The study explored bacterial and fungal communities in two commercially cultivated spinach (Spinacia oleracea L.) cultivars across five ecological niches: bulk soil, rhizosphere, root endosphere, leaf episphere, and leaf endosphere. Using high-throughput sequencing of 16S rRNA and ITS amplicons, we assessed microbial diversity, composition, co-occurrence networks, and functional potential, revealing that alpha microbial diversity was highest in bulk soil and lowest in the leaf endosphere. Beta diversity analysis demonstrated significant niche differentiation, with fungal communities exhibiting notable cultivar-driven variation, while bacterial communities were more influenced by niche. The bacterial microbiome displayed a wide range of taxa, while the fungal microbiome comprised two primary groups, with differential abundance analysis indicating niche-specific microbial enrichment in both bacterial and fungal communities. Tracking microbial contributions to different niches showed minimal influence of bulk soil on the rhizosphere, with fungal communities presenting higher niche transfer rates than bacteria. Co-occurrence network analysis highlighted cultivar-specific microbial interactions. Functional predictions indicated niche-dependent microbial metabolic adaptations, particularly in carbohydrate and amino acid metabolism. These findings offer valuable insights into the spinach microbiome, highlighting niche differentiation and cultivar-specific microbial interactions that influence plant-associated microbial communities.
