Numerical modeling and uncertainties in rate coefficients for methane utilization and TCE cometabolism by a methane-oxidizing mixed culture

On the reliable estimation of sequential Monod kinetic parameters

While dozens of studies have attempted to estimate the Monod kinetic parameters of microbial reductive dechlorination, published values in the literature vary by 2-6 orders of magnitude. This lack of consensus can be attributed in part to limitations of both experimental design and parameter estimation techniques. To address these issues, Hamiltonian Monte Carlo was used to produce more than one million sets of realistic simulated microcosm data under a variety of experimental conditions. These data were then employed in model fitting experiments using a number of parameter estimation algorithms for determining Monod kinetic parameters. Analysis of data from conventional triplicate microcosms yielded parameter estimates characterized by high collinearity, resulting in poor estimation accuracy and precision. Additionally, confidence intervals computed by commonly used classical regression analysis techniques contained true parameter values much less frequently than their nominal confidence levels. Use of an alternative experimental design, requiring the same number of analyses as conventional experiments but comprised of microcosms with varying initial chlorinated ethene concentrations, is shown to result in order-of-magnitude decreases in parameter uncertainty. A Metropolis algorithm which can be run on a typical personal computer is demonstrated to return more reliable parameter interval estimates.

Stochastic gene transcription with non-competitive transcription regulatory architecture

The transcription factors, such as activators and repressors, can interact with the promoter of gene either in a competitive or non-competitive way. In this paper, we construct a stochastic model with non-competitive transcriptional regulatory architecture and develop an analytical theory that re-establishes the experimental results with an improved data fitting. The analytical expressions in the theory allow us to study the nature of the system corresponding to any of its parameters and hence, enable us to find out the factors that govern the regulation of gene expression for that architecture. We notice that, along with transcriptional reinitiation and repressors, there are other parameters that can control the noisiness of this network. We also observe that, the Fano factor (at mRNA level) varies from sub-Poissonian regime to super-Poissonian regime. In addition to the aforementioned properties, we observe some anomalous characteristics of the Fano factor (at mRNA level) and that of the variance of protein at lower activator concentrations in the presence of repressor molecules. This model is useful to understand the architecture of interactions which may buffer the stochasticity inherent to gene transcription.

Quantifying Impacts of Microcosm Mass Loss on Kinetic Constant Estimation

Microcosm experiments to assess microbial reductive dechlorination of chlorinated aliphatic hydrocarbons typically experience 5-50% mass loss due to frequent sampling events and diffusion through septa. A literature review, however, reveals that models fit to such experiments for kinetic constant estimation have generally failed to account for experimental mass loss. To investigate possible resultant bias in best-fit parameters, a series of numerical experiments was conducted in which Monod kinetic models with and without mass loss were fit to more than 1300 synthetic data sets, generated using published microcosm data. Models that failed to account for mass loss resulted in significant fitted parameter bias. Bias ranged from 5 to 45% of the parameter magnitude for Monte Carlo simulations with low (approximately 10%) mass loss to 20-120% for simulations with high (approximately 40%) mass loss. In addition, for high mass loss simulations, best-fit values consistently fell along the bounds of the optimization range. These results suggest that failure to properly account for mass loss in microcosms may lead to inaccurate estimation of kinetic constants and may explain some of the literature-reported variability in these parameters. A model is presented that provides a method for including sampling and diffusional mass losses to improve kinetic constant estimation accuracy.

Methane Monooxygenase Gene Transcripts as Quantitative Biomarkers of Methanotrophic Activity in Methylosinus trichosporium OB3b

Methanotrophic microorganisms are characterized by their ability to oxidize methane. Globally they have a significant impact on methane emissions by attenuating net methane fluxes to the atmosphere in natural and engineered systems, though the populations are dynamic in their activity level in soils and waters. Methanotrophs oxidize methane using methane monooxygenase (MMO) enzymes, and selected subunit genes of the most common MMOs, specifically pmoA and mmoX, are used as biomarkers for the presence and abundance of populations of bacterial methanotrophs. The relative expression of these biomarker genes is dependent on copper-to-biomass ratios. Empirically derived quantitative relationships between methane oxidation biomarker transcript amounts and methanotrophic activity could facilitate determination of methane oxidation rates. In this study, pure cultures of a model type II methanotroph, Methylosinus trichosporium OB3b, were grown in hollow-fiber membrane bioreactors (HFMBR) under different steady-state methane oxidation conditions. Methanotroph biomass (DNA based) and methane oxidation biomarker mRNA transcript amounts were determined using quantitative PCR (qPCR) and reverse transcription-PCR (RT-qPCR), respectively. Under both copper-present and copper-limited conditions, per-cell pmoA mRNA transcript levels positively correlated with measured per-cell methane oxidation rates across 3 orders of magnitude. These correlations, if maintained across different methanotrophs, could prove valuable for inferring in situ oxidation rates of methanotrophs and understanding the dynamics of their impact on net methane emissions.IMPORTANCE Methanotrophs are naturally occurring microorganisms capable of oxidizing methane and have an impact on global net methane emissions. The genes pmoA and mmoX are used as biomarkers for bacterial methanotrophs. Quantitative relationships between transcript amounts of these genes and methane oxidation rates could facilitate estimation of methanotrophic activity. In this study, a strong correlation was observed between per-cell pmoA transcript levels and per-cell methane oxidation rates for pure cultures of the aerobic methanotroph M. trichosporium OB3b grown in bioreactors. If similar relationships exist across different methanotrophs, they could prove valuable for inferring in situ oxidation rates of methanotrophs and better understanding their impact on net methane emissions.

