Bacterial Evolution – The Movie

ORIGINAL: PLOS

By Roli Roberts

Posted: February 21, 2013

Recent advances in sequencing technology have brought us the complexity of microbial metagenomes from oceans, soils and guts. These massive datasets of the combined genome sequences of hundreds or thousands of cohabiting bugs are presumably capturing a mere snapshot from an incredibly dynamic interplay between mutating, competing and adapting populations. How can we hope to tease apart these tangled banks?

A research article by Matthew Herron and Michael Doebeli just published in PLOS Biology steps back and gives us, instead of a snapshot, a set of three sixteen-frame high-definition movies of one of the simplest ecosystems conceivable. And the daunting complexity it reveals raises questions about our ability to comprehend, from metagenome data alone, what on earth is going on in wild bug populations.

As time pans from left to right, green glucose lovers and blue acetate addicts emerge from the gold ancestral population (Herron & Doebeli, PLOS Biology 2013)

The study uses frozen samples (the “fossil record”) from an old experiment in which Doebeli and colleagues allowed ten E. coli populations to evolve for 1200 generations in a mixture of two tasty nutrients – glucose and acetate (think sweet and sour sauce). Under these conditions it had been found that each initially uniform population reproducibly evolved into two separate communities, each adapted to its own niche – one that efficiently burns glucose, and another that’s less efficient but can switch to running on acetate. Here they take three of those ten experimental populations and throw next-generation sequencing technology at them, generating detailed metagenome sequences for each population over sixteen timepoints.

Many fascinating things emerge from this analysis, and in fact the best way into Herron and Doebeli’s study is probably to read the superb (and very accessible) accompanying Primer by Christopher Marx. But for me, the striking thing is that these three evolutionary movies are so similar (see the above images) – the actors are given only their starting positions, but in each case the action unfolds in a spookily stereotypic way. The same genes mutate in the same order, and often with the same mutations.

Genotypes vie with each other, but no bug ever wins out, and a handful of crucial mutations can make a single species behave like two unrelated ones, each in its own niche. You’re left with the impression that despite the potential complexity, what emerges is a surprising degree of predictability or reproducibility in the evolutionary path – a triumph of determinism over happenstance?

So although it’s rather sobering to look at the complexity that can arise spontaneously from this simple experimental premise, and then to gaze helplessly on the slew of data from a single snapshot of a wild microbial ecosystem, the reproducibility does remind us that, like Hollywood, evolution has its motifs and tropes that may be replayed time and again. 

Herron, M., & Doebeli, M. (2013). Parallel Evolutionary Dynamics of Adaptive Diversification in Escherichia coli. PLOS Biology, 11 (2) DOI:10.1371/journal.pbio.1001490

Marx, C. (2013) Can You Sequence Ecology? Metagenomics of Adaptive Diversification. PLOS Biology, 11 (2) DOI: 10.1371/journal.pbio.1001487