Populations of Phytophthora rubi Show Little Differentiation and High Rates of Migration Among States in the Western United States

Population genetics is a powerful tool to understand patterns and evolutionary processes that are involved in plant-pathogen emergence and adaptation to agricultural ecosystems. We are interested in studying the population dynamics of Phytophthora rubi, the causal agent of Phytophthora root rot in raspberry. P. rubi is found in the western United States, where most of the fresh and processed raspberries are produced. We used genotyping-by-sequencing to characterize genetic diversity in populations of P. rubi sampled in the United States and other countries. Our results confirm that P. rubi is a monophyletic species with complete lineage sorting from its sister taxon P. fragariae. Overall, populations of P. rubi show low genetic diversity across the western United States. Demographic analyses suggest that populations of P. rubi from the western United States are the source of pathogen migration to Europe. We found no evidence for population differentiation at a global or regional (western United States) level. Finally, our results provide evidence of migration from California and Oregon into Washington. This report provides new insights into the evolution and structure of global and western United States populations of the raspberry pathogen P. rubi, indicating that human activity might be involved in moving the pathogen among regions and fields.

Systematic Development of Phytophthora Species-Specific Mitochondrial Diagnostic Markers for Economically Important Members of the Genus

The genus Phytophthora contains many invasive species to the U.S.A. that have the potential to cause significant damage to agriculture and native ecosystems. A genus and species-specific diagnostic assay was previously reported based on mitochondrial gene order differences that allowed for the systematic development of 14 species-specific TaqMan probes for pathogen detection ( Bilodeau et al. 2014 ). In this study, an additional 32 species-specific TaqMan probes for detection of primarily invasive species have been validated against 145 Phytophthora taxa as well as a range of Pythium and plant DNA samples. All validated probes were found to be species-specific and could be multiplexed with a genus-specific probe. The lower limit of linear detection using purified genomic DNA ranged from 1 to 100 fg in all assays. In addition, 124 unique TaqMan probes for Phytophthora spp. developed in silico are presented, which, if testing confirms they are species-specific, will provide diagnostic capabilities for approximately 89% of the genus. To enhance sensitivity of detection for several species that contained a single nucleotide polymorphism (SNP) in the reverse primer, a second primer was developed that is added in a small amount to the master mix. Furthermore, a PCR-RFLP system was developed that could be used to identify individual species when multiple species are present in a sample, without requiring cloning or sequencing. Several experiments were also conducted to compare various qPCR thermal cyclers and independent validation experiments with another research laboratory to identify possible limitations when the assays are used on a range of equipment in different labs. This system represents a comprehensive, hierarchal approach to increase the detection capability and provide tools to help prevent the introduction of invasive Phytophthora species.

Development and Application of qPCR and RPA Genus- and Species-Specific Detection of Phytophthora sojae and P. sansomeana Root Rot Pathogens of Soybean

Phytophthora root rot of soybean, caused by Phytophthora sojae, is one of the most important diseases in the Midwestern United States, and is estimated to cause losses of up to 1.2 million metric tons per year. Disease may also be caused by P. sansomeana; however, the prevalence and damage caused by this species is not well known, partly due to limitations of current diagnostic tools. Efficient, accurate, and sensitive detection of pathogens is crucial for management. Thus, multiplex qPCR and isothermal RPA (recombinase polymerase amplification) assays were developed using a hierarchical approach to detect these Phytophthora spp. The assays consist of a genus-specific probe and two species-specific probes that target the atp9-nad9 region of the mitochondrial genome that is highly specific for the genus Phytophthora. The qPCR approach multiplexes the three probes and a plant internal control. The RPA assays run each probe independently with a plant internal control multiplexed in one amplification, obtaining a result in as little as 20 mins. The multicopy mitochondrial genome provides sensitivity with sufficient variability to discern among different Phytophthora spp. The assays were highly specific when tested against a panel of 100 Phytophthora taxa and range of Pythium spp. The consistent detection level of the assay was 100 fg for the qPCR assay and 10 pg for the RPA assay. The assays were validated on symptomatic plants collected from Michigan (U.S.) and Ontario (Canada) during the 2013 field season, showing correlation with isolation. In 2014, the assays were validated with samples from nine soybean producing states in the U.S. The assays are valuable diagnostic tools for detection of Phytophthora spp. affecting soybean.

Synchronized navigation of current and prior studies using image registration improves radiologist's efficiency

PURPOSE

The purpose of this study was to investigate how the use of multi-modal rigid image registration integrated within a standard picture archiving and communication system affects the efficiency of a radiologist while performing routine interpretations of cases including prior examinations.

METHODS

Six radiologists were recruited to read a set of cases (either 16 neuroradiology or 14 musculoskeletal cases) during two crossover reading sessions. Each radiologist read each case twice, one time with synchronized navigation, which enables spatial synchronization across examinations from different study dates, and one time without. Efficiency was evaluated based upon time to read a case and amount of scrolling while browsing a case using Wilcoxon signed rank test.

RESULTS

Significant improvements in efficiency were found considering either all radiologists simultaneously, the two sections separately and the majority of individual radiologists for time to read and for amount of scrolling. The relative improvement for each individual radiologist ranged from 4 to 32% for time to read and from 14 to 38% for amount of scrolling.

CONCLUSION

Image registration providing synchronized navigation across examinations from different study dates provides a tool that enables radiologists to work more efficiently while reading cases with one or more prior examinations.

