Phytophthora pini Leonian resurrected to distinct species status

Temperature and Fungicide Sensitivity in Three Prevalent Phytophthora Species Causing Phytophthora Root Rot in Rhododendron

Temperature is an important environmental variable affecting Phytophthora spp. biology. It alters the ability of species to grow, sporulate, and infect their plant host, and it is also important in mediating pathogen responses to disease control measures. Average global temperatures are increasing as a consequence of climate change, yet there are few studies that compare the effects of temperature on Phytophthora spp. that are important to the nursery industry. To address this, we conducted a series of experiments to evaluate how temperature affects the biology and control of three soilborne Phytophthora spp. prevalent in the nursery industry. In the first set of experiments, we evaluated the mycelial growth and sporulation of several Phytophthora cinnamomi, P. plurivora, and P. pini isolates at temperatures ranging from 4 to 42°C for different amounts of time (0 to 120 h). In the second set of experiments, we evaluated the response of three isolates of each species to the fungicides mefenoxam and phosphorous acid at temperatures ranging from 6 to 40°C. Results showed that each species responds differently to temperature, with P. plurivora having the greatest optimal temperature (26.6°C), P. pini the least (24.4°C), and P. cinnamomi was intermediate between the two (25.3°C). P. plurivora and P. pini had the lowest minimum temperatures (approximately 2.4°C) compared with P. cinnamomi (6.5°C), while all three species had a similar maximum temperature (approximately 35°C). When tested against mefenoxam, all three species were generally more sensitive to mefenoxam at cool temperatures (6 to 14°C) than at warmer temperatures (22 to 30°C). P. cinnamomi was also more sensitive to phosphorous acid at cool temperatures (6 to 14°C). However, both P. plurivora and P. pini tended to be more sensitive to phosphorous acid at warmer temperatures (22 to 30°C). These findings help define the temperatures at which these pathogens will be the most damaging and help delineate the temperatures at which fungicides should be applied for maximum efficacy.

An Overview of Phytophthora Species on Woody Plants in Sweden and Other Nordic Countries

The genus Phytophthora, with 326 species in 12 phylogenetic clades currently known, includes many economically important pathogens of woody plants. Different Phytophthora species often possess a hemibiotrophic or necrotrophic lifestyle, have either a broad or narrow host range, can cause a variety of disease symptoms (root rot, damping-off, bleeding stem cankers, or blight of foliage), and occur in different growing environments (nurseries, urban and agricultural areas, or forests). Here, we summarize the available knowledge on the occurrence, host range, symptoms of damage, and aggressiveness of different Phytophthora species associated with woody plants in Nordic countries with a special emphasis on Sweden. We evaluate the potential risks of Phytophthora species to different woody plants in this geographical area and emphasize the increasing threats associated with continued introduction of invasive Phytophthora species.

Cataloging Phytophthora Species of Agriculture, Forests, Horticulture, and Restoration Outplantings in California, U.S.A.: A Sequence-Based Meta-Analysis

California contains a diverse flora, and knowledge of the pathogens that threaten those plants is essential to managing their long-term health. To better understand threats to California plant health, a meta-analysis of Phytophthora detections within the state was conducted using publicly available sequences as a primary source of data rather than published records. Accessions of internal transcribed spacer (ITS) ribosomal DNA were cataloged from 800 Californian Phytophthora isolates, analyzed, and determined to correspond to 80 taxa, including several phylogenetically distinct provisional species. A number of Phytophthora taxa not previously reported from California were identified, including 20 described species. Pathways of introduction and spread were analyzed by categorizing isolates' origins, grouped by land-use: (i) agriculture, (ii) forests and other natural ecosystems, (iii) horticulture and nurseries, or (iv) restoration outplantings. The pooled Phytophthora metacommunities of the restoration outplantings and horticulture land-use categories were the most similar, whereas the communities pooled from forests and agriculture were least similar. Phytophthora cactorum, P. pini, P. pseudocryptogea, and P. syringae were identified in all four land-use categories, while 13 species were found in three. P. gonapodyides was the most common species by number of ITS accessions and exhibited the greatest diversity of ITS haplotypes. P. cactorum, P. ramorum, and P. nicotianae were associated with the greatest number of host genera. In this analysis, the Phytophthora spp. most prevalent in California differ from those compiled from the scientific literature.

Phytophthora spp. Associated with Appalachian Oak Forests and Waterways in Pennsylvania, with P. abietivora as a Pathogen of Five Native Woody Plant Species

To document the distribution of potentially harmful Phytophthora spp. within Pennsylvania, the Pennsylvania Department of Agriculture collected 89 plant, 137 soil, and 48 water samples from 64 forested sites during 2018 to 2020. In total, 231 Phytophthora strains were isolated using baiting assays and identified based on morphological characteristics and sequences of nuclear and mitochondrial loci. Twenty-one Phytophthora spp. in nine clades and one unidentified species were present. Phytophthora abietivora, a recently described clade 7a species, was recovered from diseased tissue of 10 native broadleaved plants and twice from soil from 12 locations. P. abietivora is most likely endemic to Pennsylvania based on pathogenicity tests on six native plant species, intraspecific genetic diversity, wide distribution, and recoveries from Abies Mill. and Tsuga Carrière plantations dating back to 1989. Cardinal temperatures and morphological traits are provided for this species. Other taxa, in decreasing order of frequency, include P. chlamydospora, P. plurivora, P. pini, P. cinnamomi, P. xcambivora, P. irrigata, P. gonapodyides, P. cactorum, P. pseudosyringae, P. hydropathica, P. stricta, P. xstagnum, P. caryae, P. intercalaris, P. 'bitahaiensis', P. heveae, P. citrophthora, P. macilentosa, P. cryptogea, and P. riparia. Twelve species were associated with diseased plant tissues. This survey documented 53 new plant-Phytophthora associations and expanded the known distribution of some species.

