WP 7.3 The Effect of Oscillating Environmental Conditions and Perturbations on Microbiomes

project description

Oscillating environmental conditions (i.e., stochastic perturbations that are usually rather weak) are among the most prominent factors that shape microbial communities. More severe pulse perturbations (i.e., sudden changes in environmental conditions, which only last for a short time interval)may have long-lasting effects on microbial communities and may lead to alternative stable states. Currently, our knowledge of how complex microbial communities adapt to pulsed perturbations and the ways in which pulsed perturbations impact microbiome function, resistance, and resilience is fragmented and lacks a unifying theoretical framework.

This work package will employ concepts from temporal ecology to investigate how the recent and distant history of perturbation events, as well as their temporal pattern (i.e., single pulse, periodic regular or irregular) shape microbial communities. We hypothesize that universal mechanisms of community adaptations to pulsed perturbations exist, and result in altered community characteristics.While the projects in research theme 2 also deal with perturbation, they focus on anthropogenic perturbations, such as perturbations by environmental chemicals (project 3) or climate change (project 4).

Here, we will analyze natural perturbations of various severity across systems to elucidate the fundamental effects such perturbations have on microbial communities. The response of microbial communities to perturbations has usually been investigated in individual systems, but an overarching framework of universal mechanisms driving community adaptation to perturbations is still lacking. To identify patterns that go beyond a system-specific response, we will use four different microbiomes, which are naturally exposed to (periodic) pulsed perturbations: (i) biological soil crusts in deserts (diurnal variations in water content due to dew formation), (ii) rhizosphere microbial communities that experience diurnal oscillating input of carbon and nutrients from plant root exudations following a day-night cycle, (iii) mammalian gut microbiome, which experiences diurnal oscillations driven by the circadian clock of the host as well as inter-day variation in feeding schedules, and (iv) sewage sludge, which is exposed to diurnal peaks of nutrient inputs. We will set up experimental systems for each microbiome that allow controlled manipulation of their native perturbation regimes (rhizosphere: reverse microdialysis to simulate root exudations; gut: mouse models using complex and/or defined gut microbiota communities; and soil crusts: incubations with controlled addition of water).

We will apply the same set of perturbation regimes to all systems, and explore the emergence of community properties (resistance, resilience, substrate utilization, activity) based on the history of experienced pulsed perturbations. Specifically, after perturbation, we will measure composition of the active community using qSIP, and functional community responses by quantifying respiration, substrate utilization and enzyme activities. In addition, we will employ a model system of reduced complexity, such as a lab-cultured consortia of selected microbial strains, which will allow us to follow specific interactions in more detail.

By compiling the results from the different microbiome systems and combining it with theoretical modeling, we aim to identify fundamental mechanisms of community adaptation to perturbations, and develop a nuanced understanding of how perturbation type and frequency drive community adaptation processes. Given the high prevalence of pulsed perturbations and environmental oscillations in nature, a better understanding of their effect on the functioning of microbiomes will be essential for managing natural ecosystems, and for developing engineered systems.