Development of Rapid Isothermal Amplification Assays for Detection of Phytophthora spp. in Plant Tissue

Several isothermal amplification techniques recently have been developed that are tolerant of inhibitors present in many plant extracts, which can reduce the need for obtaining purified DNA for running diagnostic assays. One such commercially available technique that has similarities with real-time polymerase chain reaction (PCR) for designing primers and a labeled probe is recombinase polymerase amplification (RPA). This technology was used to develop two simple and rapid approaches for detection of Phytophthora spp.: one genus-specific assay multiplexed with a plant internal control and the other species-specific assays for Phytophthora ramorum and P. kernoviae. All assays were tested for sensitivity (ranging from 3 ng to 1 fg of DNA) and specificity using DNA extracted from more than 136 Phytophthora taxa, 21 Pythium spp., 1 Phytopythium sp., and a wide range of plant species. The lower limit of linear detection using purified DNA was 200 to 300 fg of DNA in all pathogen RPA assays. Six different extraction buffers were tested for use during plant tissue maceration and the assays were validated in the field by collecting 222 symptomatic plant samples from over 50 different hosts. Only 56 samples were culture positive for Phytophthora spp. whereas 91 were positive using the Phytophthora genus-specific RPA test and a TaqMan real-time PCR assay. A technique for the generation of sequencing templates from positive RPA amplifications to confirm species identification was also developed. These RPA assays have added benefits over traditional technologies because they are rapid (results can be obtained in as little as 15 min), do not require DNA extraction or extensive training to complete, use less expensive portable equipment than PCR-based assays, and are significantly more specific than current immunologically based methods. This should provide a rapid, field-deployable capability for pathogen detection that will facilitate point-of-sample collection processing, thereby reducing the time necessary for accurate diagnostics and making management decisions.

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.

Phytophthora database 2.0: update and future direction

The online community resource Phytophthora database (PD) was developed to support accurate and rapid identification of Phytophthora and to help characterize and catalog the diversity and evolutionary relationships within the genus. Since its release in 2008, the sequence database has grown to cover 1 to 12 loci for ≈2,600 isolates (representing 138 described and provisional species). Sequences of multiple mitochondrial loci were added to complement nuclear loci-based phylogenetic analyses and diagnostic tool development. Key characteristics of most newly described and provisional species have been summarized. Other additions to improve the PD functionality include: (i) geographic information system tools that enable users to visualize the geographic origins of chosen isolates on a global-scale map, (ii) a tool for comparing genetic similarity between isolates via microsatellite markers to support population genetic studies, (iii) a comprehensive review of molecular diagnostics tools and relevant references, (iv) sequence alignments used to develop polymerase chain reaction-based diagnostics tools to support their utilization and new diagnostic tool development, and (v) an online community forum for sharing and preserving experience and knowledge accumulated in the global Phytophthora community. Here we present how these improvements can support users and discuss the PD's future direction.

Analyses of the population structure in a global collection of Phytophthora nicotianae isolates inferred from mitochondrial and nuclear DNA sequences

Genetic variation within the heterothallic cosmopolitan plant pathogen Phytophthora nicotianae was determined in 96 isolates from a wide range of hosts and geographic locations by characterizing four mitochondrial (10% of the genome) and three nuclear loci. In all, 52 single-nucleotide polymorphisms (SNPs) (an average of 1 every 58 bp) and 313 sites with gaps representing 5,450 bases enabled the identification of 50 different multilocus mitochondrial haplotypes. Similarly, 24 SNPs (an average of 1 every 69 bp), with heterozygosity observed at each locus, were observed in three nuclear regions (hyp, scp, and β-tub) differentiating 40 multilocus nuclear genotypes. Both mitochondrial and nuclear markers revealed a high level of dispersal of isolates and an inconsistent geographic structuring of populations. However, a specific association was observed for host of origin and genetic grouping with both nuclear and mitochondrial sequences. In particular, the majority of citrus isolates from Italy, California, Florida, Syria, Albania, and the Philippines clustered in the same mitochondrial group and shared at least one nuclear allele. A similar association was also observed for isolates recovered from Nicotiana and Solanum spp. The present study suggests an important role of nursery populations in increasing genetic recombination within the species and the existence of extensive phenomena of migration of isolates that have been likely spread worldwide with infected plant material.

Small RNA profiling reveals phosphorus deficiency as a contributing factor in symptom expression for citrus huanglongbing disease

Huanglongbing (HLB) is a devastating citrus disease that is associated with bacteria of the genus 'Candidatus Liberibacter' (Ca. L.). Powerful diagnostic tools and management strategies are desired to control HLB. Host small RNAs (sRNA) play a vital role in regulating host responses to pathogen infection and are used as early diagnostic markers for many human diseases, including cancers. To determine whether citrus sRNAs regulate host responses to HLB, sRNAs were profiled from Citrus sinensis 10 and 14 weeks post grafting with Ca. L. asiaticus (Las)-positive or healthy tissue. Ten new microRNAs (miRNAs), 76 conserved miRNAs, and many small interfering RNAs (siRNAs) were discovered. Several miRNAs and siRNAs were highly induced by Las infection, and can be potentially developed into early diagnosis markers of HLB. miR399, which is induced by phosphorus starvation in other plant species, was induced specifically by infection of Las but not Spiroplasma citri that causes citrus stubborn-a disease with symptoms similar to HLB. We found a 35% reduction of phosphorus in Las-positive citrus trees compared to healthy trees. Applying phosphorus oxyanion solutions to HLB-positive sweet orange trees reduced HLB symptom severity and significantly improved fruit production during a 3-year field trial in south-west Florida. Our molecular, physiological, and field data suggest that phosphorus deficiency is linked to HLB disease symptomology.

Membrane-based oligonucleotide array developed from multiple markers for the detection of many Phytophthora species

Most Phytophthora spp. are destructive plant pathogens; therefore, effective monitoring and accurate early detection are important means of preventing potential epidemics and outbreaks of diseases. In the current study, a membrane-based oligonucleotide array was developed that can detect Phytophthora spp. reliably using three DNA regions; namely, the internal transcribed spacer (ITS), the 5' end of cytochrome c oxidase 1 gene (cox1), and the intergenic region between cytochrome c oxidase 2 gene (cox2) and cox1 (cox2-1 spacer). Each sequence data set contained ≈250 sequences representing 98 described and 15 undescribed species of Phytophthora. The array was validated with 143 pure cultures and 35 field samples. Together, nonrejected oligonucleotides from all three markers have the ability to reliably detect 82 described and 8 undescribed Phytophthora spp., including several quarantine or regulated pathogens such as Phytophthora ramorum. Our results showed that a DNA array containing signature oligonucleotides designed from multiple genomic regions provided robustness and redundancy for the detection and differentiation of closely related taxon groups. This array has the potential to be used as a routine diagnostic tool for Phytophthora spp. from complex environmental samples without the need for extensive growth of cultures.

