Isolation and characterization of novel microorganisms producing natural compounds of possible industrial interest: an integrated genomic and metabolomic approach

Background This study investigates the discovery of bioactive natural compound (BNC)-producing microorganisms from diverse, marine and terrestrial extreme environments using an integrated genomic and metabolomic approach. BNCs, including pigments, antimicrobials, and antioxidants, play pivotal roles in microbial adaptation and constitute valuable resources for applications spanning pharmaceuticals to sustainable materials. To enhance the likelihood of isolating BMC producers, a pigmentation-guided strategy was applied across three ecologically distinct and extreme environments: alpine glacier snow, volcanic marine sediments, and marine holobionts exposed to natural CO 2 emissions. Results This approach yielded 51 pigmented microbial isolates, encompassing both bacteria and fungi across multiple phyla. From this collection, seven representative strains exhibiting high growth rate and consistent and intense pigmentation were selected for in-depth characterization. Whole-genome sequencing and biosynthetic gene cluster (BGC) analysis revealed extensive biosynthetic potential, with 61 BGCs identified, including pathways associated with terpenes, polyketide synthases (PKS), and non-ribosomal peptide synthetases (NRPS). Complementary metabolomic profiling via UPLC-QTOF-MS confirmed the production of a broad spectrum of BNC, with 58 natural products being detected, including carotenoids, antimicrobial compounds, biosurfactants, and polyketide-derived pigments. Functional assays further demonstrated the ability of these strains to metabolize amylaceous substrates and plant-derived carbohydrates, highlighting their suitability for sustainable biotechnological processes based on renewable feedstocks. Notably, two isolates affiliated with Alkalihalobacillus algicola and Cytobacillus oceanosediminis exhibited genomic divergence below species-level thresholds, suggesting the presence of previously uncharacterized lineages. Conclusion Overall, this work underscores the effectiveness of coupling pigmentation-based screening with omics-driven analyses to uncover microorganisms as candidate cell factory for BNC production. The identified strains represent promising candidates for sustainable biotechnological applications, including the production of natural pigments, antimicrobials, and bio-based materials, thereby contributing to the advancement of circular and eco-friendly industrial systems.