Integrated metagenomic and culturomic strategies to mine and validate beneficial rhizosphere Actinobacteria from lavender

Introduction: The lavender industry faces significant constraints from soil salinization and continuous cropping obstacles. However, systematic exploration and functional analysis of beneficial rhizosphere microbial resources, particularly Actinobacteria, remain inadequate. Methods: To address this, we integrated metagenomic and culturomic strategies to investigate the rhizosphere and endophytic microbiomes in saline-alkaline lavender cultivation areas in Huocheng, China (soil pH ~8.04, salt ~0.074%). Metagenomic functional annotation and soil factor correlation analysis guided a subsequent culturomics approach to isolate strains. Isolates were screened for plant growth-promoting (PGP) traits, and selected strains were evaluated in pot inoculation experiments with Arabidopsis thaliana. Results: High-throughput sequencing revealed that Actinomycetota dominated the microbial communities, with Streptomyces and Nocardioides as key genera. Metagenomic analysis showed the community was enriched with functional genes related to saline-alkaline stress response, secondary metabolite synthesis, and nutrient cycling, whose distribution correlated significantly with soil pH and salinity. From this resource, 10 actinobacterial strains with multiple PGP traits (e.g., P-solubilization, siderophore production, IAA, ACC deaminase, and nitrogenase activity) were obtained. Pot experiments confirmed that these saline-alkaline-derived actinobacteria, both as single strains and as a bacterial consortium (C4 + A1), significantly promoted the growth of A. thaliana. Discussion: This study achieves a closed-loop verification from in silico functional prediction to empirical validation of beneficial strains. It provides the first systematic elucidation of the functional adaptation mechanisms of the lavender rhizosphere actinobacterial community under saline-alkaline stress and identifies elite microbial resources with both stress tolerance and PGP functions. The findings offer novel microbial agents and a theoretical foundation for developing specialized inoculants to mitigate saline-alkaline obstacles in lavender cultivation.