Biodiscovery of Actinomycetota through metabolo-genomics reveals functional diversity across contrasting Mexican ecosystems

Discovery of novel bioactive natural products from <i>Actinomycetota</i> has decreased, motivating the exploration of rare ecosystems. In this work, we integrated genomics and untargeted metabolomics to profile the biosynthetic capacity of <i>Streptomyces</i> and <i>Nocardia</i> strains isolated from two contrasting, Ramsar-listed Mexican biomes with well-defined ecological features: Cuatro Ciénegas, a semi-arid, oligotrophic karst basin with high microbial endemism, and Calakmul, a tropical rainforest characterized by high biodiversity, seasonal wetlands and limestone-derived alkaline soils. We hypothesized that bacteria isolated from contrasting environments would encode for novel and distinctive subsets of secondary metabolites. Using different metabolo-genomic approaches, a diverse collection of <i>Streptomyces</i> and <i>Nocardia</i> strains was identified, including several potentially novel species. Genome mining revealed a large repertoire of biosynthetic gene clusters (BGCs), many without matches to known metabolites, while molecular networking and dereplication (GNPS, SNAP-MS) exposed extensive chemical diversity within the isolates. Targeted synteny/ortholog analyses (CORASON) linked subsets of metabolites to BGCs, confirming actinomycin and collismycin and identifying komodoquinone-, nocardiopsistin- and rubiginone-like clusters. Notably, bioactivity assays of crude extracts demonstrated effective antifungal effects against <i>Candida albicans</i> SC5314 biofilms and planktonic growth, suggesting their potential therapeutic use. These findings reveal a significant untapped chemical space encoded by <i>Actinomycetota</i> from Ramsar sites, while reinforcing the need for improved tools to connect genomic and metabolomic data for natural product discovery.