ArticleMicrobial ecology2026
Host genotype Impacts the Assembly and Functional Potential of Bacterial Communities in the Spinach Phyllosphere Within Commercial Organic Farming Systems.
Article in Microbial ecology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
Understanding how host genotype influences phyllosphere microbiome assembly and functional potential is crucial for enhancing crop health in commercial organic production systems. We characterized the diversity, composition, ecological assembly processes, core taxa, and predicted functions of the spinach (Spinacia oleracea L.) phyllosphere across eight commercial cultivars grown under organic management at two locations in California. Absolute qPCR revealed variation in bacterial abundance across samples, although cultivars did not differ significantly. Alpha diversity was broadly similar among cultivars, whereas sampling location and plant age showed stronger effects. Beta diversity analyses revealed that community composition was primarily structured by location, with cultivar-associated differences detectable but minor. Niche breadth patterns were comparable across cultivars. Ecological assembly analyses indicated that phyllosphere communities were shaped by a combination of stochastic dispersal and deterministic selection, with stochastic processes predominating within cultivars. A conserved core microbiome, including genera such as Pseudarthrobacter, Sphingomonas, and Nocardioides, was consistently detected across cultivars, suggesting a stable phyllosphere consortium under organic field conditions. Functional predictions indicated a dominance of chemoheterotrophy and moderate representation of nitrogen-cycling pathways, with modest cultivar-specific variation in carbon and nitrogen transformations. Overall, geographic location emerged as the primary driver of spinach phyllosphere assembly, while a stable core microbiome and conserved functional potential persisted across cultivars. These results show that environmental filtering, random dispersal, and small effects of host genotype all affect the structure and function of the phyllosphere in organic farming. This gives us a basis for microbiome-informed strategies to improve crop resilience and food safety.
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