Abstracts

Rinke van Tatenhove-Pel, TU Delft

Population dynamics in spatially structured environments

Microorganisms are often studied in well-mixed environments, but their behaviour in spatially structured environments, which occur often in nature, is different. In this presentation, I will discuss three topics related to population dynamics in spatially structured environments. The first one focuses on understanding evolution in spatially structured environments. Using Saccharomyces cerevisiae as an example, I will show how non-structured environments favour strains with a high growth and a low biomass yield, while in a spatially structured environment mutants with a low growth rate and a high biomass yield are enriched. The second part focusses on evolution of microbial consortia in spatially structured environments. We will look at a defined consortium of Lactococcus cremoris strains, and identify in which conditions growth in spatially structured environments can enrich for cooperative interactions. The third part focuses on predicting microbial interactions. I will show how growth in spatially structured environments combined with FACS sorting allows us to predict interactions between microorganisms in a consortium.

Orkun Soyer,  The University of Warwick

Physics of cyanobacterial motility leads to macroscopic formations and influences assembly of spatially organized, stable communities

Microbes in Nature rarely exist in isolation, but commonly form spatially organised assemblies including macroscopic aggregates. The formation of such spatially organised microbial systems, and the spatio-temporal dynamics of species and interactions within them is not fully understood. Studies in this direction have so far focussed on “constructed” assemblies of few species, forming biofilms on agar, while natural systems can be structurally and taxonomically more complex and difficult to study in situ.

We have ‘adapted’ a freshwater community to the lab under lack of carbon source and application of a 12hr light-dark cycle. This resulted in a microbial community dominated by a filamentous cyanobacteria and capable of reproducible spatial structure formation, including cm-scale granules. We found that this community maintains species composition stably over a 2-year period of serial passaging and presents metabolic exchanges among member species and expression of anoxygenic functions by specific ones. We show that the formation of macroscopic granules is underpinned by the gliding motility of the filamentous cyanobacteria, through emergent collective behaviours. We find these granules to harbour anoxic microenvironments, which could explain the expression of the anoxygenic functions and some of the species co-existence dynamics.

Our findings show that structural organisation driven by one species can significantly shape microenvironments and determine assembly, stability, and function of a larger microbial community. The presented system can acts as a model for understanding the formation of cyanobacterial mats and granules found in Nature and how they function to underpin biogeochemical cycling of key compounds. At the same time, the presented (or similar) mid-complexity system can be adapted to biotechnological applications in carbon capture, and sunlight to chemical conversion.

Relevant publications:

https://www.biorxiv.org/content/10.1101/2022.12.13.520286v2 

https://elifesciences.org/reviewed-preprints/100768 

Raghuveer Parthasarathy,  University of Oregon

Gut Microbes and their Physical Concerns

In any ecosystem, the structure of the landscape and the activities of its resident organisms influence one another. This holds in the gut as well, where legions of microbes cooperate, compete, and influence their hosts. In intestinal ecosystems, however, we know little about the spatial structure, physical forces, and bacterial behaviors present, limiting our ability to understand and perhaps engineer the gut flora. To address this, my lab uses light sheet fluorescence microscopy to observe gut bacteria, peering into live larval zebrafish, a model organism that enables a high degree of experimental control. I will focus on experiments that have revealed that antibiotics can cause collapses in gut populations by altering bacterial shape, and that bacteria can alter intestinal mechanical activity through interactions with the host immune system.

Nicolas Desprat,  Ecole normale supérieure Paris

Multiscale organisation of  rod-shaped bacterial micro-colonies

Biofilms are close-packed communities, in which cells can interact on very short length scales. These local interactions have been shown to promote the emergence of collective effects. In this talk, I will discuss the physics of microcolony formation, from the macroscopic down to the molecular scale.

Katja Taute, Peter Debye Institute for Soft Matter Physics, Leipzig University

Bacterial navigation in complex environments

Bacteria navigate natural habitats with a wide range of mechanical properties, from the ocean to the digestive tract and soil, by rotating helical flagella like propellers. They are able to bias their direction of motion relative to external sensory stimuli, in particular to dissolved chemicals – a behavior termed chemotaxis. 

In the lab, bacterial motility and chemotaxis have mostly been studied in uniform aqueous buffer solutions. We use high-throughput 3D bacterial tracking in microfluidically controlled environments to investigate bacterial chemotactic navigation strategies in more complex environments that mimic natural bacterial habitats. 

I will discuss how the pathogen Vibrio alginolyticus adapts its navigation strategies to different environments that mimic its natural range of habitats. 

Susann Müller, Department of Applied Microbial Ecology, Helmholtz Centre for Environmental Research, Leipzig

Ecological forces dictate microbial community assembly processes in bioreactor systems

Microbial communities are indispensable for future biotechnology to produce valuable platform chemicals and reduce the exploitation of fossil resources. Yet, the stability of microbial communities in classical continuous reactor set ups is best brief or non-existent. This is due to ecological forces such as stochastic and deterministic properties of communities that contribute to rapid changes in structure and function to varying degrees. The talk highlights the differences between these two properties, provides tools for their estimation and gives an outlook on overcoming instabilities of microbial communities in biotechnological reactor systems.