Rapid Evolution of Simple Microbial Communities in the Laboratory

Classical models predict that asexual populations evolve in simple unstructured environments by clonal replacement, yet laboratory evolutionary studies have uncovered persistent polymorphism, driven either by frequency-dependent selection or mutualistic interactions. We have studied the evolution of microbes in simple unstructured environments as a way to illuminate the evolution of biodiversity. We sought to understand how complexity arises in an Escherichia coli population founded by a single clone and propagated under glucose limitation for >770 generations. When coevolved clones are cultured separately, their transcriptional profiles differ from their common ancestor in ways that are consistent with our understanding of how E. coli adapts to glucose limitation. A majority of the 180 differentially expressed genes shared between coevolved clones is controlled by the global regulators RpoS, Crp, and CpxR. Clone-specific expression differences include upregulation of genes whose products scavenge overflow metabolites such as acetate, enabling cross-feeding. Unexpectedly, we find that when coevolved clones are cultured together, the community expression profile more closely resembles that of minority clones cultured in isolation rather than that of the majority clone cultured in isolation. We attribute this to habitat modification and regulatory feedback arising from consumption of overflow metabolites by niche specialists. Targeted and whole-genome sequencing reveal acs, glpR, and rpoS mutations in the founder that likely predispose evolution of niche specialists. Several mutations bringing about specialization are compensatory rather than gain-of-function. Biocomplexity can therefore arise on a single limiting resource if consumption of that resource results in the creation of others that are differentially accessible to adaptive mutants. These observations highlight the interplay of founder genotype, biotic environment, regulatory mutations, and compensatory changes in the adaptive evolution of asexual species and somatic cells.