- Perspective on community-function landscapes out in Cell Systems. (PDF)
- Dispatch by Karna and Seppe on work from Newman lab.
- Vaibhhav Sinha joins the lab as a post doc!
- New preprint on algal control of bacterial community assembly - work by Kaumudi Prabhakara.
Quantitative Microbial Ecology and Evolution
Department of Ecology & Evolution
Center for the Physics of Evolving Systems
The University of Chicago
What we do: Evolution has constructed persistent and functional biological systems from the molecular to organismal and ecological scales. What are the principles by which evolution has generated these systems? What aspects of eco-evolutionary processes can be predicted? We are asking these questions at the ecological level in the context of microbial communities - key metabolic players in the global eco-evolutionary process. In particular, we would like to know: How do microbial communities function? What are the molecular mechanisms? Why has evolution resulted in the microbial community structures we observe in Nature?
The successes of physics in describing non-living matter have taught us that we must do phenomenology first -- that is, provide quantitative, phenomenological, descriptions of precisely how microbial communities function. In essence, we need to establish which are the right variables to describe microbial community structure, metabolic function, and dynamics. Armed with this knowledge we can then ask - what are the molecular and mechanistic bases of these variables? Finally, why has the evolutionary process resulted in the collective variables we observe? To accomplish this we:
(1) Study ensembles of communities with well-defined functional properties and uncover the relevant variables for mapping structure to function using statistical and phenomenological methods.
(2) Understand what molecular players and mechanisms are responsible for the collective variables describing community structure and function -- interactions, gene expression, metabolism.
(3) Using synthetic communities in the laboratory and observations on natural ecosystems we hope to determine why the structure-function relationships we observe in (1) and the mechanisms of (2) are present in natural microbial ecosystems.
We ask the questions posed above in three related types of microbial communities where the structure (taxonomic, metagenomic, abundances) and function (metabolic) are sharply defined and quantifiable:
(1) Denitrifying bacterial communities.
(2) Self-sustaining closed microbial biospheres.
(3) Phototroph-heterotroph microbial communities.
We are a group of physicists, applied mathematicians, ecologists, and evolutionary biologists. We are always looking for new members who are excited about biology, ecology, and making new measurements - get in touch! Our group is part of a new Department of Education funded training grant in Quantitative Ecology.