Genomic and Functional Analysis of Two Halophilic IAA-Producing Vreelandella Strains

Soil salinization poses a crucial challenge to agriculture; in fact, it reduces both growth and crop yields. Vreelandella species emerged as promising plant-growth-promoting-rhizobacteria (PGPR) capable of thriving in saline environments. Our study illustrates a comparative genomic analysis of two Vreelandella species: Vreelandella titanicae (QH24) and Vreelandella alkaliphila (QH23), isolated from the rhizosphere of quinoa cultivated in the presence of salt. Genome sequencing, functional annotation, and protein interaction network modeling were used to explore their adaptive mechanisms to salinity and their potential to plant growth promotion, with a specific focus on indole-3-acetic acid (IAA) biosynthesis under salt stress. Both genomes revealed several genes involved in osmotic stress response, including those associated with ectoine, glycine betaine, and proline metabolism. PGPR-related genes, particularly those involved in IAA biosynthesis, siderophore production, and phosphate metabolism, were identified in both species, although key differences emerged. In vitro assays on quinoa seedlings confirmed the PGPR potential of both strains, showing improved seedling growth and modification in root architecture. Moreover, both the strains produced more IAA in response to increasing amounts of NaCl, with QH23 exhibiting significant higher quantities respect to QH24. Network analysis revealed that aldA acts as a central regulatory hub linking auxin biosynthesis and salt-responsive metabolism in QH24, whereas amiE in QH23 is part of a wider interaction module. These findings indicate that QH24 and QH23 take different genetic strategies to coordinate IAA synthesis under saline conditions. Our results provide important information regarding the genomic basis of PGPR activity as a response to saline conditions and lay the foundations for further transcriptomic and metabolomic studies to optimize PGPR use in sustainable agricultural practices.