Novel Introductions and Epidemic Dynamics of the Sudden Oak Death Pathogen Phytophthora ramorum in Oregon Forests.

Sudden oak death caused by Phytophthora ramorum has been actively managed in Oregon since the early 2000s. To date, this epidemic has been driven mostly by the NA1 clonal lineage of P. ramorum, but an outbreak of the EU1 lineage has recently emerged. Here, we contrast the population dynamics of the NA1 outbreak first reported in 2001 to the outbreak of the EU1 lineage first detected in 2015. We performed tests to determine whether any of the lineages were introduced more than once. Infested regions of the forest were sampled between 2013 and 2018 (n = 903), and strains were genotyped at 15 microsatellite loci. Most genotypes observed were transient, with 272 of 358 unique genotypes emerging during one year and disappearing the next year. The diversity of EU1 was very low and isolates were spatially clustered (less than 8 km apart), suggesting a single EU1 introduction. Some forest isolates are genetically similar to isolates collected from a local nursery in 2012, suggesting the introduction of EU1 from this nursery or simultaneous introduction to both the nursery and latently into the forest. In contrast, the older NA1 populations were more polymorphic and spread more than 30 km2. A principal component analysis supported two to four independent NA1 introductions. The NA1 and EU1 epidemics infest the same area but show disparate demographics because of the initial introductions of the lineages spaced 10 years apart. Comparing these epidemics provides novel insight regarding patterns of emergence of clonal pathogens in forest ecosystems.

Population Structure of Phytophthora plurivora on Rhododendron in Oregon Nurseries.

Phytophthora plurivora is a recently described plant pathogen, formerly recognized as P. citricola. Recent sampling of Pacific Northwest nurseries frequently encountered this pathogen, and it has been shown to be among the most damaging Phytophthora pathogens on ornamentals. We characterized the population structure of P. plurivora in a survey of four Oregon nurseries across three different counties with focus on Rhododendron hosts. Isolates were identified to the species level by Sanger sequencing and/or a PCR-RFLP assay of the internal transcribed spacer (ITS) region. We used genotyping-by-sequencing to determine genetic diversity. Variants were called de novo, resulting in 284 high-quality variants for 61 isolates after stringent filtering. Based on Fst and AMOVA, populations were moderately differentiated among nurseries. Overall, population structure suggested presence of one dominant clonal lineage in all nurseries, as well as isolates of cryptic diversity mostly found in one nursery. Within the clonal lineage, there was a broad range of sensitivity to mefenoxam and phosphorous acid. Sensitivity of the two fungicides was correlated. P. plurivora was previously assumed to spread clonally, and the low genotypic diversity observed within and among isolates corroborated this hypothesis. The broad range of fungicide sensitivity within the P. plurivora population found in PNW nurseries has implications for managing disease caused by this important nursery pathogen. These findings provide the first perspective into P. plurivora population structure and phenotypic plasticity in Pacific Northwest nurseries.