Integrated Metagenomic and Culturomic Strategies to Mine and Validate Beneficial Rhizosphere Actinobacteria from Lavender

Xugela Habuding^1*Jiayi Chen¹Jinfang Zhu²Guanru Wang¹Lan Ma¹Tajiguli Abulikemu^1*

• ¹Xinjiang Normal University, Urumqi, China
• ²Xinjiang Agricultural University, Urumqi, China

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. To overcome the limitations of conventional single-method approaches, this study integrated metagenomic and culturomic strategies for the first time to systematically investigate the rhizosphere and endophytic microbiomes in saline-alkaline lavender cultivation areas in Huocheng, China (soil pH ~ 8.04, salt ~ 0.074%). High-throughput sequencing revealed that the phylum Actinomycetota dominated both the rhizosphere and root endophytic communities, with Streptomyces and Nocardioides as the predominant genera. A key innovative finding, through metagenomic functional annotation combined with soil factor correlation analysis, is that this rhizosphere microbial community is enriched with functional genes related to saline-alkaline stress response, secondary metabolite synthesis, and nutrient cycling. The distribution of these genes showed significant correlations with soil pH and salinity, revealing potential genetic-level mechanisms for community adaptation to adversity. Guided by these functional predictions, a culturomics approach was used to obtain 10 strains with multiple plant growth-promoting traits (P-solubilization, siderophores, IAA, ACC deaminase, and nitrogenase activity), based on screening of colony morphology, molecular identification, and bioactivity. Furthermore, pot inoculation experiments demonstrated that actinobacteria derived from this saline-alkaline environment were effective not only as single strains but also as a bacterial consortium (C4 + A1), which showed a particularly significant growth-promoting effect on Arabidopsis thaliana. This approach achieved closed-loop verification from "functional prediction" to "empirical strain validation." This study provides the first systematic elucidation of the functional adaptation mechanisms of the lavender rhizosphere actinobacterial community under saline-alkaline conditions. Moreover, by employing an integrated strategy, it identifies elite microbial resources possessing both stress tolerance and multiple PGP functions. These findings offer novel microbial agents and a solid theoretical foundation for developing specialized inoculants aimed at mitigating saline-alkaline obstacles in lavender cultivation.