Toward Improved Bioremediation Strategies: Response of BAM-Degradation Activity to Concentration and Flow Changes in an Inoculated Bench-Scale Sediment Tank.

Compound-specific isotope analysis (CSIA) can reveal mass-transfer limitations during biodegradation of organic pollutants by enabling the detection of masked isotope fractionation. Here, we applied CSIA to monitor the adaptive response of bacterial degradation in inoculated sediment to low contaminant concentrations over time. We characterized Aminobacter sp. MSH1 activity in a flow-through sediment tank in response to a transient supply of elevated 2,6-dichlorobenzamide (BAM) concentrations as a priming strategy and took advantage of an inadvertent intermittence to investigate the effect of short-term flow fluctuations. Priming and flow fluctuations yielded improved biodegradation performance and increased biodegradation capacity, as evaluated from bacterial activity and residual concentration time series. However, changes in isotope ratios in space and over time evidenced that mass transfer became increasingly limiting for degradation of BAM at low concentrations under such stimulated conditions, and that activity decreased further due to bacterial adaptation at low BAM (µg/L) levels. Isotope ratios, in conjunction with residual substrate concentrations, therefore helped identifying underlying limitations of biodegradation in such a stimulated system, offering important insight for future optimization of remediation schemes.

Unraveling biogeochemical complexity through better integration of experiments and modeling.

The evolution of groundwater quality in natural and contaminated aquifers is affected by complex interactions between physical transport and biogeochemical reactions. Identifying and quantifying the processes that control the overall system behavior is the key driver for experimentation and monitoring. However, we argue that, in contrast to other disciplines in earth sciences, process-based computer models are currently vastly underutilized in the quest for understanding subsurface biogeochemistry. Such models provide an essential avenue for quantitatively testing hypothetical combinations of interacting, complex physical and chemical processes. If a particular conceptual model, and its numerical counterpart, cannot adequately reproduce observed experimental data, its underlying hypothesis must be rejected. This quantitative process of hypothesis testing and falsification is central to scientific discovery. We provide a perspective on how closer interactions between experimentalists and numerical modelers would enhance this scientific process, and discuss the potential limitations that are currently holding us back. We also propose a data-model nexus involving a greater use of numerical process-based models for a more rigorous analysis of experimental observations while also generating the basis for a systematic improvement in the design of future experiments.

Does It Pay Off to Explicitly Link Functional Gene Expression to Denitrification Rates in Reaction Models?

Environmental omics and molecular-biological data have been proposed to yield improved quantitative predictions of biogeochemical processes. The abundances of functional genes and transcripts relate to the number of cells and activity of microorganisms. However, whether molecular-biological data can be quantitatively linked to reaction rates remains an open question. We present an enzyme-based denitrification model that simulates concentrations of transcription factors, functional-gene transcripts, enzymes, and solutes. We calibrated the model using experimental data from a well-controlled batch experiment with the denitrifier Paracoccous denitrificans. The model accurately predicts denitrification rates and measured transcript dynamics. The relationship between simulated transcript concentrations and reaction rates exhibits strong non-linearity and hysteresis related to the faster dynamics of gene transcription and substrate consumption, relative to enzyme production and decay. Hence, assuming a unique relationship between transcript-to-gene ratios and reaction rates, as frequently suggested, may be an erroneous simplification. Comparing model results of our enzyme-based model to those of a classical Monod-type model reveals that both formulations perform equally well with respect to nitrogen species, indicating only a low benefit of integrating molecular-biological data for estimating denitrification rates. Nonetheless, the enzyme-based model is a valuable tool to improve our mechanistic understanding of the relationship between biomolecular quantities and reaction rates. Furthermore, our results highlight that both enzyme kinetics (i.e., substrate limitation and inhibition) and gene expression or enzyme dynamics are important controls on denitrification rates.

Chromium (VI) removal kinetics by magnetite-coated sand: Small-scale flow-through column experiments.

