Extracellular Molecular Repertoire of Xerotolerant Actinobacteria Colonizing Serpentinite Rocks

Weathered serpentinites are extreme lithobiontic environments characterized by oligotrophy, high heavy metal content, and desiccation stress; yet, the adaptive mechanisms of colonizing actinobacteria remain poorly understood. This study aimed to isolate and characterize xerotolerant actinobacteria from serpentinite and to profile their secondary metabolites involved in stress tolerance. Three lithobiontic strains were isolated and identified by whole-genome sequencing (dDDH and ANI) as Rhodococcus oxybenzonivorans SK11, Paenarthrobacter nitroguajacolicus SK18, and Rhodococcus qingshengii SK25. Desiccation tolerance was assessed using PEG-8000, siderophore production on CAS agar with metal substitution (Fe³⁺, Al³⁺, Cu²⁺, Ga³⁺), and biosurfactant activity via emulsification assays. Genome mining identified biosynthetic gene clusters for compatible solutes, siderophores, and biosurfactants. All strains maintained viability at 50% PEG. Compatible solute pathways included ectoine (ectABC) in SK18 and SK25, glycine betaine (gbsAB) only in SK18, and trehalose (TreYZ) and proline (ProABC) pathways in all three. Genome mining of Rhodococcus strains revealed a number of NRPS-dependent clusters, some of which are predicted to encode siderophores (rhodochelin, heterobactins), while SK18 used an NRPS-independent desferrioxamine E pathway together with a unique lanthipeptide cluster. Biosurfactant production was condition-dependent, with SK25 achieving complete emulsification (E₂₄ = 100%) in hexadecane-supplemented medium. These findings demonstrate that weathered serpentinite actinobacteria employ an extracellular molecular repertoire of compatible solutes, siderophores, and biosurfactants to survive extreme oligotrophy, desiccation, and metal stress.