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, or changes in an organism's behavior and physiology that follow a 24 hour, cyclical pattern, are found throughout the tree of life—, , and mammals all have them. But what about bacteria? Do these ubiquitous microbes also have circadian rhythms?

Circadian rhythms are regulated by that facilitate daily oscillations in gene expression. For many years, bacteria were thought to be clockless. This assumption was rooted in the , which suggests that selection for circadian clocks in bacteria is unlikely given that their reproductive cycle is often shorter than 24 hours. In other words, what use is a clock that ticks longer than your lifetime?

However, with the 1980s came discoveries in cyanobacteria, a group of photosynthesizing microbes found in soil and water, that turned this long-held assumption on its head. shows that . Even the gut microbiota, a dense and diverse microbial community, exhibits daily . Learning more about bacterial circadian rhythms could help researchers understand the microbes that play a pivotal role in human health.

Circadian Rhythms in Cyanobacteria

Cyanobacteria are ubiquitous in . Not only are they the , they were the first prokaryotes in which a circadian clock was discovered, and the only bacteria in which such mechanisms have been robustly characterized.

to identify rhythmicity in cyanobacterial gene expression. In these experiments, Synechococcus elongatus, a species widely recognized as the , was transformed with a plasmid expressing luciferase genes driven by the promoter of a S. elongatus photosynthesis gene. By tracking the bioluminescence of S. elongatus cells under periods of constant light or during light-dark cycles, scientists found that the rhythm of bioluminescence (and thus activity of the photosynthetic gene promoter) was consistent with :

1. Free-running and following a 24-hour period. "Free-running" means a rhythm occurs approximately every 24 hours, even under constant environmental conditions. The S. elongatus circadian rhythm continues regardless of whether cells are incubated under constant light or cycles of light and dark.
2. Able to entrain to environmental cues. Although circadian clocks are endogenous, they are inextricably linked to the external world. , called (German for “time-givers”), including light and . People experience jet lag, for instance, when their clocks are in the midst of entraining their sleep cycle to a new time zone. In the case of cyanobacteria, photosynthetic gene expression resets in response to different light-dark patterns.
3. Temperature-compensated. A hallmark of circadian rhythms is that they continue over a range of physiological temperatures. This ensures that the timing of physiological and behavioral processes is not thrown out of whack if the environment is a bit cold one minute and a bit hot the next. Scientists found that the at 25, 30 or 36℃.

Given photosynthesis is linked to light, the observation that this process exhibits circadian rhythmicity in cyanobacteria makes sense. However, it has since been demonstrated that , perhaps , is under circadian control.

With so much genomic rhythmicity, one has to wonder: is having a circadian rhythm useful for these bacteria? By with different circadian periods in various light-dark cycles (Zeitgebers), researchers found that strains whose endogenous rhythm most closely aligned with the Zeitgeber cycle survived better than their competitors, suggesting that the ability to biologically track time imparts a fitness advantage to cyanobacteria.

In the 30 years since these initial discoveries, scientists have also . The : KaiA, KaiB and KaiC. Under periods of light, KaiC is autophosphorylated at 2 residues, a process promoted by interactions with KaiA. As darkness falls, KaiC is sequentially dephosphorylated, which is facilitated by KaiB-mediated displacement of KaiA. In both its phosphorylated and dephosphorylated states, KaiC indirectly modulates gene expression via interactions with other protein regulators. The 24-hour cycle of KaiC phosphorylation and dephosphorylation is how the cyanobacterial circadian clock ticks. In fact, the clock will still tick (i.e., undergo its phosphorylation cycles) in vitro when the with adenosine triphosphate (ATP) in a test tube.

Circadian Rhythms in Non-Photosynthesizing Bacteria

Support for circadian rhythms in cyanobacteria is rich, but what about non-photosynthesizing bacteria? Here, the evidence is less clear. , but the cycles fail to meet all criteria for a circadian rhythm, such as temperature compensation. are present in diverse bacterial species, though whether they function as timekeepers is not well understood.

Still, there are intriguing reports. One study found that a clinical isolate of the gut bacterium, Klebsiella aerogenes (referred to as Enterobacter aerogenes by the authors), in the expression of the motility gene, motA. The rhythms of multiple biological replicates synchronized when cells were incubated in vitro with melatonin, a hormone under host circadian control. These findings suggest that the circadian clock of K. aerogenes may entrain to host cues in vivo. Indeed, in the absence of melatonin, there was greater variability in the circadian phases of different cultures. Of note, only 31-44% of cultures exhibited circadian patterns in motA expression—why those cultures demonstrated rhythmicity while others did not is not clear. Ultimately, more research is required to better understand the nuances of the K. aerogenes rhythm.

Another recent study illustrated that in the expression of genes involved in light detection and biofilm formation. Using a luciferase bioluminescence assay similar to that employed in cyanobacteria, the authors showed that the promoters of these genes controlled expression in 24-hour cycles that entrain to light-dark cycles and compensate for temperature. These rhythms were only observed when B. subilitis formed biofilms, suggesting that circadian rhythms may confer an adaptive advantage in bacterial communities where cells coordinate their behavior to thrive within a given environment.

Circadian Rhythms and the Gut Microbiota

The identification of circadian rhythmicity in gut-associated bacteria is intriguing in light of research showing that the . That is, the abundance of certain taxa peaks during one part of the day (morning) then crashes in another (night). These changes are influenced by Zeitgebers associated with host circadian processes, as . This underscores the close relationship between host and microbiota, in which processes in one (e.g., circadian rhythms) regulate and are regulated by the other.

Studies in mice have shown that , , and disrupt the rhythmicity of the microbiota. Disruptions in host and microbiota rhythms have important health consequences. In both mice and humans, and alters community composition to promote obesity and glucose intolerance, a precursor for type 2 diabetes. Another study found , which could potentially serve as a biomarker of disease.

The negative health outcomes associated with dysregulated microbiota rhythmicity may be tied to altered metabolite production by gut bacteria. For instance, , a compound produced by the microbiota and a key modulator in host intestinal homeostasis. Mice on a high-fat diet, however, lose this rhythmicity and are prone to obesity. Thus, rhythmic changes in microbiota metabolic function may be one of the many ways in which gut bacteria influence health and susceptibility to disease.

Whether gut microbiota rhythmicity is regulated by endogenous bacterial clocks, or is simply a reflection of the community responding to host circadian processes is unclear. In other words, daily fluctuations in microbiota structure and function are not evidence of bona fide bacterial circadian rhythms. Still, given the findings in K. aerogenes and B. subtilis, it is not entirely unlikely that gut bacteria harbor circadian clocks. This raises a number of questions: Which species have circadian rhythms and which ones don't? What, if anything, can this tell us about the physiology and adaptation of diverse bacteria within the gut? Are there species that drive the rhythm of the gut microbial community at large by coordinating with other bacteria, as hinted by the biofilm-dependent rhythmicity of B. subtilis?

Answers to these questions would bolster our understanding of circadian rhythms within the bacterial world. Moreover, they could teach us how to exploit bacterial circadian clocks, and harmonize their ticking with our own, to promote and maintain our health and well-being.

Without cyanobacteria, life as we know it wouldn't exist. Check out this next article to learn how cyanobacteria catalyzed the great oxidation event, which led to the release of oxygen in Earth's atmosphere and the evolution of aerobic metabolism.