Magnetite nanoparticles are promising materials for treating toxic Cr(VI), but safe handling is challenging due to their small size. We prepared flow-through columns containing 10% or 100% (v/v) magnetite-coated sand. Cr(VI) removal efficiency was determined for different Cr(VI) concentrations (0.1 or 1.0 mM), neutral or alkaline pH, and oxic/anoxic conditions. We formulated a reactive-transport model that accurately predicted total Cr removal, accounting for reversible and irreversible (chemi)sorption reactions. Our results show that the material removes and irreversibly sequesters Cr(VI). For the concentration range used 10% and 100% (v/v) -packed columns removed > 99% and 72% of influent Cr(VI), respectively. Two distinct parameter sets were necessary to fit the identical model formulation to the 10 or 100% (v/v) columns (e.g., maximum sorption capacities (qmax) of 1.37 µmol Cr/g sand and 2.48 µmol Cr/g, respectively), which we attributed to abrasion-driven magnetite micro-particle detachment during packing yielding an increase in reactive surface area. Furthermore, experiments under oxic conditions showed that, even when handled in the presence of O2, the magnetite-coated sand maintained a high removal capacity (47%). Our coupled experimental and modelling analyses indicates that magnetite-coated sand is a promising and suitable medium for treating Cr(VI)-contaminated water in fixed-bed reactors or permeable reactive barriers.

Mass-Transfer-Limited Biodegradation at Low Concentrations-Evidence from Reactive Transport Modeling of Isotope Profiles in a Bench-Scale Aquifer.

Organic contaminant degradation by suspended bacteria in chemostats has shown that isotope fractionation decreases dramatically when pollutant concentrations fall below the (half-saturation) Monod constant. This masked isotope fractionation implies that membrane transfer is slow relative to the enzyme turnover at µg L-1 substrate levels. Analogous evidence of mass transfer as a bottleneck for biodegradation in aquifer settings, where microbes are attached to the sediment, is lacking. A quasi-two-dimensional flow-through sediment microcosm/tank system enabled us to study the aerobic degradation of 2,6-dichlorobenzamide (BAM), while collecting sufficient samples at the outlet for compound-specific isotope analysis. By feeding an anoxic BAM solution through the center inlet port and dissolved oxygen (DO) above and below, strong transverse concentration cross-gradients of BAM and DO yielded zones of low (µg L-1) steady-state concentrations. We were able to simulate the profiles of concentrations and isotope ratios of the contaminant plume using a reactive transport model that accounted for a mass-transfer limitation into bacterial cells, where apparent isotope enrichment factors *ε decreased strongly below concentrations around 600 µg/L BAM. For the biodegradation of organic micropollutants, mass transfer into the cell emerges as a bottleneck, specifically at low (µg L-1) concentrations. Neglecting this effect when interpreting isotope ratios at field sites may lead to a significant underestimation of biodegradation.

Magnitude of Diffusion- and Transverse Dispersion-Induced Isotope Fractionation of Organic Compounds in Aqueous Systems.

Determining whether aqueous diffusion and dispersion lead to significant isotope fractionation is important for interpreting the isotope ratios of organic contaminants in groundwater. We performed diffusion experiments with modified Stokes diaphragm cells and transverse-dispersion experiments in quasi-two-dimensional flow-through sediment tank systems to explore isotope fractionation for benzene, toluene, ethylbenzene, 2,6-dichlorobenzamide, and metolachlor at natural isotopic abundance. We observed very small to negligible diffusion- and transverse-dispersion-induced isotope enrichment factors (ε < -0.4 ‰), with changes in carbon and nitrogen isotope values within ±0.5‰ and ±1‰, respectively. Isotope effects of diffusion did not show a clear correlation with isotopologue mass with calculated power-law exponents ß close to zero (0.007 < ß < 0.1). In comparison to ions, noble gases, and labeled compounds, three aspects stand out. (i) If a mass dependence is derived from collision theory, then isotopologue masses of polyatomic molecules would be affected by isotopes of multiple elements resulting in very small expected effects. (ii) However, collisions do not necessarily lead to translational movement but can excite molecular vibrations or rotations minimizing the mass dependence. (iii) Solute-solvent interactions like H-bonds can further minimize the effect of collisions. Modeling scenarios showed that an inadequate model choice, or erroneous choice of ß, can greatly overestimate the isotope fractionation by diffusion and, consequently, transverse dispersion. In contrast, available data for chlorinated solvent and gasoline contaminants at natural isotopic abundance suggest that in field scenarios, a potential additional uncertainty from aqueous diffusion or dispersion would add to current instrumental uncertainties on carbon or nitrogen isotope values (±1‰) with an additional ±1‰ at most.