Evaluating alternate biokinetic models for trace pollutant cometabolism

Mathematical models of cometabolic biodegradation kinetics can improve our understanding of the relevant microbial reactions and allow us to design in situ or in-reactor applications of cometabolic bioremediation. A variety of models are available, but their ability to describe experimental data has not been systematically evaluated for a variety of operational/experimental conditions. Here five different models were considered: first-order; Michaelis-Menten; reductant; competition; and combined models. The models were assessed on their ability to fit data from simulated batch experiments covering a realistic range of experimental conditions. The simulated observations were generated by using the most complex model structure and parameters based on the literature, with added experimental error. Three criteria were used to evaluate model fit: ability to fit the simulated experimental data, identifiability of parameters using a colinearity analysis, and suitability of the model size and complexity using the Bayesian and Akaike Information criteria. Results show that no single model fits data well for a range of experimental conditions. The reductant model achieved best results, but required very different parameter sets to simulate each experiment. Parameter nonuniqueness was likely to be due to the parameter correlation. These results suggest that the cometabolic models must be further developed if they are to reliably simulate experimental and operational data.

Characterization and biodegradation kinetics of a new cold-adapted carbamazepine-degrading bacterium, Pseudomonas sp. CBZ-4

Carbamazepine is frequently detected in waters and hardly eliminated during conventional wastewater treatment processes due to its complicated chemical structure and resistance to biodegradation. A carbamazepine-degrading bacterium named CBZ-4 was isolated at a low temperature (10 degreeC) from activated sludge in a municipal wastewater treatment plant. Strain CBZ-4, which can use carbamazepine as its sole source of carbon and energy, was identified as Pseudomonas sp. by the 16S rRNA gene sequence. The composition and percentage of fatty acids, which can reveal the cold-adaptation mechanism of strain CBZ-4, were determined. Strain CBZ-4 can effectively degrade carbamazepine at optimal conditions: pH 7.0, 10 degreeC, 150 r/min rotation speed, and 13% inoculation volume. The average removal rate of carbamazepine was 46.6% after 144 hr of incubation. The biodegradation kinetics of carbamazepine by CBZ-4 was fitted via the Monod model. Vmax and Ks were found to be 0.0094 hr-1 and 32.5 mg/L, respectively.

Trichloroethylene aerobic cometabolism by suspended and immobilized butane-growing microbial consortia: a kinetic study

A kinetic study of butane uptake and trichloroethylene (TCE) aerobic cometabolism was conducted by two suspended-cell (15 and 30°C) and two attached-cell (15 and 30°C) consortia obtained from the indigenous biomass of a TCE-contaminated aquifer. The shift from suspended to attached cells resulted in an increase of butane (15 and 30°C) and TCE (15°C) biodegradation rates, and a significant decrease of butane inhibition on TCE biodegradation. The TCE 15°C maximum specific biodegradation rate was equal to 0.011 mg(TCE ) mg(protein)(-1) d(-1) with suspended cells and 0.021 mg(TCE) mg(protein)(-1) d(-1) with attached cells. The type of mutual butane/TCE inhibition depended on temperature and biomass conditions. On the basis of a continuous-flow simulation, a packed-bed PFR inoculated with the 15 or 30°C attached-cell consortium could attain a 99.96% conversion of the studied site's average TCE concentration with a 0.4-0.5-day hydraulic residence time, with a low effect of temperature on the TCE degradation performances.

Aerobic biotransformation of N-nitrosodimethylamine and N-nitrodimethylamine in methane and benzene amended soil columns

Aerobic biotransformation of N-nitrosodimethylamine (NDMA), an emerging contaminant of concern, and its structural analog N-nitrodimethylamine (DMN), was evaluated in benzene and methane amended groundwater passed through laboratory scale soil columns. Competitive inhibition models were used to model the kinetics for NDMA and DMN cometabolism accounting for the concurrent degradation of the growth and cometabolic substrates. Transformation capacities for NDMA and DMN with benzene (13 and 23μg (mgcells)(-1)) and methane (0.14 and 8.4μg (mgcells)(-1)) grown cultures, respectively are comparable to those presented in the literature, as were first order endogenous decay rates estimated to be 2.1×10(-2)±1.7×10(-3)d(-1) and 6.5×10(-1)±7.1×10(-1)d(-1) for the methane and benzene amended cultures, respectively. These studies highlight possible attenuation mechanisms and rates for NDMA and DMN biotransformation in aerobic aquifers undergoing active remediation, natural attenuation or managed aquifer recharge with treated wastewater (i.e., reclaimed water).

