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

Diversity of Phytophthora Communities across Different Types of Mediterranean Vegetation in a Nature Reserve Area

Research Highlights: Protected natural areas are a reservoir of Phytophthora species and represent the most suitable sites to study their ecology, being less disturbed by human activities than other environments. Background and Objectives: The specific objective of this study was to correlate the diversity and distribution of Phytophthora species with the vegetation in aquatic, riparian and terrestrial habitats within a protected area in Eastern Sicily, Southern Italy. Materials and Methods: Environmental samples (water and soil) were sourced from two streams running through the reserve and six different types of vegetation, including Platano-Salicetum pedicellatae, the Sarcopoterium spinosum community, Myrto communis-Pistacietum lentisci, Pistacio-Quercetum ilicis,Oleo-Quercetum virgilianae and a gallery forest dominated by Nerium oleander (Natura 2000 classification of habitats). Phytophthora species were recovered from samples using leaf baiting and were classified on the basis of morphological characteristics and sequencing of internal transcribed spacer (ITS) regions of ribosomal DNA (rDNA). Results: As many as 11 Phytophthora species, within five different ITS clades, were identified, including P. asparagi, P. bilorbang, P. cryptogea, P. gonapodyides, P. lacustris, P. multivora, P. nicotianae, P. oleae, P. parvispora, P. plurivora and P. syringae. No Phytophthora species were found in the Sarcopoterium spinosum comm. Phytophthora asparagi, P. lacustris and P. plurivora were the prevalent species in the other five plant communities, but only P. plurivora was present in all of them. Overall aquatic species from clade 6 (100 out of 228 isolates) were the most common; they were recovered from all five types of vegetation, streams and riparian habitats. Phytophthora populations found in the Platano-Salicetum pedicellatae and Oleo-Quercetum virgilianae show the highest diversity, while no correlation was found with the physicochemical characteristics of the soil. Conclusions: The vegetation type and the aquatic or terrestrial habitat were identified as major environmental factors correlated with the diversity of Phytophthora communities in this reserve.

Genomic biosurveillance of forest invasive alien enemies: A story written in code

The world's forests face unprecedented threats from invasive insects and pathogens that can cause large irreversible damage to the ecosystems. This threatens the world's capacity to provide long-term fiber supply and ecosystem services that range from carbon storage, nutrient cycling, and water and air purification, to soil preservation and maintenance of wildlife habitat. Reducing the threat of forest invasive alien species requires vigilant biosurveillance, the process of gathering, integrating, interpreting, and communicating essential information about pest and pathogen threats to achieve early detection and warning and to enable better decision-making. This process is challenging due to the diversity of invasive pests and pathogens that need to be identified, the diverse pathways of introduction, and the difficulty in assessing the risk of establishment. Genomics can provide powerful new solutions to biosurveillance. The process of invasion is a story written in four chapters: transport, introduction, establishment, and spread. The series of processes that lead to a successful invasion can leave behind a DNA signature that tells the story of an invasion. This signature can help us understand the dynamic, multistep process of invasion and inform management of current and future introductions. This review describes current and future application of genomic tools and pipelines that will provide accurate identification of pests and pathogens, assign outbreak or survey samples to putative sources to identify pathways of spread, and assess risk based on traits that impact the outbreak outcome.

Advances in Diagnostics of Downy Mildews: Lessons Learned from Other Oomycetes and Future Challenges

