Genomics Research in Ecology & Evolution in Nature

The group investigates ecological and evolutionary processes in (infectious) microbial communities. We aim to understand the genotype-phenotype-fitness relationships within (evolving) communities. Additionally, we investigate the effect of microbial interactions on the evolution of antibiotic resistance. We study these eco-evolutionary processes using molecular biological tools, by performing phenotypic and growth measurements, and modelling. We currently focus on bacterial isolates from persons suffering from urinary tract infections as a model system. Additionally, we investigate the interactions between pathogens and benign bacteria discovered in the urinary tract of healthy persons. By unveiling the fundamental ecological and evolutionary microbial processes in infectious disease, we hope to improve and contribute to strategies that can alleviate infectious diseases and limit the spread of antibiotic resistance.

In my group we use ecological and evolutionary theory to unravel the causes and the consequences of free-living and host-associated microbial communities. On the one hand we are interested in understanding how microbiomes are formed (causes of microbial diversity) and what processes (stochastic determinism) and mechanisms (selection though competition or environmental filtering, dispersal, drift, speciation) lead to the development of microbial communities. On the other hand I am interested in determining what are the consequences of this microbial diversity for the functioning of the environment the microbiome is associated with – being that a host or a soil – and understanding the mechanisms determining the diversity effect. We address these topics in a range of environments (agricultural soil, salt marshes soils) and hosts (plants, arthropods, birds, mice and humans), by combining experimental procedures (field, microcosm, mesocosm, manipulative experiments), modelling, microbiological and molecular techniques, metagenomic and bioinfomatic approaches.

We strive to unravel the mechanism underlying the immense diversity of life. How do organisms adapt, differentiate and diversify? How do they shape and are shaped by the communities and ecosystems they occur in? To do so, we study a wide array of organisms and systems – from exotic viruses to their unicellular eukaryotic hosts, from endophytic fungi to carnivorous plants, and from open-ocean cyanobacteria to coastal soil microbiomes. Our focus lies in understanding processes that drive and accelerate evolution in these systems, such as horizontal gene transfer via mobile genetic elements, viruses or vesicles.

For our research, we harness the power of genomics and big data, leveraging cutting-edge sequencing technologies and devising workflows and software to maximize their use. Moreover, we are developing tools for data exploration, integration and interpretation with a focus on genomics data visualization. Combining these efforts, we aim to gain new insights into the concert of ecology and evolution that brings forth the wondrous living world around us.

Every living organism, from bacteria and archaea to plants and humans, is expected to harbor several viruses. These obligate cellular parasites represent one of the most diverse biological entities known to us, and we just began to explore this diversity.

RNA viruses are characterized by a relatively small genome size of around 10-30 kb, a high mutation rate about one million times higher than their hosts, and big population size. These features translate into considerable genetic diversity within each host, better pictured by the existence of a population of variants (micro-evolution). Because of these features, evolutionary rates of viruses (macro-evolution) are usually several hundreds of times faster than for prokaryotes or eukaryotes.

Our research aims to characterize evolutionary pressures and dynamics that impact the evolution of viruses across scales, from within- to between-hosts, from small transmission chains to epidemics and from deep to recent evolutionary processes. Because viral evolution takes place at the same time scale as viral ecological processes, its study can uncover some insights into virus ecology: How do they spread? Where do they come from? What is their host range? All critical pieces of information to understand and manage their impact on us, on our domesticated animals and plants, on our ecosystems and even on our whole biosphere.

To explore these questions, we use an integrated combination of "wet" (controlled experiments, field work, high-throughput sequencing) and "dry" (bioinformatics, phylodynamics, modeling and simulations) approaches.

The research of our group focuses on specialized metabolism in plants and the many ways we can utilize those metabolites. Currently we investigate the mechanisms that govern environmental stress tolerance in different crops by integrating functional genomics, metabolomics, as well as protein biochemical and genetic approaches with a focus on terpene metabolic networks. Additional interests of ours are the interactions of plants with their environment and the advancement of regenerative farming.

The aim of our research is to understand the diversity of colour in plants and animals. We study the proximate (pigments, structure) and ultimate (fitness, visual function, temperature) underlying this diversity. We particularly focus on the colours of flowers and insects: how do they create their colours, and how are these colours perceived in the eyes of their natural observers (pollinators, mates, antagonists)?

Plants in natural ecosystems are confronted with a highly variable environment. Within the lifetime of a plant they can encounter hot and cold spells, drought and flooding events, as well as salt stress. Our group studies how plants adapt and acclimatize to variable environments and adverse conditions. To this end we compare genotypes or species with contrasting behaviour, investigate their physiology (growth, architecture, gas/solute exchange, hormones, metabolism) and seek the underlying gene regulatory networks with the help of sequencing technology. By tracing the functional changes that plant species underwent to optimize their performance in stressful environments we aim to provide insights where limitations and opportunities lie for climate resilient crops and agriculture.