Global invasion history of the emerging plant pathogen Phytophthora multivora

Background

global trade in living plants and plant material has significantly increased the geographic distribution of many plant pathogens. As a consequence, several pathogens have been first found and described in their introduced range where they may cause severe damage on naïve host species. Knowing the center of origin and the pathways of spread of a pathogen is of importance for several reasons, including identifying natural enemies and reducing further spread. Several Phytophthora species are well-known invasive pathogens of natural ecosystems, including Phytophthora multivora. Following the description of P. multivora from dying native vegetation in Australia in 2009, the species was subsequently found to be common in South Africa where it does not cause any remarkable disease. There are now reports of P. multivora from many other countries worldwide, but not as a commonly encountered species in natural environments.

Results

a global collection of 335 isolates from North America, Europe, Africa, Australia, the Canary Islands, and New Zealand was used to unravel the worldwide invasion history of P. multivora, using 10 microsatellite markers for all isolates and sequence data from five loci from 94 representative isolates. Our population genetic analysis revealed an extremely low heterozygosity, significant non-random association of loci and substantial genotypic diversity suggesting the spread of P. multivora readily by both asexual and sexual propagules. The P. multivora populations in South Africa, Australia, and New Zealand show the most complex genetic structure, are well established and evolutionary older than those in Europe, North America and the Canary Islands.

Conclusions

according to the conducted analyses, the world invasion of P. multivora most likely commenced from South Africa, which can be considered the center of origin of the species. The pathogen was then introduced to Australia, which acted as bridgehead population for Europe and North America. Our study highlights a complex global invasion pattern of P. multivora, including both direct introductions from the native population and secondary spread/introductions from bridgehead populations.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08363-5.

Current status of Phytophthora in Australia

Among the most economically relevant and environmentally devastating diseases globally are those caused by Phytophthora species. In Australia, production losses in agriculture and forestry result from several well-known cosmopolitan Phytophthora species and infestation of natural ecosystems by Phytophthora cinnamomi have caused irretrievable loss to biodiversity especially in proteaceous dominated heathlands. For this review, all available records of Phytophthora in Australia were collated and curated, resulting in a database of 7 869 records, of which 2 957 have associated molecular data. Australian databases hold records for 99 species, of which 20 are undescribed. Eight species have no records linked to molecular data, and their presence in Australia is considered doubtful. The 99 species reside in 10 of the 12 clades recognised within the complete phylogeny of Phytophthora. The review includes discussion on each of these species' status and additional information provided for another 29 species of concern. The first species reported in Australia in 1900 was Phytophthora infestans. By 2000, 27 species were known, predominantly from agriculture. The significant increase in species reported in the subsequent 20 years has coincided with extensive surveys in natural ecosystems coupled with molecular taxonomy and the recognition of numerous new phylogenetically distinct but morphologically similar species. Routine and targeted surveys within Australian natural ecosystems have resulted in the description of 27 species since 2009. Due to the new species descriptions over the last 20 years, many older records have been reclassified based on molecular identification. The distribution of records is skewed toward regions with considerable activity in high productivity agriculture, horticulture and forestry, and native vegetation at risk from P. cinnamomi. Native and exotic hosts of different Phytophthora species are found throughout the phylogeny; however, species from clades 1, 7 and 8 are more likely to be associated with exotic hosts. One of the most difficult challenges to overcome when establishing a pest status is a lack of reliable data on the current state of a species in any given country or location. The database compiled here for Australia and the information provided for each species overcomes this challenge. This review will aid federal and state governments in risk assessments and trade negotiations by providing a comprehensive resource on the current status of Phytophthora species in Australia. Citation: Burgess TI, Edwards J, Drenth A, et al. 2021. Current status of Phytophthora in Australia. Persoonia 47: 151-177. https://doi.org/10.3767/persoonia.2021.47.05.

Virulence of Five Phytophthora Species Causing Rhododendron Root Rot in Oregon

Phytophthora root rot is a destructive disease of rhododendron that causes substantial losses of this nursery crop in infested field and container production areas. Historically, Phytophthora cinnamomi was considered the main causal agent of the disease. However, a recent survey of soilborne Phytophthora species from symptomatic rhododendrons in Oregon revealed that P. plurivora is more common than P. cinnamomi, and that several other Phytophthora species may be involved. We investigated the ability of the five most abundant species from the survey to cause root rot: P. plurivora, P. cinnamomi, P. pini, P. pseudocryptogea, and P. cambivora. Three to four isolates were selected for each species from across six Oregon nurseries. Media of containerized Rhododendron catawbiense 'Boursault' was infested with single isolates in a randomized complete block design in a greenhouse. Phytophthora cinnamomi, P. pini, and P. plurivora rapidly caused ≥90% of severe root rot, whereas P. pseudocryptogea caused more moderate disease (46% of severe root rot). Phytophthora cambivora failed to produce enough inoculum and was used at a lower inoculum density than the other four species; however, occasionally, it caused severe root rot (5% incidence). No differences in virulence were observed among isolates of the same species, except for one isolate of P. plurivora that caused less disease than other P. plurivora isolates. This study demonstrates that all five Phytophthora species, which were representative of 94% of the survey isolates, are capable of causing severe root rot and plant death, but that not all species are equally virulent.

