Composition of the microbiomes from spinach seeds infested or non-infested with Peronospora effusa or Verticillium dahliae

The worldwide distribution of plant seeds can disseminate beneficial and plant pathogenic microorganisms. This phenomenon is of particular concern where seed production is geographically isolated from crop production, as is the case with spinach in the United States. We aimed to characterize the structure and function of spinach seed microbiomes in commercial spinach seed lots originating from Europe and New Zealand. The seed lots we analyzed were infested with Peronospora effusa and Verticillium dahliae, only infested with V. dahliae, or not infested with either of these pathogens. The microbial taxonomic composition and gene function (assessed by Gene Ontology (GO) terms) of spinach seeds were highly influenced by geographic origin and the status of pathogen infestation. Through taxonomic profiling, we found that potentially plant beneficial bacterial genera such as Pseudomonas and Pantoea were the most abundant taxa both in infested and non-infested seeds, and Stenotrophomonas was observed in seed lots infested with P. effusa and V. dahliae. Many potential plant pathogens that are not known to be associated with spinach seed were also discovered by metagenomic analysis, including Sclerotinia sclerotiorum, Botrytis cinerea, Bipolaris sorokiniana, Fusarium pseudograminearum, Alternaria brassicae, Parastagonospora nodorum, and Pyrenophora teres f. teres. Our analysis of the function of prokaryotic genes in de novo assembled metagenomes revealed distinct GO terms associated with the geographic origin of seed lots. This work provides an important first step toward identifying spinach seed-borne microorganisms that could be utilized to improve plant health and plant pathogens that could be inadvertently carried to new locations.