7th joint conference "Joint Microbiology & Infection Conference 2024" of the DGHM and VAAM

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Evolution across environmental nutrient concentrations: How microbes evolve and maintain low half-saturation for growth rate

Microbial Ecology & Evolution

Microbes grow faster when they have more of a limiting nutrient. The relationship between nutrient concentration and population growth rate is critical to predict how members of microbial communities respond to environmental perturbations. Models of this response, such as the widely used Monod model, are generally characterized by a maximum growth rate and a half-saturation concentration of the resource. What values should we expect for these half-saturation concentrations, and how should they depend on the resource concentration in nature?We survey growth response data across a wide range of resources and microbial taxa, including many phytoplankton. We find that the half-saturation concentrations vary across orders of magnitude, even for the same organism and resource. To explain this variation, we develop an evolutionary model to show that demographic fluctuations (genetic drift) can constrain the adaptation of half-saturation concentrations. We find that this effect fundamentally differs depending on the type of population dynamics: Populations undergoing periodic bottlenecks of fixed size will adapt their half-saturation concentrations in proportion to the environmental resource concentrations, but populations undergoing periodic dilutions of fixed size will evolve half-saturation concentrations that are largely decoupled from the environmental concentrations.Our model provides testable predictions on how the ability for low concentration growth is distributed across microbial habitats and along resource gradients, but it also reveals how an evolved half-saturation concentration may not reflect the organism&quot;s environment. In particular, this explains how taxa in resource-rich environments can still evolve fast growth at low resource concentrations.

Abstract Speaker

Oral Presentation

Evolution on a microscale: Empowering adaptation and selection through a microfluidic chip

IntroductionAdaptive laboratory evolution (ALE) is a key tool to investigate fundamental questions about the processes underlying the evolution of life and how microbial populations adapt to their environments, such as the emergence of antibiotic resistance. Microfluidics have fundamentally changed the field of microbial ALE as it can mimic naturally occurring microenvironments promoting the growth of biofilms alongside planktonic cells.[1]GoalsA microfluidic ALE chip device that features adjustable, spatially defined physico-chemical stressor gradients should be developed employing an in-flow gradient aligned parallel to the flow direction to enhance the robustness of ALE process including the efficient on-chip screening of the complete entire cell population.Materials &amp; MethodsThe evo.S (evolution under stress) microfluidic chip was designed using CAD and fabricated from PDMS (polydimethylsiloxane) and used for the adaptation of microbial cells to stressors in a customizable stressor concentration gradient.[2]ResultsThe controlled generation of different gradient profiles across the interconnected compartments leads to adaptation of Escherichia coli to the presence of antibiotics and revealed the chip's capacity to differentiate between persistence and resistance. Importantly, this approach was effectively employed for the discovery of previously unknown mutations conferring resistance to nalidixic acid in E. coli. Recently, the chip was modified to successfully adapt the thermophilic organism Thermus thermophilus to kanamycin.SummaryThe evo.S chip enhances the occurrence of mutations, resulting in the generation of stress-resistant strains. This kind of miniaturized chip-based ALE offers crucial insights into the mechanism of antibiotic resistance and can be applied to adapt virtually any microorganism.References[1] Zoheir, A. E., Stolle, C., Rabe, K. S., Appl. Microbiol. Biotechnol. 2024, 108, 162.[2] Zoheir, A. E., Späth, G. P., Niemeyer, C. M., Rabe, K. S., Small 2021, 17, 2007166.

Tracking the Dynamics of Interacting Microbial Populations

Microbes exhibit diverse interactions including predation, symbiosis, and competition. These interactions impact the dynamics of microbial populations and therefore shape ecological outcomes within microbial communities. This study focuses on the interactions between Dictyostelium discoideum (Dicty) and bacteria. Dicty is a social amoeba that feeds on soil bacteria by phagocytosis and develops into multicellular aggregates and forms fruiting bodies in the absence of a food source. It has been reported that some Pseudomonads produce toxic compounds that prevent amoebal predation. We hypothesize that the dynamics of these interactions are largely dependent on the population sizes and spatial distribution of the interacting microbes. We seek to understand predatory, foraging, and defence behaviours between Dicty and different bacteria species.We developed experimental setups that allow microscopic imaging of the interaction between Dicty and bacteria in liquid suspension and on agar. The images are analyzed using ImageJ/Mtrack/Labkit and MATLAB. The results obtained will ultimately be compared with mathematical models.By combining population dynamics experiments with mathematical models, we intend to provide a better insight into how interactions mediated by natural products can affect the balance of microbial ecosystems. This understanding would help in the development of solutions to ecological, agricultural, clinical, or environmental problems, as well as the advancement of natural product research.

