude oil with ligninolytic enzymes encapsulated in calcium-alginate beads

The degradation of crude and weathered crude oil following the application of crude and calcium-alginate encapsulated ligninolytic enzymes was studied using in situ microcosms. Changes in the chemical composition of the oil were monitored in crude enzyme extracts, as well as a sediment matrix, for as long as 70 days. Compound-specific effects of ligninolytic enzymes applied to the sediments were observed over time through changes in concentration of total petroleum hydrocarbons (TPH), polycyclic aromatic hydrocarbons (PAHs) and fractions of saturates, aromatics, resins and asphaltenes (SARA). As the oil weathered, most TPH and PAH fractions showed a rapid decrease in concentration. As sediment oil concentrations decreased following treatment with ligninolytic enzymes, the microbial population was enriched with hydrocarbon-degrading species. This trend demonstrates that the oil fractions initially not bioavailable for microbial degradation, were subsequently released to the sediment via catalytic conversion with laccase and manganese peroxidase, and the oil continues to be biodegraded by microbial populations.

Microbial Degradation of Phenanthrene in Pristine and Contaminated Sandy Soils

Phenanthrene mineralisation studies in both pristine and contaminated sandy soils were undertaken through detailed assessment of the activity and diversity of the microbial community. Stable isotope probing (SIP) was used to assess and identify active ¹³C-labelled phenanthrene degraders. Baseline profiling indicated that there was little difference in fungal diversity but a significant difference in bacterial diversity dependent on contamination history. Identification of dominant fungal and bacterial species highlighted the presence of organisms capable of degrading various petroleum-based compounds together with other anthropogenic compounds, regardless of contamination history. Community response following a simulated contamination event (¹⁴C-phenanthrene) showed that the microbial community in deep pristine and shallow contaminated soils adapted most to the presence of phenanthrene. The similarity in microbial community structure of well-adapted soils demonstrated that a highly adaptable fungal community in these soils enabled a rapid response to the introduction of a contaminant. Ten fungal and 15 bacterial species were identified as active degraders of phenanthrene. The fungal degraders were dominated by the phylum Basidiomycota including the genus Crypotococcus, Cladosporium and Tremellales. Bacterial degraders included the genera Alcanivorax, Marinobacter and Enterococcus. There was little synergy between dominant baseline microbes, predicted degraders and those that were determined to be actually degrading the contaminant. Overall, assessment of baseline microbial community in contaminated soils provides useful information; however, additional laboratory assessment of the microbial community's ability to degrade pollutants allows for better prediction of the bioremediation potential of a soil.

Biodegradation of hexadecane using sediments from rivers and lagoons of the Southern Gulf of Mexico

The Southern Gulf of Mexico is an area highly impacted by crude oil extraction, refining activities and the presence of natural petroleum seepage. Oceanic currents in the Gulf of Mexico continually facilitate the transport of hydrocarbons to lagoons and rivers. This research evaluated hexadecane (HXD) degradation in marine sediment samples from lagoons and rivers that are fed by the Southern Gulf of Mexico, specifically six samples from rivers, three samples from lagoons, and one sample from a marine outfall. The highest rates of biodegradation were observed in sediments from the mouths of the Gonzalez River and the Champotón Lagoon. The lowest consumption rate was found in sediment from the mouth of the Coatzacoalcos River. With regards to the Ostión Lagoon and the Grijalva River, there was a low rate of consumption, but a high efficiency of degradation which took place at the end of the experiments. No correlation was found between the consumption rate and the environmental physicochemical parameters.

