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Microbial activities and the versatility gained through adaptation to xenobiotic compounds are the main biological forces to counteract environmental pollution. The current results present a new adaptive mechanism that is mediated through posttranslational modifications. Strains of Delftia acidovorans incapable of growing autochthonously on 2,4-dichlorophenoxyacetate (2,4-D) were cultivated in a chemostat on 2,4-D in the presence of (R)-2-(2,4-dichlorophenoxy)propionate. Long-term cultivation led to enhanced 2,4-D degradation, as demonstrated by improved values of the Michaelis–Menten constant Km for 2,4-D and the catalytic efficiency kcat/Km of the initial degradative key enzyme (R)-2-(2,4-dichlorophenoxy)propionate/α-ketoglutarate-dependent dioxygenases (RdpA). Analyses of the rdpA gene did not reveal any mutations, indicating a nongenetic mechanism of adaptation. 2-DE of enzyme preparations, however, showed a series of RdpA forms varying in their pI. During adaptation increased numbers of RdpA variants were observed. Subsequent immunoassays of the RdpA variants showed a specific reaction with 2,4-dinitrophenylhydrazine (DNPH), characteristic of carbonylation modifications. Together these results indicate that posttranslational carbonylation modified the substrate specificity of RdpA. A model was implemented explaining the segregation of clones with improved degradative activity within the chemostat. The process described is capable of quickly responding to environmental conditions by reversibly adapting the degradative potential to various phenoxyalkanoate herbicides.

Most natural environments are characterized by frequent changes of their abiotic conditions. Microorganisms can respond to such changes by switching their physiological state between activity and dormancy allowing them to endure periods of unfavorable abiotic conditions. As a consequence, the competitiveness of microbial species is not simply determined by their growth performance under favorable conditions but also by their ability and readiness to respond to periods of unfavorable environmental conditions. The present study investigates the relevance of factors controlling the abundance and activity of individual bacterial species competing for an intermittently supplied substrate. For this purpose, numerical experiments were performed addressing the response of microbial systems to regularly applied feeding pulses. Simulation results show that community dynamics may exhibit a non-trivial link to the frequency of the external constraints and that for a certain combination of these environmental conditions coexistence of species is possible. The ecological implication of our results is that even non-dominant, neglected species can have a strong influence on realized species composition of dominant key species, due to their invisible presence enable the coexistence between important key species and by this affecting provided function of the system.

Spatial distribution of soil microorganisms is relevant for the functioning and performance of many ecosystem processes such as nutrient cycling or biodegradation of organic matters and contaminants. Beside the multitude of abiotic environmental factors controlling the distribution of microorganisms in soil systems, many microbial species exhibit chemotactic behavior by directing their movement along concentration gradients of nutrients or of chemoattractants produced by cells of their own kind. This chemotactic ability has been shown to promote the formation of complex distribution patterns even in the absence of environmental heterogeneities. Microbial population patterns in heterogeneous soil systems might be, hence, the result of the interplay between the heterogeneous environmental conditions and the microorganisms' intrinsic pattern formation capabilities.In this modeling study, we combined an individual-based modeling approach with a reactive pore-network model to investigate the formation of bacterial patterns in homogeneous and heterogeneous porous media. We investigated the influence of different bacterial chemotactic sensitivities (toward both substrate and bacteria) on bacterial distribution patterns. The emerging population patterns were classified with the support of a geostatistical approach, and the required conditions for the formation of any specific pattern were analyzed.Results showed that the chemotactic behavior of the bacteria leads to non-trivial population patterns even in the absence of environmental heterogeneities. The presence of structural pore scale heterogeneities had also an impact on bacterial distributions. For a range of chemotactic sensitivities, microorganisms tend to migrate preferably from larger pores toward smaller pores and the resulting distribution patterns thus resembled the heterogeneity of the pore space. The results clearly indicated that in a porous medium like soil the distribution of bacteria may not only be related to the external constraints but also to the chemotactic behavior of the bacterial cells.

Vertical flow systems filled with porous medium have been shown to efficiently remove volatile organic contaminants (VOCs) from contaminated groundwater. To apply this semi-natural remediation strategy it is however necessary to distinguish between removal due to biodegradation and due to volatile losses to the atmosphere. Especially for (potentially) toxic VOCs, the latter needs to be minimized to limit atmospheric emissions. In this study, numerical simulation was used to investigate quantitatively the removal of volatile organic compounds in two pilot-scale water treatment systems: an unplanted vertical flow filter and a planted one, which could also be called a vertical flow constructed wetland, both used for the treatment of contaminated groundwater. These systems were intermittently loaded with contaminated water containing benzene and MTBE as main VOCs. The highly dynamic but permanently unsaturated conditions in the porous medium facilitated aerobic biodegradation but could lead to volatile emissions of the contaminants. Experimental data from porous material analyses, flow rate measurements, solute tracer and gas tracer test, as well as contaminant concentration measurements at the boundaries of the systems were used to constrain a numerical reactive transport modeling approach. Numerical simulations considered unsaturated water flow, transport of species in the aqueous and the gas phase as well as aerobic degradation processes, which made it possible to quantify the rates of biodegradation and volatile emissions and calculating their contribution to total contaminant removal. A range of degradation rates was determined using experimental results of both systems under two operation modes and validated by field data obtained at different operation modes applied to the filters. For both filters, simulations and experimental data point to high biodegradation rates, if the flow filters have had time to build up their removal capacity. For this case volatile emissions are negligible and total removal can be attributed to biodegradation, only. The simulation study thus supports the use of both of these vertical flow systems for the treatment of groundwater contaminated with VOCs and the use of reactive transport modeling for the assessment of VOCs removal and operation modes in these high performance treatment systems.

