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First Look Plant Disease article

First reports of Phytophthora ramorum clonal lineages NA1 and EU1 causing Sudden Oak Death on tanoaks in Del Norte County, California

Matteo Garbelotto, Francesco Dovana, Douglas Schmidt, Cameron Chee, Chris Lee, Valerie Fieland, Niklaus J. Grünwald, and Yana Valachovic


A year of forest health surveys has led to the first detection of Phytophthora ramorum in Del Norte County followed by the first wildland detection of the EU1 clonal lineage (Grunwald et al. 2009) of this pathogen in California. In July 2019, leaves were sampled from two tanoaks (Notholithocarpus densiflorus) and 16 California bay laurels (Umbellularia californica) in Jedediah Smith State Park in Del Norte County, the northernmost coastal County of California. Leaves displayed lesions normally associated with Sudden Oak Death (SOD) caused by P. ramorum and were discovered during the citizen science-based survey known as SOD Blitz (Meentemeyer et al. 2015). Samples were surface sterilized using 75% Ethanol and plated on PARPH-V8 agar (Jeffers and Martin 1986). After plating, DNA was extracted and amplified using two P. ramorum-specific assays (Hayden et al. 2006, Kroon et al. 2004). Leaves from two tanoaks exhibiting twig die-back had typical SOD lesions along the midvein, gave positive PCR results and yielded cultures with colony morphology, sporangia and chlamydospores typical of the NA1 lineage of P. ramorum originally isolated in California from tanoaks and coast live oaks (Quercus agrifolia) (Rizzo et al. 2002). The ITS locus and a portion of the Cox-1 locus were sequenced from DNA extracts of each culture using primers DC6-ITS4 (Bonants et al. 2004) and COXF4N-COXR4N (Kroon et al. 2004), respectively. ITS sequences (GB MN540639-40) were typical of P. ramorum and Cox-1 sequences (GB MN540142-3) perfectly matched the Cox-1 sequence of the NA1 lineage (GB DQ832718) (Kroon et al. 2004). Microsatellite alleles were generated as described in Croucher et al. (2013) for the two Del Norte cultures and for eight P. ramorum cultures, representative of the four main multilocus genotypes (MLGs) present in California, namely c1 (Santa Cruz/Commercial Nurseries), c3 (San Francisco Bay Area), c2 (Monterey County), and c4 (Humboldt County) (Croucher et al. 2013). The two Del Norte MLGs were identical to one another and most similar to MLG c1, with a single repeat difference at a single locus. SSR results suggest the inoculum source may not be from Humboldt County, neighboring to the South, but from a yet unidentified outbreak, possibly associated with ornamental plants. Jedediah Smith State Park was surveyed for 12 months following the initial detection, however the pathogen has yet to be re-isolated in that location. In July 2020, SOD symptomatic leaves from two tanoak trees exhibiting twig cankers were collected 8 Km north of Jedediah Smith State Park, where three additional tanoak trees displayed rapidly browned dead canopies consistent with late stage SOD. Leaves were processed as above. Colonies from these samples produced chlamydospores and sporangia typical of P. ramorum on PARPH-V8 agar, but displayed a growth rate faster than that of NA1 genotypes and were characterized by aerial hyphae, overall resembling the morphology of EU1 lineage colonies (Brasier 2003). The EU1 lineage was confirmed by the perfect match of the sequence of a portion of the Cox-1 gene (GB MW349116-7) with the Cox-1 sequence of EU1 genotypes (GB EU124926). The EU1 clonal lineage has been previously isolated from tanoaks in Oregon forests, approximately 55 Km to the North (Grünwald et al. 2016), but this is the first report for California wildlands and will require containment and government regulations. It is unknown whether the EU1 strains in Del Norte County originated from Oregon forests or elsewhere.

New Forests article November 2020

Phytophthora Introductions in Restoration Areas: Responding to Protect California Native Flora from Human-Assisted Pathogen Spread.

Frankel, S.J.; Conforti, C.; Hillman, J.; Ingolia, M.; Shor, A.; Benner, D.; Alexander, J.M.; Bernhardt, E.; Swiecki, T.J.