Species tree estimation for the late blight pathogen, Phytophthora infestans, and close relatives

To better understand the evolutionary history of a group of organisms, an accurate estimate of the species phylogeny must be known. Traditionally, gene trees have served as a proxy for the species tree, although it was acknowledged early on that these trees represented different evolutionary processes. Discordances among gene trees and between the gene trees and the species tree are also expected in closely related species that have rapidly diverged, due to processes such as the incomplete sorting of ancestral polymorphisms. Recently, methods have been developed for the explicit estimation of species trees, using information from multilocus gene trees while accommodating heterogeneity among them. Here we have used three distinct approaches to estimate the species tree for five Phytophthora pathogens, including P. infestans, the causal agent of late blight disease in potato and tomato. Our concatenation-based "supergene" approach was unable to resolve relationships even with data from both the nuclear and mitochondrial genomes, and from multiple isolates per species. Our multispecies coalescent approach using both Bayesian and maximum likelihood methods was able to estimate a moderately supported species tree showing a close relationship among P. infestans, P. andina, and P. ipomoeae. The topology of the species tree was also identical to the dominant phylogenetic history estimated in our third approach, Bayesian concordance analysis. Our results support previous suggestions that P. andina is a hybrid species, with P. infestans representing one parental lineage. The other parental lineage is not known, but represents an independent evolutionary lineage more closely related to P. ipomoeae. While all five species likely originated in the New World, further study is needed to determine when and under what conditions this hybridization event may have occurred.

Mitochondrial haplotype analysis for differentiation of isolates of Phytophthora cinnamomi

Although Phytophthora cinnamomi is heterothallic, there are few instances of successful crossing in laboratory experiments, and analysis of field populations indicates a clonally reproducing population. In the absence of sexual recombination, the ability to monitor mitochondrial haplotypes may provide an additional tool for identification of clonal isolates and analysis of population structure. To determine mitochondrial haplotypes for this species, seven mitochondrial loci spanning a total of 6,961 bp were sequenced for 62 isolates representing a geographically diverse collection of isolates with A1 and A2 mating type. Three of the regions were primarily intergenic regions between trnG and rns, rns and nad3, and nad6 and cox1, while the remaining loci spanned cox2, nad9, rps10, and secY coding regions and some of the flanking spacer regions. In total, 45 mitochondrial haplotypes were identified (75% of the total isolates examined) with differences due to single-nucleotide polymorphisms (SNPs, totaling 152 bp) and length mutations (17 indels >2 bp representing a total of 910 bp in length). SNPs were the predominate mutation in the four coding regions and their flanking intergenic regions, while both SNPs and length mutations were observed in the three primarily intergenic regions. Some of the length mutations in these regions were due to addition or loss of unique sequences while others were due to variable numbers of subrepeats (in the trnG-rns region, there were 3 to 12 copies of a 24-bp subrepeat sequence that differentiated 17 haplotypes). Network analysis of the haplotypes identified eight primary clades, with the most divergent clade representing primarily A1 isolates collected from Papua New Guinea. The isolate grouping in the network corresponded to mating type and previously published isozyme classifications, with three exceptions: a haplotype representing an A1 mating type (H29) was placed well within the A2 mating type haplotype grouping, one haplotype (H26) had isolates with two isozyme classifications, and one isozyme group was represented on separate network clades, suggesting that recombination has occurred in the past. Among the 62 isolates examined, several examples were identified of isolates recovered from different geographic regions having the same mitochondrial haplotype, suggesting movement of isolates via plant material. Analysis of the data set to determine whether fewer loci could be sequenced to classify haplotypes indicated that the trnG-rns and rns-nad6 loci would classify 87% of the haplotypes identified in this study, while additional sequencing of the nad9 or secY loci would further differentiate the remaining six haplotypes. Based on conservation of gene order in Phytophthora spp., the trnG-rns locus should be useful for mitochondrial haplotype classification in other species, as should the cox2, nad9, rps10, and secY loci. However, the rns-nad3 and nad6-cox1 loci span regions that can have a different gene order in some Phytophthora spp.

DNA barcoding of oomycetes with cytochrome c oxidase subunit I and internal transcribed spacer

Oomycete species occupy many different environments and many ecological niches. The genera Phytophthora and Pythium for example, contain many plant pathogens which cause enormous damage to a wide range of plant species. Proper identification to the species level is a critical first step in any investigation of oomycetes, whether it is research driven or compelled by the need for rapid and accurate diagnostics during a pathogen outbreak. The use of DNA for oomycete species identification is well established, but DNA barcoding with cytochrome c oxidase subunit I (COI) is a relatively new approach that has yet to be assessed over a significant sample of oomycete genera. In this study we have sequenced COI, from 1205 isolates representing 23 genera. A comparison to internal transcribed spacer (ITS) sequences from the same isolates showed that COI identification is a practical option; complementary because it uses the mitochondrial genome instead of nuclear DNA. In some cases COI was more discriminative than ITS at the species level. This is in contrast to the large ribosomal subunit, which showed poor species resolution when sequenced from a subset of the isolates used in this study. The results described in this paper indicate that COI sequencing and the dataset generated are a valuable addition to the currently available oomycete taxonomy resources, and that both COI, the default DNA barcode supported by GenBank, and ITS, the de facto barcode accepted by the oomycete and mycology community, are acceptable and complementary DNA barcodes to be used for identification of oomycetes.

