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The effects of cultivar, production system, and nursery on the composition of the rhizosphere microbiome of cultivated rhododendrons in Oregon
Zachary Foster: USDA ARS; Jerry Weiland: USDA ARS; Carolyn Scagel: USDA ARS; Niklaus Grunwald: USDA ARS
<div>The composition of plant microbiomes influences important agricultural processes such as nutrient absorption and plant health. Plant genotype and environment affect the microbiome, but the nature and relative importance of these effects are not well understood. We evaluated the effect of host genotype, nursery, and production system (potted versus in-ground planting) on the composition of the fungal and oomycete rhizosphere microbiome of rhododendrons in Oregon nurseries. Rhizosphere and roots were sampled from randomly selected, potted and in-ground plants of 3 host cultivars at 4 nurseries. ITS1 amplicons were sequenced using the Illumina MiSeq. Sequences were clustered and assigned to taxa using vsearch. Organism trophic mode was inferred using the FUNGuild database. Diversity statistics, ordination plots, and heat trees were calculated in R with vegan and metacoder. There was little difference in alpha diversity between potted and in-ground plants, but nurseries that grew plants with both production systems had higher diversity overall. Cultivar did not account for observed differences in community composition; however, nursery and production system had a significant effect. Ordination results suggest that production system had the dominant effect on microbiome composition, followed by a moderate effect from nursery, and no effect from cultivar. Most fungal species were predicted to be saprotrophs (50%), followed by pathogens (12%) and symbionts (6%). </div>

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