Natural attenuation and enhanced bioremediation of organic contaminants in groundwater

Groundwater contamination and natural attenuation capacity at a petroleum spilled facility in Korea

As a remedial option, the natural attenuation capacity of a petroleum contaminated groundwater at a military facility was examined. Hydrogeological conditions, such as high water level, permeable uppermost layer and frequent heavy rainfall, were favorable to natural attenuation at this site. The changes in the concentrations of electron acceptors and donors, as well as the relevant hydrochemical conditions, indicated the occurrence of aerobic respiration, denitrification, iron reduction, manganese reduction and sulfate reduction. The calculated BTEX expressed biodegradation capacity ranged between 20.52 and 33.67 mg/L, which appeared effective for the reduction of the contaminants levels. The contribution of each electron accepting process to the total biodegradation was in the order: denitrification > iron reduction > sulfate reduction > aerobic respiration > manganese reduction. The BTEX and benzene point attenuation rates were 0.0058-0.0064 and 0.0005-0.0032 day(-1), respectively, and the remediation time was 0.7-1.2 and 2.5-30 years, respectively. The BTEX and benzene bulk attenuation rates were 8.69 x 10(-4) and 1.05 x 10(-3) day(-1), respectively, and the remediation times for BTEX and benzene were 7.2 and 17.5 years, respectively. However, most of the natural attenuation occurring in this site can be attributed to dilution and dispersion. Consequently, the biodegradation and natural attenuation capacities were good enough to lower the contaminants levels, but their rates appeared to be insufficient to reach the remediation goal within a reasonable time frame. Therefore, some active remedial measures would be required.

Assessing the correlation between anaerobic toluene degradation activity and bssA concentrations in hydrocarbon-contaminated aquifer material

The assessment of biodegradation activity in contaminated aquifers is critical to demonstrate the performance of bioremediation and natural attenuation and to parameterize models of contaminant plume dynamics. Real time quantitative PCR (qPCR) was used to target the catabolic bssA gene (coding for benzylsuccinate synthase) and a 16S rDNA phylogenetic gene (for total Bacteria) as potential biomarkers to infer on anaerobic toluene degradation rates. A significant correlation (P = 0.0003) was found over a wide range of initial toluene concentrations (1-100 mg/l) between toluene degradation rates and bssA concentrations in anaerobic microcosms prepared with aquifer material from a hydrocarbon contaminated site. In contrast, the correlation between toluene degradation activity and total Bacteria concentrations was not significant (P = 0.1125). This suggests that qPCR targeting of functional genes might offer a simple approach to estimate in situ biodegradation activity, which would enhance site investigation and modeling of natural attenuation at hydrocarbon-contaminated sites.

Current approaches for the assessment of in situ biodegradation

Considering the high costs and technical difficulties associated with conventional remediation strategies, in situ biodegradation has become a promising approach for cleaning up contaminated aquifers. To verify if in situ biodegradation of organic contaminants is taking place at a contaminated site and to determine if these processes are efficient enough to replace conventional cleanup technologies, a comprehensive characterization of site-specific biodegradation processes is essential. In recent years, several strategies including geochemical analyses, microbial and molecular methods, tracer tests, metabolite analysis, compound-specific isotope analysis, and in situ microcosms have been developed to investigate the relevance of biodegradation processes for cleaning up contaminated aquifers. In this review, we outline current approaches for the assessment of in situ biodegradation and discuss their potential and limitations. We also discuss the benefits of research strategies combining complementary methods to gain a more comprehensive understanding of the complex hydrogeological and microbial interactions governing contaminant biodegradation in the field.

Resolution of natural microbial community dynamics by community fingerprinting, flow cytometry, and trend interpretation analysis