Tween 80 surfactant-enhanced bioremediation: toward a solution to the soil contamination by hydrophobic organic compounds

The occurrence of hydrophobic organic compounds (HOCs) in the soil has become a highly significant environmental issue. This problem has been exacerbated by the strong sorption of HOCs to the soils, which makes them unavailable for most remediation processes. More and more works show that surfactant-enhanced biological technologies offer a great potential to clear up HOCs-contaminated soils. This article is a critical review of HOCs removal from soils using Tween 80 (one of the mostly used nonionic surfactants) aided biological remediation technologies. The review begins with a discussion of the fundamentals of Tween 80-enhanced desorption of HOCs from contaminated soils, with special emphasis on the biotoxicity of Tween 80. Successful results obtained by Tween 80-enhanced microbial degradation and phytoremediation are documented and discussed in section 3 and section 4, respectively. Results show Tween 80-enhanced biotechnologies are promising for treating HOCs-contaminated soils. However, considering the fact that most of these scientific studies have only been conducted at the laboratory-scale, many improvements are required before these technologies can be scaled up to the full-scale level. Moreover, further research on mechanisms related to the interaction of Tween 80 with degrading microorganisms and the plants is in high demand.

Mild acid and alkali treated clay minerals enhance bioremediation of polycyclic aromatic hydrocarbons in long-term contaminated soil: A 14C-tracer study

Bioremediation of polycyclic aromatic hydrocarbon (PAH)-contaminated soils requires a higher microbial viability and an increased PAH bioavailability. The clay/modified clay-modulated bacterial degradation could deliver a more efficient removal of PAHs in soils depending on the bioavailability of the compounds. In this study, we modified clay minerals (smectite and palygorskite) with mild acid (HCl) and alkali (NaOH) treatments (0.5-3 M), which increased the surface area and pore volume of the products, and removed the impurities without collapsing the crystalline structure of clay minerals. In soil incubation studies, supplements with the clay products increased bacterial growth in the order: 0.5 M HCl ≥ unmodified ≥ 0.5 M NaOH ≥ 3 M NaOH ≥ 3 M HCl for smectite, and 0.5 M HCl ≥ 3 M NaOH ≥ 0.5 M NaOH ≥ 3 M HCl ≥ unmodified for palygorskite. A¹⁴C-tracing study showed that the mild acid/alkali-treated clay products increased the PAH biodegradation (5-8%) in the order of 0.5 M HCl ≥ unmodified > 3 M NaOH ≥ 0.5 M NaOH for smectite, and 0.5 M HCl > 0.5 M NaOH ≥ unmodified ≥ 3 M NaOH for palygorskite. The biodegradation was correlated (r = 0.81) with the bioavailable fraction of PAHs and microbial growth as affected particularly by the 0.5 M HCl and 0.5 M NaOH-treated clay minerals. These results could be pivotal in developing a clay-modulated bioremediation technology for cleaning up PAH-contaminated soils and sediments in the field.

Bacterial mineralization of phenanthrene on thermally activated palygorskite: A 14C radiotracer study

Clay-bacterial interaction can significantly influence the biodegradation of organic contaminants in the environment. A moderate heat treatment of palygorskite could alter the physicochemical properties of the clay mineral and thus support the growth and function of polycyclic aromatic hydrocarbon (PAH)-degrading bacteria. By using ¹⁴C-labelled phenanthrene and a model bacterium Burkholderia sartisoli, we studied the mineralization of phenanthrene on the surface of a moderately heat-treated (up to 400°C) palygorskite. The heat treatment at 400°C induced a reduction of binding sites (e.g., by the elimination of organic matter and/or channel shrinkage) in the palygorskite and thus imparted a weaker sequestration of phenanthrene on its surface and within the pores. As a result, a supplement with the thermally modified palygorskite (400°C) significantly increased (20-30%; p<0.05) the biomineralization of total phenanthrene in a simulated soil slurry system. These results are highly promising to develop a clay mineral based technology for the bioremediation of PAH contaminants in water and soil environments.

Biostimulation of Indigenous Microbial Community for Bioremediation of Petroleum Refinery Sludge

