The bacterial diversity of seeds, transmission of bacteria from seed to phyllosphere, and fate of seed-transmitted bacteria on mature plants are poorly characterized. Understanding the dynamics of microbial communities is important for finding bio-control or mitigation strategies for human and plant pathogens. Bacterial populations colonizing spermosphere and phyllosphere of spinach (Spinacia oleracea) seedlings and plants were characterized using pyrosequencing of 16S rRNA gene amplicons. Spinach seed microbiota was composed of three bacterial phyla: Proteobacteria, Firmicutes and Actinobacteria, belonging to > 250 different operational taxonomic units (OTUs). Seed and cotyledon bacterial communities were similar in richness and diversity. Richness of 3-4 leaf-stage of development plants increased markedly to > 850 OTUs classified within 11 phyla. Although some bacterial OTUs were detected on seeds, cotyledons and plants, the breadth of new sequences indicates the importance of multiple sources outside the seed in shaping phyllosphere community. Most classified sequences were from previously undescribed taxa, highlighting the benefits of pyrosequencing in describing seed diversity and phyllosphere bacterial communities. Bacterial community richness increased from 250 different OTUs for spinach seeds and cotyledons, to 800 OTUs for seedlings. To our knowledge this is the first comprehensive characterization of the spinach microbiome, complementing previous culture-based and clone library studies.

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