First Report of Phytophthora pini Causing Foliage Blight and Shoot Dieback of Rhododendron pulchrum in China

During a 2019-2020 survey for plant pathogenic oomycetes in Nanjing, China, severe foliage blight and dieback were observed on approximately 20 Rhododendron pulchrum plants at three public parks and gardens. Approximately 25% of leaves and shoots were affected. Symptoms included brown to black lesions on leaves and stems, dieback of shoot tips, and wilting. Diseased tissues were collected from a five-year-old shrub with typical disease symptoms at Xuanwuhu Park. They were cut into 10×10 mm2 squares, immersed in 70% ethanol for 30 sec, and placed onto fresh clarified V8 juice agar (cV8A) containing pimaricin, ampicillin, rifampicin, and pentachloronitrobenzene. Phytophthora-like hypae were transferred to new cV8A plates daily. A total of five isolates were obtained after five days of incubation at 25°C. After approximately 20 days, all isolates were identical in morphological traits including semi-papillate sporangia and gametangia (homothallic). Thirty sporangia of a representative isolate Ppi were randomly selected and examined. They were mostly ovoid and sometimes obpyriform, averaging 41.0 ± 3.9 × 24.8 ± 3.2 µm. Antheridia of 30 randomly selected gametangia were paragynous, averaging 16.7 ± 0.7 × 12.4 ± 1.5 µm. Average diameters of oogonia and plerotic oospores were 29.2 ± 0.3 µm and 26.4 ± 1.6 µm, respectively. Chlamydospores were not observed. The above morphological traits suggested the causal agent belonging to the "P. citricola-complex". Isolate Ppi was subjected to sequencing of the rDNA internal transcribed spacer (ITS) region and the ras-related GTP-binding protein 1 (Ypt1) gene. ITS sequence of Ppi (GenBank ACN. MT672594) has 100% identity to that of P. pini (MG865565). It has a 3-nt difference from the ITS sequences of P. acerina (MG518642) and P. citricola (MG865475) and a 4-nt difference from that of P. plurivora (FJ665225). Ypt1 sequence of Ppi (MT680000) has 100% identity to that of P. pini (MK058416). Pathogenicity of Ppi on R. pulchrum was tested using both detached-leaf and whole-plant assays. In the former assay, each of six asymptomatic leaves was symmetrically wounded at both sides using a sterile inoculation needle. A 5×5 mm2 Ppi-colonized cV8A plug was placed on each wound of five leaves. Sterile agar plugs were used for a control leaf. All six leaves were placed on a wet filter paper in a closed container at 25°C. This assay was repeated twice. On the fifth day, all inoculated leaves had necrotic tissues around the wounds, while the control leaves remained asymptomatic. In the whole-plant assay, 20-inch-tall plants were used. Five attached leaves and the twig base of each plant were wounded. A control plant was inoculated in the same manner above, while sterile agar plugs were used. Each plant was covered with a plastic bag and maintained at 25°C. Wet cotton balls were placed in the bags to maintain humidity. After two days, the bag containing cotton balls was removed. This assay was repeated three times. After two weeks, all three inoculated plants in the three replicated trials had severe foliage blight and dieback, whereas control plants remained healthy. Phytophthora isolates recovered from artificially inoculated tissues were identical to isolate Ppi in morphological characters. Rhododendron diseases caused by P. pini were reported in the USA and Finland . This is the first report of P. pini causing foliage blight and dieback on R. pulchrum, an important nursery and landscape plant in China. Additional surveys are ongoing to determine the distribution of this pathogen in Nanjing. Management programs are under development to contain the spread of P. pini and treat diseased plants.

Phytophthora Diversity in Pennsylvania Nurseries and Greenhouses Inferred from Clinical Samples Collected over Four Decades

The increasing movement of exotic pathogens calls for systematic surveillance so that newly introduced pathogens can be recognized and dealt with early. A resource crucial for recognizing such pathogens is knowledge about the spatial and temporal diversity of endemic pathogens. Here, we report an effort to build this resource for Pennsylvania (PA) by characterizing the identity and distribution of Phytophthora species isolated from diverse plant species in PA nurseries and greenhouses. We identified 1137 Phytophthora isolates cultured from clinical samples of >150 plant species submitted to the PA Department of Agriculture for diagnosis from 1975 to 2019 using sequences of one or more loci and morphological characteristics. The three most commonly received plants were Abies, Rhododendron, and Pseudotsuga. Thirty-six Phytophthora species identified represent all clades, except 3 and 10, and included a distinct subgroup of a known species and a prospective new species. Prominent pathogenic species such as P. cactorum, P. cinnamomi, P. nicotianae, P. drechsleri, P. pini, P. plurivora, and P. sp. kelmania have been found consistently since 1975. One isolate cultured from Juniperus horizontalis roots did not correspond to any known species, and several other isolates also show considerable genetic variation from any authentic species or isolate. Some species were isolated from never-before-documented plants, suggesting that their host range is larger than previously thought. This survey only provides a coarse picture of historical patterns of Phytophthora encounters in PA nurseries and greenhouses because the isolation of Phytophthora was not designed for a systematic survey. However, its extensive temporal and plant coverage offers a unique insight into the association of Phytophthora with diverse plants in nurseries and greenhouses.