Forests 2020, 11, 1291. https://doi.org/10.3390/f11121291


Over the past several years, plantings of California native plant nursery stock in restoration areas have become recognized as a pathway for invasive species introductions, in particular Phytophthora pathogens, including first in the U.S. detections (Phytophthora tentaculata, Phytophthora quercina), new taxa, new hybrid species, and dozens of other soilborne species. Restoration plantings may be conducted in high-value and limited habitats to sustain or re-establish rare plant populations. Once established, Phytophthora pathogens infest the site and are very difficult to eradicate or manage—they degrade the natural resources the plantings were intended to enhance. To respond to unintended Phytophthora introductions, vegetation ecologists took a variety of measures to prevent pathogen introduction and spread, including treating infested areas by solarization, suspending plantings, switching to direct seeding, applying stringent phytosanitation requirements on contracted nursery stock, and building their own nursery for clean plant production. These individual or collective actions, loosely coordinated by the Phytophthoras in Native Habitats Work Group ensued as demands intensified for protection from the inadvertent purchase of infected plants from commercial native plant nurseries. Regulation and management of the dozens of Phytophthora species and scores of plant hosts present a challenge to the state, county, and federal agriculture officials and to the ornamental and restoration nursery industries. To rebuild confidence in the health of restoration nursery stock and prevent further Phytophthora introductions, a voluntary, statewide accreditation pilot project is underway which, upon completion of validation, is planned for statewide implementation.

Early view Forest Pathology article November 2020

The influence of time, soil moisture and exogenous factors on the survival potential of oospores and chlamydospores of Phytophthora cinnamomi. 

Jamba Gyeltshen, William A. Dunstan, Andrew H. Grigg, Treena I. Burgess, and Giles E. St. J. Hardy



The mode of persistence of Phytophthora cinnamomi, a highly aggressive soil‐ and water‐borne pathogen, remains unclear. This study investigated the survival of viable oospores and chlamydospores of P. cinnamomi when present as free propagules in untreated soil, or in soil subject to four exogenous treatments: smoke water, fish emulsion and two fungicides (ridomil and furalaxyl). The exogenous treatments were applied under moist and dry soil conditions. Spore viability was determined by the thiazolyl blue tetrazolium bromide (MTT) staining technique, with a qPCR assay used to compare general patterns of decline. Over 96% of oospores lost viability over a period of 48 weeks irrespective of soil moisture conditions. The mean percentage viability for oospores decreased from 91% at time zero to 72, 35, 20 and 1% after 6, 12, 24 and 48 weeks, respectively. Reduction in viability of chlamydospores was more rapid than oospores, with viability declining from 92% to zero after 12 weeks. There was no significant difference between untreated soil and the exogenous treatments. The RNA‐based qPCR assay indicated a strong presence of viable oospores of P. cinnamomi up to week 12 for moist soil and week 3 for dry soil, but thereafter failed to detect RNA even though viable oospores could be detected by MTT staining. Based on the MTT staining, this study indicated that viability of P. cinnamomi oospores may be entirely lost within 1 year and that of chlamydospores within 3 months for the soil type tested. Therefore, oospores and chlamydospores when existing as free propagules in soil appear unlikely to be involved in the long‐term survival of P. cinnamomi.

New "Forests" article January 2020

A Survey in Natural Forest Ecosystems of Vietnam Reveals High Diversity of both New and Described Phytophthora Taxa including P. ramorum.

Jung, T.; Scanu, B.; Brasier, C.M.; Webber, J.; Milenković, I.; Corcobado, T.; Tomšovský, M.; Pánek, M.; Bakonyi, J.; Maia, C.; Bačová, A.; Raco, M.; Rees, H.; Pérez-Sierra, A.; Horta Jung, M.

Forests 2020, 11, 93. https://www.mdpi.com/1999-4907/11/1/93

In 2016 and 2017, surveys of Phytophthora diversity were performed in 25 natural and semi-natural forest stands and 16 rivers in temperate and subtropical montane and tropical lowland regions of Vietnam. Using baiting assays from soil samples and rivers and direct isolations from naturally fallen leaves, 13 described species, five informally designated taxa and 21 previously unknown taxa of Phytophthora were isolated from 58 of the 91 soil samples (63.7%) taken from the rhizosphere of 52 of the 64 woody plant species sampled (81.3%) in 20 forest stands (83.7%), and from all rivers: P. capensis, P. citricola VII, VIII, IX, X and XI, P. sp. botryosa-like 2, P. sp. meadii-like 1 and 2, P. sp. tropicalis-like 2 and P. sp. multivesiculata-like 1 from Phytophthora major phylogenetic Clade 2; P. castaneae and P. heveae from Clade 5; P. chlamydospora, P. gregata, P. sp. bitahaiensis-like and P. sp. sylvatica-like 1, 2 and 3 from Clade 6; P. cinnamomi (Pc), P. parvispora, P. attenuata, P. sp. attenuata-like 1, 2 and 3 and P. ×heterohybrida from Clade 7; P. drechsleri, P. pseudocryptogea, P. ramorum (Pr) and P. sp. kelmania from Clade 8, P. macrochlamydospora, P. sp. ×insolita-like, P. sp. ×kunnunara-like, P. sp. ×virginiana-like s.l. and three new taxa, P. sp. quininea-like, P. sp. ×Grenada 3-like and P. sp. ×Peru 4-like, from Clade 9; and P. sp. gallica-like 1 and 2 from Clade 10. The A1 and A2 mating types of both Pc and Pr co-occurred. The A2 mating type of Pc was associated with severe dieback of montane forests in northern Vietnam. Most other Phytophthora species, including Pr, were not associated with obvious disease symptoms. It is concluded that (1) Vietnam is within the center of origin of most Phytophthora taxa found including Pc and Pr, and (2) Phytophthora clades 2, 5, 6, 7, 8, 9, and 10 are native to Indochina.


