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

Authors: Kandel, Shyam; Henry, Peter; Goldman, Polly; Mou, Beiquan; Klosterman, Steven

Submitted to: Phytobiomes Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/3/2021
Publication Date: 2/17/2022
Citation: Kandel, S.L., Henry, P.M., Goldman, P.H., Mou, B., Klosterman, S.J. 2022. Composition of the microbiomes from spinach seeds infested or noninfested with Peronospora effusa or Verticillium dahliae. Phytobiomes Journal. 6(2):169-180. https://doi.org/10.1094/PBIOMES-05-21-0034-R.
DOI: https://doi.org/10.1094/PBIOMES-05-21-0034-R

Interpretive Summary: Spinach seeds are produced in a few specific locations in both the northern and southern hemisphere due to the long day length requirement for seed production. Movement of spinach seeds from these locations to other parts of the world may also move microbes on seeds that are beneficial or harmful to crop production. Verticillium dahliae is a broad host range fungal pathogen for example that is carried on spinach seeds and planted in soils which affects subsequent crops grown in rotation. Peronospora effusa is the organism that causes downy mildew on spinach directly. In this study we examined DNA sequences of microbes obtained from spinach seeds infested with either Peronospora effusa or Verticillium dahliae, or not infested and from two different geographic areas. Analysis of the DNA sequences in total indicate divergence in seed microbes between those derived from different geographic regions and types of pathogen infestation and may be helpful identify beneficial microorganisms for improving plant health.

Technical Abstract: 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 noninfested 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, A. solani, 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 seedborne microorganisms that could be utilized to improve plant health and plant pathogens that could be inadvertently carried to new locations.