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 F_st 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.

Metabarcoding reveals a high diversity of woody host-associated Phytophthora spp. in soils at public gardens and amenity woodlands in Britain

Forests and woodlands worldwide are being severely impacted by invasive Phytophthora species, with initial outbreaks in some cases occurring on host trees located in public parks and gardens. These highly disturbed sites with diverse planting practices may indeed act as harbours for invasive Phytophthora pathogens which are particularly well adapted to surviving in soil. High throughput Illumina sequencing was used to analyse Phytophthora species diversity in soil samples collected from 14 public garden/amenity woodland sites in northern Britain. Bioinformatic analyses revealed some limitations to using internal transcribed spacer as the barcode region; namely reporting of false positives and ambiguous species matches. Taking this into account, 35 distinct sequences were amplified across the sites, corresponding to 23 known Phytophthora species as well as twelve oomycete sequences with no match to any known Phytophthora species. Phytophthora pseudosyringae and P. austrocedri, both of which cause serious damage to trees and are regarded as fairly recent introductions to Britain, were the two most abundant Phytophthora species detected. There was no evidence that any of the detected Phytophthora species were more associated with any one type of host, healthy or otherwise. This study has demonstrated the ubiquity and diversity of Phytophthora species endemic in highly managed, extensively planted soil environments in Britain. Suggested improvements to the methodology and the practical implications of the findings in terms of mitigating Phytophthora spread and impact are discussed.

Phytophthora Species Detected in Two Ozark Forests with Unusual Patterns of White Oak Mortality

Widespread decline and mortality of white oaks (Quercus alba) occurred in Missouri Ozark forests between 2011 and 2017. Symptoms included rapid crown death with bronzing of leaves, retention of dead leaves, crown dieback and thinning, and loss of large limbs within one year of death. Decline and mortality were associated with hillside drainages and fit descriptions of European oak forests predisposed to decline by pathogenic Phytophthora species. A survey was performed at two locations in 2014 and 2015 to assess the distribution of dead and declining white oaks, and the occurrence and distribution of Phytophthora species. Multiple Phytophthora species were detected, including P. cinnamomi, P. cactorum, P. europaea, and P. pini. P. cinnamomi was the most common and widely distributed species among plots at both locations. The detection of P. cinnamomi at the base of white oaks was not associated with poor crown vigor. However, more quantitative survey techniques are necessary to clearly evaluate this relationship. P. cinnamomi kills fine roots of white and red oaks in North America and has been associated with the decline of white oaks in the United States (Ohio) and other countries. Further studies are needed to determine the importance of P. cinnamomi in oak decline within the Ozark highlands.

Thermal Inactivation of Inoculum of Two Phytophthora Species by Intermittent Versus Constant Heat

Research on solarization efficacy has examined the critical temperature and minimum exposure time to inactivate soilborne pathogens. Most mathematical models focus on survival of inoculum subjected to a constant heat regime rather than an intermittent heat regime that better simulates field conditions. To develop a more accurate predictive model, we conducted controlled lab experiments with rhododendron leaf disks infested with Phytophthora ramorum and P. pini. Focused in vitro experiments with P. ramorum showed significantly longer survival of inoculum exposed to intermittent versus constant heat, indicating that intermittent heat is less damaging. A similar trend was observed in soil. Damage was evaluated by comparing the reduction in subsequent survival time of inoculum subjected to different intensities of sublethal heat treatments. Inoculum exposure to continuous heat reflected an increasing rate of damage accumulation. Multiple sublethal heat events resulted in a constant rate of damage accumulation which allowed us to calculate total damage as the sum of damage from each heat event. A model including a correction for an intermittent heat regime significantly improved the prediction of thermal inactivation under a temperature regime that simulated field conditions.

Canker and decline diseases caused by soil- and airborne Phytophthora species in forests and woodlands

Most members of the oomycete genus Phytophthora are primary plant pathogens. Both soil- and airborne Phytophthora species are able to survive adverse environmental conditions with enduring resting structures, mainly sexual oospores, vegetative chlamydospores and hyphal aggregations. Soilborne Phytophthora species infect fine roots and the bark of suberized roots and the collar region with motile biflagellate zoospores released from sporangia during wet soil conditions. Airborne Phytophthora species infect leaves, shoots, fruits and bark of branches and stems with caducous sporangia produced during humid conditions on infected plant tissues and dispersed by rain and wind splash. During the past six decades, the number of previously unknown Phytophthora declines and diebacks of natural and semi-natural forests and woodlands has increased exponentially, and the vast majority of them are driven by introduced invasive Phytophthora species. Nurseries in Europe, North America and Australia show high infestation rates with a wide range of mostly exotic Phytophthora species. Planting of infested nursery stock has proven to be the main pathway of Phytophthora species between and within continents. This review provides insights into the history, distribution, aetiology, symptomatology, dynamics and impact of the most important canker, decline and dieback diseases caused by soil- and airborne Phytophthora species in forests and natural ecosystems of Europe, Australia and the Americas.

