top of page

Microbial dynamics in fluctuating environments​

The microbial community structure is driven by many biological and environmental factors and environmental change has a significant impact on the diversity and activity of microbial communities. Our work focuses on understanding the role of diverse environmental changes (e.g. pH, temperature, moisture, land use, fertilisation history, hydrocarbons, and grazing) in soil microbial dynamics in fluctuating environments, to understand how environmental perturbation impact microbial processes. This research combines wet and dry lab approaches to analyse the physiological, ecological and evolutionary adaptation of microbial activity from the cellular to the community level.

Growth and activity of soil ammonia oxidisers

Picture 1.png

Ammonia oxidisers play a crucial role in the terrestrial nitrogen cycle and three main types of ammonia oxidisers have been discovered so far: the ammonia oxidising archaea, the ammonia oxidising bacteria and the comammox. In soil, the growth and activity of these ammonia oxidisers are influenced by various factors such as soil pH, nitrogen fertiliser source, temperature, or moisture content. Our research analyses the growth of each of those groups, and the different taxonomic phylotypes within, under diverse environmental conditions to better understand niche specialisation. Understanding the mechanisms behind their growth and activity is important for managing soil fertility and mitigating environmental issues such as greenhouse gas emissions. Ongoing research in this field aims to reveal the complex interactions between ammonia oxidisers and their environment.

Community assembly processes

I.2_Community assembly processes.png

Soil is a highly heterogeneous environment, and small-scale abiotic fluxes within the microenvironments affect the abundance and distribution of microbial communities. The community structure of microbial populations is driven by many biological and environmental factors, and our work is analysing the diverse underlying controlling mechanisms, among which selection, divergence, HGT. Our studies analysed a range of abiotic factors including soil pH, temperature, soil water content, land use, fertilisation history, grazing, hydrocarbons and microplastics. They focus on a range of spatial and temporal scales, including fluctuating environments.

Evolutionary diversification processes

I.3_Growth and activity of soil ammonia oxidizers.png

Understanding the speciation and extinction processes occurring across millions of years of microbial evolution is enabled by phylogenetic reconstructions and comparative phylogenetic approaches. We relate several genomic mechanisms (lateral gene transfer, gene duplication and gene loss) to the microbial adaptation to the environment, either during drastic environmental changes (e.g. terrestrial to marine colonisation) or during closely related niches (e.g. topsoil versus subsoil). Our work also analyses the transitions between multiple phenotypic states across microbial evolutionary histories.

Life trait strategies

I.4_ Life trait strategies.png

Dormancy is a key survival mechanism in microbes, allowing them to withstand changes in their environment that are not favourable for growth. While microbial ecology has mainly used resident microbes as a proxy of microbial adaptation, we are investigating multiple life trait strategies (dormancy, activity and death) of microbes in natural habitats including soil. This trait refinement will enable determining key mechanisms of adaptation on microbial communities.

Niche breadth

I.5_Niche breadth.png

Organisms may be defined as specialists or generalists by the range of environments in which they thrive (their niche). Conventional wisdom in ecology of higher organisms predicts a strong trade-off between niche breadth and fitness. Our group studies the niche breadth trait and its effects on fitness in numerous contexts, including environmental change. How niche breadth affects community assembly and diversity in the context of environmental change in natural environments is of particular interest

Host-microbe specialisation 

I.6_Host-microbe specialisation.jpg

Host-associated microbes are central to the ecology and evolution of many eukaryotic hosts, through supporting the hosts in diverse functions. This relationship is essential for various important systems, such as microbiome associated to sea sponges, crop roots or floral systems. In all these host microbe association, host specificity range from generalists (acquired from the surrounding environment) to highly specialised endosymbionts (inherited from parents and only present in specific hosts). We aim to unravel the existence of phylosymbiosis processes to better understand the evolution of these essential relationships, and how they affect community resilience in a changing environment.

Experimental evolution

I.7_Experimental evolution.png

Microbial experimental evolution enables studying the evolutionary responses of populations to various kinds of environmental perturbation under multiple generations in a controlled environment. Our work focus on evolving E. coli, ammonia oxidising archaea and ammonia oxidising bacteria, comparing mechanisms across the two domains of life. This approach allows observing phenotyping patterns in a relatively short timeframe and linking phenotypes to genotypic changes.

bottom of page