Process-based modeling of arsenic(III) oxidation by manganese oxides under circumneutral pH conditions.

Numerous experimental studies have identified a multi-step reaction mechanism to control arsenite (As(III)) oxidation by manganese (Mn) oxides. The studies highlighted the importance of edge sites and intermediate processes, e.g., surface passivation by reaction products. However, the identified reaction mechanism and controlling factors have rarely been evaluated in a quantitative context. In this study, a process-based modeling framework was developed to delineate and quantify the relative contributions and rates of the different processes affecting As(III) oxidation by Mn oxides. The model development and parameterization were constrained by experimental observations from literature studies involving environmentally relevant Mn oxides at circumneutral pH using both batch and stirred-flow reactors. Our modeling results highlight the importance of a transitional phase, solely evident in the stirred-flow experiments, where As(III) oxidation gradually shifts from fast reacting Mn(IV) to slowly reacting Mn(III) edge sites. The relative abundance of these edge sites was the most important factor controlling the oxidation rate, whereas surface passivation restricted oxidation only in the stirred-flow experiment. The Mn(III) edge sites were demonstrated to play a crucial role in the oxidation and therefore in controlling the long-term fate of As. This study provided an improved understanding of Mn oxide reactivity and the significance in the cycling of redox-sensitive metal(loid)s in the environment.

AQDS and Redox-Active NOM Enables Microbial Fe(III)-Mineral Reduction at cm-Scales.

Redox-active organic molecules such as anthraquinone-2,6-disulfonate (AQDS) and natural organic matter (NOM) can act as electron shuttles thus facilitating electron transfer from Fe(III)-reducing bacteria (FeRB) to terminal electron acceptors such as Fe(III) minerals. In this research, we examined the length scale over which this electron shuttling can occur. We present results from agar-solidified experimental incubations, containing either AQDS or NOM, where FeRB were physically separated from ferrihydrite or goethite by 2 cm. Iron speciation and concentration measurements coupled to a diffusion-reaction model highlighted clearly Fe(III) reduction in the presence of electron shuttles, independent of the type of FeRB. Based on our fitted model, the rate of ferrihydrite reduction increased from 0.07 to 0.19 µmol d-1 with a 10-fold increase in the AQDS concentration, highlighting a dependence of the reduction rate on the electron-shuttle concentration. To capture the kinetics of Fe(II) production, the effective AQDS diffusion coefficient had to be increased by a factor of 9.4. Thus, we postulate that the 2 cm electron transfer was enabled by a combination of AQDS molecular diffusion and an electron hopping contribution from reduced to oxidized AQDS molecules. Our results demonstrate that AQDS and NOM can drive microbial Fe(III) reduction across 2 cm distances and shed light on the electron transfer process in natural anoxic environments.

Spatial and temporal evolution of groundwater arsenic contamination in the Red River delta, Vietnam: Interplay of mobilisation and retardation processes.