An expanded phylogeny for the genus Phytophthora

A comprehensive phylogeny representing 142 described and 43 provisionally named Phytophthora species is reported here for this rapidly expanding genus. This phylogeny features signature sequences of 114 ex-types and numerous authentic isolates that were designated as representative isolates by the originators of the respective species. Multiple new subclades were assigned in clades 2, 6, 7, and 9. A single species P. lilii was placed basal to clades 1 to 5, and 7. Phytophthora stricta was placed basal to other clade 8 species, P. asparagi to clade 6 and P. intercalaris to clade 10. On the basis of this phylogeny and ancestral state reconstructions, new hypotheses were proposed for the evolutionary history of sporangial papillation of Phytophthora species. Non-papillate ancestral Phytophthora species were inferred to evolve through separate evolutionary paths to either papillate or semi-papillate species.

Genotypic Diversity of Phytophthora cinnamomi and P. plurivora in Maryland's Nurseries and Mid-Atlantic Forests

Genetic diversity of two Phytophthora spp.-P. cinnamomi (102 isolates), commonly encountered in Maryland nurseries and forests in the Mid-Atlantic United States, and P. plurivora (186 isolates), a species common in nurseries-was characterized using amplified fragment length polymorphism. Expected heterozygosity and other indices suggested a lower level of diversity among P. cinnamomi than P. plurivora isolates. Hierarchical clustering showed P. cinnamomi isolates separated into four clusters, and two of the largest clusters were closely related, containing 80% of the isolates. In contrast, P. plurivora isolates separated into six clusters, one of which included approximately 40% of the isolates. P. plurivora isolates recovered from the environment (e.g., soil and water) were genotypically more diverse than those found causing lesions. For both species, isolate origin (forest versus nursery or among nurseries) was a significant factor of heterozygosity. Clonal groups existed within P. cinnamomi and P. plurivora and included isolates from both forest and nurseries, suggesting that a pathway from nurseries to forests or vice versa exists.

Distribution and diversity of Phytophthora across Australia

The introduction and subsequent impact of Phytophthora cinnamomi within native vegetation is one of the major conservation issues for biodiversity in Australia. Recently, many new Phytophthora species have been described from Australia’s native ecosystems; however, their distribution, origin, and potential impact remain unknown. Historical bias in Phytophthora detection has been towards sites showing symptoms of disease, and traditional isolation methods show variable effectiveness of detecting different Phytophthora species. However, we now have at our disposal new techniques based on the sampling of environmental DNA and metabarcoding through the use of high-throughput sequencing. Here, we report on the diversity and distribution of Phytophthora in Australia using metabarcoding of 640 soil samples and we compare the diversity detected using this technique with that available in curated databases. Phytophthora was detected in 65% of sites, and phylogenetic analysis revealed 68 distinct Phytophthora phylotypes. Of these, 21 were identified as potentially unique taxa and 25 were new detections in natural areas and/or new introductions to Australia. There are 66 Phytophthora taxa listed in Australian databases, 43 of which were also detected in this metabarcoding study. This study revealed high Phytophthora richness within native vegetation and the additional records provide a valuable baseline resource for future studies. Many of the Phytophthora species now uncovered in Australia’s native ecosystems are newly described and until more is known we need to be cautious with regard to the spread and conservation management of these new species in Australia’s unique ecosystems.

A unique species in Phytophthora clade 10, Phytophthora intercalaris sp. nov., recovered from stream and irrigation water in the eastern USA

A novel species of the genus Phytophthora was recovered during surveys of stream and nursery irrigation water in Maryland, Massachusetts, North Carolina, Virginia and West Virginia in the USA. The novel species is heterothallic, and all examined isolates were A1 mating type. It produced rare ornamented oogonia and amphigynous antheridia when paired with A2 mating type testers of Phytophthora cinnamomi and Phytophthora cryptogea. Sporangia of this novel species were non-papillate and non-caducous. Thin-walled intercalary chlamydospores were abundant in hemp seed agar and carrot agar, while they were produced only rarely in aged cultures grown in clarified V8 juice agar. Phylogenetic analyses based on sequences of the internal transcribed spacer region and the β-tubulin and mitochondrial cytochrome-c oxidase 1 (cox1) genes indicated that the novel species is phylogenetically close to Phytophthora gallica in Phytophthora clade 10. The novel species has morphological and molecular features that are distinct from those of other species in Phytophthora clade 10. It is formally described here as Phytophthora intercalaris sp. nov. Description of this unique clade-10 species is important for understanding the phylogeny and evolution of Phytophthora clade 10.