Context dependency of community ecology and keystone species in a synthetic gut bacterial community

Microbe-microbe interactions are critical for gut microbiome function. A challenging task to understand health and disease-related microbiome signatures is to move beyond descriptive community-level profiling towards disentangling microbial interaction networks. Using a synthetic gut bacterial community (OMM12), we aimed to study the role of individual members in community assembly, identify putative keystone species and test their influence across different environments. Single-species dropout experiments revealed that bacterial strain relationships strongly vary not only in different regions of the murine gut, but also across several standard culture media. Mechanisms involved in environment-dependent keystone functions in vitro included exclusive access to polysaccharides as well as bacteriocin production. Further, Bacteroides caecimuris and Blautia coccoides were found to play keystone roles in gnotobiotic mice by impacting community composition, the metabolic landscape and inflammatory responses. In summary, this work highlights the strong interdependency between bacterial community ecology and the biotic and abiotic environment. Our results question the concept of universal keystone species in the gastrointestinal ecosystem and underline the context-dependency of both, keystone functions and bacterial interaction networks.

Evolution of flagellar assembly regulation in host-associated bacteria: a case study on plant commensal Acidovorax delafieldii isolates

In host-associated bacteria, benefits of traits common in their free-living counterparts, such as flagellar motility, can be offset by energetic costs and the risk of triggering immune responses. While the conserved and immunogenic flagellin gene is often lost, we expect other genes of the flagellar assembly pathway to undergo diversifying selection, in particular the master regulator flhDC. FlhDC has been shown to integrate environmental signals and regulate processes other than flagellar assembly, including virulence of pathogenic bacteria. We were also interested in how loss of flhC would affect the transcriptional landscape of two closely related flhC+ and flhC- Acidovorax delafieldii strains, isolated from Lotus japonicus.Firstly, we mined 1839 reference Proteobacteria genomes for elements of the flagellar assembly pathway using hidden Markov models. Quantity and quality of each sequence were analyzed in a phylogenetic framework, comparing statistics across environmental and host-associated strains. We constructed knock-out and revertant mutants for the flhC+ isolate and tested their motility. We cultivated the subjects in media spiked with crude extracts from Lotus japonicus, axenic or infected by Rhizophagus irregularis, an arbuscular mycorrhizal fungus. After sequencing the transcriptome, we analyzed differential expression and regulation of ecologically relevant genes and studied differences in transcriptional networks topology.We detected lower prevalence, number of copies and scores for most flagellar assembly genes of host-associated strains. However, flhDC shows similar prevalence in both groups, but lower scores in host-associated strains. This suggests that mutation might be more beneficial than loss. As a case study, flhC- co-expression networks show widespread deregulation, with effects on several plant-associated traits and an altered transcriptional balance between type II and VI secretion systems.Our study provides insights into evolutionary dynamics of the flagella and examines a loss of regulation scenario, showing how effects on the phenotype can extend beyond motility, indirectly affecting host-microbe-microbe relationships.

Influence of nutrient richness on Escherichia coli growth dynamics, cellular stress response and denovo emergence of resistance to rifampicin.

Introduction: Emergence of antibiotic resistance is a major threat to global health, limiting the available options for treating infectious diseases. External factors such as nutrient richness or chemical composition of the media can influence the antibiotic stress response, survival, cellular adaptations, population dynamics and adaptive evolution of antibiotic tolerance and resistance in bacteria.Goals: To investigate the influence of nutrient richness on Escherichia coli (E. coli) population growth dynamics and cellular stress response to rifampicin. Probability estimation and genetic analysis of the adaptive evolution of rifampicin resistance in E. coli. Materials and methods: We investigated E. coli (BW25113) rifampicin susceptibility under nutrient rich and poor conditions (Neidhardt's MOPS rich or minimal medium, with added glucose) by quantitatively determining the population growth dynamics, frequency of pre-existing rifampicin resistance and denovo emergence of resistance, live cell microscopy and genetic sequencing of ancestral and evolved strains.Results: Our investigation revealed contrasting growth dynamics on rich and poor media near the minimum inhibitory concentration of rifampicin. Under the nutrient poor condition, rifampicin led to reduced growth rate, whereas in the nutrient rich condition an extended lag phase was observed followed by stochastic exit from the lag phase, which also corresponded to the emergence of phenotypic rifampicin resistance. Further investigation revealed that the resistance emerged denovo under rifampicin treatment in the nutrient rich condition. We further investigated the cellular heterogeneity and genetic variations in the rifampicin resistance determining region of rpoB in the denovo rifampicin resistant strains.Conclusions: Nutrient richness resulted in increased rifampicin extended lag phase, cellular heterogeneity and denovoemergence of rifampicin resistance in E. coli.

Oral Session
Microbial Ecology & Evolution II

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Oral SessionMicrobial Ecology & Evolution II

Appointment

Chair

Topic

Programme

Oral Session
Microbial Ecology & Evolution II