Research

Our goal is to understand how microbes within communities adapt to environmental change. This is not an easy task. On the one hand, microbial communities consist of a large number of different species resulting in a complex interaction network that is constantly changing over time. On the other hand, with recent advances in single-cell techniques, we are only now beginning to identify and characterise microbial individual’s traits relevant for adaptation. In our lab we use an interdisciplinary approach to understand how individual cell variation influence evolutionary dynamics, and how community dynamics in turn influence evolutionary outcomes, i.e. eco-evolutionary feedback loops.

Our general working approach is to build mathematical models to formulate specific predictions. We then test these predictions by doing experiments in highly controlled environments. The overall expectation from these experiments is to generate general concepts that extend beyond specific bacterial species and communities.

RESEARCH LINES

I) MICROBIAL EVOLUTION IN A COMMUNITY CONTEXT. We study how species interactions give rise to emergent properties at the community level that feedback to influence the evolution of populations and how this evolution affects the stability and functionality of microbial communities.

Three major questions that drive our research are:

  • How do higher-order interactions and indirect effects shape the evolution of multi-species systems?
  • How do species interactions evolve and give rise to new community functionalities; e.g. novel collective metabolism?
  • What type of species interactions lead to community-level cohesion?

To address these questions, we use a bottom-up approach. That is, we use communities of reduced complexity – synthetic communities– to measure and quantify species interactionsin highly controlled environments. Once we have a mechanistic understanding on species interactions, we experimentally expose these synthetic communities to a desired condition for hundreds of generations and we use whole-genome sequencing to see what mutations accumulated in each population at the end of the experiment.

As a postdoctoral fellow with Martin Ackermann, Alejandra optimised an experimental system currently used in the lab to address some of the research questions. In this system (left fluorescence image), Acinetobacter johnsonii (in red) and Pseudomonas putida (in green) switch their interactions from competitive to exploitative depending on the carbon source provided (Rodriguez-Verdugo et al. 2019).

 

II) MICROBIAL PHENOTYPIC RESPONSES TO ENVIRONMENTAL CHANGE. We are studying how individual cells behave before and after an environmental perturbation (e.g. abiotic stress) and how these acclimation responses influence adaptation.

Two major questions that drive our research are:

  • How does phenotypic plasticity influence population level responses to pertubations?
  • What phenotypic traits are under selection under abiotic stress?

To tackle these questions, we use microfluidics coupled with time-lapse microscopy. This cutting-edge technology provides three unique advantages; it allows: 1) to quantify single-cell growth parameters; 2) to track cell lineages for many generations before the appearance and selection of beneficial mutations; 3) to simulate conditions close to what bacteria experience in nature (e.g. fast fluctuating environments, spatial heterogeneity) with high level of experimental control.

During her postdoc, Alejandra grew Escherichia coli‘s cells in microfluidic flow-cells in stressful and non-stressful conditions. Click here to see the time-lapse movie of these cells growing in a non-stressful environment.