Phytophthora species recovered from the Connecticut River Valley in Massachusetts, USA

Little is currently known about the assemblage of Phytophthora species in northeastern North America, representing a gap in our understanding of species incidence. Therefore, Phytophthora species were surveyed at 20 sites in Massachusetts, with 16 occurring in the Connecticut River Valley. Many of the sampled waterways were adjacent to active agricultural lands, yet were buffered by mature floodplain forests composed of Acer, Platanus, Populus and Ulmus. Isolates were recovered with three types of baits (rhododendron leaves, pear, green pepper) in 2013 and water filtration in 2014. Overall, 457 isolates of Phytophthora were recovered and based on morphological characters and rDNA internal transcribed spacer (ITS), β-tubulin (β-tub) and cytochrome oxidase c subunit I (cox1) sequences, 18 taxa were identified, including three new species: P. taxon intercalaris, P. taxon caryae and P. taxon pocumtuck. In addition, 49 isolates representing five species of Phytopythium also were identified. Water filtration captured a greater number of taxa (18) compared to leaf and fruit baits (12). Of the three bait types rhododendron leaves yielded the greatest number of isolates and taxa, followed by pear and green pepper, respectively. Despite the proximity to agricultural lands, none of the Phytophthora species baited are considered serious pathogens of vegetable crops in the region. However, many of the recovered species are known woody plant pathogens, including four species in the P. citricola s.l. complex that were identified: P. plurivora, P. citricola III, P. pini and a putative novel species, referred to here as P. taxon caryae. An additional novel species, P. taxon pocumtuck, is a close relative of P. borealis based on cox1 sequences. The results illustrate a high level of Phytophthora species richness in the Connecticut River Valley and that major rivers can serve as a source of inoculum for pathogenic Phytophthora species in the northeast.

Diversity of Foliar Phytophthora Species on Rhododendron in Oregon Nurseries

The genus Phytophthora contains some of the most notorious plant pathogens affecting nursery crops. Given the recent emergence of the sudden oak death pathogen Phytophthora ramorum, particularly in association with Rhododendron spp., characterization of Phytophthora communities associated with this host in nursery environments is prudent. Many taxa may present symptoms similar to P. ramorum but we do not necessarily know their identity, frequency, and importance. Here, we present a survey of Phytophthora taxa observed from seven nurseries in the U.S. state of Oregon. Incidence and diversity of Phytophthora communities differed significantly among nurseries and among seasons within nursery. The taxa P. syringae and P. plurivora were widespread and detected at most of the nurseries sampled. Nine other taxa were also detected but were found either in a single nursery or were shared among only a few nurseries. Characterization of the Phytophthora communities present in nurseries is an important step toward understanding the ecology of these organisms as well as an aid to nursery managers in determining what risks may be present when symptomatic plants are observed. This study builds on an increasing literature, which characterizes Phytophthora community structure in nurseries.

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.

Phytophthora terminalis sp. nov. and Phytophthora occultans sp. nov., two invasive pathogens of ornamental plants in Europe

In the past decade several Phytophthora strains were isolated from diseased Pachysandra terminalis plants suffering stem base and root rot, originating from the Netherlands and Belgium. All isolates were homothallic and had a felt-like colony pattern, produced semi-papillate sporangia, globose oogonia and had a maximum growth at ~ 27 C. Several additional Phytophthora strains were isolated from diseased Buxus sempervirens plants, originating from the Netherlands and Belgium, which had sustained stem base and root rot; similar strains also were isolated from Acer palmatum, Choisya ternata and Taxus in the United Kingdom. All isolates were homothallic and had a stellate colony pattern, produced larger semi-papillate sporangia and smaller globose oogonia than the isolates from Pa. terminalis and had a maximum growth temperature of ~ 30 C. Phylogenetic analyses of both species using the internal transcribed spacer region of the nuc rDNA (ITS), mt cytochrome oxidases subunit I gene (CoxI) and nuc translation elongation factor 1-α gene (TEF1α) revealed that all sequences of each species were identical at each locus and unique to that species, forming two distinct clusters in subclade 2a. Sequence analysis of partial β-tubulin genes showed that both taxa share an identical sequence that is identical to that of Ph. himalsilva, a species originating from Asia, suggesting a common Asian origin. Pathogenicity trials demonstrated disease symptoms on their respective hosts, and re-isolation and re-identification of the inoculated pathogens confirmed Koch's postulates.

Phytophthora Populations in Nursery Irrigation Water in Relationship to Pathogenicity and Infection Frequency of Rhododendron and Pieris

Phytophthora spp. are waterborne plant pathogens that are commonly found in streams, rivers, and reclaimed irrigation water. Rhododendron and Pieris trap plants at two commercial nurseries were irrigated with water naturally infested with Phytophthora spp. during the 2011 and 2012 growing seasons to assess the frequency of disease. Phytophthora spp. were consistently recovered from water samples at every collection time but detected on only 2 of the 384 trap plants during the two growing seasons. Pathogenicity assays proved that Phytophthora hydropathica and Phytophthora taxon PgChlamydo, commonly recovered taxa in irrigation water at the nurseries, were foliar pathogens of Rhododendron and Pieris; however, neither species was able to cause root rot on these same hosts. Overall, Phytophthora spp.-infested irrigation water did not act as a primary source of infection on Rhododendron and Pieris, even though foliar pathogenic species of Phytophthora were present in the water.

