Phylogeography of the wide-host range panglobal plant pathogen Phytophthora cinnamomi.

Various hypotheses have been proposed regarding the origin of the plant pathogen Phytophthora cinnamomi. P. cinnamomi is a devastating, highly invasive soilborne pathogen associated with epidemics of agricultural, horticultural and forest plantations and native ecosystems worldwide. We conducted a phylogeographic analysis of populations of this pathogen sampled in Asia, Australia, Europe, southern and northern Africa, South America, and North America. Based on genotyping-by-sequencing, we observed the highest genotypic diversity in Taiwan and Vietnam, followed by Australia and South Africa. Mating type ratios were in equal proportions in Asia as expected for a sexual population. Simulations based on the index of association suggest a partially sexual, semi-clonal mode of reproduction for the Taiwanese and Vietnamese populations while populations outside of Asia are clonal. Ancestral area reconstruction provides new evidence supporting Taiwan as the ancestral area, given our sample, indicating that this region might be near or at the centre of origin for this pathogen as speculated previously. The Australian and South African populations appear to be a secondary centre of diversity following migration from Taiwan or Vietnam. Our work also identified two panglobal, clonal lineages PcG1-A2 and PcG2-A2 of A2 mating type found on all continents. Further surveys of natural forests across Southeast Asia are needed to definitively locate the actual centre of origin of this important plant pathogen.

Soilborne Phytophthora and Pythium Diversity From Rhododendron in Propagation, Container, and Field Production Systems of the Pacific Northwest.

Rhododendron root rot is a severe disease that causes significant mortality in rhododendrons. Information is needed about the incidence and identity of soilborne Phytophthora and Pythium species causing root rot in Pacific Northwest nurseries in order to better understand the disease etiology and to optimize disease control strategies. The last survey focusing solely on soilborne oomycete pathogens in rhododendron production was conducted in 1974. Since then, advances in pathogen identification have occurred, new species may have been introduced, pathogen communities may have shifted, and little is known about Pythium species affecting this crop. Therefore, a survey of root-infecting Phytophthora and Pythium species was conducted at seven nurseries from 2013 to 2017 to (i) document the incidence of root rot damage at each nursery and stage of production, (ii) identify soilborne oomycetes infecting rhododendron, and (iii) determine whether there are differences in pathogen diversity among nurseries and production systems. Rhododendrons from propagation, container, and field systems were sampled and Phytophthora and Pythium species were isolated from the roots and collar region. Root rot was rarely evident in propagation systems, which were dominated by Pythium species. However, severe root rot was much more common in container and field systems where the genus Phytophthora was also more prevalent, suggesting that Phytophthora species are the primary cause of severe root rot and that most contamination by these pathogens comes in after the propagation stage. In total, 20 Pythium species and 11 Phytophthora species were identified. Pythium cryptoirregulare, Pythium aff. macrosporum, Phytophthora plurivora, and Phytophthora cinnamomi were the most frequently isolated species and the results showed that Phytophthora plurivora has become much more common than in the past. Phytophthora diversity was also greater in field systems than in propagation or container systems. Risks for Phytophthora contamination were commonly observed during the survey and included placement of potting media in direct contact with field soil, the presence of dead plants that could serve as continuous sources of inoculum, and the presence of excess water as a result of poor drainage, overirrigation, or malfunctioning irrigation equipment. In the past, research on disease development and root rot disease control in rhododendron focused almost exclusively on Phytophthora cinnamomi. More research is needed on both of these topics for the other root-infecting species identified in this survey.

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.

The Irish potato famine pathogen Phytophthora infestans originated in central Mexico rather than the Andes.

