van Gestel Group

Evolution of microbial development

Both eukaryotic and prokaryotic microbes display astonishing forms of primitive development, affecting how cells organise themselves into simple collectives that propagate in both space and time. The van Gestel group studies how microbial development evolves in the context of predation, a major ecological driver of evolutionary innovation, using a combination of microfluidics, functional genomics and high-content expression libraries.

Previous and current research

The vast majority of both eukaryotic and prokaryotic biodiversity on our planet is microscopic. Although most microbes can propagate as single cells, many display primitive forms of collective development, such as cell-to-cell communication (i.e., quorum-sensing, Figure 1, van Gestel et al., Nat Comm 2021), cell differentiation (van Gestel et al., PLoS Biol 2015; van Gestel et al., Nature Eco & Evo 2020) and spatial patterning (van Gestel & Tarnita, PNAS 2017; van Gestel & Wagner, PLoS Biol 2021). Despite the widespread occurrence of such developmental phenotypes, their regulatory underpinnings and ecological implications often remain elusive. How do developmental mechanisms evolve in time, and how do they affect the emergent properties of collectives and their propagation in their natural ecology? We address these questions by studying how microbial development evolves under predation – one of the prominent ecological causes of evolutionary innovation.

Predator-prey interactions abound: in just a pinch of soil thousands of protozoan predators scavenge their bacterial prey (Figure 2). These predator-prey interactions unleash a fierce evolutionary arms race: bacteria evolve mechanisms that either prevent them from being phagocytized and/or support escape from the phagosome, while conversely protozoans evolve sophisticated hunting strategies to find, kill, and digest their prey. In this arms race, both predators and prey often form collectives that show adaptive emergent properties (Figure 3). For example, protozoans can invade bacterial communities through collective motility, while bacteria can withstand predation by adhering together. What is more, the tug of war between predator and prey can sometimes also profoundly change character, leading to the emergence of host-symbiont or host-pathogen interactions.

We study how predator-prey co-evolution impacts microbial development using an interdisciplinary approach – combining quantitative single-cell microscopy, microfluidics, functional genomics, high-content CRISPR libraries, experimental evolution, and mathematical modelling. Our goal is to identify the mechanisms that underlie predation and predation evasion, determine how these mechanisms are regulated and how their evolution impacts the interaction between protozoans and bacteria. Our starting point is the interaction between Bacillus subtilis and Dictyostelium discoideum, two soil-dwelling organisms with well-studied collective phenotypes, but, ultimately, we will explore natural communities of co-evolving protozoans and bacteria (Figure 3).

As part of both the Developmental Biology Unit and the Microbial Ecosystems Transversal Theme at EMBL, we have a growing network of collaborators within EMBL (e.g., Typas group, Vincent group) and outside (e.g., Gross lab at University of California San Francisco and Tarnita lab at Princeton University).

Future projects and goals

We are at the very beginning of uncovering the impact of predation on microbial development. Thus, many questions remain to be addressed, while others remain to be formulated. Some medium-term questions are:

  • How do protozoan cells coordinate their behavior in predation?
  • How can bacterial collectives evade predation?
  • How are predation and predation evasion mechanisms induced?
  • How do the underlying developmental mechanisms evolve in time?
  • What factors shape the selective feedback between predator and prey?
  • How does predator-prey co-evolution attenuate or facilitate the emergence of host-pathogen or host-symbiont interactions?

Figure showing cell-to-cell communication in a population of signal producing (blue) and signal receiving (red) bacterial cells
Figure 1: Cell-to-cell communication in a population of signal producing (blue) and signal receiving (red) bacterial cells. Cells express yellow fluorescent protein in response to signal molecules. Data points and grid surface show observed and expected signal response respectively. Figure adopted from van Gestel et al., Nat Comm 2021.
Figure 2: Movie of amoebae preying on bacteria.
figure showing Microbial collectives
Figure 3: Microbial collectives emerging in the context of predation.