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

Adaptive radiation of a single lineage into novel ecological niches underpins the evolution of biodiversity. 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. Over 3000 generations, replicate populations showed parallel loss of sporulation, morphological transitions to fragmenting hyphae and diversification in carbon source utilisation. Genomic analyses revealed mutations in developmental and metabolic genes, while reintroduction of the actinorhodin cluster demonstrated pervasive negative epistasis affecting antibiotic production. These findings reveal adaptive diversification and antagonistic interactions in regulatory pathways under relaxed selection, providing insights into the evolution of complex multicellular bacteria and informing industrial antibiotic production strategies.Code associated with the Streptomyces LTEE is here https://github.com/PaulHoskisson/StreptomycesLTEE/tree/main