Nutrient deficiency severely impairs the catabolic activity of indigenous microorganisms in hydrocarbon rich environments (HREs) and limits the rate of intrinsic bioremediation. The present study aimed to characterize the microbial community in refinery waste and evaluate the scope for biostimulation based in situ bioremediation. Samples recovered from the wastewater lagoon of Guwahati refinery revealed a hydrocarbon enriched [high total petroleum hydrocarbon (TPH)], oxygen-, moisture-limited, reducing environment. Intrinsic biodegradation ability of the indigenous microorganisms was enhanced significantly (>80% reduction in TPH by 90 days) with nitrate amendment. Preferred utilization of both higher- (>C30) and middle- chain (C20-30) length hydrocarbons were evident from GC-MS analysis. Denaturing gradient gel electrophoresis and community level physiological profiling analyses indicated distinct shift in community's composition and metabolic abilities following nitrogen (N) amendment. High throughput deep sequencing of 16S rRNA gene showed that the native community was mainly composed of hydrocarbon degrading, syntrophic, methanogenic, nitrate/iron/sulfur reducing facultative anaerobic bacteria and archaebacteria, affiliated to γ- and δ-Proteobacteria and Euryarchaeota respectively. Genes for aerobic and anaerobic alkane metabolism (alkB and bssA), methanogenesis (mcrA), denitrification (nirS and narG) and N2 fixation (nifH) were detected. Concomitant to hydrocarbon degradation, lowering of dissolve O2 and increase in oxidation-reduction potential (ORP) marked with an enrichment of N2 fixing, nitrate reducing aerobic/facultative anaerobic members [e.g., Azovibrio, Pseudoxanthomonas and Comamonadaceae members] was evident in N amended microcosm. This study highlighted that indigenous community of refinery sludge was intrinsically diverse, yet appreciable rate of in situ bioremediation could be achieved by supplying adequate N sources.

Citric acid- and Tween(®) 80-assisted phytoremediation of a co-contaminated soil: alfalfa (Medicago sativa L.) performance and remediation potential

A pot experiment was designed to assess the phytoremediation potential of alfalfa (Medicago sativa L.) in a co-contaminated (i.e., heavy metals and petroleum hydrocarbons) soil and the influence of citric acid and Tween(®) 80 (polyethylene glycol sorbitan monooleate), applied individually and combined together, for their possible use in chemically assisted phytoremediation. The results showed that alfalfa plants could tolerate and grow in a co-contaminated soil. Over a 90-day experimental time, shoot and root biomass increased and negligible plant mortality occurred. Heavy metals were uptaken by alfalfa to a limited extent, mostly by plant roots, and their concentration in plant tissues were in the following order: Zn > Cu > Pb. Microbial population (alkane-degrading microorganisms) and activity (lipase enzyme) were enhanced in the presence of alfalfa with rhizosphere effects of 9.1 and 1.5, respectively, after 90 days. Soil amendments did not significantly enhance plant metal concentration or total uptake. In contrast, the combination of citric acid and Tween(®) 80 significantly improved alkane-degrading microorganisms (2.4-fold increase) and lipase activity (5.3-fold increase) in the rhizosphere of amended plants, after 30 days of experiment. This evidence supports a favorable response of alfalfa in terms of tolerance to a co-contaminated soil and improvement of rhizosphere microbial number and activity, additionally enhanced by the joint application of citric acid and Tween(®) 80, which could be promising for future phytoremediation applications.

A quantitative PCR approach for quantification of functional genes involved in the degradation of polycyclic aromatic hydrocarbons in contaminated soils

Polycyclic aromatic hydrocarbons (PAHs) are major pollutants globally and due to their carcinogenic and mutagenic properties their clean-up is paramount. Bioremediation or using PAH degrading microorganisms (mainly bacteria) to degrade the pollutants represents cheap, effective methods. These PAH degraders harbor functional genes which help microorganisms use PAHs as source of food and energy. Most probable number (MPN) and plate counting methods are widely used for counting PAHs degraders; however, as culture based methods only count a small fraction (<1%) of microorganisms capable of carrying out PAH degradation, the use of culture-independent methodologies is desirable.•

This protocol presents a robust, rapid and sensitive qPCR method for the quantification of the functional genes involved in the degradation of PAHs in soil samples.

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This protocol enables us to screen a vast number of PAH contaminated soil samples in few hours.

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This protocol provides valuable information about the natural attenuation potential of contaminated soil and can be used to monitor the bioremediation process.

