Researchers replicate evolution in the lab using microbes and feeding them with subtly different sugars, and observing how their adaptations diverge

In a parallel universe sci-fi plot, a change of one choice leads to endless possibilities. Taking a train to a destination instead of the usual bus unfolds a series of different experiences, but culminates in a logical and predictable ending. Does nature have similar ways? For example, a change in food led to Darwin's finches adapting their beaks differently. How different do the food sources have to be to push species into different evolutionary outcomes? Can this be achieved even if there are subtle variations in food? And, can we predict the fate of these populations in any way? These fundamental questions in evolutionary biology have baffled scientists for several decades.

Researchers from the Department of Chemical Engineering, Indian Institute of Technology Bombay (IIT Bombay), embarked on understanding this process in the microscopic world. In two of their recent studies, the team used two microbes, a well-known bacterium, Escherichia coli , or E.coli, and a eukaryotic yeast, Saccharomyces cerevisiae , to explore how they process and evolve when identical sugars are served differently. E. coli is a common gut bacterium, and yeast is a common ingredient in baking.

Evolution is how living things change over time, as differences build up over generations. These studies show, for the first time, that subtle variations in otherwise identical environments can lead to evolutionary divergence. For their experiments, the researchers gave a mix of sugars—glucose and galactose, found in dairy products—to one group of microbes. The other groups received either melibiose or lactose, which are complex sugars made up of the same glucose and galactose.

Essentially, the microbial populations were fed equal amounts of glucose and galactose but packaged differently. The food sources are termed as ‘synonymous’, which means they are the same sugars, with subtle variations in their packaging. It is similar to rice and dal versus dosa, the same ingredients with different packaging. The researchers’ team allowed the microbes to multiply for several hundred generations in these three sugar environments, facilitating the evolution process in the microbial world.

“ We picked sugars that are chemically related. Our goal was to see if microbes care about how the meal is served ,” says Prof Supreet Saini, who led the study from IIT Bombay.

Over generations, subtle variation in the food acts as a fork in the road leading to separate evolutionary paths. After 300 generations, one set of bacteria showed a higher growth rate, while the other group had more biomass (total weight), showing two distinct growth traits. Similar diverged outcomes were observed in yeast groups as well. Based on the sugar composition, each group of microbes adapts into two unpredictable evolutionary paths. The genetic study revealed that several mutations led to this adaptation.

“ We didn’t expect these subtle differences (in food/nutrients) to create completely distinct adaptive paths. The findings suggest that the way a cell responds to a nutrient can influence which mutations are beneficial and what paths evolution can take ,” shares Neetika Ahlawat, a post-doctoral researcher and author on both studies.

Microbial adaptation to a specific food source can influence their behaviour in a new environment. This spill-over effect is referred to as pleiotropic response or a side effect of adaptation in a given environment. Surprisingly, when the researchers transferred these evolved populations of both E. coli and yeast to a new set of sugar sources, their growth showed a predictable pattern. Thus, while the performance of the populations in the environments in which they were grown was unpredictable, the side effects of evolution could be predicted successfully!

“ It’s a nice reminder that evolution is both flexible and constrained. In identical environments, the outcome was unpredictable, demonstrating a possible flexibility in evolution. However, the pleiotrophic side effects of that evolution in new environments were surprisingly consistent. How well an evolved population performed elsewhere could be predicted based on how its ancestor had behaved, ” adds Pavithra Venkataraman, a former PhD student at IIT Bombay, and an author of the study on E. coli.

The findings can be scaled to large-scale industrial applications. Tweaking resource combinations may aid in microbes exhibiting beneficial traits. Microbes with improved growth rate and better metabolite yields can be utilised for commercial applications such as food and beverages, pharmaceuticals, and the biofuels industry.

“ We could imagine using resources to limit the evolutionary paths available to pathogens, making it harder for antibiotic resistance to emerge. It’s still early days, but the prospect is exciting ,” suggests Prof Saini.

Like a fiction story with multiple plots, evolution can create endless variations. Both have commonality: a similar beginning, a tiny twist, and different experiences, with a predictable ending based on the hidden rules. The findings show that we can not only witness the outcome of the game, but also predict it by learning the hidden rules!

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