Microbacterium sp. Y107 Is Associated with Enhanced Lingonberry Root Growth and Transcriptional Changes Under Gnotobiotic Conditions

Lingonberry (Vaccinium vitis-idaea L.) has a weak root system and limited nutrient acquisition capacity. Plant growth-promoting rhizobacteria (PGPR) can promote plant growth by regulating rhizosphere nutrient cycling and host metabolism, but the underlying mechanisms in Ericaceae remain unclear. In this study, the strain Microbacterium sp. Y107 was isolated from the rhizosphere of lingonberry. Using growth-promoting assays (with 9 independent biological replicates, each consisting of 3 plants per bottle as the experimental unit, an inoculum density of OD600 = 1.0, a cultivation period of 60 days, and whole-plant harvesting), GC–MS-based metabolite analysis, axenic coculture, analyses of the rhizosphere environment and gene expression, transcriptome sequencing (3 biological replicates per treatment), and qRT–PCR validation, we systematically evaluated the effects of strain Y107 on lingonberry growth, rhizosphere conditions, and host gene expression. CK (control) plants were defined as those inoculated with sterile LB liquid medium. Pearson correlation analysis was also used to assess the relationships among plant growth, soil traits, and physiological indices. Compared with the CK treatment, strain Y107 significantly promoted lingonberry growth (p < 0.05), increasing the fresh weight of the roots by 157.65% and the whole-plant fresh weight by 33.85%, respectively, and increasing peroxidase (POD) activity by 61.11%, while reducing the contents of reducing sugars and proline. Strain Y107 stably colonized the lingonberry root surface and formed biofilms. Y107 treatment resulted in detectable levels of soil microbial biomass carbon and nitrogen, indicating successful microbial colonization. The ammonium nitrogen content significantly increased, increasing nitrogen availability and promoting root nutrient uptake. Transcriptome analysis revealed that the expression of genes enriched in photosynthesis-related pathways, as well as those involved in carbon and nitrogen metabolism and redox regulation, was altered in strain Y107, which upregulated key photosynthesis-related genes such as psbP and ndhU and significantly enriched the cytosolic ribosomal large subunit gene set in a negative direction. Correlation analysis further revealed that strain Y107 optimized the association between lingonberry growth and soil nutrients. Overall, strain Y107 promoted lingonberry growth through stable colonization, enhanced nutrient cycling, promoted lingonberry growth, and altered the expression patterns of genes involved in photosynthesis-related pathways.