Phytophthora-ID.org: A Sequence-Based Phytophthora Identification Tool

Contemporary species identification relies strongly on sequence-based identification, yet resources for identification of many fungal and oomycete pathogens are rare. We developed two web-based, searchable databases for rapid identification of Phytophthora spp. based on sequencing of the internal transcribed spacer (ITS) or the cytochrome oxidase (cox) 1 and 2 spacer region, followed by BLAST searching the databases. Both databases are highly selective. For ITS, only sequences associated with published Phytophthora spp. descriptions or classic Phytophthora phylogenetics references are included. For the cox spacer region, only data obtained by resequencing select isolates reported in published work were included. Novel taxa tentatively named are selectively included in the database and labeled as Phytophthora taxon "X"; as in, for example, P. taxon "asparagi". The database was validated with 700 Phytophthora isolates collected from nursery environments during 2006 to 2009. This resource, found at www.Phytophthora-ID.org , is a robust and validated tool for molecular identification of Phytophthora spp. and is regularly being updated.

The receptor-like kinase SERK3/BAK1 is required for basal resistance against the late blight pathogen phytophthora infestans in Nicotiana benthamiana

BACKGROUND

The filamentous oomycete plant pathogen Phytophthora infestans causes late blight, an economically important disease, on members of the nightshade family (Solanaceae), such as the crop plants potato and tomato. The related plant Nicotiana benthamiana is a model system to study plant-pathogen interactions, and the susceptibility of N. benthamiana to Phytophthora species varies from susceptible to resistant. Little is known about the extent to which plant basal immunity, mediated by membrane receptors that recognise conserved pathogen-associated molecular patterns (PAMPs), contributes to P. infestans resistance.

PRINCIPAL FINDINGS

We found that different species of Phytophthora have varying degrees of virulence on N. benthamiana ranging from avirulence (incompatible interaction) to moderate virulence through to full aggressiveness. The leucine-rich repeat receptor-like kinase (LRR-RLK) BAK1/SERK3 is a major modulator of PAMP-triggered immunity (PTI) in Arabidopsis thaliana and N. benthamiana. We cloned two NbSerk3 homologs, NbSerk3A and NbSerk3B, from N. benthamiana based on sequence similarity to the A. thaliana gene. N. benthamiana plants silenced for NbSerk3 showed markedly enhanced susceptibility to P. infestans infection but were not altered in resistance to Phytophthora mirabilis, a sister species of P. infestans that specializes on a different host plant. Furthermore, silencing of NbSerk3 reduced the cell death response triggered by the INF1, a secreted P. infestans protein with features of PAMPs.

CONCLUSIONS/SIGNIFICANCE

We demonstrated that N. benthamiana NbSERK3 significantly contributes to resistance to P. infestans and regulates the immune responses triggered by the P. infestans PAMP protein INF1. In the future, the identification of novel surface receptors that associate with NbSERK3A and/or NbSERK3B should lead to the identification of new receptors that mediate recognition of oomycete PAMPs, such as INF1.

Evaluation of image quality of a 32-channel versus a 12-channel head coil at 1.5T for MR imaging of the brain

BACKGROUND AND PURPOSE

Multichannel phased-array head coils are undergoing exponential escalation of coil element numbers. While previous technical studies have found gains in SNR and spatial resolution with the addition of element coils, it remains to be determined how these gains affect clinical reading. The purpose of this clinical study was to determine if the SNR and spatial resolution characteristics of a 32-channel head coil result in improvements in perceived image quality and lesion evaluation.

MATERIALS AND METHODS

Twenty-one patients underwent MR imaging of the brain at 1.5T sequentially with both a 12-channel and a 32-channel receive-only phased-array head coil. Axial T2WIs, T1WIs, FLAIR images, and DWIs were acquired. Anonymized images were compared side-by-side and by sequence for image quality, lesion evaluation, and artifacts by 3 neuroradiologists. Results of the comparison were analyzed for the preference for a specific head coil.

RESULTS

FLAIR and DWI images acquired with the 32-channel coil showed significant improvement in image quality in several parameters. T2WIs also improved significantly with acquisition by the 32-channel coil, while T1WIs improved in a limited number of parameters. While lesion evaluation also improved with acquisition of images by the 32-channel coil, there was no apparent improvement in diagnostic quality. There was no difference in artifacts between the 2 coils.

CONCLUSIONS

Improvements in SNR and spatial resolution attributed to image acquisition with a 32-channel head coil are paralleled by perceived improvements in image quality.

First Report of Bud Rot Caused by Phytophthora palmivora on African Oil Palm in Colombia

A bud rot disease, referred to as "pudricion del cogollo" or PC (for its name in Spanish), is a major disease of oil palm in four production areas of Colombia. Even though the disease has been studied for more than 40 years in Central and South America, the causal agent remained unknown (1). Infection first develops in the palm heart (cogollo) above the meristematic zone. Initial external symptoms appear as necrotic lesions on the sides of the spear leaf (youngest, unexpanded leaf) and the sizes of the lesions remain static as tissues emerge, expand, and mature. Under favorable environmental conditions (temperature around 26°C and relative humidity above 80%), further rotting of the heart eventually destroys the bud. A baiting technique with papaya and cocoa fruits was successfully used to trap the causal agent from symptomatic spear leaf tissue collected from the provinces of Nariño and Santander (2), where the disease is severe. Small, triangular-shaped pieces were removed from healthy fruits that had been surface sterilized, and a corresponding piece of diseased oil palm tissue was inserted into the hole and sealed with the removed fruit tissue. The whole fruit was wrapped with plastic and incubated at 25°C. Once the fruit traps showed initial necrotic symptoms, fruit tissue from the advancing point of the lesions was plated on Phytophthora-selective media. Four isolates of Phytophtora palmivora, all A2 mating type, were obtained during this study and each presented similar white and depressed mycelium when grown on oatmeal agar (OMA) medium. Papillated, ellipsoidal sporangia with short pedicels had an average size of 37.1 (breadth) × 52.8 μm (length). Chlamydospores averaged 35.1 μm in diameter and were similar to those observed in diseased palm tissue. DNA from the Phytophthora isolates was used as a template for PCR using ITS1/ITS4 primers. BLASTn analysis of the ITS sequences (GenBank Accession No. GQ398157) showed 99.9% homology with P. palmivora. The sequences of the four isolates were identical. For pathogenicity testing, cultures were grown on OMA. Two milliliters of distilled water containing 40,000 sporangia were injected into the base of the spear leaf of 105 nursery palms; the same number of palms was injected with 2 ml of distillated water as controls. Initial PC symptoms were observed 3 to 4 days after inoculation on 85% of inoculated palms and 15% of these palms developed typical bud rot symptoms under favorable conditions. No symptoms were observed on the controls. The presence of Phytophthora was confirmed by light microscopy and P. palmivora was reisolated from symptomatic palms with the fruit-baiting technique. The presence of Phytophthora in the four Colombian growing areas was also confirmed using Agdia (Elkhart, IN) immunostrips followed by DNA extraction from the Immunostrip wick and ITS sequencing to confirm the species. To our knowledge, this is the first report of P. palmivora causing PC on oil palm in Colombia. References: (1) H. de Franqueville. Exp. Agric. 39:225, 2003. (2) G. Sarria et al. Rev. Palmas, Colombia. 29(3):31, 2008.