New Plant Pathology article Jan 2020

Phytophthora agathidicida: research progress, cultural perspectives and knowledge gaps in the control and management of kauri dieback in New Zealand.

Bradshaw, RE, Bellgard, SE, Black, A, Burns, BR, Gerth, ML, McDougal, RL, Scott, PM, Waipara, NW, Weir, BS, Williams, NM, Winkworth, RC, Ashcroft, T, Bradley, EL, Dijkwel, PP, Guo, Y, Lacey, RF, Mesarich, CH, Panda, P, Horner, IJ.

Plant Pathology (2020) 69, 3–16, https://bsppjournals.onlinelibrary.wiley.com/doi/full/10.1111/ppa.13104

Kauri (Agathis australis), which is one of the world's largest and longest‐living conifer species, is under threat from a root and collar dieback disease caused by the oomycete pathogen Phytophthora agathidicida. The noted incidence of kauri dieback has increased in the past decade, and even trees >1000 years old are not immune. This disease has profound effects on both forest ecosystems and human society, particularly indigenous Māori, for whom kauri is a taonga or treasure of immense significance. This review brings together existing scientific knowledge about the pathogen and the devastating disease it causes, as well as highlighting important knowledge gaps and potential approaches for disease management. The life cycle of P. agathidicida is similar to those of other soilborne Phytophthora pathogens, with roles for vegetative hyphae, zoospores and oospores in the disease. However, there is comparatively little known about many aspects of the biology of P. agathidicida, such as its host range and disease latency, or about the impact on the disease of abiotic and biotic factors such as soil health and co‐occurring Phytophthora species. This review discusses current and emerging tools and strategies for surveillance, diagnostics and management, including a consideration of genomic resources, and the role these play in understanding the pathogen and how it causes this deadly disease. Key aspects of indigenous Māori knowledge, which include rich ecological and historical knowledge of kauri forests and a holistic approach to forest health, are highlighted.


New Environmental Science & Policy article Nov. 2019

Global biogeography and invasion risk of the plant pathogen genus Phytophthora

Peter Scott; Martin K.-F. Bader; Treena Burgess; Giles Hardy; Nari Williams

New Environmental Science & Policy Volume 101, November 2019, Pages 175-182

Abstract: A global database of the pathogen genus Phytophthora, comprising ca. 12,500 disease reports over 142 years, was collated to benchmark and examine the genus-wide distribution and invasiveness. Rarefaction was used to estimate global Phytophthora species richness. We applied a framework, leveraging geographically and economically biased pathogen data against environmental and socioeconomic metrics to model their distribution. Hierarchical clustering of host and country range allowed characterisation of invasion potential. Phytophthora descriptions rose to 86 by the year 2000, surging to over 180 species to date driven primarily by novel molecular techniques, resulting in a species richness estimate of 326 (95% CI: 274–378). Countries with diverse ecosystems and entrenched agricultural and forestry industries supported by intensive research programmes reported the highest diversity. Constructing principal components from enviro-socioeconomic factors highlighted national data deficits, showing that two-thirds of trading nations have reported lower-than-predicted species numbers. Phytophthora species clustered into two main invasiveness groups as either cosmopolitan generalists or specialists, historically tied to agriculture. Further spread and detection of Phytophthora pathogens are inevitable with increasing global trade, especially in developing and emerging economies. Adoption of best practice diagnostics and enhanced resource and data sharing are crucial for coordinated global pathogen surveillance and biosecurity.

