Big picture: the dreams
Video: Mikhail Tikhonov - “Microbial ecology as a new frontier for theoretical physics” (Stanford Physics/Applied Physics colloquium)
Beyond discreteness: "species" in the microbial world
Most of classical ecology relies on the assumption that organisms can be naturally partitioned into discrete types. But how well does this intuition actually apply to microbes? Asexual reproduction, evolution, horizontal gene transfer: all these mechanisms render the "partitioning assumption" questionable. It is clear that "species" is a useful concept. However, right now, this is not the best language we have, it is the only one we have – and many fascinating examples, like the stories of Methanobacillus omelianskii or Chlorochromatium aggregatum, make one wonder just how good this discrete language really is.
Unfortunately, no alternative currently exists. Our experimental studies report the "number of species" in the gut. Our models investigate dynamics of "species abundance", as shaped by "species interactions". Data analysis packages cluster sequences into "taxonomic units". Thus the partitioning assumption shapes our questions, our models, and even our approach to data. How else could we describe microbial ecosystems, if not in these terms?
The implications of high dimensionality
Our understanding of ecological and evolutionary mechanisms derives predominantly from analysis of low-dimensional models (with few species). However, natural communities are famously highly diverse, with hundreds of phenotypes coexisting and interacting. In physics, we know that when the number of degrees of freedom becomes large, the behavior of the system may change completely. What is qualitatively different about the high-diversity regime in ecology?
There exists a long tradition of "large-N ecology", starting with the classic work of Robert May. However, the focus has traditionally been on composition, e.g. the number of coexisting species. What are the specifically functional implications of high diversity? And how should this modify the familiar low-dimensional intuition we have of ecological and evolutionary processes?
Blurring the species boundaries
If research groups had mascots, we'd be proudly represented by the duck-rabbit!
While our primary motivation is theoretical, the active projects are a roughly equal split between theory, data analysis and experimental collaborations.
Statistical physics of resource competition
One classic way to link composition and function is provided by MacArthur's resource competition model from the late 60's. It was extensively studied for N = 1 and N = 2 resources, in particular by Tilman, who developed a highly influential geometric intuition.
In natural communities, however, the number of relevant metabolites is in the dozens. Remarkably, the high-diversity regime of the MacArthur model can be solved analytically, using methods of statistical physics of disordered systems. This exactly solvable model provides a rich platform to investigate the implications of high dimensionality for both ecological and evolutionary dynamics.
Tikhonov M, Monasson R (2017) Collective phase in resource competition in a highly diverse ecosystem. PRL
Tikhonov M, Monasson R (2018) Innovation rather than improvement: a solvable high-dimensional model highlights the limitations of scalar fitness. J Stat Phys
Natural microbial ecosystems do not just exchange members: they frequently come into contact as entire communities. For instance, think of a leaf falling on the ground, or a dog licking your hand. These events have been dubbed "community coalescence". A frequent, yet largely unstudied natural occurrence, they are expected to be an important factor shaping community structure, and are also of significant medical interest (e.g. fecal matter transplants are one of the few effective therapies against C. difficile infections). Interpreted as community-level competition, community coalescence is a very intriguing phenomenon also from a theoretical standpoint.
In collaboration with Alvaro Sanchez (Yale) and Pankaj Mehta (Boston U), we are investigating community coalescence both theoretically and experimentally.
Rillig MC et al. (2015) Interchange of entire communities: microbial community coalescence. Trends Ecol Evo
Tikhonov M (2016) Community-level cohesion without cooperation. eLife
Goldford J, Lu N et al. (2017) Emergent simplicity in microbial community assembly. Science
Lu N et al. (2018) Cohesiveness in microbial community coalescence (bioRxiv)
Other ongoing projects cover a diverse set of topics, including:
- metabolically driven spatial assembly of multi-species consortia (see our paper in PNAS);
- an intriguing exact mapping of MacArthur's resource competition onto learning theory;
- a theoretical construct of "weakly structured" ecologies where the number of species is ill-defined.
We expect to develop additional collaborations with groups at the WashU medical campus and the Center for Genome Sciences & Systems Biology.