The promise and pitfalls of sequence-based identification of plant-pathogenic fungi and oomycetes

Sequences of selected marker loci have been widely used for the identification of specific pathogens and the development of sequence-based diagnostic methods. Although such approaches offer several advantages over traditional culture-based methods for pathogen diagnosis and identification, they have their own pitfalls. These include erroneous and incomplete data in reference databases, poor or oversimplified interpretation of search results, and problems associated with defining species boundaries. In this letter, we outline the potential benefits and drawbacks of using sequence data for identification and taxonomic deduction of plant-pathogenic fungi and oomycetes, using phytophthora as a primary example. We also discuss potential remedies for these pitfalls and address why coordinated community efforts are essential to make such remedies more efficient and robust.

Viability of Oomycete Propagules Following Ingestion and Excretion by Fungus Gnats, Shore Flies, and Snails

Sporangia of Phytophthora capsici and P. nicotianae, as well as hyphal swellings of Pythium splendens, P. sylvaticum, and P. ultimum, were ingested by adult shore flies but none were viable after passing through the digestive tract. Oospores of Pythium aphanidermatum retained their viability following ingestion by adult shore flies. Larval stages of fungus gnats and shore flies ingested sporangia of Phytophthora capsici, P. nicotianae, and P. ramorum, but they were not viable upon excretion. In contrast, hyphal swellings of Pythium splendens, P. sylvaticum, and P. ultimum, chlamydospores of Phytophthora ramorum, and oospores of Pythium aphanidermatum, retained their viability after passage through the digestive tract of these larvae. Snails were capable of ingesting and excreting viable sporangia and chlamydospores of P. ramorum, which upon excretion infected detached leaves. Although the impact of larvae and snails in the rapid dissemination of pathogen propagules is unknown, this work does highlight the possibility that some often-ignored animal-fungus interactions should be considered in long-range dispersal of pathogen propagules via food webs.

Evaluation of molecular markers for Phytophthora ramorum detection and identification: testing for specificity using a standardized library of isolates

Given the importance of Phytophthora ramorum from a regulatory standpoint, it is imperative that molecular markers for pathogen detection are fully tested to evaluate their specificity in detection of the pathogen. In an effort to evaluate 11 reported diagnostic techniques, we assembled a standardized DNA library using accessions from the World Phytophthora Genetic Resource Collection for 315 isolates representing 60 described Phytophthora spp. as well as 11 taxonomically unclassified isolates. These were sent blind to collaborators in seven laboratories to evaluate published diagnostic procedures using conventional (based on internal transcribed spacer [ITS] and cytochrome oxidase gene [cox]1 and 2 spacer regions) and real-time polymerase chain reaction (based on ITS and cox1 and 2 spacer regions as well as beta-tubulin and elicitin genes). Single-strand conformation polymorphism (SSCP) analysis using an automated sequencer for data collection was also evaluated for identification of all species tested. In general, the procedures worked well, with varying levels of specificity observed among the different techniques. With few exceptions, all assays correctly identified all isolates of P. ramorum and low levels of false positives were observed for the mitochondrial cox spacer markers and most of the real-time assays based on nuclear markers (diagnostic specificity between 96.9 and 100%). The highest level of false positives was obtained with the conventional nested ITS procedure; however, this technique is not stand-alone and is used in conjunction with two other assays for diagnostic purposes. The results indicated that using multiple assays improved the accuracy of the results compared with looking at a single assay alone, in particular when the markers represented different genetic loci. The SSCP procedure accurately identified P. ramorum and was helpful in classification of a number of isolates to a species level. With one exception, all procedures accurately identified P. ramorum in blind evaluations of 60 field samples that included examples of plant infection by 11 other Phytophthora spp. The SSCP analysis identified eight of these species, with three identified to a species group.

Phytophthora Database: A Forensic Database Supporting the Identification and Monitoring of Phytophthora

Phytophthora spp. represent a serious threat to agricultural and ecological systems. Many novel Phytophthora spp. have been reported in recent years, which is indicative of our limited understanding of the ecology and diversity of Phytophthora spp. in nature. Systematic cataloging of genotypic and phenotypic information on isolates of previously described species serves as a baseline for identification, classification, and risk assessment of new Phytophthora isolates. The Phytophthora Database (PD) was established to catalog such data in a web-accessible and searchable format. To support the identification of new Phytophthora isolates via comparison of their sequences at one or more loci with the corresponding sequences derived from the isolates archived in the PD, we generated and deposited sequence data from more than 1,500 isolates representing the known diversity in the genus. Data search and analysis tools in the PD include BLAST, Phyloviewer (a program for building phylogenetic trees using sequences of selected isolates), and Virtual Gel (a program for generating expected restriction patterns for given sequences). The PD also provides a customized means of storing and sharing data via the web. The PD serves as a model that easily can be adopted to develop databases for other important pathogen groups.