Development of a multiplex assay for genus- and species-specific detection of Phytophthora based on differences in mitochondrial gene order

A molecular diagnostic assay for Phytophthora spp. that is specific, sensitive, has both genus- and species-specific detection capabilities multiplexed, and can be used to systematically develop markers for detection of a wide range of species would facilitate research and regulatory efforts. To address this need, a marker system was developed based on the high copy sequences of the mitochondrial DNA utilizing gene orders that were highly conserved in the genus Phytophthora but different in the related genus Pythium and plants to reduce the importance of highly controlled annealing temperatures for specificity. An amplification primer pair designed from conserved regions of the atp9 and nad9 genes produced an amplicon of ≈340 bp specific for the Phytophthora spp. tested. The TaqMan probe for the genus-specific Phytophthora test was designed from a conserved portion of the atp9 gene whereas variable intergenic spacer sequences were used for designing the species-specific TaqMan probes. Specific probes were developed for 13 species and the P. citricola species complex. In silico analysis suggests that species-specific probes could be developed for at least 70 additional described and provisional species; the use of locked nucleic acids in TaqMan probes should expand this list. A second locus spanning three tRNAs (trnM-trnP-trnM) was also evaluated for genus-specific detection capabilities. At 206 bp, it was not as useful for systematic development of a broad range of species-specific probes as the larger 340-bp amplicon. All markers were validated against a test panel that included 87 Phytophthora spp., 14 provisional Phytophthora spp., 29 Pythium spp., 1 Phytopythium sp., and 39 plant species. Species-specific probes were validated further against a range of geographically diverse isolates to ensure uniformity of detection at an intraspecific level, as well as with other species having high levels of sequence similarity to ensure specificity. Both diagnostic assays were also validated against 130 environmental samples from a range of hosts. The only limitation observed was that primers for the 340 bp atp9-nad9 locus did not amplify Phytophthora bisheria or P. frigida. The identification of species present in a sample can be determined without the need for culturing by sequencing the genus-specific amplicon and comparing that with a reference sequence database of known Phytophthora spp.

A high-temperature tolerant species in clade 9 of the genus Phytophthora: P. hydrogena sp. nov

A previously unknown Phytophthora species was isolated from irrigation water in Virginia, USA. This novel species produces abundant noncaducous and nonpapillate sporangia in soil water extract solution. It sometimes produces chlamydospores and hyphal swellings in aged cultures and in Petri's solution. This species has optimum vegetative growth at 30 C and grows well at 35 C. The lowest and highest temperatures for growth are 5 and 40 C. All isolates examined in this study are compatibility type A1 and produce mostly plerotic oospores when paired with an A2 mating-type tester of P. cinnamomi. Sequence analyses of the rDNA internal transcribed spacer (ITS) regions and the mitochondrially encoded cytochrome c oxidase 1 (cox 1) gene placed this species in clade 9 of the genus Phytophthora. These characteristics support the description of this taxon as a new species for which we propose the name P. hydrogena sp. nov. Further phylogenetic and physiological investigations of clade 9 species revealed a high-temperature tolerant cluster including P. hydrogena, P. aquimorbida, P. hydropathica, P. irrigata, P. chrysanthemi, P. insolita, P. polonica and P. parsiana. These species all grow well at 35 C. The monophyly of the species in this heat-tolerant cluster except P. insolita and P. polonica is highly supported by the maximum-likelihood analyses of the ITS and cox 1 sequences.

Movement of Phytophthora spp. in Maryland's Nursery Trade

Phytophthora spp. cause major losses in the nursery industry worldwide. However, a clear demonstration of the route of movement has not been previously shown. A survey of 10 Maryland nurseries was conducted over a 3-year period to investigate the presence of Phytophthora spp. on newly arrived plants, mainly from West Coast suppliers. Local nursery plants, irrigation water, and potting media were also sampled for Phytophthora spp. Isolates were identified using a combination of morphological characteristics and DNA sequencing. Species identified included Phytophthora cactorum, P. cambivora, P. cinnamomi, P. citrophthora, P. drechsleri, P. elongata, P. gonapodyides, P. hydropathica, P. irrigata, P. lacustris, P. multivora, P. nicotianae, P. pini, P. plurivora, and P. syringae. P. taxon pgchlamydo was also isolated from irrigation water. Eight of the abovementioned Phytophthora spp. were isolated in association with incoming material, indicating that the movement of these pathogens continues to occur. Asymptomatic plant material was the main route of introduction of Phytophthora spp. to Maryland nurseries. Results also indicated that several Phytophthora spp. could be found in Maryland nurseries in association with infested potting media of asymptomatic plants. Although P. ramorum was not detected, our surveys underscore the significance of nursery practices that allow introductions of these significant plant pathogens to new geographic locations.