Use of on-site bioreactors to estimate the biotransformation rate of N-ethyl perfluorooctane sulfonamidoethanol (N-EtFOSE) during activated sludge treatment

Accurate rates are needed for models that predict the fate of xenobiotic chemicals and impact of inhibitors at full-scale wastewater treatment plants. On-site rates for aerobic biotransformation of N-ethyl perfluorooctane sulfonamidoethanol (N-EtFOSE), a fluorinated repellent, were determined by continuously pumping mixed liquor from an aeration basin into two well-mixed acrylic bioreactors (4-L) operated in parallel. Known masses of N-EtFOSE and bromide were continuously added to the reactors. Reactor effluents were then monitored for bromide, N-EtFOSE, and metabolites of N-EtFOSE. Of the six transformation products reported in batch studies, only N-ethyl perfluorooctane sulfonamido acetate (N-EtFOSAA) was detected in the effluents. Bromide addition to the reactors enabled rate estimates despite variations in flow rate. Pseudo-second order rate coefficients for the N-EtFOSE biotransformation to N-EtFOSAA, predicted using a dynamic model of the reactor system, were k=2.0 and 2.4Lg(-1)VSSd(-1) for the two reactors, which are slower than the rates previously obtained using batch reactors. Given the relatively slow rate of N-EtFOSE transformation, its sorption and volatilization may be important in wastewater processes. The methodology used in this study should be suitable for similar on-site rate assessments with other contaminants or inhibitors.

The kinetics of process dependent ammonia inhibition of methanogenesis from acetic acid

Advanced anaerobic digestion processes aimed at improving the methanization of sewage sludge may be potentially impaired by the production of inhibitory compounds (e.g. free ammonia). The result of methanogenic inhibition is relatively high effluent concentrations of acetic acid and other soluble organics, as well as reduced methane yields. An extreme example of such an advanced process is the thermal hydrolytic pretreatment of sludge prior to high solids digestion (THD). Compared to a conventional mesophilic anaerobic digestion process (MAD), THD operates in a state of constant inhibition driven by high free ammonia concentrations, and elevated pH values. As such, previous investigations of the kinetics of methanogenesis from acetic acid under uninhibited conditions do not necessarily apply well to the modeling of extreme processes such as THD. By conducting batch ammonia toxicity assays using biomass from THD and MAD reactors, we compared the response of these communities over a broad range of ammonia inhibition. For both processes, increased inhibitor concentrations resulted in a reduction of biomass growth rate (r(max) = μ(max)∙X) and a resulting decrease in the substrate half saturation coefficient (K(S)). These two parameters exhibited a high degree of correlation, suggesting that for a constant transport limited system, the K(S) was mostly a linear function of the growth rate. After correcting for reactor pH and temperature, we found that the THD and MAD biomass were both able to perform methanogenesis from acetate at high free ammonia concentrations (equivalent to 3-5 g/L total ammonia nitrogen), albeit at less than 30% of their respective maximum rates. The reduction in methane production was slightly less pronounced for the THD biomass than for MAD, suggesting that the long term exposure to ammonia had selected for a methanogenic pathway less dependent on those organisms most sensitive to ammonia inhibition (i.e. aceticlastic methanogens).

Modeling arsenite oxidation by chemoautotrophic Thiomonas arsenivorans strain b6 in a packed-bed bioreactor

Arsenic is a major toxic pollutant of concern for the human health. Biological treatment of arsenic contaminated water is an alternative strategy to the prevalent conventional treatments. The biological treatment involves a pre-oxidation step transforming the most toxic form of arsenic, As (III), to the least toxic form, As (V), respectively. This intermediate process improves the overall efficiency of total arsenic removal from the contaminated water. As (III) oxidation by the chemoautotrophic bacterium Thiomonas arsenivorans strain b6 was investigated in a fixed-film reactor under variable influent As (III) concentrations (500-4000 mg/L) and hydraulic residence times (HRTs) (0.2-1 day) for a duration of 137 days. During the entire operation, seven steady-state conditions were obtained with As (III) oxidation efficiency ranging from 48.2% to 99.3%. The strong resilience of the culture was exhibited by the recovery of the bioreactor from an As (III) overloading of 5300±400 mg As (III)/L day operated at a HRT of 0.2 day. An arsenic mass balance revealed that As (III) was mainly oxidized to As (V) with unaccounted arsenic (≤4%) well within the analytical error of measurement. A modified Monod flux expression was used to determine the biokinetic parameters by fitting the model against the observed steady-state flux data obtained from operating the bioreactor under a range of HRTs (0.2-1 day) and a constant influent As (III) concentration of 500 mg/L. Model parameters, k=0.71±0.1 mg As (III)/mg cells h, and K(s)=13.2±2.8 mg As (III)/L were obtained using a non-linear estimation routine and employing the Marquardt-Levenberg algorithm. Sensitivity analysis revealed k to be more sensitive to model simulations of As (III) oxidation under steady-state conditions than parameter K(s).