Phytophthora bisheria sp. nov., a new species identified in isolates from the Rosaceous raspberry, rose and strawberry in three continents

A homothallic semipapillate slow growing Phytophthora species associated with root rot of strawberries from greenhouse-grown plants in North Carolina, USA, root rot of roses in the Netherlands, and root rot of raspberry in Knoxfield, Australia, was identified. The main character of this organism is the production of paragynous antheridia with broad attachment to the oogonial wall. The morphology of the pathogen does not match that of any of the more than 85 described Phytophthora species. Phylogenetic analysis based on sequences of the internal transcribed spacer rDNA region (ITS1-5.8S-ITS2) of this taxon and those from other Phytophthora species from GenBank supports the conclusion that this organism is an unreported new species. In the phylogenetic tree with other reported Phytophthora species at the GenBank, the new species is more closely related to others in ITS clade 2 comprising semipapillate taxa including P. botryosa, P. citrophthora, P. colocasiae, P. meadii, P. citricola, P. inflata, P.tropicalis, P. capsici, Phytophthora sp. 'glovera' and P. multivesiculata. The most closely related species is P. multivesiculata isolated from Cymbidium orchid in the Netherlands. In this paper we describe the morphological characteristics and the phylogenetic relationships that support the description of this taxon as a new species Phytophthora bisheria sp. nov.

Plant pathogen culture collections: it takes a village to preserve these resources vital to the advancement of agricultural security and plant pathology

ABSTRACT Plant pathogen culture collections are essential resources in our fight against plant disease and for connecting discoveries of the present with established knowledge of the past. However, available infrastructure in support of culture collections is in serious need of improvement, and we continually face the risk of losing many of these collections. As novel and reemerging plant pathogens threaten agriculture, their timely identification and monitoring depends on rapid access to cultures representing the known diversity of plant pathogens along with genotypic, phenotypic, and epidemiological data associated with them. Archiving such data in a format that can be easily accessed and searched is essential for rapid assessment of potential risk and can help track the change and movement of pathogens. The underexplored pathogen diversity in nature further underscores the importance of cataloguing pathogen cultures. Realizing the potential of pathogen genomics as a foundation for developing effective disease control also hinges on how effectively we use the sequenced isolate as a reference to understand the genetic and phenotypic diversity within a pathogen species. In this letter, we propose a number of measures for improving pathogen culture collections.

Treatment of cervical pregnancy with cerclage, curettage and balloon tamponade. A report of three cases

BACKGROUND

Cervical pregnancy is a rare form of ectopic pregnancy, historically requiring hysterectomy to control life-threatening hemorrhage. However, with early diagnosis, conservative procedures can preserve the uterus and fertility.

CASES

Three cases of cervical pregnancy were treated successfully with curettage. Two cases utilizing precurettage and postcurettage hemostatic techniques were treated with curettage alone. A third case, not employing precurettage hemostatic maneuvers, required uterine artery embolization to control bleeding and avoid hysterectomy.

CONCLUSION

Curettage alone, when preceded by cervical infiltration with a vasoconstricting agent, placement of a cerclage suture high on the cervix and followed by cervical canal tamponade with a Foley catheter balloon, can successfully treat early cervical pregnancy.

Cosegregation of Avr4 and Avr6 in Phytophthora sojae

The F2 progeny resulting from a cross of Phytophthora sojae race 2 (avirulent on Rps4 and Rps6) and race 7 (virulent on Rps4 and Rps6) were tested for their ability to cause disease on soybean plants carrying the Rps4 or the Rps6 resistance genes. Of 55 F2 progeny analyzed, 41 individuals were avirulent on both of these genes and 14 were virulent on Rps4 and Rps6, indicating that avirulence on Rps4 and Rps6 is dominant and linked. These results support the suggestion that the soybean–Phytophthora relationship is a gene for gene interaction and that the presumptive Avr4 and Avr6 genes are either tightly linked or identical. Keywords: avirulence, genetic mapping, Glycine max, incomplete dominance, Phytophthora megasperma f.sp. glycinea.

In vitro cell injury by oxidized low density lipoprotein involves lipid hydroperoxide-induced formation of alkoxyl, lipid, and peroxyl radicals

Mounting evidence supports current theories linking lipoprotein oxidation to atherosclerosis. We sought the cellular biochemical mechanism by which oxidized LDL inflicts cell injury. Inhibitors of candidate pathways of cell death were used to treat human fibroblast target cells exposed to oxidized LDL.. Ebselen, which degrades lipid hydroperoxides, inhibited oxidized LDL toxicity, consistent with our recent report that 7 beta-hydroperoxycholesterol (7 beta-OOH chol) is the major cytotoxin of oxidized LDL. Intracellular chelation of metal ions inhibited, while preloading cells with iron enhanced, toxicity, Inhibition of oxidized LDL and 7 beta-OOH chol toxicity by 2-keto-4-thiolmethyl butyric acid, a putative alkoxyl radical scavenger and by vitamin E, probucol and diphenylphenylenediamine, putative scavengers of peroxyl radicals was consistent with the involvement of these radicals in the lethal sequence. Cell death was thus postulated to occur due to lipid peroxidation via a sequence involving lipid hydroperoxide-induced, iron-mediated formation of alkoxyl, lipid, and peroxyl radicals. Pathways involving other reactive oxygen species, new protein synthesis, or altered cholesterol metabolism were considered less likely, since putative inhibitors failed to lessen toxicity. Understanding the mechanism of cell injury by oxidized LDL and its toxic moiety, 7 beta-OOH chol, may indicate specific interventions in the cell injury believed to accompany vascular lesion development.

