02 Fakultät Bau- und Umweltingenieurwissenschaften
Permanent URI for this collectionhttps://elib.uni-stuttgart.de/handle/11682/3
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Item Open Access Microbial biostabilization in fine sediments(2022) Gerbersdorf, Sabine Ulrike; Wieprecht, Silke (Prof. Dr.-Ing.)Microbial biostabilization has increasingly received attention over the last years due to its significance for the dynamics of fine sediments in fluvial and coastal systems with implications for ecology, economy and human-health. This habilitation thesis highlights the contributions of the applicant and her team to this multi-disciplinary research area and is based on eight core publications that are presented in seven chapters. First, the topic of biofilm and biostabilization is introduced and second, the materials and methods applied are presented before own research findings are discussed. To start with, the stabilization potential of heterotrophic bacterial assemblages has been emphasised as well as the adhesive properties of the protein moieties within the EPS (extracellular polymeric substances) that are more significant than previously thought. Furthermore, the engineering potential of estuarine prokaryotic and eukaryotic assemblages has been studied separately and combined to reveal the effective cooperation of mixed biofilm that resulted in highest substratum stabilization although the effects were not clearly synergistic (=more than additive). The significance of biostabilization could be evidenced as well for freshwaters where highest adhesive capacity and sediment stability occurred during spring. Microbial community composition differed accordingly to result in mechanically highly diverse biofilm. Moreover, the importance of two of the most influential abiotic conditions, light intensity and hydrodynamics, was shown for biofilm growth, species composition and functionality - here biostabilization. In order to test adhesive properties at the relevant mesoscale (mm-cm) but non-destructively and highly sensitive, MagPI (Magnetic Particle Induction) has been applied. The last chapter concerns technical aspects to further improve its performance while demonstrating the impact of material and geometry and the importance of both, magnetic field strength and field gradient for the physics of the MagPI approach.Item Open Access Microbial stabilization of lotic fine sediments(Stuttgart : Eigenverlag des Instituts für Wasser- und Umweltsystemmodellierung der Universität Stuttgart, 2018) Schmidt, Holger; Wieprecht, Silke (Prof. Dr.-Ing.)The microbial stabilization of fine sediments constitutes an essential ecosystem function with great ecological and economic implications e.g. in the context of reservoir and waterway management. Although this process is well researched in intertidal mudflats, there is still a major lack of knowledge for lotic systems. To perform fundamental research in this field and to account for the associated very high level of complexity, expertise of natural and engineering science was combined in an interdisciplinary approach. A highly sophisticated mesocosm setup was designed and constructed to guarantee fully controllable and reproducible natural-like boundary conditions during biofilm formation. The overall aim of the performed studies in this doctoral thesis was a comprehensive investigation of all relevant parameters of the cultivated biofilms, such as the microbial biomass, the produced extracellular polymeric substances (EPS), and the composition of the microbial community as well as the stability of the biofilm. This extensive approach should allow the identification of functional key parameters of the biofilm as well as essential interactions and their impact on the overall biofilm ecosystem and resulting biostabilization. In a series of long-term experiments, different influencing factors on biofilm development and corresponding biostabilization were assessed. The first potential impact factor that was analyzed was the experimental setup itself. Furthermore, the influence of the seasonal changes of the microbial community in the utilized river water and the effects of different levels of bed shear stress and illumination intensity were assessed. The results of these different experiments provided essential new insights into the process of biostabilization of lotic fine sediments. Firstly, the reliability of the used experimental setup could be proven, as no significant differences could be detected in biofilm formation and biostabilization comparing different mesocosm sections. The fact that very similar biofilms were developing when the boundary conditions were identical was a crucial prerequisite for any further investigations. In addition, the relevance of biostabilization in lotic systems, which was doubted for a long time, could be proven. However, freshwater and brackish habitat can be very different (e.g. in terms of nutrient availability). This was exemplarily indicated by significantly lower microbial biomass in the analyzed freshwater biofilms compared to biofilms from well-studied intertidal mudflats. Moreover, the very complex interplays between bacteria and diatoms in the biofilm matrix were underlined which led to a focus on this subject during further subsequent studies via an extensive genetic and microscopic profiling. Secondly, the important role of EPS during biostabilization could be demonstrated, whereby the significance of extracellular proteins, such as adhesives produced by sessile diatoms, was suggested. This observation may extend the current EPS research which focusses on extracellular carbohydrates due to their high quantitative fraction in the EPS matrix. Furthermore, the interactions between the microbes, the extracellular matrix and the overall stability of the biofilm system appeared to be much more complex than formerly assumed. Thirdly, the importance of the microbial community in the biofilm system could be elucidated. Even though a high correlation between mere microbial biomass and biostabilization could be detected, especially the seasonality experiments emphasized the impact of the life style of key players among the diatoms. These insights could be extended during the experiments analyzing the different levels of abiotic boundary conditions, where differently stable biofilms were clearly dominated by different assemblages of dominant bacteria. These observations constitute very important new insights into microbial biostabilization as a direct correlation between microbial ecology and the overall, actually measurable ecosystem function of the biofilm could be shown for the first time. Concluding, the insights into the fundamental principles of biostabilization gathered during this thesis can be seen as important steps for further fundamental research. The construction of a reliable unique setup is complete, the reproducible biofilm cultivation in this setup is verified and first investigations of different driving factors during biostabilization were performed. These analyses paved the way for further studies to analyze currently hardly assessed boundary conditions and deeper assessments in order to generate a sound database for future modelling approaches of the dynamics of microbially stabilized lotic fine sediments.Item Open Access Mixed-dimension models for flow and transport processes in porous media with embedded tubular network systems(Stuttgart: Eigenverlag des Instituts für Wasser- und Umweltsystemmodellierung der Universität Stuttgart, 2020) Koch, Timo; Flemisch, Bernd (apl. Prof. Dr. rer. nat.)Flow in vascularized biological tissue, root water uptake, or flow around injection or extraction wells can be modeled by coupled mixed-dimensional PDE systems. Conceptually, such systems can be described as porous media with embedded tubular transport networks. We describe numerical methods for the simulation of such systems. The compartments are spatially discretized by non-matching computational grids: a three-dimensional mesh for the porous medium domain, and a geometrically embedded mesh of connected line segments for the network domain. A generalized abstract form of mixed-dimension embedded models is presented which summarizes several existing methods. A particularity of solutions to mixed-dimensional PDEs with dimensional gap two (0D-2D or 1D-3D) is the occurrence of singularities where the network center-lines intersect the porous domain. We introduce a new numerical scheme which removes these singularities by smoothing kernels, and exhibits improved convergence behavior and accuracy for coarse grid resolutions. The method is developed for isotropic, as well as anisotropic porous media. Furthermore, a new mixed-dimension embedded model for tissue perfusion and NMR signal generation is presented. Detailed perfusion simulations on the capillary scale are shown to reproduce image contrast of clinical (organ-scale) MRI data from multiple sclerosis patients. Similar modeling techniques and methods are then used to simulate root water uptake. For the implementation of such applications, a common software framework is developed by use of the open-source simulator DuMux. The framework allows the implementation of coupled mixed- and equidimensional models in a unified way, using software abstractions. Possible framework applications go beyond the methods presented in this work.Item Open Access Modelling biogeochemical and mass transport processes in the subsurface: investigation of microbially induced calcite precipitation(Stuttgart : Eigenverlag des Instituts für Wasser- und Umweltsystemmodellierung der Universität Stuttgart, 2016) Hommel, Johannes; Class, Holger (apl. Prof. Dr.-Ing.)