Geogenic arsenic (As) contamination of groundwater poses a major threat to global health, particularly in Asia. To mitigate this exposure, groundwater is increasingly extracted from low-As Pleistocene aquifers. This, however, disturbs groundwater flow and potentially draws high-As groundwater into low-As aquifers. Here we report a detailed characterisation of the Van Phuc aquifer in the Red River Delta region, Vietnam, where high-As groundwater from a Holocene aquifer is being drawn into a low-As Pleistocene aquifer. This study includes data from eight years (2010-2017) of groundwater observations to develop an understanding of the spatial and temporal evolution of the redox status and groundwater hydrochemistry. Arsenic concentrations were highly variable (0.5-510 µg/L) over spatial scales of <200 m. Five hydro(geo)chemical zones (indicated as A to E) were identified in the aquifer, each associated with specific As mobilisation and retardation processes. At the riverbank (zone A), As is mobilised from freshly deposited sediments where Fe(III)-reducing conditions occur. Arsenic is then transported across the Holocene aquifer (zone B), where the vertical intrusion of evaporative water, likely enriched in dissolved organic matter, promotes methanogenic conditions and further release of As (zone C). In the redox transition zone at the boundary of the two aquifers (zone D), groundwater arsenic concentrations decrease by sorption and incorporations onto Fe(II) carbonates and Fe(II)/Fe(III) (oxyhydr)oxides under reducing conditions. The sorption/incorporation of As onto Fe(III) minerals at the redox transition and in the Mn(IV)-reducing Pleistocene aquifer (zone E) has consistently kept As concentrations below 10 µg/L for the studied period of 2010-2017, and the location of the redox transition zone does not appear to have propagated significantly. Yet, the largest temporal hydrochemical changes were found in the Pleistocene aquifer caused by groundwater advection from the Holocene aquifer. This is critical and calls for detailed investigations.

Mass Transfer Limitation during Slow Anaerobic Biodegradation of 2-Methylnaphthalene.

While they are theoretically conceptualized to restrict biodegradation of organic contaminants, bioavailability limitations are challenging to observe directly. Here we explore the onset of mass transfer limitations during slow biodegradation of the polycyclic aromatic hydrocarbon 2-methylnaphthalene (2-MN) by the anaerobic, sulfate-reducing strain NaphS2. Carbon and hydrogen compound specific isotope fractionation was pronounced at high aqueous 2-MN concentrations (60 µM) (εcarbon = -2.1 ± 0.1‰/εhydrogen = -40 ± 7‰) in the absence of an oil phase but became significantly smaller (εcarbon = -0.9 ± 0.3‰/εhydrogen = -6 ± 3‰) or nondetectable when low aqueous concentrations (4 µM versus 0.5 µM) were in equilibrium with 80 or 10 mM 2-MN in hexadecane, respectively. This masking of isotope fractionation directly evidenced mass transfer limitations at (sub)micromolar substrate concentrations. Remarkably, oil-water mass transfer coefficients were 60-90 times greater in biotic experiments than in the absence of bacteria (korg-aq2-MN = 0.01 ± 0.003 cm h-1). The ability of isotope fractionation to identify mass transfer limitations may help study how microorganisms adapt and navigate at the brink of bioavailability at low concentrations. For field surveys our results imply that, at trace concentrations, the absence of isotope fractionation does not necessarily indicate the absence of biodegradation.

An Electron-Balance Based Approach to Predict the Decreasing Denitrification Potential of an Aquifer.

Numerical models for reactive transport can be used to estimate the breakthrough of a contaminant in a pumping well or at other receptors. However, as natural aquifers are highly heterogeneous with unknown spatial details, reactive transport predictions on the aquifer scale require a stochastic framework for uncertainty analysis. The high computational demand of spatially explicit reactive-transport models hampers such analysis, thus motivating the search for simplified estimation tools. We suggest performing an electron balance between the reactants in the infiltrating solution and in the aquifer matrix to obtain the hypothetical time of dissolved-reactant breakthrough at a receptor if the reaction with the matrix was instantaneous. This time we denote as the advective breakthrough time for instantaneous reaction (τinst ). It depends on the amount of the reaction partner present in the matrix, the mass flux of the dissolved reactant, and the stoichiometry. While the shape of the reactive-species breakthrough curve depends on various kinetic parameters, the overall timing scales with τinst . We calculate the latter by particle tracking. The effort of computing τinst is so low that stochastic calculations become feasible. We apply the concept to a two-dimensional test case of aerobic respiration and denitrification. A detailed spatially explicit reactive-transport model includes microbial dynamics. Scaling the time of local breakthrough curves observed at individual points by τinst decreased the variability of electron-donor breakthrough curves significantly. We conclude that the advective breakthrough time for instantaneous reaction is efficient in estimating the time over which an aquifer retains its degradation potential.