Potential Role of Elicitins in the Interaction between Phytophthora Species and Tobacco

The potential role of extracellular elicitor proteins (elicitins) from Phytophthora species as avirulence factors in the interaction between Phytophthora and tobacco was examined. A survey of 85 Phytophthora isolates representing 14 species indicated that production of elicitin is almost ubiquitous except for isolates of Phytophthora parasitica from tobacco. The production of elicitins by isolates of P. parasitica correlated without exception with low or no virulence on tobacco. Genetic analysis was conducted by using a cross between two isolates of P. parasitica , segregating for production of elicitin and virulence on tobacco. Virulence assays of the progeny on tobacco confirmed the correlation between production of elicitin and low virulence.

A gene encoding a host-specific elicitor protein of Phytophthora parasitica

Extracellular elicitor proteins (elicitins) from Phytophthora species induce local and distal defense responses specifically in plants of the Solanaceae and Cruciferae. Based on elicitin amino acid sequences, elicitin-coding sequences from P. parasitica were amplified by the polymerase chain reaction. A genomic clone containing a complete elicitin gene, parA1, was isolated and sequenced. Elicitin was confirmed to be encoded as a precursor protein containing a 20-amino acid signal peptide that is processed before secretion. Bacterial expression of the cloned elicitin gene as a translational fusion protein containing glutathione S-transferase yielded a biologically active protein capable of inducing a hypersensitive response in tobacco, suggesting that fungus-specific postranslational modifications of elicitin are not required for its activity. Southern blot analysis indicated that elicitin genes occur as a multigene family (at least two to 10 copies) in P. parasitica, P. capsici, P. citricola, P. citrophthora, P. cryptogea, P. drechsleri, P. megasperma, and P. palmivora. Some isolates of P. parasitica that did not produce elicitins still contained elicitin-coding sequences but did not accumulate elicitin mRNA.

Transformation of the oomycete pathogen Phytophthora megasperma f. sp. glycinea occurs by DNA integration into single or multiple chromosomes

A procedure for stable transformation was developed for Phytophthora megasperma f. sp. glycinea, an oomycete pathogen of soybean. Transformants were obtained using a bacterial hygromycin resistance gene fused to a promoter and terminator from the ham34 gene of another oomycete, Bremia lactucae. Vector DNA, alone or complexed to cationic liposomes, was introduced into protoplasts using polyethylene glycol and CaCl2. DNA and RNA hybridization, and phosphotransferase assays, confirmed the presence and expression of vector DNA in the transformants. Hybridization to electrophoretically separated chromosomes of P. m. glycinea showed that vector DNA had integrated into only one chromosome in four transformants, and into multiple chromosomes in one transformant.

Characterization of microorganisms involved in accelerated biodegradation of metalaxyl and metolachlor in soils

The metabolism of the chemically related fungicide metalaxyl and the herbicide metolachlor was studied in soils and in liquid culture. Experiments with [14C]metalaxyl demonstrated that it was readily metabolized in a soil (E9) with a history of fungicide treatment, but not in a control soil. The respective half-lives of metalaxyl and metolachlor in the E9 soil were 14 and 56 days. Fourteen soil microorganisms were isolated, identified, and tested for their relative ability to degrade [14C]metalaxyl and [14C]metolachlor. With single microorganisms, breakdown of metalaxyl ranged from 36–52% after 25 days, and up to 75% with mixtures of either fungi or bacteria. Four products of metalaxyl metabolism, isolated by two-dimensional thin-layer chromatography, were tested for their antifungal activity using Phytophthora boehmeriae as a sensitive bioassay organism. All four breakdown products were inactive at concentrations up to 2.5 μg/mL, contrasting with an effective concentration for 50% inhibition of growth of P. boehmeriae for metalaxyl of 0.02 μg/mL. Rates of breakdown of metolachlor ranged from 4 to 86% with different microorganisms. Products of metolachlor breakdown possessed no herbicidal activity at concentrations up to 10 μg/mL. Cell-free extracts of four species of soil bacteria were also active in metalaxyl degradation.

An ultrastructural study of the late-blight fungus Phytophthora infestans and its interaction with the foliage of two potato cultivars possessing different levels of general (field) resistance

In the susceptible reaction of foliage of the cultivar Majestic there was extensive colonization of the host tissue prior to the onset of necrosis. The development of intracellular hyphae was confined to the initially parasitized palisade cells. Thereafter the fungus grew as intercellular hyphae, which penetrated host cells and formed haustoria. Haustorial morphology was highly variable, ranging in type from small spherical to much larger digitlike structures. Haustorial formation was preceded by the laying down of a moderately electron-dense penetration matrix bounded by the host plasmalemma. This material probably constituted the extrahaustorial matrix once haustorial development had taken place. The matrical material stained with silver proteinate reagent, and this reaction was blocked by dimedone, indicating that it was carbohydrate in nature. In the resistant reaction of foliage of the cultivar Shamrock, the epidermal cells rapidly became necrotic. Quantities of exceedingly electron-dense granules appeared in the necrotic host cells. Host organelles were no longer recognizable, but the fungal cytoplasm remained intact. In adjoining host cells, thin cell wall appositions were formed, which had a heterogeneous composition. On occasions when the fungus attempted to invade an underlying mesophyll cell, papillae usually formed in that cell at the site of incipient penetration.