Autohydrogenotrophic perchlorate reduction kinetics of a microbial consortium in the presence and absence of nitrate

This is the first study to model the effects of nitrate on autohydrogenotrophic perchlorate biokinetics. Batch experiments demonstrated that the presence of nitrate significantly inhibited perchlorate degradation by a hydrogen-oxidizing, perchlorate-reducing microbial consortium. However, the consortium was capable of significant perchlorate reduction while the bulk of the nitrate was still present. Results showed that a modified competitive inhibition model successfully predicted autohydrogenotrophic perchlorate degradation in the presence of nitrate (initial concentrations of ∼230 μg ClO(4)(-)/L and 2.2-4.6 mg NO(3)(-)-N/L). The model describes perchlorate degradation as a function of the biomass, perchlorate, hydrogen, and nitrate concentrations, as well as the single-component perchlorate (28 μg/L), hydrogen (2.3 × 10(-6) M (aq)), and nitrate (0.15 mg/L as N) half-saturation coefficients (K(s)) and perchlorate maximum substrate utilization rate (k) (1.8 μg ClO(4)(-)/mg TSS-hr). Single-component parameters were obtained through a series of batch experiments performed under perchlorate-, nitrate-, and hydrogen-limiting conditions with initial concentrations of 80-340 μg ClO(4)(-)/L, 2.7-3.6 mg NO(3)(-)-N/L, and 1%-3% H(2) (g) by volume.

Chloroform aerobic cometabolism by butane-growing Rhodococcus aetherovorans BCP1 in continuous-flow biofilm reactors

This work focuses on chloroform (CF) cometabolism by a butane-grown aerobic pure culture (Rhodococcus aetherovorans BCP1) in continuous-flow biofilm reactors. The goals were to obtain preliminary information on the feasibility of CF biodegradation by BCP1 in biofilm reactors and to evaluate the applicability of the pulsed injection of growth substrate and oxygen to biofilm reactors. The attached-cell tests were initially conducted in a 0.165-L bioreactor and, then, scaled-up to a 1.772-L bioreactor. Glass cylinders were utilized as biofilm carriers. The continuous supply of growth substrate (butane), which led to the attainment of the highest CF degradation rate (8.4 mg(CF) day(-1) m (biofilm surface)(-2)), was compared with four schedules of butane and oxygen pulsed feeding. The pulsed injection technique allowed the attainment of a ratio of CF mass degraded per unit mass of butane supplied equal to 0.16 mg(CF) mg (butane)(-1), a value 4.4 times higher than that obtained with the continuous substrate supply. A procedure based on the utilization of integral mass balances and of average concentrations along the bioreactors resulted in a satisfactory match between the predicted and the experimental CF degradation performances, and can therefore be utilized to provide a guideline for optimizing the substrate pulsed injection schedule.

Performance and biofilm activity of nitrifying biofilters removing trihalomethanes

Nitrifying biofilters seeded with three different mixed-culture sources removed trichloromethane (TCM) and dibromochloromethane (DBCM) with removals reaching 18% for TCM and 75% for DBCM. In addition, resuspended biofilm removed TCM, bromodichloromethane (BDCM), DBCM, and tribromomethane (TBM) in backwash batch kinetic tests, demonstrating that the biofilters contained organisms capable of biotransforming the four regulated trihalomethanes (THMs) commonly found in treated drinking water. Upon the initial and subsequent increased TCM addition, total ammonia nitrogen (TOTNH(3)) removal decreased and then reestablished, indicating an adjustment by the biofilm bacteria. In addition, changes in DBCM removal indicated a change in activity related to DBCM. The backwash batch kinetic tests provided a useful tool to evaluate the biofilm's bacteria. Based on these experiments, the biofilters contained bacteria with similar THM removal kinetics to those seen in previous batch kinetic experiments. Overall, performance or selection does not seem based specifically on nutrients, source water, or source cultures and most likely results from THM product toxicity, and the use of GAC media appeared to offer benefits over anthracite for biofilter stability and long-term performance, although the reasons for this advantage are not apparent based on research to date.

Cometabolic degradation and inhibition kinetics of 1,2-dichloroethane (1,2-DCA) in suspended-growth nitrifying systems

Cometabolic degradation of 1,2-dichloroethane (1,2-DCA) and its inhibitory impact on nitrification were investigated by the use of a mixed suspended-growth culture enriched for nitrifiers. 1,2-DCA was found to be cometabolically degradable by the nitrifier culture. This degradation rate was found to be dependent on the initial 1,2-DCA level. The first-order 1,2-DCA degradation rate constants ranged between 0.42 and 0.87 L (g VSS)(-1) h(-1). Increase in NH4-N utilization favoured cometabolic degradation of 1,2-DCA. The amount of 1,2-DCA degraded per unit mass of NH4-N strongly correlated with initial NH4-N and 1,2-DCA concentrations, ranging between 50 mg L(-1) and 200 mg L(-1) and 1600 microg L(-1) and 100,000 microg L(-1), respectively. The presence of 1,2-DCA caused inhibition of oxygen uptake and NH4-N utilization. In spite of the adverse effect of 1,2-DCA on the nitrifying biomass, the system had a high capacity for cometabolic removal of this compound even at inhibitory concentrations. 1,2-DCA had mainly mixed inhibitor characteristics, but at low concentrations (< 25,000 microg/L) it acted rather as a competitive inhibitor. The inhibition constants belonging to 1,2-DCA, K(ic) (the dissociation constant of the enzyme-inhibitory compound complex) and K(iu) (the dissociation constant of the enzyme-substrate-inhibitory compound complex) were determined to be 6000-8000 microg L(-1) and 188,000-200,000 microg L(-1), respectively.

