Niche-specific microbial diversity, interactions, and functional potential within the spinach microbiome

Understanding the spatial organization and functional diversity of microbiomes across plant compartments is essential for unraveling the complex interactions between plants and their associated microbial consortia. This study examined the microbial communities associated with spinach (<i>Spinacia oleracea</i> L.) across five ecological niches, using 16S rRNA and ITS amplicon sequencing, in two commercial conventional cultivars: Hammerhead and Traverse. Microbial diversity, community composition, co-occurrence networks, and functional potential showed cultivar-specific effects, especially in the fungal community. The niche was a significant factor influencing all microbiome parameters, showing the same pattern in both cultivars: highest in bulk soil, followed by the rhizosphere, leaf episphere, and finally the root and leaf endosphere. We observed clear niche differentiation and enrichment of niche-specific genera. A core microbiome was identified, comprising 10 bacterial and 6 fungal taxa, with <i>Streptomyces, Bacillus</i>, and <i>Rubrobacter</i> being the key bacterial genera, and <i>Alternaria</i> and <i>Cladosporium</i> being the dominant fungi. SourceTracker2 analysis revealed a limited contribution of bulk soil to the rhizosphere (∼25 %), while the rhizosphere and leaf episphere were the primary sources for endosphere communities. Fungal communities showed higher transfer rates (75-96 %) between niches compared to bacterial communities (19-93 %). Co-occurrence network analysis revealed that Traverse had a denser microbial network than Hammerhead, with key hubs such as <i>Streptomycetaceae</i> and <i>Chaetomiaceae.</i> Inferred functional potential suggested metabolic capabilities in microbial communities across spinach niches, including those of potential plant pathogens. The microbial spatial distribution and identification of spinach from this study lays the foundation for designing targeted strategies to mitigate pathogen risks and introduce beneficial microbial functions into crops.