Natural microbial communities generally have an unknown structure and composition because of their still not yet cultivable members. Therefore, understanding the relationships among the bacterial members, prediction of their behaviour, and controlling their functions are difficult and often only partly successful endeavours to date. This study aims to test a new idea that allows to follow community dynamics on the basis of a simple concept. Terminal restriction fragment length polymorphism (T-RFLP) analysis of bacterial 16S ribosomal RNA genes was used to describe a community profile that we define as composition of a community. Flow cytometry and analysis of DNA contents and forward scatter characteristics of the single cells were used to describe a community profile, which we define as structure of a community. Both approaches were brought together by a non-metric multidimensional scaling (n-MDS) for trend interpretation of changes in the complex community data sets. This was done on the basis of a graphical evaluation of the cytometric data, leading to the newly developed Dalmatian plot tool, which gave an unexpected insight into the dynamics of the unknown bacterial members of the investigated natural microbial community. The approach presented here was compared with other techniques described in the literature. The microbial community investigated in this study was obtained from a BTEX contaminated anoxic aquifer. The indigenous bacteria were allowed to colonise in situ microcosms consisting of activated carbon. These microcosms were amended with benzene and one of the electron acceptors nitrate, sulphate or ferric iron to stimulate microbial growth. The data obtained in this study indicated that the composition (via T-RFLP) and structure (via flow cytometry) of the natural bacterial community were influenced by the hydro-geochemical conditions in the test site, but also by the supplied electron acceptors, which led to distinct shifts in relative abundances of specific community members. It was concluded that engineered environments can be successfully monitored by single cell analytics in combination with established molecular tools and sophisticated statistical analyses, a combination that holds great promise for studying and monitoring natural microbial community behaviour.

Knowledge explosion in phytotechnologies for environmental solutions

Bioremediation using biotechnology and biodiversity--a multiscale approach.

Idling time of swimming bacteria near particulate surfaces contributes to apparent adsorption coefficients at the macroscopic scale under static conditions

Static capillary assays were performed to observe the distribution of Escherichia coli and several mutant strains at the interface between an aqueous solution and a Gelrite particulate suspension, used as a model porous medium. Motile smooth-swimming mutant bacteria (E. coli HCB437) accumulated at the interface, but did not penetrate very far into the Gelrite suspension. Motile wild-type bacteria (E. coli HCB1) penetrated much further than the smooth-swimming mutant, but did not accumulate to the same extent at the interface. Nonmotile tumbly mutant bacteria (E. coli HCB359) did not accumulate or penetrate to a significant degree. Computer simulations using a Monte Carlo algorithm, with input parameters based on bacterial swimming properties in static bulk aqueous systems, appeared to underestimate the bacterial idling time associated with solid surfaces. To account for physicochemical, biological and geometrical influences, an additional component of the bacterial idling time was included. The third component of the idling time was further analyzed semiquantitatively with a 1-D population-scale transport model with first-order association (k(on)) and dissociation (k(off)) adsorption-like kinetics. Computer simulation results suggested that this additional bacterial idling time not only increased the magnitudes of k(on) and k(off), but also enhanced the ratio of k(on) to k(off). This further implies that motile bacteria may tend to accumulate at the boundaries of low-permeable regions in groundwater systems, which is beneficial for bioremediation of residual contamination that may not be accessible by conventional remediation approaches.

Bioaugmentation in a newly established LECA-based horizontal flow soil filter reduces the adaptation period and enhances denitrification

The possibility of enhancing the denitrification of a newly established LECA-based horizontal subsurface flow (HSSF) soil filter receiving pretreated wastewater from a vertical flow filter was studied. The pilot-scale experiment offers evidence regarding the survival and reproduction of introduced microbes taken from an LECA-based HSSF constructed wetland (CW) that has similar internal conditions, after bioaugmentation into newly established LECA-based HSSF CW mesocosms. Bioaugmentation resulted in a trend towards higher and more stable denitrification in the supplemented mesocosms during the nearly half-year study period.

