Bioremediation Field Research Articles

Variably saturated flow and multicomponent biogeochemical reactive transport modeling of a uranium bioremediation field experiment

Three-dimensional, coupled variably saturated flow and biogeochemical reactive transport modeling of a 2008 in situ uranium bioremediation field experiment is used to better understand the interplay of transport and biogeochemical reactions controlling uranium behavior under pulsed acetate amendment, seasonal water table variation, spatially variable physical (hydraulic conductivity, porosity) and geochemical (reactive surface area) material properties. While the simulation of the 2008 Big Rusty acetate biostimulation field experiment in Rifle, Colorado was generally consistent with behaviors identified in previous field experiments at the Rifle IFRC site, the additional process and property detail provided several new insights. A principal conclusion from this work is that uranium bioreduction is most effective when acetate, in excess of the sulfate-reducing bacteria demand, is available to the metal-reducing bacteria. The inclusion of an initially small population of slow growing sulfate-reducing bacteria identified in proteomic analyses led to an additional source of Fe(II) from the dissolution of Fe(III) minerals promoted by biogenic sulfide. The falling water table during the experiment significantly reduced the saturated thickness of the aquifer and resulted in reactants and products, as well as unmitigated uranium, in the newly unsaturated vadose zone. High permeability sandy gravel structures resulted in locally high flow rates in the vicinity of injection wells that increased acetate dilution. In downgradient locations, these structures created preferential flow paths for acetate delivery that enhanced local zones of TEAP reactivity and subsidiary reactions. Conversely, smaller transport rates associated with the lower permeability lithofacies (e.g., fine) and vadose zone were shown to limit acetate access and reaction. Once accessed by acetate, however, these same zones limited subsequent acetate dilution and provided longer residence times that resulted in higher concentrations of TEAP reaction products when terminal electron donors and acceptors were not limiting. Finally, facies-based porosity and reactive surface area variations were shown to affect aqueous uranium concentration distributions with localized effects of the fine lithofacies having the largest impact on U(VI) surface complexation. The ability to model the comprehensive biogeochemical reaction network, and spatially and temporally variable processes, properties, and conditions controlling uranium behavior during engineered bioremediation in the naturally complex Rifle IFRC subsurface system required a subsurface simulator that could use the large memory and computational performance of a massively parallel computer. In this case, the eSTOMP simulator, operating on 128 processor cores for 12 h, was used to simulate the 110-day field experiment and 50 days of post-biostimulation behavior.

Bacteria-mediated PAH degradation in soil and sediment

Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous in the natural environment and easily accumulate in soil and sediment due to their low solubility and high hydrophobicity, rendering them less available for biological degradation. However, microbial degradation is a promising mechanism which is responsible for the ecological recovery of PAH-contaminated soil and sediment for removing these recalcitrant compounds compared with chemical degradation of PAHs. The goal of this review is to provide an outline of the current knowledge of biodegradation of PAHs in related aspects. Over 102 publications related to PAH biodegradation in soil and sediment are compiled, discussed, and analyzed. This review aims to discuss PAH degradation under various redox potential conditions, the factors affecting the biodegradation rates, degrading bacteria, the relevant genes in molecular monitoring methods, and some recent-year bioremediation field studies. The comprehensive understanding of the bioremediation kinetics and molecular means will be helpful for optimizing and monitoring the process, and overcoming its limitations in practical projects.

Uranium 238U/235U Isotope Ratios as Indicators of Reduction: Results from an in situ Biostimulation Experiment at Rifle, Colorado, U.S.A.

