A clock for all seasons: ecology and evolution of circadian clocks

Abstract

Circadian clocks are intrinsic biological timers with a period of about 24 hours that can be synchronized to the environmental daily cycle and allow for prediction and anticipation of important cyclic events. These clocks are widespread across the tree of life and are found even in bacteria. Photosynthetic bacteria (i.e. cyanobacteria) have become crucial to understanding the adaptive value of circadian clocks, but much is still unclear about how circadian clocks have evolved and continue to evolve. In this dissertation, I discuss early and future circadian clock evolution, and leverage bacteria – both cyanobacteria and the gut microbiome – as a model system for understanding this evolution. First, I report evidence of bona fide photoperiodism in cyanobacteria, showing that cyanobacteria can use daylength as a cue of future environmental conditions and preemptively change their gene expression and lipid membrane desaturation index in a way that allows for increased survival to cold temperatures. Similar to what is often observed in eukaryotic photoperiodism, this phenomenon takes multiple cycles to develop and requires a functional circadian clock. Next, I use the gut microbiome as a model system to understand how host rhythmicity and arrhythmicity impact the composition of a community. We learned that the gut community can be quite stable to host arrhythmicity, but when the community is perturbed by antibiotics, it can only recover its original composition if the host is rhythmic. We also identify certain bacterial species that appear to be selected for/against in rhythmic conditions. Overall, this dissertation advances the chronobiology field by establishing cyanobacteria as a model for photoperiodic time-measurement and demonstrating the effect that host rhythmicity can have upon the structure of microbial communities.