Oxidative cleavage of diverse ethers by an extracellular fungal peroxygenase

Many litter-decay fungi secrete heme-thiolate peroxygenases that oxidize various organic chemicals, but little is known about the role or mechanism of these enzymes. We found that the extracellular peroxygenase of Agrocybe aegerita catalyzed the H2O2-dependent cleavage of environmentally significant ethers, including methyl t-butyl ether, tetrahydrofuran, and 1,4-dioxane. Experiments with tetrahydrofuran showed the reaction was a two-electron oxidation that generated one aldehyde group and one alcohol group, yielding the ring-opened product 4-hydroxybutanal. Investigations with several model substrates provided information about the route for ether cleavage: (a) steady-state kinetics results with methyl 3,4-dimethoxybenzyl ether, which was oxidized to 3,4-dimethoxybenzaldehyde, gave parallel double reciprocal plots suggestive of a ping-pong mechanism (K(m)((peroxide)), 1.99 +/- 0.25 mM; K(m)((ether)), 1.43 +/- 0.23 mM; k(cat), 720 +/- 87 s(-1)), (b) the cleavage of methyl 4-nitrobenzyl ether in the presence of H2(18)O2 resulted in incorporation of 18O into the carbonyl group of the resulting 4-nitrobenzaldehyde, and (c) the demethylation of 1-methoxy-4-trideuteromethoxybenzene showed an observed intramolecular deuterium isotope effect [(k(H)/k(D))(obs)] of 11.9 +/- 0.4. These results suggest a hydrogen abstraction and oxygen rebound mechanism that oxidizes ethers to hemiacetals, which subsequently hydrolyze. The peroxygenase appeared to lack activity on macromolecular ethers, but otherwise exhibited a broad substrate range. It may accordingly have a role in the biodegradation of natural and anthropogenic low molecular weight ethers in soils and plant litter.

Enhancement of aerobic biodegradation in an oxygen-limiting environment using a saponin-based microbubble suspension

This study investigated the ability of a saponin-based microbubble suspension to enhance aerobic biodegradation of phenanthrene by subsurface delivery. As the microbubble suspension flowed through a sand column pressure buildup and release was repeatedly observed, which delivered oxygen to the less permeable regions. Burkholderia cepacia RPH1, a phenanthrene-degrading bacterium, was mainly transported in a suspended form in the microbubble suspension. When three pore volumes of the microbubble suspension containing B. cepacia RPH1 was introduced into a column contaminated with phenanthrene (100 mg/kg), the oxygen content declined to 5% from an initial value of 20% within 5 days and correspondingly, 34.4% of initial phenanthrene was removed in 8 days. The addition of two further three pore volumes enhanced the biodegradation efficiency by a factor of 2.2. Our data suggest that a saponin-based microbubble suspension could be a potential carrier for enhancing the aerobic biodegradation under an oxygen-limiting environment.

Enhanced transverse migration of bacteria by chemotaxis in a porous T-sensor

Subsurface bioremediation is often hindered by the inability to achieve good mixing between injected bacteria and residual contaminants. Chemotaxis, which is the ability of bacteria to migrate preferentially toward higher concentrations of certain chemical attractants, could potentially increase bacterial transport into the contaminated zone. To observe and quantify this chemotactic enhancement to bacterial dispersion transverse to groundwater flow, a microfluidic device--a porous T-sensor-was created. It allowed two streams of equal flow rate to enter side-by-side into a porous channel; the transverse mixing of the two streams was controlled primarily by dispersion. When a suspension of the chemotactic bacteria Escherichia coli HCB1 and a solution of chemical attractant alpha-methylaspartate were injected as the two incoming streams, enhanced bacterial migration into the attractant stream was observed relative to a control experiment with dispersion alone. Chemotaxis was observed under lower flow rates comparable to natural groundwaterflow. The chemotactic response was greater than that predicted by an advection-dispersion equation model using a chemotactic coefficient derived under quiescent experimental conditions, which suggests that flow in porous media may further enhance transverse migration for chemotactic bacteria. This study provided direct evidence of the significance of bacterial chemotactic transverse migration at groundwater flow rates.

In situ bioremediation of monoaromatic pollutants in groundwater: a review

Monoaromatic pollutants such as benzene, toluene, ethylbenzene and mixture of xylenes are now considered as widespread contaminants of groundwater. In situ bioremediation under natural attenuation or enhanced remediation has been successfully used for removal of organic pollutants, including monoaromatic compounds, from groundwater. Results published indicate that in some sites, intrinsic bioremediation can reduce the monoaromatic compounds content of contaminated water to reach standard levels of potable water. However, engineering bioremediation is faster and more efficient. Also, studies have shown that enhanced anaerobic bioremediation can be applied for many BTEX contaminated groundwaters, as it is simple, applicable and economical. This paper reviews microbiology and metabolism of monoaromatic biodegradation and in situ bioremediation for BTEX removal from groundwater under aerobic and anaerobic conditions. It also discusses the factors affecting and limiting bioremediation processes and interactions between monoaromatic pollutants and other compounds during the remediation processes.

