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Fungal and oomycete microbiome of Rhododendron roots in Oregon nurseries

dataset
posted on 2024-06-11, 06:14 authored by Oregon State University
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.

Funding

U.S. Department of Agriculture, 2072-22000-039-00D

History

Data contact name

BioProject Curation Staff

Publisher

National Center for Biotechnology Information

Temporal Extent Start Date

2019-08-22

Theme

  • Non-geospatial

ISO Topic Category

  • biota

National Agricultural Library Thesaurus terms

sequence analysis

Pending citation

  • No

Public Access Level

  • Public

Accession Number

PRJNA561631

Preferred dataset citation

It is recommended to cite the accession numbers that are assigned to data submissions, e.g. the GenBank, WGS or SRA accession numbers. If individual BioProjects need to be referenced, state that "The data have been deposited with links to BioProject accession number PRJNA561631 in the NCBI BioProject database (https://www.ncbi.nlm.nih.gov/bioproject/)."

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