Turnover and legacy of sediment-associated PAH in a baseflow-dominated river.

Polycyclic Aromatic Hydrocarbons (PAH) ubiquitously occur in rivers and threaten the aquatic ecosystem. Understanding their fate and behaviour in rivers can help in improving management strategies. We develop a particle-facilitated transport model considering suspended sediments with sorbed PAH from different origins to investigate the turnover and legacy of sediment-bound PAH in the baseflow-dominated Ammer River in southwest Germany. Our model identifies the contributions of dissolved and particle-bound PAH during wet and dry periods to the annual load. The analysis of in-stream processes enables investigating the average turnover times of sediments and attached PAH for the main stem of the river. The legacy of sediment-bound PAH is studied by running the model assuming a 50% reduction in PAH emissions after the introduction of environmental regulation in the 1970s. Our results show that sediment-bound and dissolved PAH account for 75% and 25% of the annual PAH load, respectively. PAH are mainly emitted from urban areas that contribute over 74% to the total load. In steep reaches, the turnover times of sediments and attached PAH are similar, whereas they differ by 1-2 orders of magnitude in reaches with very mild slopes. Flow rates significantly affect PAH fluxes between the mobile water and the riverbed over the entire river. Total PAH fluxes from the river bed to the mobile water are simulated to occur when the discharge is larger than 5 m3s -1. River segments with large sediment storage show a potential of PAH legacy, which may have caused a PAH release over 10-20 years after the implementation of environmental regulation. This study is useful for assessing environmental impacts of PAH in rivers (e.g., their contribution to the river-water toxicity) and exemplifies that the longitudinal distribution, turnover, and legacy potential of PAH in a river system require a mechanistic understanding of river hydraulics and sediment transport.

Microplastic-Contaminant Interactions: Influence of Nonlinearity and Coupled Mass Transfer.

Microplastic particles are ubiquitously detected in the environment. Despite intensive public and scientific discussions, their potential to transport contaminants in rivers and oceans under environmental conditions is still under assessment. In the present study we measured sorption isotherms and kinetics in batch experiments using phenanthrene (as a typical hydrophobic wastewater contaminant) and microplastic particles of different sizes and materials. We observed a linear sorption isotherm for polyethylene, in contrast to nonlinear sorption of polyamide and polystyrene, which could be best described by the Freundlich and the Polanyi-Dubinin-Manes isotherms, respectively. We modeled sorption kinetics as a combination of external mass transfer governed by diffusion through an aqueous boundary layer and intraparticle diffusion within the plastic. Which of these processes controls the kinetics depends on the sorption strength, particle size, diffusion coefficients, and time. We used semi-analytical and numerical methods to simulate the coupled mass transfer for both linear and nonlinear sorption. We successfully applied the semi-analytical model to polyethylene and the numerical code to polyamide and polystyrene, reproducing the measured kinetics and obtaining reasonable values for mass transfer and intraparticle diffusion coefficients. Subsequently, we used these coefficients to estimate the transport potential and relevant time scales for microplastic-bound contaminants under environmental conditions. Environ Toxicol Chem 2019;38:1635-1644. © 2019 SETAC.

Fate of wastewater contaminants in rivers: Using conservative-tracer based transfer functions to assess reactive transport.

