Effect of Rhizosphere Microbiome on Nutrients Composition of Soil and Fruits Metabolites of Highbush Blueberry (<em>Vaccinium</em> <em>corymbosum</em> L.) Grown in Open Ground Conditions and Greenhouses

This study revealed that highbush blueberry (Vaccinium corymbosum L.) plants cultivated in distinct cultivation systems (greenhouse vs. open field) exhibited significant differences in rhizosphere microbiota, soil nutrient profiles, and fruit metabolites. Metabolite profiling revealed a significant trade-off: fruits from the open field accumulated significantly higher levels of secondary metabolites, including anthocyanins (9.5% higher; 1.85 ± 0.03 vs. 1.69 ± 0.03 μmol/g; p = 0.002), flavonoids (56.0% higher; 0.39 ± 0.01 vs. 0.25 ± 0.03 mg/g; p = 0.007), and ascorbic acid (15.6% higher; 144.71 ± 3.80 vs. 125.19 ± 3.99 μg/g; p = 0.003). In contrast, greenhouse fruits were enriched in primary metabolites such as water-soluble sugars (28.3% higher; 109.96 ± 4.73 vs. 85.70 ± 2.91 mg/g; p = 0.006) and total organic acids (30.2% higher; 19.39 ± 0.31 vs. 14.89 ± 0.55 mg/g; p &lt; 0.001). These divergent profiles were associated with distinct rhizosphere microenvironments: the open field treatment sustained higher OC and microbial α-diversity (Shannon index), while the greenhouse system formed a high-availability cation niche characterized by lower pH, higher EC, and elevated levels of exchangeable Ca²⁺, Mg²⁺, and available potassium (APO). The cultivation systems re-engineered the rhizosphere microbiota assembly, resulting in distinct communities (assessed by principal coordinates analysis (PCO) based on UniFrac distances). Notably, the greenhouse soil was associated with a higher relative abundance of copiotrophic bacterial taxa such as Streptomyces and Bacillus. Their relative abundances showed strong positive correlations with cation availability (e.g., Streptomyces vs. Ca²⁺, *r* = 0.827), suggesting a potential ecological linkage, though causation cannot be inferred from these correlative data alone. Multivariate correlation and principal component analysis (PCA) integrated these patterns and revealed that soil cations (Ca²⁺, Mg²⁺, APO) were negatively correlated with fruit antioxidants but positively linked to sugars/acids, and the key microbial taxa (e.g., Bacillus, Chloroflexi) were major contributors to the difference of fruit quality traits. The findings highlight that the cultivation systems is strongly associated with fruit quality by selectively shaping a functionally specific rhizosphere microbiota, which co-varies with a shift in the plant's resource allocation between growth (primary metabolism) and defense (secondary metabolism). This work provides an integrative correlation and proposes framework for understanding how agricultural practices manipulate the soil-plant-microbe continuum to direct crop quality in perennial systems. Our findings, primarily correlative, reveal a consistent cultivation systems-level association between the cultivation environment, rhizosphere properties, and fruit metabolism. This work provides an integrative correlative framework for understanding how agricultural practices manipulate the soil-plant-microbe continuum to direct crop quality in perennial systems and proposes testable hypotheses for future mechanistic investigations.