This research aimed to test the following hypotheses:

•The global distribution of Phytophthora species is associated with environmental, social and economic traits of different country’s.
•Models for Phytophthora diversity, incorporating environmental, social and economic characteristics, can be used to predict a countries trade risk.
Phytophthora species biogeography and host range can be used to predict invasiveness and a country’s conduciveness to infection.


New Plant Disease article September 2019

Variation in Susceptibility of Tanoak to the NA1 and EU1 Lineages of Phytophthora ramorum, the Cause of Sudden Oak Death

Kelsey L. Søndreli, Alan Kanaskie, Susanna Keriö, and Jared M. LeBoldus

Plant Disease https://apsjournals.apsnet.org/doi/10.1094/PDIS-04-19-0831-RE


Abstract: Phytophthora ramorum, the cause of sudden oak death (SOD), kills tanoak (Notholithocarpus densiflorus) trees in southwestern Oregon and California. Two lineages of P. ramorum are now found in wildland forests of Oregon (NA1 and EU1). In addition to the management of SOD in forest ecosystems, disease resistance could be used as a way to mitigate the impact of P. ramorum. The objectives of this study were to (i) characterize the variability in resistance of N. densiflorus among families using lesion length; (ii) determine whether lineage, isolate, family, or their interactions significantly affect variation in lesion length; and (iii) determine whether there are differences among isolates and among families in terms of lesion length. The parameters isolate nested within lineage (isolate[lineage]) and family × isolate(lineage) interaction explained the majority of the variation in lesion length. There was no significant difference between the NA1 and EU1 lineages in terms of mean lesion length; however, there were differences among the six isolates. Lesions on seedlings collected from surviving trees at infested sites were smaller, on average, than lesions of seedlings collected from trees at noninfested sites (P = 0.0064). The results indicate that there is potential to establish a breeding program for tanoak resistance to SOD and that several isolates of P. ramorum should be used in an artificial inoculation assay.

New Plant Disease article July 2019

A qPCR Assay for the Detection of Phytophthora cinnamomi Including an mRNA Protocol Designed to Establish Propagule Viability in Environmental Samples | Plant Disease

Manisha B. Kunadiya, William D. Dunstan, Diane White, Giles E. St. J. Hardy, Andrew H. Grigg, and Treena I. Burgess

Plant Disease Vol. 103, No. 9, https://doi.org/10.1094/PDIS-09-18-1641-RE

Abstract: Phytophthora cinnamomi causes root and collar rot in many plant species in natural ecosystems and horticulture. A species-specific primer and probe PCIN5 were designed based on a mitochondrial locus encoding subunit 2 of cytochrome c oxidase (cox2). Eight PCR primers, including three forward and five reverse, were designed and tested in all possible combinations. Annealing temperatures were optimized for each primer pair set to maximize both specificity and sensitivity. Each set was tested against P. cinnamomi and two closely related clade 7 species, P. parvispora and P. niederhauseri. From these tests, five primer pairs were selected based on specificity and, with a species-specific P. cinnamomi probe, used to develop quantitative real-time PCR (qPCR) assays. The specificity of the two most sensitive qPCR assays was confirmed using the genomic DNA of 29 Phytophthora isolates, including 17 isolates of 11 species from clade 7, and representative species from nine other clades (all except clade 3). The assay was able to detect as little as 150 ag of P. cinnamomi DNA and showed no cross-reaction with other Phytophthora species, except for P. parvispora, a very closely related species to P. cinnamomi, which showed late amplification at high DNA concentrations. The efficiency of the qPCR protocol was evaluated with environmental samples including roots and associated soil from plants artificially infected with P. cinnamomi. Different RNA isolation kits were tested and evaluated for their performance in the isolation of RNA from environmental samples, followed by cDNA synthesis, and qPCR assay. Finally, a protocol was recommended for determining the presence of P. cinnamomi in recalcitrant environmental samples.


New Phytopathology article

Promise and Pitfalls of Endemic Resistance for Cultural ResourcesThreatened by Phytophthora ramorum.  Richard C. Cobb, Noam Ross, Katherine J. Hayden, Catherine A. Eyre, Richard S. Dodd, Susan J. Frankel, Matteo Garbelotto, and David M. Rizzo.



First Look Phytopatholgy article 6 May 2019

A microsatellite analysis identifies global pathways of movement of Phytophthora cinnamomi and the likely sources of wildland infestations in California and Mexico. https://apsjournals.apsnet.org/doi/10.1094/PHYTO-03-19-0102-R

Maria Socorro Serrano, Todd Osmundson, Alejandra Almaraz-Sanchez, Peter JP Croucher, Ted Swiecki, Dionisio Alvarado, and Matteo Garbelotto