Adaptive radiation during long-term experimental evolution of the multicellular bacterium, Streptomyces

The rapid diversification of a single lineage into novel ecological niches underpins evolution of biodiversity, with adaptive radiations being important drivers of ecological diversity across the tree of life. Experimental evolution has revolutionised our understanding of the fundamental ecological and evolutionary processes in adaptation. To study adaptation in the industrially and ecologically important bacterium Streptomyces, a long-term evolution experiment (LTEE) was undertaken in a strain lacking several antibiotic biosynthetic gene clusters, facilitating the study of epistasis in antibiotic biosynthesis. Streptomyces coelicolor is a filamentous soil organism that does not undergo sporulation under the LTEE conditions, affording the opportunity to study adaptation under relaxed selection on sporulation. Replicate populations showed parallel loss of sporulation and major morphological shifts in terms of hyphal growth and aggregate formation, where fragmenting hyphae became the dominant phenotype. Catabolic diversification was also evident across the replicate populations with extensive growth rate changes relative to the progenitor across several nutrient sources, where there is evidence for both antagonistic pleiotropy and mutation accumulation. Negative epistasis was predominant in antibiotic biosynthesis in strains from the LTEE. This system provides a foundation for studying diversification and adaption to a novel environment in a physiologically and morphologically complex organism.