ITS sequences-Effect of rhizosphere microbiome on soil nutrients and fruit metabolites of highbush blueberry (Vaccinium corymbosum L.) under greenhouse vs. open field cultivation

This study characterized 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. A clear metabolic trade-off was observed: open-field cultivation significantly enhanced fruit secondary metabolites, including anthocyanins (9.5% higher), flavonoids (56.0% higher), and ascorbic acid (15.6% higher). In contrast, greenhouse fruits were enriched in primary metabolites such as water-soluble sugars (28.3% higher) and total organic acids (30.2% higher) (p < 0.01 for all comparisons). These divergent profiles were associated with distinct rhizosphere microenvironments. The open field soil exhibited higher organic carbon and microbial alpha-diversity, while the greenhouse soil was characterized by a high-availability cation niche with lower pH, higher electrical conductivity, and elevated levels of exchangeable Ca2+, Mg2+, and available potassium. These contrasting niches were linked to shifts in the rhizosphere microbiota assembly. Notably, the greenhouse soil was associated with a higher relative abundance of copiotrophic bacterial taxa such as Streptomyces and Bacillus, whose abundances showed strong positive correlations with cation availability (e.g., Streptomyces vs. Ca2+, correlation coefficient r = 0.827, p < 0.01). Multivariate analysis integrated these patterns, revealing that soil cations were negatively correlated with fruit antioxidants but positively linked to sugars and acids. This correlative study suggests that cultivation systems are strongly associated with fruit quality, potentially by shaping functionally specific rhizosphere microbiota that co-varies with a shift in the plant's resource allocation between growth (primary metabolism) and defense (secondary metabolism). Our findings provide an integrative framework for understanding how agricultural practices manipulate the soil-plant-microbe continuum to influence crop quality in perennial systems and generate testable hypotheses for future mechanistic research.