Genome-mining revealed biosurfactant production capacity and gene co-occurrence patterns in diverse ecosystems

Biosurfactants produced by microorganisms play essential roles in ecosystem function and hold significance promise for biotechnological applications. However, their diversity and distribution remain poorly depicted due to the limitations of culture-based approaches. In this study, we conducted a large-scale genomic data mining of 142,135 microbial genomes of putative biosurfactant-producing taxa, spanning 21 distinct ecosystems, to systematically profile gene association with 10 major biosurfactant classes. Using a list of 18 key functional genes, we mapped their taxonomic and ecological distribution and analyzed patterns of gene co-occurrence. We found that rhamnolipid biosynthesis genes are nearly ubiquitous across microbial lineages, reflecting their fundamental role in microbial adaptation. In contrast, emulsan and serrawettin pathways are more restricted to plant-associated and fungal ecosystems. The highest diversity of biosurfactant-related genes was found in genomes recovered from nutrient-rich habitats, including plant-associated, algal, and wastewater ecosystems. Co-occurrence network analysis revealed two distinct organizational strategies: a rare, conserved core cluster of genes associated with fengycin, surfactin, iturin lichenysin and plipastatin production, and a widespread, modular periphery linked to rhamnolipid, emulsan, and serrawettin W1 pathways, that are likely driven by the need to adapt to environmental complexity. Notably, we identified previously unreported genomes with biosurfactant production potential, significantly expanding the known biodiversity and ecological range of potential producers. Our findings establish biosurfactant production as a key microbial trait shaped by habitat, with broad implications for microbial ecology, ecosystem monitoring and sustainable biotechnology. This work provides comprehensive genomic resource for biosurfactant research, laying the foundation for targeted bioprospecting and integrative functional studies.