Microbial contaminant degradation may either result in the utilization of the compound for growth or act as a protective mechanism against its toxicity. Bioavailability of contaminants for nutrition and toxicity has opposite consequences which may have resulted in quite different bacterial adaptation mechanisms; these may particularly interfere when a growth substrate causes toxicity at high bioavailability. Recently, it has been demonstrated that a high bioavailability of vapour-phase naphthalene (NAPH) leads to chemotactic movement of NAPH-degrading Pseudomonas putida (NAH7) G7 away from the NAPH source. To investigate the balance of toxic defence and substrate utilization, we tested the influence of the cell density on surface-associated growth of strain PpG7 at different positions in vapour-phase NAPH gradients. Controlled microcosm experiments revealed that high cell densities increased growth rates close (< 2 cm) to the NAPH source, whereas competition for NAPH decreased the growth rates at larger distances despite the high gas phase diffusivity of NAPH. At larger distance, less microbial biomass was likewise sustained by the vapour-phase NAPH. Such varying growth kinetics is explained by a combination of bioavailability restrictions and NAPH-based inhibition. To account for this balance, a novel, integrated ‘Best Equation’ describing microbial growth influenced by substrate availability and inhibition is presented.

Reactive transport simulations are a common approach for the quantitative assessment of contaminant biodegradation in the subsurface. To use knowledge on microbial kinetics for the simulation of in situ biodegradation, the mass transfer processes controlling the bioavailability of the contaminants need to be described appropriately. A common approach to account for this problem is using a linear exchange model controlling the link between bulk and bioavailable concentration. Assuming that the subsequent degradation is controlled by the bioavailable concentration, only, these two steps can be combined to an analytical expression for the overall reaction rate know as the Best-Equation. In our work, we evaluate this approach for its ability to describe biodegradation kinetics limited by pore-scale mass transfer. Results from explicit numerical and analytical simulations of mass transport and reactive consumption at the pore scale are used to test the accuracy of results obtained using the Best-Equation. Our analysis shows that strictly spoken the Best-Equation is not valid. However, a good approximation can be achieved with errors of less than 6% in cases of moderate bioavailability and much lower errors in cases of either low or high bioavailability. These results support the description of mass transfer processes used in many reactive transport models. Furthermore, we present a method to obtain an accurate estimate of the unknown rate parameter controlling the diffusive mass transfer processes at the pore scale.

The global-scale quantification of organic carbon (Corg) degradation pathways in marine sediments is difficult to achieve experimentally due to the limited availability of field data. In the present study, a numerical modeling approach is used as an alternative to quantify the major metabolic pathways of Corg oxidation (Cox) and associated fluxes of redox-sensitive species fluxes along a global ocean hypsometry, using the seafloor depth (SFD) as the master variable. The SFD dependency of the model parameters and forcing functions is extracted from existing empirical relationships or from the NOAA World Ocean Atlas. Results are in general agreement with estimates from the literature showing that the relative contribution of aerobic respiration to Cox increases from 80% in deep-sea sediments. Sulfate reduction essentially follows an inversed SFD dependency, the other metabolic pathways (denitrification, Mn and Fe reduction) only adding minor contributions to the global-scale mineralization of Corg. The hypsometric analysis allows the establishment of relationships between the individual terminal electron acceptor (TEA) fluxes across the sediment-water interface and their respective contributions to the Corg decomposition process. On a global average, simulation results indicate that sulfate reduction is the dominant metabolic pathway and accounts for approximately 76% of the total Cox, which is higher than reported so far by other authors. The results also demonstrate the importance of bioirrigation for the assessment of global species fluxes. Especially at shallow SFD most of the TEAs enter the sediments via bioirrigation, which complicates the use of concentration profiles for the determination of total TEA fluxes by molecular diffusion. Furthermore, bioirrigation accounts for major losses of reduced species from the sediment to the water column prohibiting their reoxidation inside the sediment. As a result, the total carbon mineralization rate exceeds the total flux of oxygen into the sediment by a factor of 2 globally.