A quantitative histological and ultrastructural analysis of interactions between the flax rust and near-isogenic host lines varying in their degree of incompatibility

Histological differences were evident in the leaves of eight near-isogenic lines of flax infected with the rust fungus Melampsora lini. Compared with the compatible L9 and M1 interactions, fungal growth was progressively more restricted in the moderately incompatible K and M4, incompatible M and P, and highly incompatible L and M3 interactions. This restriction took place in advance of appreciable necrosis of host cells in K, M4, M, and P. At 72 h the proportion of haustoria-containing cells which were necrotic was only 10–15% in K and M4. In M at 72 h necrosis was 80% or more at infection sites with small colonies but was negligible at sites with large colonies. In P, by contrast, a similar proportion of necrosis, 40% at 72 h, was present at all infection sites. However, in L and M3 host necrosis was much more rapid and the fungus was restricted to a few host cells. An early ultrastructural event was the appearance of extensive fibrillar deposits in the initially electron-lucent extrahaustorial matrices of both the incompatible M and P and moderately incompatible M4 and K interactions. A positive reaction with silver proteinate indicated that these matrical deposits contained carbohydrate, possibly a mucopolysaccharide or glycoprotein, but they were not extracted by either cellulase, pectinase, or chitinase. The extrahaustorial membrane, surrounding the haustoria in the compatible L9 and M1 interactions and the moderately incompatible K interaction was not stained by the periodic acid – phosphotungstic acid – chromic acid (PACP) procedure believed specific for the plasmalemma. In incompatible reactions clusters of electron-dense particles sometimes replaced starch in plastids of infected host cells. This event usually coincided with the appearance of extensive matrical deposits around fungal haustoria. At the same time particles were also found in plastids in uninfected host cells immediately adjacent to infection sites, particularly in the M and P interactions. These particles were extracted from thin sections by using pullulanase followed by α-amylase, indicating that they consisted of highly branched amylopectin.

Cytochemical specialization at the haustorial interface of a biotrophic fungal parasite, Albugo Candida

The haustorial apparatus of Albugo candida consisted of a narrow neck attached to a spherical body, which was packed with mitochondria. Covering the haustorial body was an electron-dense matrix which was bounded by the extrahaustorial membrane. This membrane, a continuation of the host cell plasmalemma, was highly convoluted with many short tentacles extending into the surrounding host cytoplasm. Single cisternae of host rough endoplasmic reticulum were always closely associated with the distal portion of the haustorial neck. Silver proteinate staining indicated that both the penetration jacket, a distinct zone surrounding the proximal part of the haustorial neck, and the extrahaustorial matrix were polysaccharide in nature, possibly complexed to other macromolecules such as proteins. The haustorial cell wall reacted only slightly with the silver proteinate, and in the distal region of the neck, there was no reaction. The fungal plasmalemma reacted strongly with the stain, except in the distal neck region, where there was no staining. With PACP, a staining procedure believed specific for the plasmalemma, the extrahaustorial membrane did not stain, whilst the host plasmalemma continuous with it did stain. The distal region of the haustorial neck wall also stained intensely with PACP clearly differentiating it cytochemically from the much lighter staining proximal neck and haustorial body walls. The penetration jacket stained more intensely than the extrahaustorial matrix with PACP, which might suggest a different chemical composition. Following incubation in 0.8 M sucrose osmoticum, the extrahaustorial membrane pulled away from the proximal neck wall, but remained tightly affixed to the distal neck wall, indicating that a tight junction existed between that membrane and the fungal cell wall in that region. Enzymic digestion with either cellulase or an endo-β-1,3-glucanase removed neither the haustorial body wall nor the extrahaustorial matrix. The significance of this finding is briefly discussed.

Plasmolysis of rusted flax: a fine-structural study of the host–pathogen interface

Plasmolysis of rust-infected flax tissue after treatment with sucrose, mannitol, or calcium chloride solutions caused withdrawal of the host plasmalemma from the cell wall and movement of the host protoplast towards the haustorium. The extrahaustorial membrane, however, was not displaced from its position along the haustorial neck or around the haustorial body. In sucrose and mannitol solutions the extrahaustorial matrix was unchanged in volume, which suggests that it is either a more rigid structure than has usually been suggested or an artifact of fixation. After calcium chloride treatment, the matrix was frequently slightly distended and some plasmolysis of the haustorial protoplast was generally observed; this did not occur in the sucrose or mannitol solutions. The possible significance of these findings is briefly discussed.

A fine-structural study of the pea downy mildew fungus Peronospora pisi in its host Pisum sativum

Downy mildew disease of the cultivated pea Pisum sativum L. caused by the fungus Peronospora pisi Sydow was studied in mature leaves and young shoots of the host plant. Particularly in systemic infections of young shoot tissue, a common occurrence was an extremely electron-opaque membrane-bound, hemispherical deposit extending through the host cell wall into the host cytoplasm. This material which abutted directly onto the intercellular hyphal wall was termed the penetration matrix. Its formation was apparently the result of a specific interaction between the host and obligate fungal parasite. Similar apparently solid or gellike material constituted the matrix surrounding the digitlike intracellular haustorium. This membrane-bound extrahaustorial matrix was present through the penetrated host cell wall and formed a relatively thick layer around haustoria in young shoot tissue, but was much thinner distally around haustoria in mature leaf mesophyll cells. An unusual, regularly arranged, tubular network of ribosome-free endoplasmic reticulum was occasionally found in the host cytoplasm in systemically infected shoot tissue adjacent to haustoria.

Acid phosphatase and protease release by the insectivorous plant Drosera rotundifolia

The leaves of the insectivorous plant Drosera rotundifolia L. produced extracellular hydrolytic enzymes in response to feeding with gelatin. Enzyme release was first detected 1 to 2 days after feeding, reached a maximum on day 4, and then gradually declined. Optimal activity of both acid phosphatase (orthophosphoric-monoester phosphohydrolase (acid optimum), EC 3.1.3.2) and protease enzymes was in the acidic range of pH. The acid phosphatase attacked a range of phosphorylated compounds but its p-nitrophenylphosphatase (PNPPase) and ribonucleoside triphosphatase activities were highest. It displayed relatively low phosphomonoesterase (EC 3.1.3.1, 3.1.3.2) activity. Both acid phosphatase and protease enzymes were insensitive to the sulphydryl inhibitor N-ethylmaleimide. The acid phosphatase was strongly inhibited by fluoride and orthophosphate. The nature of the apparent induction of hydrolase enzyme activity is briefly discussed.