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

## TL;DR

This study explores the microbial communities in different parts of spinach plants, finding that each part has unique microbes that may support plant health.

## Contribution

The study identifies niche-specific microbial taxa and interactions in spinach, revealing cultivar-specific patterns and functional potential.

## Key findings

- Microbial diversity is highest in bulk soil and roots enriched in Streptomyces.
- Co-occurrence networks show positive interactions supporting plant health.
- Fungal communities transfer more readily between niches than bacterial ones.

## Abstract

•Amplicon sequencing analyzed bacterial and fungal microbiomes in spinach niches.•Microbial diversity varied by niche, highest in bulk soil and roots enriched in Streptomyces.•Compartments showed niche-specific core and enriched microbial taxa.•Co-occurrence networks revealed positive interactions supporting plant health.•Functional predictions indicated niche-driven traits and limited bulk soil-phyllosphere links.

Amplicon sequencing analyzed bacterial and fungal microbiomes in spinach niches.

Microbial diversity varied by niche, highest in bulk soil and roots enriched in Streptomyces.

Compartments showed niche-specific core and enriched microbial taxa.

Co-occurrence networks revealed positive interactions supporting plant health.

Functional predictions indicated niche-driven traits and limited bulk soil-phyllosphere links.

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 (Spinacia oleracea 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 Streptomyces, Bacillus, and Rubrobacter being the key bacterial genera, and Alternaria and Cladosporium 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 Streptomycetaceae and Chaetomiaceae. 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.

Image, graphical abstract