The degradation of organic matter, including organic contaminants, in subsurface environments is controlled by the abundances and functional capabilities of the resident microorganisms. As a consequence, modeling approaches simulating the fate of organics and related changes in redox conditions have to account for the effects of microbial activity on the degradation kinetics, as well as for the spatial and temporal distributions of the chemical species (e.g., terminal electron acceptors, nutrients or toxic substances) that control microbial activity. The present paper reviews the principal modeling approaches that are used to simulate the degradation of organic matter in water-saturated porous media. Special attention is devoted to modeling the bioavailability of chemical substrates of microbial reactions, and the sequential occurrence of terminal electron accepting pathways. While the various model approaches found in the literature are capable of reproducing field data sets from various environmental settings, they are rarely compared in terms of performance and predictive ability. Most approaches incorporate simplifications or empirical rate laws, which limit their range of application. Thus, there remains a need for further development of more general, process-based modeling concepts to represent microbially mediated reactive processes.

At field sites with varying redox conditions, different redox-specific microbial degradation pathways contribute to total contaminant degradation. The identification of pathway-specific contributions to total contaminant removal is of high practical relevance, yet difficult to achieve with current methods. Current stable-isotope-fractionation-based techniques focus on the identification of dominant biodegradation pathways under constant environmental conditions. We present an approach based on dual stable isotope data to estimate the individual contributions of two redox-specific pathways. We apply this approach to carbon and hydrogen isotope data obtained from reactive transport simulations of an organic contaminant plume in a two-dimensional aquifer cross section to test the applicability of the method. To take aspects typically encountered at field sites into account, additional simulations addressed the effects of transverse mixing, diffusion-induced stable-isotope fractionation, heterogeneities in the flow field, and mixing in sampling wells on isotope-based estimates for aerobic and anaerobic pathway contributions to total contaminant biodegradation. Results confirm the general applicability of the presented estimation method which is most accurate along the plume core and less accurate towards the fringe where flow paths receive contaminant mass and associated isotope signatures from the core by transverse dispersion. The presented method complements the stable-isotope-fractionation-based analysis toolbox. At field sites with varying redox conditions, it provides a means to identify the relative importance of individual, redox-specific degradation pathways.

Vertical flow filters (unplanted) and vertical flow constructed wetlands (planted), simple and inexpensive technologies to treat effectively volatile organic compounds (VOCs) contaminated water, consist of containers filled with granular material which is intermittently fed with contaminated water. Contaminants are removed from the water percolating through the filter due to a combination of biodegradation, volatilization and root uptake as the main removal processes. While biodegradation is the desired process, volatile emission might restrict the application of such systems. The focus of this thesis is on the assessment and quantification of individual removal processes in pilot-scale outdoor vertical filters and wetlands, located in Leuna, Germany used for VOCs contaminated groundwater treatment. Numerical reactive transport simulations were performed to extrapolate findings from a pilot-scale intermittently loaded system used for domestic waste water treatment to predict the performance of such a system for treatment of water containing ammonium and two VOCs: benzene and methyl tertiary butyl ether – MTBE. Model simulations considered aerobic degradation and volatilization assuming different scenarios. Model results predicted depth and frequency of the intermittent water loading, as well as the degradation kinetics and material properties are relevant for the contribution of the individual processes to total VOCs removal. An appropriate combination of injection depth and composition of the filter material would result in increasing biodegradation enhanced by oxygen recharge, at a limited emission of volatiles. For a selected pilot-scale vertical flow filter in Leuna, benzene and MTBE volatilization and biodegradation were investigated by a combination of field measurements and conservative numerical model simulations. Non-reactive tracer tests and flow rate measurements showed highly transient flow and heterogeneous transport regime in this filter system. Radon-222 (naturally occurring in the treated water and measured at the in- and out-flow of the filter) behavior reproduced by numerical simulations and extrapolated for benzene and MTBE, indicated high volatilization potential. In contrast, relatively low volatile concentrations were detected by passive samplers on top of the filter. Qualitative assessment of biodegradation by catabolic genes analysis at different depths of the filter; and semi-quantitative assessment by stable isotope fractionation analysis indicated high potential for aerobic degradation. Thus, despite the high volatilization potential, biodegradation is dominating the contaminant mass removal: VOCs entering the soil air are subject to subsequent biodegradation in the upper filter layer acting, which is acting as a biofilter and reducing atmospheric VOCs emissions. Removal processes in a pilot-scale vertical flow filter and a vertical flow constructed wetland showing high VOCs removal, were analyzed by numerical reactive transport model simulations. Model calibration was based on porous material analyses, flow rate measurements, conservative solute and gas tracer tests, and in- and out-flow contaminant concentrations measurement. Numerical modeling results suggested very high biodegradation rates at both filters avoided volatile atmospheric emissions attributing the observed removal to biodegradation only. The simulation study thus supports the use of both of these vertical flow systems for the treatment of contaminated groundwater and the use of reactive transport modeling for the assessment of volatile organic compound removal in these high performance treatment systems.