Potential impact of soil microbial heterogeneity on the persistence of hydrocarbons in contaminated subsurface soils

In situ bioremediation is potentially a cost effective treatment strategy for subsurface soils contaminated with petroleum hydrocarbons, however, limited information is available regarding the impact of soil spatial heterogeneity on bioremediation efficacy. In this study, we assessed issues associated with hydrocarbon biodegradation and soil spatial heterogeneity (samples designated as FTF 1, 5 and 8) from a site in which in situ bioremediation was proposed for hydrocarbon removal. Test pit activities showed similarities in FTF soil profiles with elevated hydrocarbon concentrations detected in all soils at 2 m below ground surface. However, PCR-DGGE-based cluster analysis showed that the bacterial community in FTF 5 (at 2 m) was substantially different (53% dissimilar) and 2-3 fold more diverse than communities in FTF 1 and 8 (with 80% similarity). When hydrocarbon degrading potential was assessed, differences were observed in the extent of (14)C-benzene mineralisation under aerobic conditions with FTF 5 exhibiting the highest hydrocarbon removal potential compared to FTF 1 and 8. Further analysis indicated that the FTF 5 microbial community was substantially different from other FTF samples and dominated by putative hydrocarbon degraders belonging to Pseudomonads, Xanthomonads and Enterobacteria. However, hydrocarbon removal in FTF 5 under anaerobic conditions with nitrate and sulphate electron acceptors was limited suggesting that aerobic conditions were crucial for hydrocarbon removal. This study highlights the importance of assessing available microbial capacity prior to bioremediation and shows that the site's spatial heterogeneity can adversely affect the success of in situ bioremediation unless area-specific optimizations are performed.

Hexadecane and pristane degradation potential at the level of the aquifer--evidence from sediment incubations compared to in situ microcosms

Monitored natural attenuation is widely accepted as a sustainable remediation method. However, methods providing proof of proceeding natural attenuation within the water-unsaturated (vadose) zone are still relying on proxies such as measurements of reactive and non-reactive gases, or sediment sampling and subsequent mineralisation assays, under artificial conditions in the laboratory. In particular, at field sites contaminated with hydrophobic compounds, e.g. crude oil spills, an in situ evaluation of natural attenuation is needed, because in situ methods are assumed to provide less bias than investigations applying either proxies for biodegradation or off-site microcosm experiments. In order to compare the current toolbox of methods with the recently developed in situ microcosms, incubations with direct push-sampled sediments from the vadose and the aquifer zones of a site contaminated with crude oil were carried out in conventional microcosms and in situ microcosms. The results demonstrate the applicability of the in situ microcosm approach also outside water-saturated aquifer conditions in the vadose zone. The sediment incubation experiments demonstrated turnover rates in a similar range (vadose, 4.7 mg/kg*day; aquifer, 6.4 mghexadecane/kgsoil/day) of hexadecane degradation in the vadose zone and the aquifer, although mediated by slightly different microbial communities according to the analysis of fatty acid patterns and amounts. Additional experiments had the task of evaluating the degradation potential for the branched-chain alkane pristane (2,6,10,14-tetramethylpentadecane). Although this compound is regarded to be hardly degradable in comparison to n-alkanes and is thus frequently used as a reference parameter for indexing the extent of biodegradation of crude oils, it could be shown to be degraded by means of the incubation experiments. Thus, the site had a high inherent potential for natural attenuation of crude oils both in the vadose zone and the aquifer.

Assessing impediments to hydrocarbon biodegradation in weathered contaminated soils

In this study, impediments to hydrocarbon biodegradation in contaminated soils were assessed using chemical and molecular methodologies. Two long-term hydrocarbon contaminated soils were utilised which were similar in physico-chemical properties but differed in the extent of hydrocarbon (C10-C40) contamination (S1: 16.5 g kg(-1); S2: 68.9 g kg(-1)). Under enhanced natural attenuation (ENA) conditions, hydrocarbon biodegradation was observed in S1 microcosms (26.4% reduction in C10-C40 hydrocarbons), however, ENA was unable to stimulate degradation in S2. Although eubacterial communities (PCR-DGGE analysis) were similar for both soils, the alkB bacterial community was less diverse in S2 presumably due to impacts associated with elevated hydrocarbons. When hydrocarbon bioaccessibility was assessed using HP-β-CD extraction, large residual concentrations remained in the soil following the extraction procedure. However, when linear regression models were used to predict the endpoints of hydrocarbon degradation, there was no significant difference (P>0.05) between HP-β-CD predicted and microcosm measured biodegradation endpoints. This data suggested that the lack of hydrocarbon degradation in S2 resulted primarily from limited hydrocarbon bioavailability.

