Integrating Antibiotic Concentrations and Microbial Resistance Selection in Soils: Mechanistic Modelling Approaches for Risk Assessment

Abstract

Antimicrobial resistance (AMR) is increasingly recognized as an environmental as well as a clinical problem. While resistance has traditionally been studied in the context of human and veterinary medicine, there is growing evidence that environmental compartments play a central role in the emergence and spread of resistance. Environmental systems host large and diverse microbial communities that are continuously exposed to low concentrations of antibiotics and other stressors, creating conditions under which resistance can be selected, maintained, and potentially transferred between organisms. Soils are of particular relevance in this context. They receive antibiotics, among other sources, through manure and sludge application and wastewater irrigation, resulting in long-term, low-level exposure of complex microbial communities. Unlike clinical settings, environmental systems are characterized by strong heterogeneity, spatial structure, and temporal variability. Microorganisms in soils experience highly localized conditions with respect to pH, nutrient availability and water content all of which influence both antibiotic fate and biological responses. These features complicate the assessment of antibiotic effects and make it difficult to directly relate observed environmental concentrations to resistance risks. A central challenge in environmental resistance research is that observed or extracted concentrations do not directly represent the dose experienced by microorganisms. Antibiotics in soils are subject to a range of fate processes, including sorption, diffusion into soil particles, and degradation, which modify both their availability. Apparent dissipation inferred from declining extractable concentrations may reflect the potentially reversible formation of non-extractable residues rather than complete mineralization, meaning that external concentrations alone provide an incomplete description of exposure. In addition, non-extractable residues further complicate the concept of bioavailability, as their formation mechanisms and long-term behaviour remain unclear. This thesis uses a mechanistic modelling approach to investigate how environmental antibiotic concentrations translate into resistance selection in soils. The modelling framework explicitly links three classes of processes: environmental fate processes in soils, cellular uptake and intracellular accumulation, and microbial population dynamics. Environmental fate is represented through sorption, diffusion into soil particles, and degradation, which together determine bioavailability. Cellular uptake is described mechanistically based on acid-base speciation, membrane permeability, and electrochemical gradients, allowing intracellular concentrations to be derived from environmental conditions. Microbial competition is modelled at the population level by coupling intracellular antibiotic exposure to growth inhibition and fitness costs of resistance. The results indicate that apparent dissipation of antibiotics in soils is often dominated by the formation of non-extractable residues rather than complete mineralization. In particular, intra-particle diffusion provides a plausible mechanistic explanation for the rapid initial decline in extractable concentrations, as antibiotics may diffuse into slowly accessible domains within soil particles or aggregates. This process can buffer environmental exposure by sustaining low-level concentrations over extended periods, even when extractable residues decline. At the cellular level, acid-base speciation and environmental pH strongly control intracellular antibiotic exposure. For weak acids, ion trapping can lead to intracellular accumulation when pKa values overlap with environmentally relevant pH ranges, resulting in predicted enrichment factors of up to two orders of magnitude based on speciation alone. These uptake processes imply that small changes in environmental pH can translate into large differences in intracellular concentrations and biological effects. Selection occurs when inhibition through antibiotic pressure exceeds the fitness disadvantage of resistant strains, which can already happen at concentrations far below the minimum inhibitory concentration, defined by the minimum selective concentration. Processes that amplify intracellular exposure, such as ion trapping, can therefore shift systems across selective thresholds even when environmental concentrations remain low, while limited uptake or slow equilibration can delay or prevent resistance selection. Temporal exposure dynamics further modify resistance outcomes. Periodic antibiotic inputs generate short concentration peaks followed by prolonged low-level exposure, and such pulsed dynamics can promote resistance selection even when average concentrations remain below the minimum selective concentration. In addition, exposure to multiple antibiotics introduces interaction effects that can be synergistic, additive, neutral, or antagonistic, thereby altering selective pressure relative to single-compound exposure. Taken together, the results demonstrate that resistance selection in environmental systems is governed by some key mechanisms that regulate intracellular antibiotic exposure. pH-dependent uptake, sorption and formation of non-extractable residues, temporal input dynamics, and mixture interactions jointly determine selective pressure, whereas total environmental concentrations and degradation alone are insufficient predictors of resistance risk.

Die Dissertation ist gesperrt bis zum 24.04.2028 !