Advances in monitoring of catabolic genes during bioremediation

Biodegradation of xenobiotic compounds by microbes is exploited in the clean up of contaminated environments by bioremediation. Catabolic (or functional) genes encode for specific enzymes in catabolic pathways such as key enzymes in xenobiotic degradation pathways. By assessing the abundance or the expression of key genes in environmental samples one can get a potential measure of the degradation activity. One way of assessing the abundance and expression of specific catabolic genes is by analyzing the metagenomic DNA and RNA from environmental samples. Three major challenges in the detection and quantification of catabolic genes in bioremediation studies are 1) the accurate and sensitive quantification from environmental samples 2) the coverage of the enzymatic potential by the targeted genes 3) the validation of the correlation with actual observed degradation activities in field cases. New advances in realtime PCR, functional gene arrays and meta-transcriptomics have improved the applicability of catabolic gene assessment during bioremediation.

Biodegradation in contaminated aquifers: incorporating microbial/molecular methods

In order to evaluate natural attenuation in contaminated aquifers, there has been a recent recognition that a multidisciplinary approach, incorporating microbial and molecular methods, is required. Observed decreases in contaminant mass and identified footprints of biogeochemical reactions are often used as evidence of intrinsic bioremediation, but characterizing the structure and function of the microbial populations at contaminated sites is needed. In this paper, we review the experimental approaches and microbial methods that are available as tools to evaluate the controls on microbially mediated degradation processes in contaminated aquifers. We discuss the emerging technologies used in biogeochemical studies and present a synthesis of recent studies that serve as models of integrating microbiological approaches with more traditional geochemical and hydrogeologic approaches in order to address important biogeochemical questions about contaminant fate.

Microbial diversity and genomics in aid of bioenergy

In view of the realization that fossil fuels reserves are limited, various options of generating energy are being explored. Biological methods for producing fuels such as ethanol, diesel, hydrogen (H2), methane, etc. have the potential to provide a sustainable energy system for the society. Biological H2 production appears to be the most promising as it is non-polluting and can be produced from water and biological wastes. The major limiting factors are low yields, lack of industrially robust organisms, and high cost of feed. Actually, H2 yields are lower than theoretically possible yields of 4 mol/mol of glucose because of the associated fermentation products such as lactic acid, propionic acid and ethanol. The efficiency of energy production can be improved by screening microbial diversity and easily fermentable feed materials. Biowastes can serve as feed for H2 production through a set of microbial consortia: (1) hydrolytic bacteria, (2) H2 producers (dark fermentative and photosynthetic). The efficiency of the bioconversion process may be enhanced further by the production of value added chemicals such as polydroxyalkanoate and anaerobic digestion. Discovery of enormous microbial diversity and sequencing of a wide range of organisms may enable us to realize genetic variability, identify organisms with natural ability to acquire and transmit genes. Such organisms can be exploited through genome shuffling for transgenic expression and efficient generation of clean fuel and other diverse biotechnological applications.

Evidence for in situ degradation of mono-and polyaromatic hydrocarbons in alluvial sediments based on microcosm experiments with 13C-labeled contaminants

A microcosm study was conducted to investigate the degradation of mono- and polyaromatic hydrocarbons under in situ-like conditions using alluvial sediments from the site of a former cokery. Benzene, naphthalene, or acenaphthene were added to the sediments as (13)C-labeled substrates. Based on the evolution of (13)C-CO(2) determined by gas chromatography isotope-ratio mass spectrometry (GC-IRMS) it was possible to prove mineralization of the compound of interest in the presence of other unknown organic substances of the sediment material. This new approach was suitable to give evidence for the intrinsic biodegradation of benzene, naphthalene, and acenaphthene under oxic and also under anoxic conditions, due to the high sensitivity and reproducibility of (13)C/(12)C stable isotope analysis. This semi-quantitative method can be used to screen for biodegradation of any slowly degrading, strongly sorbing compound in long-term experiments.

Household hazardous waste disposal to landfill: using LandSim to model leachate migration

Municipal solid waste (MSW) landfill leachate contains a number of aquatic pollutants. A specific MSW stream often referred to as household hazardous waste (HHW) can be considered to contribute a large proportion of these pollutants. This paper describes the use of the LandSim (Landfill Performance Simulation) modelling program to assess the environmental consequences of leachate release from a generic MSW landfill in receipt of co-disposed HHW. Heavy metals and organic pollutants were found to migrate into the zones beneath a model landfill site over a 20,000-year period. Arsenic and chromium were found to exceed European Union and US-EPA drinking water standards at the unsaturated zone/aquifer interface, with levels of mercury and cadmium exceeding minimum reporting values (MRVs). The findings demonstrate the pollution potential arising from HHW disposal with MSW.

