Location: Horticultural Crops Disease and Pest Management Research Unit
Project Number: 2072-22000-045-065-A
Project Type: Cooperative Agreement
Start Date: Sep 1, 2026
End Date: Aug 31, 2030
Objective:
Objective 1: Survey forest and nursery isolates of Phytophthora ramorum for the presence of hybrids and validate hybrid diagnostic assay. Surveying is critical for determining the extent and frequency of hybridization events. Additionally, assembling a comprehensive collection of hybrids is essential for reconstructing their evolutionary histories, assessing their trajectories, and developing new evidence-based management strategies. The Oregon Department of Forestry and the US Forest Service currently survey the (Sudden Oak Death) SOD outbreak and provide samples to the cooperator on a weekly basis for diagnostics. The CFDA and ODA also survey nursery plants for P. ramorum and regularly provide samples to the USDA-ARS. Up to now, the identification of hybrids has not been routinely conducted, as their existence was not known.
Objective 2: Compare the relative aggressiveness among lineages and hybrids on common plant species in nurseries and forests. The high evolutionary potential of hybrids may alter fitness, and understanding these changes is essential for developing or revising mitigation strategies. Important traits are aggressiveness, host range, and sporulation.
Objective 3: Conduct 5-year re-measurement of permanent-plot network in southwest Oregon. A total of 88 plots were established in 2020 and 2021 in the forests of southwest Oregon. These plots encompassed treated sites, control stands, and untreated infestations. We will remeasure these sites to evaluate the impact of disease development and treatment on forest dynamics.
Objective 4: Evaluate the effect of host stress and fungicide application (metalaxyl) on P. ramorum genome stability. In other Phytophthora spp. stress has been demonstrated to affect genome stability, fitness, and fungicide resistance. We will evaluate how P. ramorum will respond to host and fungicide induced stress at the genome level. Isolates with these changes are less aggressive and sporulate less. Understanding this process could lead to novel management approaches for P. ramorum.
Objective 5: Compare disease resistance and genetic diversity of residual surviving tanoak trees to that of the broader population. Not all tanoak trees have been killed by the SOD. We will compare the relative levels of resistance of seedlings grown from these parent trees with seedlings grown from tanoak trees in healthy stands.
Objective 6: Determine how long P. ramorum can survive in tanoak logs after harvest. Currently, the regulations for southwest Oregon prevent the movement of tanoak logs outside of the quarantine area prior to processing. Determining the length of time P. ramorum is viable in harvested tanoak trees could have potential implications for the use and movement of logs outside the quarantine area.
Approach:
Obj. 1: In addition to testing the samples we regularly receive, we will conduct bucket surveys, intensively targeting regions of Oregon where the distribution of EU1 and NA2 overlap. We will use tanoak baited buckets to sample rainwater. Fifty infected tanoak trees, in the regions where NA2 and EU1 overlap will be selected for sampling. Five one-gallon buckets will be distributed around the base of the infected trees, in the drip line of the canopy. In each bucket, 1 liter of sterile distilled water will be added along with 5 healthy tanoak leaves so that flagellate zoospores that land in the bucket will infect the bait leaves. Every two weeks, for 6 months leaves will be collected, the liner replaced, and new water and leaves will be added to the bucket. Leaf samples will be brought back to the lab for pathogen isolation and initial genotyping and whole genome sequencing, if appropriate. Initial genotyping will be conducted using the USDA developed CRISPR-dx assays. We anticipate sequencing approximately 50 isolates of P. ramorum.
Obj. 2: A total of 20 common nursery species will each be inoculated separately with three isolates, each representing a distinct hybrid origin of P. ramorum. Controls will include three isolates from each of the clonal lineages NA1, NA2, and EU1. We will inoculate by placing a plug of mycelium on the stem of the plant and wrapping the two in parafilm. We will also harvest sporangia to compare sporulation. After seven days the lesion lengths will be measured, and sporangia harvested and counted, and these parameters will be compared to lesions and sporulation caused by isolates of clonal lineages. All experiments will be repeated twice.
Obj. 3: To assess how SOD and treatments have affected southwest Oregon forest communities, we will remeasure all vegetation in our permanent plot network. Measurements will include plant height, DBH, percent cover, canopy closure, soil samples, disease severity, fuels surveys, and other sample collections. Results will be compared to baseline data collected in 2020–2021.
Obj. 4: We will inoculate tanoak stems with five isolates from NA1, NA2, and EU1. After several weeks, isolates will be re isolated and sequenced to assess genomic changes. In parallel, five isolates of each lineage will be grown in liquid media amended with metalaxyl and sequenced to evaluate genomic responses.
Obj. 5: We will collect 200 acorns from surviving tanoaks and 200 from unexposed stands. Seedlings will be grown in the greenhouse. Using pool seq, we will genotype seedlings and parent trees to compare genetic diversity. Controlled inoculations in our APHIS certified facility will assess resistance of both groups to NA1, EU1, and NA2.
Obj. 6: To determine how long P. ramorum survives in tanoak logs, we will select 100 infected trees across the SOD range. After confirming infection, trees will be felled and resampled monthly to determine pathogen viability. Sampling will continue until two consecutive negative culture periods occur.