The attenuation of groundwater contamination via chemical reaction is traditionally evaluated by monitoring contaminant concentration through time. However, this method can be confounded by common transport processes (e.g., dilution, sorption). Isotopic techniques bypass the limits of concentration methods, and so may provide improved accuracy in determining the extent of reaction. We apply measurements of 238U/235U to a U bioremediation field experiment at the Rifle Integrated Field Research Challenge Site in Rifle, Colorado. An array of monitoring and injection wells was installed on a 100 m2 plot where U(VI) contamination was present in the groundwater. Acetate-amended groundwater was injected along an up-gradient gallery to encourage the growth of dissimilatory metal reducing bacteria (e.g., Geobacter species). During amendment, U concentration dropped by an order of magnitude in the experiment plot. We measured 238U/235U in samples from one monitoring well by MC-ICP-MS using a double isotope tracer method. A significant approximately 1.00 per thousand decrease in 238U/235U occurred in the groundwater as U(VI) concentration decreased. The relationship between 238U/235U and concentration corresponds approximately to a Rayleigh distillation curve with an effective fractionation factor (alpha) of 1.00046. We attribute the observed U isotope fractionation to a nuclear field shift effect during enzymatic reduction of U(VI)(aq) to U(IV)(s).

Microbial communities involved in the bioremediation of an aged recalcitrant hydrocarbon polluted soil by using organic amendments

An 8-month field bioremediation experiment using fresh (FS) and composted (CS) sewage sludge and unamended soil (US) was carried out on an aged hydrocarbon contaminated semi-arid soil. FS treatments led to the highest percentage of hydrocarbon degradation (46%) and the highest bacterial and fungal population. Denaturing gradient gel electrophoresis analysis demonstrated differences in bacterial and fungal community structure of treated compared to uncontaminated soil (control). Time of sampling accounted for most of the differences than type of treatment. The principal phyla observed in bioremediation treatments were Actinobacteria and Ascomycota. Results pointed to the addition of organic amendments, particularly sewage sludge, as an useful strategy for improving the effectiveness of landfarming biodegradation processes in hydrocarbon polluted soils.

Characterization of Co(III) EDTA-Reducing Bacteria in Metal- and Radionuclide-Contaminated Groundwater

The Waste Area Grouping 5 (WAG5) site at Oak Ridge National Laboratory has a potential to be a field site for evaluating the effectiveness of various bioremediation approaches and strategies. The site has been well studied in terms of its geological and geochemical properties over the past decade. However, despite the importance of microorganisms in bioremediation processes, the microbiological populations at the WAG5 site and their potential in bioremediation have not been similarly evaluated. In this study, we initiated research to characterize the microbial populations in WAG5 groundwater. Approximately 100 isolates from WAG5 groundwater were isolated and selected based on colony morphology. Fifty-five unique isolates were identified by BOX-PCR and subjected to further characterization. 16S rRNA sequences indicated that these isolates belong to seventeen bacterial genera including Alcaligenes (1 isolate), Aquamonas (1), Aquaspirillum (1), Bacillus (10), Brevundimonas (5), Caulobacter (7), Dechloromonas (2), Janibacter (1), Janthinobacterium (2), Lactobacillus (1), Paenibacillus (4), Pseudomonas (9), Rhodoferax (1), Sphingomonas (1), Stenotrophomonas (6), Variovorax (2), and Zoogloea (1). Metal respiration assays identified several isolates, which phylogenically belong or are close to Caulobacter, Stenotrophomonas, Bacillus, Paenibacillus and Pseudomonas, capable of reducing Co(III)EDTA− to Co(II)EDTA2 − using the defined M1 medium under anaerobic conditions. In addition, using WAG5 groundwater directly as the inoculants, we found that organisms associated with WAG5 groundwater can reduce both Fe(III) and Co(III) under anaerobic conditions. Further assays were then performed to determine the optimal conditions for Co(III) reduction. These assays indicated that addition of various electron donors including ethanol, lactate, methanol, pyruvate, and acetate resulted in metal reduction. These experiments will provide useful background information for future bioremediation field experiments at the WAG5 site.