Interpreting the fate of wastewater contaminants in streams is difficult because their inputs vary in time and several processes synchronously affect reactive transport. We present a method to disentangle the various influences by performing a conservative-tracer test while sampling a stream section at various locations for chemical analysis of micropollutants. By comparing the outflow concentrations of contaminants with the tracer signal convoluted by the inflow time series, we estimated reaction rate coefficients and calculated the contaminant removal along a river section. The method was tested at River Steinlach, Germany, where 38 contaminants were monitored. Comparing day-time and night-time experiments allowed distinguishing photo-dependent degradation from other elimination processes. While photo-dependent degradation showed to be highly efficient for the removal of metroprolol, bisoprolol, and venlafaxine, its impact on contaminant removal was on a similar scale to the photo-independent processes when averaged over 24 h. For a selection of compounds analyzed in the present study, bio- and photodegradation were higher than in previous field studies. In the Steinlach study, we observed extraordinarily effective removal processes that may be due to the higher proportion of treated wastewater, temperature, DOC and nitrate concentrations, but also a higher surface to volume ratio from low flow conditions that favorizes photodegradation through the shallow water column and a larger transient storage than observed in comparable studies.

An Open, Object-Based Framework for Generating Anisotropy in Sedimentary Subsurface Models.

The spatial distribution of hydraulic properties in the subsurface controls groundwater flow and solute transport. However, many approaches to modeling these distributions do not produce geologically realistic results and/or do not model the anisotropy of hydraulic conductivity caused by bedding structures in sedimentary deposits. We have developed a flexible object-based package for simulating hydraulic properties in the subsurface-the Hydrogeological Virtual Realities (HyVR) simulation package. This implements a hierarchical modeling framework that takes into account geological rules about stratigraphic bounding surfaces and the geometry of specific sedimentary structures to generate realistic aquifer models, including full hydraulic-conductivity tensors. The HyVR simulation package can create outputs suitable for standard groundwater modeling tools (e.g., MODFLOW), is written in Python, an open-source programming language, and is openly available at an online repository. This paper presents an overview of the underlying modeling principles and computational methods, as well as an example simulation based on the Macrodispersion Experiment site in Columbus, Mississippi. Our simulation package can currently simulate porous media that mimic geological conceptual models in fluvial depositional environments, and that include fine-scale heterogeneity in distributed hydraulic parameter fields. The simulation results allow qualitative geological conceptual models to be converted into digital subsurface models that can be used in quantitative numerical flow-and-transport simulations, with the aim of improving our understanding of the influence of geological realism on groundwater flow and solute transport.

Modeling of Contaminant Biodegradation and Compound-Specific Isotope Fractionation in Chemostats at Low Dilution Rates.

We present a framework to model microbial transformations in chemostats and retentostats under transient or quasi-steady state conditions. The model accounts for transformation-induced isotope fractionation and mass-transfer across the cell membrane. It also verifies that the isotope fractionation ϵ can be evaluated as the difference of substrate-specific isotope ratios between inflow and outflow. We explicitly considered that the dropwise feeding of substrate into the reactor at very low dilution rates leads to transient behavior of concentrations and transformation rates and use this information to validate conditions under which a quasi-steady state treatment is justified. We demonstrate the practicality of the code by modeling a chemostat experiment of atrazine degradation at low dilution/growth rates by the strain Arthrobacter aurescens TC1. Our results shed light on the interplay of processes that control biodegradation and isotope fractionation of contaminants at low (µg/L) concentration levels. With the help of the model, an estimate of the mass-transfer coefficient of atrazine through the cell membrane was achieved (0.0025 s-1).

In-situ mass spectrometry improves the estimation of stream reaeration from gas-tracer tests.

