Research
There is high interest in understanding the factors that determine whether microbes proliferate or not in a given environment. Invasions are a double-edged-sword, generally considered detrimental to environmental and human health due to the spread of pathogens and antibiotic resistance, but with beneficial applications such as probiotics and bioinoculants. Our research incorporates fundamental ecological theory to predict the factors that regulate invasion success.
Microbial invasions
Antibiotic resistance spread
The spread of antibiotic-resistant organisms is major threat to global health. Our research combines synthetic microbial communities, theoretical simulations and microscopy to understand how antibiotic resistance genes spread on surfaces. A key aspect of this research is the influence of the spatial positioning of individual cells, whose patterns are a major driver of resistance spread.
Plant-microbe symbioses
Microbes can afford multiple beneficial functions to plants, and harnessing such functions for plant production is of great interest. Our aim is to bring beneficial microbes found in the wild ancestors of crops into plantations as a way to recover microbial functions that might have been lost during plant domestication. Working on the applied case of rooibos tea, we found that mixing rhizobial communities from cultivated and wild plants can increase the growth and mineral nutrition of this important cash crop.
Microbial biogeography
Since the recognition that microbes display geographical ranges, there has been increasing interest in understanding what factors underlie such distributions. In particularly extreme habitats, revealing these drivers is relevant to understand potential responses to global warming. We explore biogeographical patterns of microbes across a wide range of environments.
Genome-based prediction of microbial traits
We combine genomics and predictive approaches to learn about the phenotypic traits of many microbial taxa that remain uncharacterized - from metabolic traits such as amino acid biosynthesis to morphological traits such as flagellar production. This work expands what we know about the characteristics that make microbes so adaptable in our planet, and allows the selection of taxa with particularly interesting functions in agriculture and biotechnology.
Microbial environmental preferences
Environmental preferences determine when and where any given microbe will grow, but the environmental preferences of most microbial taxa remain undetermined. Using the massive analysis of sequencing information and machine learning, we establish validated inferences on the environmental preferences of the majority of microbes that are still uncharacterized. This is relevant to predicting microbial responses to environmental changes, the design of beneficial consortia, and the improvement of microbial cultivation conditions.