Bioaccumulation of heavy metals by Vibrio alginolyticus isolated from wastes of Iron and Steal Factory, Helwan, Egypt

The isolation of bacteria resistant to heavy metals is a topic of interest in the field bioremediation of contaminated water, soil and sediments. We report here the isolation of bacteria that is resistant to high concentration of a mixture of heavy metals namely cadmium, cupper, lead and zinc. The bacterial isolate was obtained from a site receiving heavy metal waste from the iron and steal factory; a major factory located in El-tebeen, south Helwan. The isolate was identified as Vibrio alginolyticus using the API system. The maximum tolerable concentration was 2.5 mM, 4 mM, 2.5 mM and 3.5 mM for cadmium, copper, lead and zinc respectively. Transmission electron micrograph of Vibrio alginolyticus grown in nutrient broth containing a mixture of the four tested heavy metals, showed bioaccumulation of heavy metal(s) on the bacterial cell wall. At the same time, there was an over all reduction in the concentration of heavy metals in culture supernatant; the percentage reduction was 20% for cadmium, 31% for cupper 40% for lead and 45%for zinc. The reduction occurred after 4 hrs incubation at 30°C for all metals, cupper, lead, and zinc while cadmium required 24 hrs incubation were required to achieve maximum reduction. This isolate could be used to accelerate the in situ bioremediation of sites contaminated by loads of mixed metals.

Microarray and Real-Time PCR Analyses of the Responses of High-Arctic Soil Bacteria to Hydrocarbon Pollution and Bioremediation Treatments

High-Arctic soils have low nutrient availability, low moisture content, and very low temperatures and, as such, they pose a particular problem in terms of hydrocarbon bioremediation. An in-depth knowledge of the microbiology involved in this process is likely to be crucial to understand and optimize the factors most influencing bioremediation. Here, we compared two distinct large-scale field bioremediation experiments, located at the Canadian high-Arctic stations of Alert (ex situ approach) and Eureka (in situ approach). Bacterial community structure and function were assessed using microarrays targeting the 16S rRNA genes of bacteria found in cold environments and hydrocarbon degradation genes as well as quantitative reverse transcriptase PCR targeting key functional genes. The results indicated a large difference between sampling sites in terms of both soil microbiology and decontamination rates. A rapid reorganization of the bacterial community structure and functional potential as well as rapid increases in the expression of alkane monooxygenases and polyaromatic hydrocarbon-ring-hydroxylating dioxygenases were observed 1 month after the bioremediation treatment commenced in the Alert soils. In contrast, no clear changes in community structure were observed in Eureka soils, while key gene expression increased after a relatively long lag period (1 year). Such discrepancies are likely caused by differences in bioremediation treatments (i.e., ex situ versus in situ), weathering of the hydrocarbons, indigenous microbial communities, and environmental factors such as soil humidity and temperature. In addition, this study demonstrates the value of molecular tools for the monitoring of polar bacteria and their associated functions during bioremediation.

Multicomponent reactive transport modeling of uranium bioremediation field experiments

A reaction network integrating abiotic and microbially mediated reactions has been developed to simulate biostimulation field experiments at a former Uranium Mill Tailings Remedial Action (UMTRA) site in Rifle, Colorado. The reaction network was calibrated using data from the 2002 field experiment, after which it was applied without additional calibration to field experiments performed in 2003 and 2007. The robustness of the model specification is significant in that (1) the 2003 biostimulation field experiment was performed with 3 times higher acetate concentrations than the previous biostimulation in the same field plot (i.e., the 2002 experiment), and (2) the 2007 field experiment was performed in a new unperturbed plot on the same site. The biogeochemical reactive transport simulations accounted for four terminal electron-accepting processes (TEAPs), two distinct functional microbial populations, two pools of bioavailable Fe(III) minerals (iron oxides and phyllosilicate iron), uranium aqueous and surface complexation, mineral precipitation and dissolution. The conceptual model for bioavailable iron reflects recent laboratory studies with sediments from the UMTRA site that demonstrated that the bulk (∼90%) of initial Fe(III) bioreduction is associated with phyllosilicate rather than oxide forms of iron. The uranium reaction network includes a U(VI) surface complexation model based on laboratory studies with Rifle site sediments and aqueous complexation reactions that include ternary complexes (e.g., calcium–uranyl–carbonate). The bioreduced U(IV), Fe(II), and sulfide components produced during the experiments are strongly associated with the solid phases and may play an important role in long-term uranium immobilization.

Potential of Penicillium species in the bioremediation field.