Carbon conversion efficiency and limits of productive bacterial degradation of methyl tert-butyl ether and related compounds

The utilization of the fuel oxygenate methyl tert-butyl ether (MTBE) and related compounds by microorganisms was investigated in a mainly theoretical study based on the Y(ATP) concept. Experiments were conducted to derive realistic maintenance coefficients and K(s) values needed to calculate substrate fluxes available for biomass production. Aerobic substrate conversion and biomass synthesis were calculated for different putative pathways. The results suggest that MTBE is an effective heterotrophic substrate that can sustain growth yields of up to 0.87 g g(-1), which contradicts previous calculation results (N. Fortin et al., Environ. Microbiol. 3:407-416, 2001). Sufficient energy equivalents were generated in several of the potential assimilatory routes to incorporate carbon into biomass without the necessity to dissimilate additional substrate, efficient energy transduction provided. However, when a growth-related kinetic model was included, the limits of productive degradation became obvious. Depending on the maintenance coefficient m(s) and its associated biomass decay term b, growth-associated carbon conversion became strongly dependent on substrate fluxes. Due to slow degradation kinetics, the calculations predicted relatively high threshold concentrations, S(min), below which growth would not further be supported. S(min) strongly depended on the maximum growth rate mu(ma)(x), and b and was directly correlated with the half maximum rate-associated substrate concentration K(s), meaning that any effect impacting this parameter would also change S(min). The primary metabolic step, catalyzing the cleavage of the ether bond in MTBE, is likely to control the substrate flux in various strains. In addition, deficits in oxygen as an external factor and in reduction equivalents as a cellular variable in this reaction should further increase K(s) and S(min) for MTBE.

Environmental biocatalysis: from remediation with enzymes to novel green processes

Modern biocatalysis is developing new and precise tools to improve a wide range of production processes, which reduce energy and raw material consumption and generate less waste and toxic side-products. Biocatalysis is also achieving new advances in environmental fields, from enzymatic bioremediation to the synthesis of renewable and clean energies and biochemical cleaning of 'dirty' fossil fuels. Despite the obvious benefits of biocatalysis, the major hurdles hindering the exploitation of the repertoire of enzymatic processes are, in many cases, the high production costs and the low yields obtained. This article will discuss these issues, pinpointing specific new advances in recombinant DNA techniques amenable to future biocatalyst development, in addition to drawing the attention of the biotechnology community to the active pursuit and development of environmental biocatalysis, from remediation with enzymes to novel green processes.

Assessment of biogeochemical natural attenuation and treatment of chlorinated solvents, Altus Air Force Base, Altus, Oklahoma

Biogeochemical reductive dechlorination (BiRD) is a newly recognized method for the remediation or natural attenuation of chlorinated solvents. Chlorinated solvents are rapidly treated by abiotic reaction with reduced mineral iron sulfides. Iron sulfides are formed by naturally occurring sulfate-reducing bacteria when sufficient SO(4)(2-) and organic carbon are present or supplied to sediments containing mineral iron. An example of site characterization focusing on BiRD is presented focusing on mineral phases. Methods demonstrated here may be employed at other sites to evaluate naturally occurring BiRD or to evaluate an engineered BiRD remediation. A field investigation was performed at a TCE contaminated site at Altus AFB with naturally high concentrations of SO(4)(2-) and Fe(III) minerals and where an accidental fuel spill provided organic carbon. In the area of this fuel spill significant mineral iron sulfides were found, sulfate was almost completely removed, and TCE was absent. Only small amounts of daughter products were found, further indicating that the BiRD pathway was operative. Mass balance data indicates all of the remaining TCE (182 kg) could be treated by the remaining FeS (66.5 kg) in the upper aquifer; however, the FeS was not co-located with TCE to enable complete reaction. Laboratory microcosm tests with FeS amended and FeS-rich sediment from Altus AFB also suggest that BiRD is capable of destroying TCE. The results suggest that an engineered BiRD treatment is possible for this site.