Development of new polymorphic microsatellite markers for three closely related plant-pathogenic Phytophthora species using 454-pyrosequencing and their potential applications

Phytophthora spp. (oomycetes) are causal agents of devastating diseases on a high number of crops, ornamentals, and native plants worldwide. Neutral molecular markers are increasingly being used to investigate the genetic population structure and possible pathways of spread of different plant pathogens, including Phytophthora spp. In this study, polymorphic microsatellite markers were developed for three species of the former Phytophthora citricola species complex-namely, P. multivora, P. plurivora, and P. pini (P. citricola I)-using the 454-pyrosequencing technique. In total, 35 polymorphic microsatellite loci were found and further characterized: 11 for P. plurivora, 16 for P. multivora, and 8 for P. pini. Microsatellites with dinucleotide motifs repeated 6 to 10 times were the most common for all three species. On average, 65 alleles per species and 5.3 alleles per locus were detected. Most loci were characterized by a low observed heterozygosity, which might be due to the homothallic mating system of the three Phytophthora spp. targeted. Cross amplification of the newly developed markers was tested on 17 Phytophthora spp. belonging to five different internal transcribed spacer clades. Transferability success was generally low and decreased with increasing genetic distance from the species to the three target species. A set of four loci was selected to easily discriminate P. plurivora, P. multivora, and P. pini on the basis of presence or absence of a polymerase chain reaction amplicon on an agarose gel.

Diversity and Mefenoxam Sensitivity of Phytophthora spp. Associated with the Ornamental Horticulture Industry in the Southeastern United States

Phytophthora isolates associated with ornamental plants or recovered from irrigation water in six states in the southeastern United States (Georgia, North Carolina, South Carolina, Tennessee, Texas, and Virginia) were identified and screened for sensitivity to mefenoxam. Isolates from forest and suburban streams in Georgia and Virginia were included for comparison. A new in vitro assay, utilizing 48-well tissue culture plates, was used to screen for mefenoxam sensitivity; this assay allowed high throughput of isolates and used less material than the traditional petri plate assay. In total, 1,483 Phytophthora isolates were evaluated, and 27 species were identified with Phytophthora nicotianae, P. hydropathica, and P. gonapodyides, the most abundant species associated with plants, irrigation water, and streams, respectively. Only 6% of isolates associated with plants and 9% from irrigation water were insensitive to mefenoxam at 100 μg a.i./ml. Approximately 78% of insensitive isolates associated with plants were P. nicotianae, and most of these (67%) came from herbaceous annual plants. Most of the insensitive isolates recovered from irrigation water were P. gonapodyides, P. hydropathica, P. megasperma, and P. pini, and 83% of the insensitive isolates from streams were P. gonapodyides. Overall, this study suggests that mefenoxam should continue to be a valuable tool in the management of Phytophthora diseases affecting ornamental plants in the southeastern United States.

Identification and Detection of Phytophthora: Reviewing Our Progress, Identifying Our Needs

With the increased attention given to the genus Phytophthora in the last decade in response to the ecological and economic impact of several invasive species (such as P. ramorum, P. kernoviae, and P. alni), there has been a significant increase in the number of described species. In part, this is due to the extensive surveys in historically underexplored ecosystems (e.g., forest and stream ecosystems) undertaken to determine the spread of invasive species and the involvement of Phytophthora species in forest decline worldwide (e.g., oak decline). The past decade has seen an approximate doubling in the number of described species within the genus Phytophthora, and the number will likely continue to increase as more surveys are completed and greater attention is devoted to clarifying phylogenetic relationships and delineating boundaries in species complexes. The development of molecular resources, the availability of credible sequence databases to simplify identification of new species, and the sequencing of several genomes have provided a solid framework to gain a better understanding of the biology, diversity, and taxonomic relationships within the genus. This information is much needed considering the impact invasive or exotic Phytophthora species have had on natural ecosystems and the regulatory issues associated with their management. While this work is improving our ability to identify species based on phylogenetic grouping, it has also revealed that the genus has a much greater diversity than previously appreciated.

The genus Phytophthora anno 2012

Plant diseases caused by Phytophthora species will remain an ever increasing threat to agriculture and natural ecosystems. Phytophthora literally means plant destroyer, a name coined in the 19th century by Anton de Bary when he investigated the potato disease that set the stage for the Great Irish Famine. Phytophthora infestans, the causal agent of potato late blight, was the first species in a genus that at present has over 100 recognized members. In the last decade, the number of recognized Phytophthora species has nearly doubled and new species are added almost on a monthly basis. Here we present an overview of the 10 clades that are currently distinguished within the genus Phytophthora with special emphasis on new species that have been described since 1996 when Erwin and Ribeiro published the valuable monograph 'Phytophthora diseases worldwide' (35).

Phytophthora beyond agriculture

Little is known about indigenous Phytophthora species in natural ecosystems. Increasing evidence, however, suggests that a diverse, trophically complex Phytophthora community is important in many forests. The number of described species has steadily increased, with a dramatic spike in recent years as new species have been split from old and new species have been discovered through exploration of new habitats. Forest soil, streams, and the upper canopies of trees are now being explored for Phytophthora diversity, and a new appreciation for the ecological amplitude of the genus is emerging. Ten to twenty species are regularly identified in temperate forest surveys. Half or more of this Phytophthora diversity comes from species described since 2000. Taxa in internal transcribed spacer (ITS) Clade 6 are especially numerous in forest streams and may be saprophytic in this habitat. Three ecological assemblages of forest Phytophthora species are hypothesized: aquatic opportunists, foliar pathogens, and soilborne fine-root and canker pathogens. Aggressive invasive species are associated with all three groups.