The effects on the environment of pollution, particularly that caused by various industrial activities, have been responsible for the accelerated fluxes of organic and inorganic matter in the ecosphere. Xenobiotics such as phenol, phenolic compounds, polycyclic aromatic hydrocarbons (PAHs), and heavy metals, even at low concentrations, can be toxic to humans and other forms of life. Many of the remediation technologies currently being used for contaminated soil and water involve not only physical and chemical treatment, but also biological processes, where microbial activity is the responsible for pollutant removal and/or recovery. Fungi are present in aquatic sediments, terrestrial habitats and water surfaces and play a significant part in natural remediation of metal and aromatic compounds. Fungi also have advantages over bacteria since fungal hyphae can penetrate contaminated soil, reaching not only heavy metals but also xenobiotic compounds. Despite of the abundance of such fungi in wastes, penicillia in particular have received little attention in bioremediation and biodegradation studies. Additionally, several studies conducted with different strains of imperfecti fungi, Penicillium spp. have demonstrated their ability to degrade different xenobiotic compounds with low co-substrate requirements, and could be potentially interesting for the development of economically feasible processes for pollutant transformation.

Quantifying expression of Geobacter spp. oxidative stress genes in pure culture and during in situ uranium bioremediation

As part of an effort to diagnose the physiological status of Geobacter species during in situ bioremediation of uranium-contaminated groundwater, transcript levels for two genes potentially associated with oxidative stress, cydA and sodA, were quantified throughout a bioremediation field study in Rifle, CO, USA. Despite the accumulation of Fe(II) in the groundwater, which is inconsistent with the presence of dissolved oxygen, both genes were highly expressed during the bioremediation process. Therefore, the response to oxidative stress was further evaluated with Geobacter uraniireducens, an isolate from the Rifle site. When G. uraniireducens cultured with fumarate as the electron acceptor was exposed to 5% oxygen for 8 h, there was a significant increase in cydA and sodA transcripts as well as other genes associated with oxygen respiration or oxidative stress. Oxygen-exposed cells had lower transcript abundance for genes associated with anaerobic respiration, metabolism and motility. Short-term oxygen exposure had little impact on cydA transcript levels, as more than 1 h was required for increases to levels comparable to the subsurface. Abundance of cydA and sodA transcripts for the isolate G. sulfurreducens were always higher in cells cultured with Fe(III) compared with fumarate as an electron acceptor, even when fumarate-grown cells were exposed to oxygen, and Fe(III)-grown cells were grown anaerobically. These results suggest that the apparently high Geobacter cydA and sodA expression during bioremediation cannot necessarily be attributed to oxidative stress and demonstrate that diagnosis of the metabolic status of subsurface microorganisms through transcript analysis should be coupled with appropriate geochemical analyses.

Transcriptome of Geobacter uraniireducens growing in uranium-contaminated subsurface sediments

To learn more about the physiological state of Geobacter species living in subsurface sediments, heat-sterilized sediments from a uranium-contaminated aquifer in Rifle, Colorado, were inoculated with Geobacter uraniireducens, a pure culture representative of the Geobacter species that predominates during in situ uranium bioremediation at this site. Whole-genome microarray analysis comparing sediment-grown G. uraniireducens with cells grown in defined culture medium indicated that there were 1084 genes that had higher transcript levels during growth in sediments. Thirty-four c-type cytochrome genes were upregulated in the sediment-grown cells, including several genes that are homologous to cytochromes that are required for optimal Fe(III) and U(VI) reduction by G. sulfurreducens. Sediment-grown cells also had higher levels of transcripts, indicative of such physiological states as nitrogen limitation, phosphate limitation and heavy metal stress. Quantitative reverse transcription PCR showed that many of the metabolic indicator genes that appeared to be upregulated in sediment-grown G. uraniireducens also showed an increase in expression in the natural community of Geobacter species present during an in situ uranium bioremediation field experiment at the Rifle site. These results demonstrate that it is feasible to monitor gene expression of a microorganism growing in sediments on a genome scale and that analysis of the physiological status of a pure culture growing in subsurface sediments can provide insights into the factors controlling the physiology of natural subsurface communities.

