Fungal-fungal interactions drive metabolic reprogramming in root-associated endophytes of Salvia abrotanoides

Abstract Root-associated endophytic fungi are integral components of plant holobionts, where interspecific interactions shape ecological fitness and secondary metabolism. In this study, five fungal endophytes isolated from the roots of Salvia abrotanoides — Paraphoma radicina , Penicillium murcianum , Penicillago nodositata , Penicillium canescens , and Coniolariella hispanica —were investigated to evaluate how fungal–fungal interactions influence metabolic expression under co-culture conditions. Dual-culture assays on solid and liquid media revealed distinct interaction phenotypes, including distance inhibition and contact inhibition, reflecting competitive ecological strategies. LC–MS–based metabolomic profiling demonstrated that co-cultivation reshaped secondary metabolite production, leading to both suppression and induction of specific compounds. Signaling- and defense-related metabolites such as nicotinic acid, indole-3-acetic acid, and pyridoxine were differentially regulated during interaction. Notably, certain co-cultures triggered the production of metabolites absent in monocultures, including eleostearic acid and griseofulvin, indicating activation of previously silent or weakly expressed biosynthetic pathways. Among the isolates, P. nodositata was identified as a natural producer of cryptotanshinone, a diterpenoid previously associated primarily with Salvia species. However, its production was modulated under interaction conditions, suggesting context-dependent metabolic regulation. Collectively, these findings highlight the metabolic plasticity of root-associated endophytes and demonstrate that fungal–fungal interactions act as drivers of secondary metabolism reprogramming. The study underscores co-culture as an ecologically relevant strategy for uncovering interaction-mediated chemical diversity within plant-associated fungal communities.