How microbial communities assemble, and whether the state they reach is set by rules or by history.
Sebastian Correa-Gallego
I am a biologist from Jardín, on the Western Cordillera of the Colombian Andes, and I came to science through natural history before I came to it through the laboratory. At Universidad EAFIT in Medellín I joined the student research group in microbiology and astrobiology in 2022 and later coordinated it. My thesis followed the cultivable microbial community of the Organal San Antonio, a cave in Támesis, along its gradient of light, and a six-month internship at Purdue University took me inside the cell, to how yeasts divide their proteome, and into a manuscript now in preparation. I am currently applying to doctoral programs in ecology and evolution.
Convergence and contingency recur at several levels of biological organization.
A community assembles from a pool of species, an evolving lineage replayed from the same starting point may or may not repeat itself (Blount et al. 2008), and cells that once lived apart can come to depend on one another. At each of these levels some outcomes are reproducible and others turn on the order in which things happened. The answer is probably neither rules alone nor history alone but a boundary between them, and what interests me is where that boundary lies and what sets it.
The cave and the yeast cells looked at first like separate problems. One was constraint acting on a community and the other constraint acting inside a cell, and I have come to read them as one phenomenon at two resolutions. Microbial communities are where the two resolutions meet in a single experiment, because the cells can be characterized before they are combined and the community can be assembled again from the same pool. The two questions below follow from that, the first about when communities converge and the second about whether the cells that build them can predict it.
When is community assembly reproducible, and when does arrival order decide the outcome?
Communities assembled from the same species pool under identical conditions sometimes converge on one reproducible state and sometimes diverge into several, depending on the order in which members arrive (Fukami 2015). Both regimes appear in the same experimental systems. Replicate glucose-limited communities converge at the family level while their species composition diverges, and that divergence traces to multistability in the population dynamics rather than to noise (Goldford et al. 2018, Estrela et al. 2022).
Variation in growth traits alone is enough to produce more than one stable state on a single limiting resource (Manhart and Shakhnovich 2018), so the ingredients may be physiological. Ecology has candidate mechanisms for the history-dependent case, among them niche preemption, niche modification, and the size of the regional pool. What it does not have is a parameter, measured before assembly begins, that says which regime a given pool will fall into.
That parameter may lie in how each strain allocates its proteome.
Bacterial cells divide a finite proteome between ribosomes, which set growth rate, and metabolic enzymes, which set yield (Scott et al. 2010). Species traits already predict the strength of priority effects better than phylogenetic relatedness does, once they are separated into what a species requires and how it alters its environment (Vannette and Fukami 2014).
The hypothesis is that the spread of allocation strategies across a pool predicts how far replicate communities diverge. A wide spread may strengthen priority effects, if early arrivals preempt resources that later ones cannot recover, or weaken them, if complementary strategies let late arrivals establish anyway. Permuting arrival order in synthetic communities built from characterized strains distinguishes the two.