Integrated approach to PCE‐impacted site characterization, site management, and enhanced bioremediation

AbstractTetrachloroethene (PCE)‐ and trichloroethene (TCE)‐impacted sites pose significant challenges even when site characterization activities indicate that biodegradation has occurred naturally. Although site‐specific, regulatory, and economic factors play roles in the remedy‐selection process, the application of molecular biological tools to the bioremediation field has streamlined the assessment of remedial alternatives and allowed for detailed evaluation of the chosen remedial technology. The case study described here was performed at a PCE‐impacted site at which reductive dechlorination of PCE and TCE had led to accumulation of cis‐dichlorethene (cis‐DCE) with concentrations ranging from approximately 10 to 100 mg/L. Bio‐Trap® samplers and quantitative polymerase chain reaction (qPCR) enumeration of Dehalococcoides spp. were used to evaluate three remedial options: monitored natural attenuation, biostimulation with HRC®, and biostimulation with HRC‐S®. Dehalococcoides populations in HRC‐S‐amended Bio‐Traps deployed in impacted wells were on the order of 103 to 104 cells/bead but were below detection limits in most unamended and HRC‐amended Bio‐Traps. Thus the in situ Bio‐Trap study identified biostimulation with HRC‐S as the recommended approach, which was further evaluated with a pilot study. After the pilot HRC‐S injection, Dehalococcoides populations increased to 106 to 107 cells/bead, and concentrations of cis‐DCE and vinyl chloride decreased with concurrent ethene production. Based on these results, a full‐scale HRC‐S injection was designed and implemented at the site. As with the pilot study, full‐scale HRC‐S injection promoted growth of Dehalococcoides spp. and stimulated reductive dechlorination of the daughter products cis‐DCE and vinyl chloride. © 2008 Wiley Periodicals, Inc.

Bacterial Community Dynamics during Bioremediation of Diesel Oil-Contaminated Antarctic Soil

The effect of nutrient and inocula amendment in a bioremediation field trial using a nutrient-poor Antarctic soil chronically contaminated with hydrocarbons was tested. The analysis of the effects that the treatments caused in bacterial numbers and hydrocarbon removal was combined with the elucidation of the changes occurring on the bacterial community, by 16S rDNA-based terminal restriction fragment length polymorphism (T-RFLP) typing, and the detection of some of the genes involved in the catabolism of hydrocarbons. All treatments caused a significant increase in the number of bacteria able to grow on hydrocarbons and a significant decrease in the soil hydrocarbon content, as compared to the control. However, there were no significant differences between treatments. Comparison of the soil T-RFLP profiles indicated that there were changes in the structure and composition of bacterial communities during the bioremediation trial, although the communities in treated plots were highly similar irrespective of the treatment applied, and they had a similar temporal dynamics. These results showed that nutrient addition was the main factor contributing to the outcome of the bioremediation experiment. This was supported by the lack of evidence of the establishment of inoculated consortia in soils, since their characteristic electrophoretic peaks were only detectable in soil profiles at the beginning of the experiment. Genetic potential for naphthalene degradation, evidenced by detection of nahAc gene, was observed in all soil plots including the control. In treated plots, an increase in the detection of catechol degradation genes (nahH and catA) and in a key gene of denitrification (nosZ) was observed as well. These results indicate that treatments favored the degradation of aromatic hydrocarbons and probably stimulated denitrification, at least transiently. This mesocosm study shows that recovery of chronically contaminated Antarctic soils can be successfully accelerated using biostimulation with nutrients, and that this causes a change in the indigenous bacterial communities and in the genetic potential for hydrocarbon degradation.