Growth and cometabolic reduction kinetics of a uranium- and sulfate-reducing Desulfovibrio/Clostridia mixed culture: Temperature effects

Bioremediation of contaminated soils and aquifers is subject to spatial and temporal temperature changes that can alter the kinetics of key microbial processes. This study quantifies temperature effects on the kinetics of an ethanol-fed sulfate-reducing mixed culture derived from a uranium-contaminated aquifer subject to seasonal temperature fluctuations. The mixed culture contains Desulfovibrio sp. and a Clostridia-like organism. Rates of growth, ethanol utilization, decay, and uranium reduction decreased with decreasing temperature. No significant uranium reduction was observed at 10 degrees C. While both Monod saturation kinetics and pseudo second-order kinetics adequately described the rates of growth and utilization of electron donor (ethanol), model parameters for the pseudo second-order expression had smaller uncertainties. Uranium reduction kinetics were best described by pseudo second-order kinetics modified to include a term for inactivation/death of cells.

Inhibition of a U(VI)- and sulfate-reducing consortia by U(VI)

The stimulation of microbial U(VI) reduction is currently being investigated as a means to reduce uranium's mobility in groundwater, but little is known about the concentration at which U(VI) might inhibit microbial activity, or the effect of U(VI) on bacterial community structure. We investigated these questions with an ethanol-fed U(VI)- and sulfate-reducing enrichment developed from sediment from the site of an ongoing field biostimulation experiment at Area 3 of the Oak Ridge Field Research Center (FRC). Sets of triplicate enrichments were spiked with increasing concentrations of U(VI) (from 49 microm to 9.2 mM). As the U(VI) concentration increased to 224 microM, the culture's production of acetate from ethanol slowed, and at or above 1.6 mM U(VI) little acetate was produced over the time frame of the experiment. An uncoupling inhibition model was applied to the data, and the inhibition coefficient for U(VI), Ku, was found to be approximately 100 microM U(VI), or 24 mg/L, indicating the inhibitory effect is relevant at highly contaminated sites. Microbial community structure at the conclusion of the experiment was analyzed with terminal restriction fragment length polymorphism (T-RFLP) analysis. T-RFs associated with Desulfovibrio-like organisms decreased in relative abundance with increasing U(VI) concentration, whereas Clostridia-like T-RFs increased.

Modelling geochemical and microbial consumption of dissolved oxygen after backfilling a high level radiactive waste repository

Dissolved oxygen (DO) left in the voids of buffer and backfill materials of a deep geological high level radioactive waste (HLW) repository could cause canister corrosion. Available data from laboratory and in situ experiments indicate that microbes play a substantial role in controlling redox conditions near a HLW repository. This paper presents the application of a coupled hydro-bio-geochemical model to evaluate geochemical and microbial consumption of DO in bentonite porewater after backfilling of a HLW repository designed according to the Swedish reference concept. In addition to geochemical reactions, the model accounts for dissolved organic carbon (DOC) respiration and methane oxidation. Parameters for microbial processes were derived from calibration of the REX in situ experiment carried out at the Aspö underground laboratory. The role of geochemical and microbial processes in consuming DO is evaluated for several scenarios. Numerical results show that both geochemical and microbial processes are relevant for DO consumption. However, the time needed to consume the DO trapped in the bentonite buffer decreases dramatically from several hundreds of years when only geochemical processes are considered to a few weeks when both geochemical reactions and microbially-mediated DOC respiration and methane oxidation are taken into account simultaneously.

Measurement of biodegradability parameters for single unsubstituted and methylated polycyclic aromatic hydrocarbons in liquid bacterial suspensions

Substrate depletion experiments were conducted to characterize aerobic biodegradation of 20 single polycyclic aromatic hydrocarbons (PAHs) by induced Sphingomonas paucimobilis strain EPA505 in liquid suspensions. PAHs consisted of low molecular weight, unsubstituted, and methyl-substituted homologs. A material balance equation containing the Andrews kinetic model, an extension of the Monod model accounting for substrate inhibition, was numerically fitted to batch depletion data to estimate extant kinetic parameters including the maximal specific uptake rates, q(max), the affinity coefficients, K(S), and the substrate inhibition coefficients, K(I). Strain EPA505 degraded all PAHs tested. Applied kinetic models adequately simulated experimental data. A cell proliferation assay involving reduction of the tetrazolium dye WST-1 was used to evaluate the ability of strain EPA505 to utilize individual PAHs as sole energy and carbon sources. Of the 22 PAHs tested, 9 supported bacterial growth. Evaluation of the biokinetic data showed that q(max) correlated highly with transmembrane flux as theoretically estimated by a diffusion model, pointing to transmembrane transport as a potential rate-determining process. The biodegradability data generated in this study is essential for the development of quantitative structure-activity relationships (QSARs) for biodegradability and for modeling biodegradation of simple PAH mixtures.