A polyphasic approach for assessing the suitability of bioremediation for the treatment of hydrocarbon-impacted soil

Bioremediation strategies, though widely used for treating hydrocarbon-contaminated soil, suffer from lack of biodegradation endpoint accountability. To address this limitation, molecular approaches of alkB gene analysis and pyrosequencing were combined with chemical approaches of bioaccessibility and nutrient assays to assess contaminant degrading capacity and develop a strategy for endpoint biodegradation predictions. In long-term hydrocarbon-contaminated soil containing 10.3 g C10-C36 hydrocarbons kg(-1), 454 pyrosequencing detected the overrepresentation of potential hydrocarbon degrading genera such as Pseudomonas, Burkholderia, Mycobacterium and Gordonia whilst amplicons for PCR-DGGE were detected only with alkB primers targeting Pseudomonas. This indicated the presence of potential microbial hydrocarbon degradation capacity in the soil. Using non-exhaustive extraction methods of 1-propanol and HP-β-CD for hydrocarbon bioaccessibility assessment combined with biodegradation endpoint predictions with linear regression models, we estimated 33.7% and 46.7% hydrocarbon removal respectively. These predictions were validated in pilot scale studies using an enhanced natural attenuation strategy which resulted in a 46.4% reduction in soil hydrocarbon content after 320 days. When predicted biodegradation endpoints were compared to measured values, there was no significant difference (P=0.80) when hydrocarbon bioaccessibility was assessed with HP-β-CD. These results indicate that a combination of molecular and chemical techniques that inform microbial diversity, functionality and chemical bioaccessibility can be valuable tools for assessing the suitability of bioremediation strategies for hydrocarbon-contaminated soil.

Plant residues--a low cost, effective bioremediation treatment for petrogenic hydrocarbon-contaminated soil

Petrogenic hydrocarbons represent the most commonly reported environmental contaminant in industrialised countries. In terms of remediating petrogenic contaminated hydrocarbons, finding sustainable non-invasive technologies represents an important goal. In this study, the effect of 4 types of plant residues on the bioremediation of aliphatic hydrocarbons was investigated in a 90 day greenhouse experiment. The results showed that contaminated soil amended with different plant residues led to statistically significant increases in the utilisation rate of Total Petroleum Hydrocarbon (TPH) relative to control values. The maximum TPH reduction (up to 83% or 6800 mg kg(-1)) occurred in soil mixed with pea straw, compared to a TPH reduction of 57% (4633 mg kg(-1)) in control soil. A positive correlation (0.75) between TPH reduction rate and the population of hydrocarbon-utilising microorganisms was observed; a weaker correlation (0.68) was seen between TPH degradation and bacterial population, confirming that adding plant materials significantly enhanced both hydrocarbonoclastic and general microbial soil activities. Microbial community analysis using Denaturing Gradient Gel Electrophoresis (DGGE) showed that amending the contaminated soil with plant residues (e.g., pea straw) caused changes in the soil microbial structure, as observed using the Shannon diversity index; the diversity index increased in amended treatments, suggesting that microorganisms present on the dead biomass may become important members of the microbial community. In terms of specific hydrocarbonoclastic activity, the number of alkB gene copies in the soil microbial community increased about 300-fold when plant residues were added to contaminated soil. This study has shown that plant residues stimulate TPH degradation in contaminated soil through stimulation and perhaps addition to the pool of hydrocarbon-utilising microorganisms, resulting in a changed microbial structure and increased alkB gene copy numbers. These results suggest that pea straw in particular represents a low cost, effective treatment to enhance the remediation of aliphatic hydrocarbons in contaminated soils.