Geochemistry and mineralogy of arsenic in (natural) anaerobic groundwaters

Here new data from field bioremediation experiments and geochemical modeling are reported to illustrate the principal geochemical behavior of As in anaerobic groundwaters. In the field bioremediation experiments, groundwater in Holocene alluvial aquifers in Bangladesh was amended with labile water-soluble organic C (molasses) and MgSO 4 to stimulate metabolism of indigenous SO 4 -reducing bacteria (SRB). In the USA, the groundwater was contaminated by Zn, Cd and SO 4 , and contained <10 μg/L As under oxidized conditions, and a mixture of sucrose and methanol were injected to stimulate SRB metabolism. In Bangladesh, groundwater was under moderately reducing conditions and contained ∼10 mg/L Fe and ∼100 μg/L As. In the USA experiment, groundwater rapidly became anaerobic, and dissolved Fe and As increased dramatically (As > 1000 μg/L) under geochemical conditions consistent with bacterial Fe-reducing conditions. With time, groundwater became more reducing and biogenic SO 4 reduction began, and Cd and Zn were virtually completely removed due to precipitation of sphalerite (ZnS) and other metal sulfide mineral(s). Following precipitation of chalcophile elements Zn and Cd, the concentrations of Fe and As both began to decrease in groundwater, presumably due to formation of As-bearing FeS/FeS 2 . By the end of the six-month experiment, dissolved As had returned to below background levels. In the initial Bangladesh experiment, As decreased to virtually zero once biogenic SO 4 reduction commenced but increased to pre-experiment level once SO 4 reduction ended. In the ongoing experiment, both SO 4 and Fe(II) were amended to groundwater to evaluate if FeS/FeS 2 formation causes longer-lived As removal. Because As-bearing pyrite is the common product of SRB metabolism in Holocene alluvial aquifers in both the USA and Southeast Asia, it was endeavored to derive thermodynamic data for arsenian pyrite to better predict geochemical processes in naturally reducing groundwaters. Including the new data for arsenian pyrite into Geochemist’s Workbench, its stability field completely dominates in reducing Eh–pH space and “displaces” other As-sulfides (orpiment, realgar) that have been implied to be important in previous modeling exercises and reported in rare field conditions. In summary, when anaerobic bacterial metabolism is optimized by providing both electron donors and acceptors, As is mobile under Fe-reducing conditions, immobile under SO 4 -reducing conditions, and arsenian pyrite is the likely stable mineral phase formed under SO 4 -reducing conditions, instead of pure As–S phases such as realgar or orpiment.

An In Situ Device to Measure Oxygen in the Vadose Zone and in Ground Water: Laboratory Testing and Field Evaluation

AbstractOxygen probes developed to measure in situ oxygen concentrations in gaseous and aqueous environments were evaluated in laboratory tests and during long‐term field evaluation trials at contaminated sites. The oxygen probes were shown to have a linear calibration and to be accurate compared to conventional dissolved oxygen electrodes and gas chromatography, both of which require labor‐intensive sample collection and processing. The probes, once calibrated, required no maintenance or recalibration for up to a period of 7 years in low‐oxygen environments, demonstrating long‐term stability. Times to achieve 90% of the stabilized concentration (t90) after a step change in aqueous oxygen concentration were 100–120 min in laboratory experiments and up to 180 min in field experiments, which is adequate for monitoring subsurface changes. Field application data demonstrated that the oxygen probes could monitor oxygen concentrations in hydrocarbon‐contaminated ground water to a depth of 20 m below the water table or in pyritic vadose zones over extended periods. During bioremediation field trials, oxygen monitoring enabled estimation of oxygen utilization rates by microorganisms and hydrocarbon biodegradation rates. Also, probes were able to monitor the development of ground water desaturation during air sparging trials, enabling the automated assessment of the distribution of injected air.

The Prestige oil spill: bacterial community dynamics during a field biostimulation assay

A field bioremediation assay using the oleophilic fertilizer S200 was carried out 12 months after the Prestige heavy fuel-oil spill on a beach on the Cantabrian coast (north Spain). This assay showed that S200-enhanced oil degradation, particularly of high-molecular-weight n-alkanes and alkylated PAHs, suggesting an increase in the microbial bioavailability of these compounds. The bacterial community structure was determined by cultivation-independent analysis of polymerase chain reaction-amplified 16S rDNA by denaturing gradient gel electrophoresis. Bacterial community was mainly composed of alpha-Proteobacteria (Rhodobacteriaceae and Sphingomonadaceae). Representatives of gamma-Proteobacteria (Chromatiales, Moraxellaceae, and Halomonadaceae), Bacteroidetes (Flavobacteriaceae), and Actinobacteria group (Nocardiaceae and Corynebacteriaceae) were also found. The addition of the fertilizer led to the appearance of the bacterium Mesonia algae in the early stages, with a narrow range of growth substrates, which has been associated with the common alga Achrosiphonia sonderi. The presence of Mesonia algae may be attributable to the response of the microbial community to the addition of N and P rather than indicating a role in the biodegradation process. The Rhodococcus group appeared in both assay plots, especially at the end of the experiment. It was also found at another site on the Galician coast that had been affected by the same spill. This genus has been associated with the degradation of n-alkanes up to C(36). Taking into account the high content of heavy alkanes in the Prestige fuel, these microorganisms could play a significant role in the degradation of such fuel. A similar bacterial community structure was observed at another site that showed a similar degree of fuel weathering.