Experimental evaluation and mathematical modeling of microbially enhanced tetrachloroethene (PCE) dissolution

Experiments to assess metabolic reductive dechlorination (chlororespiration) at high concentration levels consistent with the presence of free-phase tetrachloroethene (PCE) were performed using three PCE-to-cis-1,2-dichloroethene (cis-DCE) dechlorinating pure cultures (Sulfurospirillum multivorans, Desulfuromonas michiganensis strain BB1, and Geobacter lovleyi strain SZ) and Desulfitobacterium sp. strain Viet1, a PCE-to-trichloroethene (TCE) dechlorinating isolate. Despite recent evidence suggesting bacterial PCE-to-cis-DCE dechlorination occurs at or near PCE saturation (0.9-1.2 mM), all cultures tested ceased dechlorinating at approximately 0.54 mM PCE. In the presence of PCE dense nonaqueous phase liquid (DNAPL), strains BB1 and SZ initially dechlorinated, but TCE and cis-DCE production ceased when aqueous PCE concentrations reached inhibitory levels. For S. multivorans, dechlorination proceeded at a rate sufficient to maintain PCE concentrations below inhibitory levels, resulting in continuous cis-DCE production and complete dissolution of the PCE DNAPL. A novel mathematical model, which accounts for loss of dechlorinating activity at inhibitory PCE concentrations, was developed to simultaneously describe PCE-DNAPL dissolution and reductive dechlorination kinetics. The model predicted that conditions corresponding to a bioavailability number (Bn) less than 1.25 x 10(-2) will lead to dissolution enhancement with the tested cultures, while conditions corresponding to a Bn greater than this threshold value can result in accumulation of PCE to inhibitory dissolved-phase levels, limiting PCE transformation and dissolution enhancement. These results suggest that microorganisms incapable of dechlorinating at high PCE concentrations can enhance the dissolution and transformation of PCE from free-phase DNAPL.

Chloroform degradation by butane-grown cells of Rhodococcus aetherovorans BCP1

The ability of a Rhodococcus aetherovorans strain, BCP1, to grow on butane and to degrade chloroform in the 0-633 microM range (0-75.5 mg l(-1)) via aerobic cometabolism was investigated by means of resting-cell assays. BCP1 degraded chloroform with a complete mineralization of the organic Cl. The resulting butane and chloroform maximum specific degradation rates were equal to 118 and 22 micromol mg(protein)(-1)day(-1), respectively. Butane inhibition on chloroform degradation was satisfactorily interpreted by means of a model of competitive inhibition, with an inhibition constant equal to 38 % of the estimated butane half-saturation constant, whereas chloroform (at 11 microM) did not inhibit butane utilization. Acetylene (1,720 microM) induced an almost complete inactivation of the degradation of both butane and chloroform, indicating that the studied cometabolic process is mediated by a monooxygenase enzyme. BCP1 proved capable of degrading vinyl chloride and 1,1,2-trichloroethane, but not 1,2-trans-dichloroethylene. BCP1 could grow on the intermediates of the most common butane metabolic pathways and on the aliphatic hydrocarbons from ethane to n-heptane. After growth on n-hexane, it was able to deplete chloroform (13 microM) with a degradation rate higher than that obtained, at the same chloroform concentration, after growth on butane.

Kinetic analysis of the inhibitory effect of trichloroethylene (TCE) on nitrification in cometabolic degradation

In this study, the inhibitory effect of TCE on nitrification process was investigated with an enriched nitrifier culture. TCE was found to be a competitive inhibitor of ammonia oxidation and the inhibition constant (K(I)) was determined as 666-802 microg/l. The TCE affinity for the AMO enzyme was significantly higher than ammonium. The effect of TCE on ammonium utilization was evaluated with linearized plots of Monod equation (e.g., Lineweaver-Burk, Hanes-Woolf and Eadie-Hofstee plots) and non-linear least square regression (NLSR). No significant differences were found among these data evaluation methods in terms of kinetic parameters obtained.

