Lydicamycins induce morphological differentiation in actinobacterial interactions.

Abstract

Streptomyces are major players in soil microbiomes; however, their interactions with other actinobacteria remain largely unexplored. Given the complex developmental cycle of actinobacteria, a multi-omics approach is essential to unravel the interactions. This study originated from the observation of induced morphogenesis between two environmental isolates from the same site, Kitasatospora sp. P9-2B1 and Streptomyces sp. P9-2B2. When co-cultivated on potato dextrose agar, P9-2B2 triggered a wave-like sporulation pattern in strain P9-2B1. Mass spectrometry imaging revealed that a suite of lydicamycins accumulated in the induced sporulation zone. Using CRISPR base editing, lydicamycin-deficient mutants were generated, and the inducible sporulation was ceased, confirming the role of lydicamycin in triggering morphological differentiation. In agar diffusion assays, pure lydicamycin was inhibitory when added concurrently with bacterial inoculation but induced sporulation when added later. The same inducible sporulation wave phenomenon was also observed in additional environmental isolates and Streptomyces coelicolor M145 and M1146. Transcriptomics analysis revealed differential gene expression linked to early aerial mycelium development at 4 days into co-culture, the transitional genes responsible for the development of spores at day 9, together with numerous genes for overall stress responses, particularly cell envelope stress responses. These findings highlight previously unrecognized actinobacteria interactions mediated by lydicamycins, suggesting a broader ecological role of bioactive metabolites in microbiomes.

Importance: Moving beyond an antibiotic discovery mindset, exploring the chemical ecology of secondary metabolites is key to maximizing their biotechnological potential. Dual cultures offer reduced complexity, enabling an in-depth analysis of these interactions via multi-omics, which provides complementary data for more robust conclusions. This study sheds light on the role of lydicamycins in dual cultures with other actinobacteria and establishes an integral roadmap for future chemical ecology work between microorganisms, particularly through mass spectrometry imaging.