Simons Collaboration on Theory of Microbial Ecosystems

Microbial life on the early Earth evolved and changed the environment, thereby enabling the evolution of more complex life. Today, microbes continue to evolve in response to an ever-changing environment, and microbial ecosystems still govern the biogeochemical cycling of the planet and profoundly affect the function of all other living organisms. With the goal of understanding microbial ecosystems and their role in sustaining life on our planet, the division supports the Simons Collaboration on Theory of Microbial Ecosystems and project awards, early-career awards and postdoctoral fellowships relevant to microbial ecology and evolution.

About this collaboration

The Simons Collaboration on Theory of Microbial Ecosystems (THE-ME) uses a combination of theoretical and experimental approaches to elucidate the principles underpinning the self-organization, structure and function of microbial communities. The group will develop experimental approaches to investigate how reproducible dynamics and function emerge from metabolic interactions between microorganisms in the absence of centralized coordination. The team will draw inspiration from the microbial communities that self-assemble around microscopic particles of organic matter in the ocean to develop much-needed model systems to study microbial ecology at the microbe scale. Culture collections of marine bacteria, fabricated microparticles and controlled microenvironments will serve as a basis for experiments to suggest and test theory. Such small-scale microbial communities underlie larger-scale microbial ecosystems, and the connections across scales will be addressed. The team of investigators, led by co-directors Otto X. Cordero and Roman Stocker, includes theorists and experimentalists with strength in diverse areas.

THE-ME research will focus on the following questions:

  • How are functions distributed in a microbial ecosystem?
  • Microbial ecosystems are distributed metabolic systems in which labor is divided across and within trophic levels. This collaboration will identify the biological, physical and chemical processes that lead to the emergence of trade-offs between metabolic functions and the eventual division of labor among cells.

  • How does resource supply shape microbial ecosystem structure and function?
  • Microbial metabolism can switch from a fast but wasteful state, in which resources are burned quickly but used inefficiently, to a slow and frugal one, in which all available energy is extracted from resources but slowly. The team will investigate how these metabolic trade-offs impact the assembly of microbial communities and the division of labor between microbes, and whether assemblies of multiple species can maximize both rate and efficiency.

  • How do environmental gradients and fluctuations impact microbial ecosystem structure and function?
  • Microbial ecosystems often have a microscale structure in which resources are localized in patches. The group will investigate how microbes optimize their behavior to grow in multiscale landscapes, and what factors drive the robustness of microbial community assembly in the face of frequent environmental fluctuations.


THE-ME Co-Directors
Otto X. Cordero
Massachusetts Institute of Technology

Roman Stocker
ETH Zurich

THE-ME Investigators

Martin Ackermann
ETH Zurich

Sebastian Bonhoeffer
ETH Zurich

Mick Follows
Massachusetts Institute of Technology

Jeff Gore
Massachusetts Institute of Technology

Terence Hwa
University of California, San Diego

Naomi Levine
University of Southern California

Mary Ann Moran
University of Georgia

Victoria Orphan
California Institute of Technology