Cometabolism of trihalomethanes by Nitrosomonas europaea

The ammonia-oxidizing bacterium Nitrosomonas europaea (ATCC 19718) was shown to degrade low concentrations (50 to 800 mug/liter) of the four trihalomethanes (trichloromethane [TCM], or chloroform; bromodichloromethane [BDCM]; dibromochloromethane [DBCM]; and tribromomethane [TBM], or bromoform) commonly found in treated drinking water. Individual trihalomethane (THM) rate constants (k1THM) increased with increasing THM bromine substitution, with TBM > DBCM > BDCM > TCM (0.23, 0.20, 0.15, and 0.10 liters/mg/day, respectively). Degradation kinetics were best described by a reductant model that accounted for two limiting reactants, THMs and ammonia-nitrogen (NH3-N). A decrease in the temperature resulted in a decrease in both ammonia and THM degradation rates with ammonia rates affected to a greater extent than THM degradation rates. Similarly to the THM degradation rates, product toxicity, measured by transformation capacity (Tc), increased with increasing THM bromine substitution. Because both the rate constants and product toxicities increase with increasing THM bromine substitution, a water's THM speciation will be an important consideration for process implementation during drinking water treatment. Even though a given water sample may be kinetically favored based on THM speciation, the resulting THM product toxicity may not allow stable treatment process performance.

Cometabolism of cis-1,2-dichloroethene by aerobic cultures grown on vinyl chloride as the primary substrate

An aerobic enrichment culture was grown on vinyl chloride (VC) as the sole source of carbon and energy. In the absence of VC, the enrichment culture cometabolized cis-1,2-dichloroethene (cDCE) and, to a lesser extent, trans1,2-dichloroethene (tDCE), beginning with oxidation to the corresponding DCE-epoxides. When provided with VC (1.3 mM) and cDCE (0.2-0.3 mM), the enrichment culture cometabolized repeated additions of cDCE for over 85 days. Cometabolism of repeated additions of tDCE was also demonstrated but at a lower ratio of nongrowth substrate to VC. VC-grown Pseudomonas aeruginosa MF1 (previously isolated from the enrichment culture) also readily cometabolizes cDCE, with an observed transformation capacity (Tc,obs) of 0.82 micromol of cDCE/mg of total suspended solids (TSS). When provided with VC and cDCE, MF1 did not begin cometabolizing cDCE until nearly all of the VC was consumed. The presence of cDCE reduces the maximum specific rate of VC utilization. A kinetic model was developed that describes these phenomena via Monod parameters for substrate and nongrowth substrate, plus inactivation and inhibition coefficients. MF1 did not show any cometabolic activity on tDCE or trichloroethene and very limited activity on 1,1-DCE (Tc,obs = 2 x 10(-5) micromol/mg TSS). Above 40 microM, tDCE and TCE noticeably increased the maximum specific rate of VC utilization, even though neither compound was consumed during or after VC consumption. High concentrations of 1,1-DCE (950 microM) completely inhibited VC biodegradation. As there is currently no evidence for aerobic biodegradation of cDCE as a sole source of carbon and energy, the results of this study provide a potential explanation for in situ disappearance of cDCE when the only other significant substrate available is VC. It is fortuitous that the VC-grown cultures tested exhibit their highest cometabolic activity toward cDCE, because it is the predominant DCE isomer formed during anaerobic reductive dechlorination of trichloroethene and tetrachloroethene.

Transition from cometabolic to growth-linked biodegradation of vinyl chloride by a Pseudomonas sp. isolated on ethene

Pseudomonas aeruginosa strain DL1 was isolated on ethene as a sole carbon and energy source. When ethene-grown DL1 was first exposed to vinyl chloride (VC), the rate of VC consumption was very rapid and then declined sharply, indicative of a cometabolic process. A lack of growth and significant release of soluble products during this interval also indicates that the initial activity on VC was cometabolic. Following the rapid initial rate of VC cometabolism, a slow rate of VC utilization continued. After an extended period of incubation (>40 days), a transition occurred that allowed DL1 to begin using VC as a primary growth substrate, with an observed yield, maximum growth rate, and Monod half saturation coefficient of 0.21 mg of total suspended solids/mg VC, 0.046 d(-1), and 1.17 microM VC, respectively, at 22 degrees C. Acetylene inhibits consumption of ethene and VC by ethene-grown cells, suggesting a monooxygenase is responsible for initiating metabolism of these alkenes. Resting cells grown on ethene cometabolized VC with an observed transformation capacity of 9.1 micromol VC/mg total suspended solids and a transformation yield of 0.22 mol VC/mol ethene. The presence of 40 microM ethene increased the rate and amount of VC cometabolized. However, consumption of higher concentrations of ethene decreased the total amount of VC consumed, and VC inhibited ethene utilization. A kinetic model was developed that describes substrate interactions during batch depletion of ethene and VC for a range of initial concentrations. The results suggest that ethene may stimulate in situ biodegradation of VC either by functioning as a primary substrate to support cometabolism of VC or by selecting for organisms that can utilize VC as a primary substrate.