Phytophthora infestans is a destructive plant pathogen best known for causing the disease that triggered the Irish potato famine and remains the most costly potato pathogen to manage worldwide. Identification of P. infestan's elusive center of origin is critical to understanding the mechanisms of repeated global emergence of this pathogen. There are two competing theories, placing the origin in either South America or in central Mexico, both of which are centers of diversity of Solanum host plants. To test these competing hypotheses, we conducted detailed phylogeographic and approximate Bayesian computation analyses, which are suitable approaches to unraveling complex demographic histories. Our analyses used microsatellite markers and sequences of four nuclear genes sampled from populations in the Andes, Mexico, and elsewhere. To infer the ancestral state, we included the closest known relatives Phytophthora phaseoli, Phytophthora mirabilis, and Phytophthora ipomoeae, as well as the interspecific hybrid Phytophthora andina. We did not find support for an Andean origin of P. infestans; rather, the sequence data suggest a Mexican origin. Our findings support the hypothesis that populations found in the Andes are descendants of the Mexican populations and reconcile previous findings of ancestral variation in the Andes. Although centers of origin are well documented as centers of evolution and diversity for numerous crop plants, the number of plant pathogens with a known geographic origin are limited. This work has important implications for our understanding of the coevolution of hosts and pathogens, as well as the harnessing of plant disease resistance to manage late blight.

Phytophthora community structure analyses in Oregon nurseries inform systems approaches to disease management.

Nursery plants are important vectors for plant pathogens. Understanding what pathogens occur in nurseries in different production stages can be useful to the development of integrated systems approaches. Four horticultural nurseries in Oregon were sampled every 2 months for 4 years to determine the identity and community structure of Phytophthora spp. associated with different sources and stages in the nursery production cycle. Plants, potting media, used containers, water, greenhouse soil, and container yard substrates were systematically sampled from propagation to the field. From 674 Phytophthora isolates recovered, 28 different species or taxa were identified. The most commonly isolated species from plants were Phytophthora plurivora (33%), P. cinnamomi (26%), P. syringae (19%), and P. citrophthora (11%). From soil and gravel substrates, P. plurivora accounted for 25% of the isolates, with P. taxon Pgchlamydo, P. cryptogea, and P. cinnamomi accounting for 18, 17, and 15%, respectively. Five species (P. plurivora, P. syringae, P. taxon Pgchlamydo, P. gonapodyides, and P. cryptogea) were found in all nurseries. The greatest diversity of taxa occurred in irrigation water reservoirs (20 taxa), with the majority of isolates belonging to internal transcribed spacer clade 6, typically including aquatic opportunists. Nurseries differed in composition of Phytophthora communities across years, seasons, and source within the nursery. These findings suggest likely contamination hazards and target critical control points for management of Phytophthora disease using a systems approach.

Pathogenicity, Fungicide Resistance, and Genetic Variability of Phytophthora rubi Isolates from Raspberry (Rubus idaeus) in the Western United States.

Root rot of raspberry (Rubus idaeus), thought to be primarily caused by Phytophthora rubi, is an economically important disease in the western United States. The objectives of this study were to determine which Phytophthora species are involved in root rot, examine the efficacy of different isolation methods (cane, root, and root/soil baiting with young raspberry plants), and determine if pathogenicity, fungicide resistance, and/or genetic variation exists among P. rubi isolates collected from raspberry fields in Washington, Oregon, and California. Of 275 samples, direct isolation from cane material resulted in a greater number of P. rubi isolates (39%), whereas root/soil baiting yielded the least (11%). Sequencing of the internal transcribed spacer region of 210 of the total 597 collected Phytophthora isolates showed that all but one isolate (identified as P. bisheria) were P. rubi. Results of the pathogenicity and fungicide resistance to mefenoxam comparing 14 total isolates from Washington, Oregon, and California showed that isolates were similarly virulent against red raspberry and the EC50 frequency distributions showed no significant difference. These results, combined with amplified fragment length polymorphism results show that P. rubi isolates from Washington, Oregon, and California represent one large mixed population. This work provides novel insights into the isolation and biology of P. rubi in western U.S. raspberry production systems.