The estimation of gas-exchange rates between streams and the atmosphere is of great importance for the fate of volatile compounds in rivers. For dissolved oxygen, this exchange process is called reaeration, and its accurate and precise estimation is essential for the quantification of metabolic rates. A common method for the determination of gas-exchange rates is through artificial gas-tracer tests with a proxy gas. We present the implementation of a portable gas-equilibrium membrane inlet mass spectrometer (GE-MIMS) to record concentrations of krypton and propane injected as tracer compound in the context of a gas-tracer test. The field-compatible GE-MIMS uses signals of atmospheric measurements for concentration standardization, and allows recording the dissolved-gas concentrations at a high temporal resolution, leading to overall low measurement uncertainty. Furthermore, the in-situ approach avoids loss of gas during the steps of sampling, transport, storage, and analysis required for ex-situ gas measurements. We compare obtained gas-exchange rate coefficients, reaeration and derived metabolic rates from the in-situ measurements to results obtained from head-space sampling of propane followed by laboratory analysis, and find much lower uncertainties with the in-situ method.

Application of Experimental Polystyrene Partition Constants and Diffusion Coefficients to Predict the Sorption of Neutral Organic Chemicals to Multiwell Plates in in Vivo and in Vitro Bioassays.

Sorption to the polystyrene (PS) of multiwell plates can affect the exposure to organic chemicals over time in in vitro and in vivo bioassays. Experimentally determined diffusion coefficients in PS ( DPS) were in a narrow range of 1.25 to 8.0 · 10-16 m2 s-1 and PS-water partition constants ( KPS/w) ranged from 0.04 to 5.10 log-units for 22 neutral organic chemicals. A kinetic model, which explicitly accounts for diffusion in the plastic, was applied to predict the depletion of neutral organic chemicals from different bioassay media by sorption to various multiwell plate formats. For chemicals with log Kow > 3, the medium concentrations decreased rapidly and considerably in the fish embryo toxicity assay but medium concentrations remained relatively constant in the cell-based bioassays with medium containing 10% fetal bovine serum (FBS), emphasizing the ability of the protein- and lipid-rich medium to compensate for losses by multiwell plate sorption. The PS sorption data may serve not only for exposure assessment in bioassays but also to model the contaminant uptake by and release from plastic packaging material and the chemical transport by PS particles in the environment.

Contaminant concentration versus flow velocity: drivers of biodegradation and microbial growth in groundwater model systems.

Aromatic hydrocarbons belong to the most abundant contaminants in groundwater systems. They can serve as carbon and energy source for a multitude of indigenous microorganisms. Predictions of contaminant biodegradation and microbial growth in contaminated aquifers are often vague because the parameters of microbial activity in the mathematical models used for predictions are typically derived from batch experiments, which don't represent conditions in the field. In order to improve our understanding of key drivers of natural attenuation and the accuracy of predictive models, we conducted comparative experiments in batch and sediment flow-through systems with varying concentrations of contaminant in the inflow and flow velocities applying the aerobic Pseudomonas putida strain F1 and the denitrifying Aromatoleum aromaticum strain EbN1. We followed toluene degradation and bacterial growth by measuring toluene and oxygen concentrations and by direct cell counts. In the sediment columns, the total amount of toluene degraded by P. putida F1 increased with increasing source concentration and flow velocity, while toluene removal efficiency gradually decreased. Results point at mass transfer limitation being an important process controlling toluene biodegradation that cannot be assessed with batch experiments. We also observed a decrease in the maximum specific growth rate with increasing source concentration and flow velocity. At low toluene concentrations, the efficiencies in carbon assimilation within the flow-through systems exceeded those in the batch systems. In all column experiments the number of attached cells plateaued after an initial growth phase indicating a specific "carrying capacity" depending on contaminant concentration and flow velocity. Moreover, in all cases, cells attached to the sediment dominated over those in suspension, and toluene degradation was performed practically by attached cells only. The observed effects of varying contaminant inflow concentration and flow velocity on biodegradation could be captured by a reactive-transport model. By monitoring both attached and suspended cells we could quantify the release of new-grown cells from the sediments to the mobile aqueous phase. Studying flow velocity and contaminant concentrations as key drivers of contaminant transformation in sediment flow-through microcosms improves our system understanding and eventually the prediction of microbial biodegradation at contaminated sites.