Modeling the kinetics of vinyl chloride cometabolism by an ethane-grown Pseudomonas sp

Pseudomonas sp strain EA1 was isolated under aerobic conditions using ethane as the sole organic carbon and electron donor source, with an observed yield of 0.99 mg total suspended solids/mg ethane (0.85 mg volatile suspended solids / mg ethane) and a maximum specific growth rate of 0.015 d(-1). When grown on ethane, EA1 cometabolizes vinyl chloride (VC) at a maximum rate of 0.350 micromol/mg volatile suspended solids/d and with a half saturation constant of 0.62 microM VC. The rate of VC use by EA1 is twice as high when ethane is also provided, even though consumption of ethane is almost completely inhibited until VC is consumed. The presence of ethane also reduces the total amount of VC cometabolized. A model was developed that adequately describes the batch kinetics of VC cometabolism in the presence and absence of ethane, as well as ethane metabolism in the presence and absence of VC. Terms are included that increase the initial rate of VC use in the presence of ethane (according to the ratio of initial ethane concentration to the half saturation coefficient) but decrease the total amount of VC cometabolized. Parameter estimates for the model were obtained using a step-wise experimental approach, with varying initial concentrations of VC and ethane. Strain EA1 completely dechlorinates VC in the presence and absence of ethane. Measurements of soluble chemical oxygen demand indicate that approximately 50% of the VC consumed is mineralized, with the balance released as soluble, nonchlorinated products. Ethene is not used as a substrate by EA1 but it does inhibit ethane metabolism and VC cometabolism. In mixtures containing all three compounds, more VC is degraded and at a faster rate compared to VC plus ethene. The results suggest that ethane-enhanced biodegradation of VC may contribute to VC removal at the aerobic fringe of groundwater plumes undergoing reductive dechlorination.

Statistical analysis of nonlinear parameter estimation for Monod biodegradation kinetics using bivariate data

A nonlinear regression technique for estimating the Monod parameters describing biodegradation kinetics is presented and analyzed. Two model data sets were taken from a study of aerobic biodegradation of the polycyclic aromatic hydrocarbons (PAHs), naphthalene and 2-methylnaphthalene, as the growth-limiting substrates, where substrate and biomass concentrations were measured with time. For each PAH, the parameters estimated were: q(max), the maximum substrate utilization rate per unit biomass; K(S), the half-saturation coefficient; and Y, the stoichiometric yield coefficient. Estimating parameters when measurements have been made for two variables with different error structures requires a technique more rigorous than least squares regression. An optimization function is derived from the maximumlikelihood equation assuming an unknown, nondiagonal covariance matrix for the measured variables. Because the derivation is based on an assumption of normally distributed errors in the observations, the error structures of the regression variables were examined. Through residual analysis, the errors in the substrate concentration data were found to be distributed log-normally, demonstrating a need for log transformation of this variable. The covariance between ln C and X was found to be small but significantly nonzero at the 67% confidence level for NPH and at the 94% confidence level for 2MN. The nonlinear parameter estimation yielded unique values for q(max), K(S), and Y for naphthalene. Thus, despite the low concentrations of this sparingly soluble compound, the data contained sufficient information for parameter estimation. For 2-methylnaphthalene, the values of q(max) and K(S) could not be estimated uniquely; however, q(max)/K(S) was estimated. To assess the value of including the relatively imprecise biomass concentration data, the results from the bivariate method were compared with a univariate method using only the substrate concentration data. The results demonstrated that the bivariate data yielded a better confidence in the estimates and provided additional information about the model fit and model adequacy. The combination of the value of the bivariate data set and their nonzero covariance justifies the need for maximum likelihood estimation over the simpler nonlinear least squares regression.

Spreadsheet method for evaluation of biochemical reaction rate coefficients and their uncertainties by weighted nonlinear least-squares analysis of the integrated monod equation

A convenient method for evaluation of biochemical reaction rate coefficients and their uncertainties is described. The motivation for developing this method was the complexity of existing statistical methods for analysis of biochemical rate equations, as well as the shortcomings of linear approaches, such as Lineweaver-Burk plots. The nonlinear least-squares method provides accurate estimates of the rate coefficients and their uncertainties from experimental data. Linearized methods that involve inversion of data are unreliable since several important assumptions of linear regression are violated. Furthermore, when linearized methods are used, there is no basis for calculation of the uncertainties in the rate coefficients. Uncertainty estimates are crucial to studies involving comparisons of rates for different organisms or environmental conditions. The spreadsheet method uses weighted least-squares analysis to determine the best-fit values of the rate coefficients for the integrated Monod equation. Although the integrated Monod equation is an implicit expression of substrate concentration, weighted least-squares analysis can be employed to calculate approximate differences in substrate concentration between model predictions and data. An iterative search routine in a spreadsheet program is utilized to search for the best-fit values of the coefficients by minimizing the sum of squared weighted errors. The uncertainties in the best-fit values of the rate coefficients are calculated by an approximate method that can also be implemented in a spreadsheet. The uncertainty method can be used to calculate single-parameter (coefficient) confidence intervals, degrees of correlation between parameters, and joint confidence regions for two or more parameters. Example sets of calculations are presented for acetate utilization by a methanogenic mixed culture and trichloroethylene cometabolism by a methane-oxidizing mixed culture. An additional advantage of application of this method to the integrated Monod equation compared with application of linearized methods is the economy of obtaining rate coefficients from a single batch experiment or a few batch experiments rather than having to obtain large numbers of initial rate measurements. However, when initial rate measurements are used, this method can still be used with greater reliability than linearized approaches.