The Potential of Metabolomics Tools in Bioremediation Studies

As a post-genomics tool, metabolomics is a young and vibrant field of science in its exponential growth phase. Metabolome analysis has become very popular recently, and novel techniques for acquiring and analyzing metabolomics data continue to emerge that are useful for a variety of biological studies. The bioremediation field has a lot to gain from the advances in this emerging area. Thus, this review article focuses on the potential of various experimental and conceptual approaches developed for metabolomics to be applied in bioremediation research, such as strategies for elucidation of biodegradation pathways using isotope distribution analysis and molecular connectivity analysis, the assessment of mineralization process using metabolic footprinting analysis, and the improvement of the biodegradation process via metabolic engineering. We demonstrate how the use of metabolomics tools can significantly extend and enhance the power of existing bioremediation approaches by providing a better overview of the biodegradation process.

Synthetic dyes decolourisation by white-rot fungi: Development of original microtitre plate method and screening

A microtitre plate-based method was developed for a fast screening of numerous fungal strains for their ability to decolourise textile dyes. In 3 days, this method allowed to estimate significant fungal decolourisation capability by measuring the absorbance decrease on up to ten dyes. More than 325 white-rot fungi (WRF) strains belonging to 76 fungal genera were compared with regards to their capability to decolourise five azo and two anthraquinone dyes as well as the dyes mixture. The most recalcitrant dyes belonged to the azo group. Several new species unstudied in the bioremediation field were found to be able to efficiently decolourise all the dyes tested.

Microbial PAH-Degradation in Soil: Degradation Pathways and Contributing Factors

Adverse effects on the environment and high persistence in the microbial degradation and environmental fate of polycyclic aromatic hydrocarbons (PAHs) are motivating interest. Many soil microorganisms can degrade PAHs and use various metabolic pathways to do so. However, both the physio-chemical characteristics of compounds as well as the physical, chemical, and biological properties of soils can drastically influence the degradation capacity of naturally occurring microorganisms for field bioremediation. Modern biological techniques have been widely used to promote the efficiency of microbial PAH-degradation and make the biodegradation metabolic pathways more clear. In this review microbial degradation of PAHs in soil is discussed, with emphasis placed on the main degradation pathways and the environmental factors affecting biodegradation.

Using Real-Time PCR to Assess Changes in the Hydrocarbon-Degrading Microbial Community in Antarctic Soil During Bioremediation

A real-time polymerase chain reaction (PCR) method to quantify the proportion of microorganisms containing alkane monooxygenase was developed and used to follow changes in the microbial community in hydrocarbon-contaminated Antarctic soil during a bioremediation field trial. Assays for the alkB and rpoB genes were validated and found to be both sensitive and reproducible (less than 2% intrarun variation and 25-38% interrun variation). Results from the real-time PCR analysis were compared to analysis of the microbial population by a culture-based technique [most probable number (MPN) counts]. Both types of analysis indicated that fertilizer addition to hydrocarbon-contaminated soil stimulated the indigenous bacterial population within 1 year. The proportion of alkB containing microorganisms was positively correlated to the concentration of n-alkanes in the soil. After the concentration of n-alkanes in the soil decreased, the proportion of alkane-degrading microorganisms decreased, but the proportion of total hydrocarbon-degrading microorganisms increased, indicating another shift in the microbial community structure and ongoing biodegradation.