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ARS Home » Pacific West Area » Corvallis, Oregon » Horticultural Crops Research » Research » Publications at this Location » Publication #364402

Research Project: Integrated Disease Management of Exotic and Emerging Plant Diseases of Horticultural Crops

Location: Horticultural Crops Research

Title: The composition of the fungal and oomycete microbiome of Rhododendron roots under varying growth conditions, nurseries, and cultivars

Author
item FOSTER, Z - Oregon State University
item Weiland, Jerry
item Scagel, Carolyn
item Grunwald, Niklaus - Nik

Submitted to: Phytobiomes Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/17/2020
Publication Date: 2/19/2020
Citation: Foster, Z.S., Weiland, G.E., Scagel, C.F., Grunwald, N.J. 2020. The composition of the fungal and oomycete microbiome of Rhododendron roots under varying growth conditions, nurseries, and cultivars. Phytobiomes Journal. 4(2):156-164. https://doi.org/10.1094/PBIOMES-09-19-0052-R.
DOI: https://doi.org/10.1094/PBIOMES-09-19-0052-R

Interpretive Summary: The microbial community of agricultural crops, often called the microbiome, influences plant processes such as nutrient absorption, drought stress, and susceptibility to pathogens. Interactions between a plant’s genotype and its environment influence the composition of the microbiome, but these interactions are not well understood. We compared how the microbiomes of rhododendrons from Oregon nurseries differed among cultivars, growth conditions, and nurseries. We focused on fungi and fungal like organisms commonly referred to as water molds. Roots were sampled from container and field-grown plants of 3 cultivars of rhododendron at 4 nurseries. We determined the diversity of species in the root microbiome using DNA sequencing. Few water molds were found and fungal communities were dominated by saprobes and mutualists. Nurseries that grew plants in containers and in field soil had a significantly higher diversity of fungi than those that only grew plants in containers. Microbiome composition differed significantly among growth conditions and nurseries, but not among cultivars. Our work suggests that environment is important in structuring the root microbiome, while cultivar is not.

Technical Abstract: The microbiome of agricultural crops influences processes such as nutrient absorption, drought stress, and susceptibility to pathogens. Interactions between a plant’s genotype and its environment influence the composition of the microbiome, but these interactions are not well understood. We compared how the fungal and oomycete microbiomes of rhododendrons from Oregon nurseries differed among cultivars, growth conditions, and nurseries. Roots were sampled from randomly selected, container and field-grown plants of 3 cultivars of rhododendron at 4 nurseries. The ITS1 barcode was sequenced with the Illumina MiSeq using two sets of primers specific to fungi and oomycetes, respectively. Sequences were used to infer community composition using VSEARCH and a custom reference database combining curated fungal and oomycete sequences. Comparisons of diversity and community composition were conducted in R using the vegan and metacoder packages. Organism lifestyle was inferred using the FUNGuild database. Few oomycetes were found and fungal communities were dominated by saprobes and mutualists. Nurseries that grew plants in containers and in field had a significantly higher diversity of fungi than those that only grew plants in containers. Microbiome composition differed significantly among growth conditions and nurseries, but not among cultivars. This suggests that, among these cultivars of rhododendron, environment is important in structuring the root microbiome, but cultivar is not.