Downy mildews are plant pathogens that damage crop quality and yield worldwide. Among the most severe and notorious crop epidemics of downy mildew occurred on grapes in the mid-1880s, which almost destroyed the wine industry in France. Since then, there have been multiple outbreaks on sorghum and millet in Africa, tobacco in Europe, and recent widespread epidemics on lettuce, basil, cucurbits, and spinach throughout North America. In the mid-1970s, loss of corn to downy mildew in the Philippines was estimated at US$23 million. Today, crops that are susceptible to downy mildews are worth at least $7.5 billion of the United States' economy. Although downy mildews cause devastating economic losses in the United States and globally, this pathogen group remains understudied because they are difficult to culture and accurately identify. Early detection of downy mildews in the environment is critical to establish pathogen presence and identity, determine fungicide resistance, and understand how pathogen populations disperse. Knowing when and where pathogens emerge is also important for identifying critical control points to restrict movement and to contain populations. Reducing the spread of pathogens also decreases the likelihood of sexual recombination events and discourages the emergence of novel virulent strains. A major challenge in detecting downy mildews is that they are obligate pathogens and thus cannot be cultured in artificial media to identify and maintain specimens. However, advances in molecular detection techniques hold promise for rapid and in some cases, relatively inexpensive diagnosis. In this article, we discuss recent advances in diagnostic tools that can be used to detect downy mildews. First, we briefly describe downy mildew taxonomy and genetic loci used for detection. Next, we review issues encountered when identifying loci and compare various traditional and novel platforms for diagnostics. We discuss diagnosis of downy mildew traits and issues to consider when detecting this group of organisms in different environments. We conclude with challenges and future directions for successful downy mildew detection.

Advanced molecular diagnostic techniques for detection of food-borne pathogens: Current applications and future challenges

The elimination of disease-causing microbes from the food supply is a primary goal and this review deals with the overall techniques available for detection of food-borne pathogens. Now-a-days conventional methods are replaced by advanced methods like Biosensors, Nucleic Acid-based Tests (NAT), and different PCR-based techniques used in molecular biology to identify specific pathogens. Bacillus cereus, Staphylococcus aureus, Proteus vulgaris, Escherichia coli, Campylobacter, Listeria monocytogenes, Salmonella spp., Aspergillus spp., Fusarium spp., Penicillium spp., and pathogens are detected in contaminated food items that cause always diseases in human in any one or the other way. Identification of food-borne pathogens in a short period of time is still a challenge to the scientific field in general and food technology in particular. The low level of food contamination by major pathogens requires specific sensitive detection platforms and the present area of hot research looking forward to new nanomolecular techniques for nanomaterials, make them suitable for the development of assays with high sensitivity, response time, and portability. With the sound of these, we attempt to highlight a comprehensive overview about food-borne pathogen detection by rapid, sensitive, accurate, and cost affordable in situ analytical methods from conventional methods to recent molecular approaches for advanced food and microbiology research.

Identification of the Dominant Genotypes of Phytophthora infestans in Canada Using Real-Time PCR with ASO-PCR Assays

Phytophthora infestans, a pathogenic oomycete that is the causal agent of potato and tomato late blight, has devastating effects worldwide. The genetic composition of P. infestans populations in Canada has changed considerably over the last few years, with the appearance of several new genotypes showing different mating types and sensitivity to the fungicide metalaxyl. Genetic markers allowing for a rapid assessment of genotypes from small amounts of biological material would be beneficial for the early detection and control of this pathogen throughout Canada. Mining of the P. infestans genome revealed several regions containing single-nucleotide polymorphisms (SNP) within both nuclear genes and flanking sequences of microsatellite loci. Allele-specific oligonucleotide polymerase chain reaction (ASO-PCR) assays were developed from 14 of the 50 SNP found by sequencing. Nine optimized ASO-PCR assays were validated using a blind test comprising P. infestans and other Phytophthora spp. The assays revealed diagnostic profiles unique to each of the five dominant genotypes present in Canada. The markers developed in this study can be used with environmental samples such as infected leaves, and will contribute to the genomic toolbox available to assess the genetic diversity of P. infestans at the intraspecific level. For late blight management, early warning about P. infestans genotypes present in potato and tomato fields will help growers select the most appropriate fungicides and application strategies.

Detection of Phytophthora ramorum in Nurseries and Forest Lands in California in 2004 to 2009

From December 2004 through May 2009, samples were collected from California nurseries and wild lands to survey for Phytophthora ramorum and comply with federal regulations of nursery stock. Samples were prescreened by an enzyme-linked immunosorbent assay (ELISA) that detects Phytophthora spp. and tested by culture, P. ramorum-specific real-time polymerase chain reaction (PCR), and nested PCR. Yearly percentages of infected samples ranged from 0.6 to 2.3%. Camellia spp., Rhododendron spp., Magnolia spp., Pieris spp., and Laurus nobilis tested positive the most frequently in the nurseries and Lithocarpus densiflorus, Umbellularia californica, and Quercus agrifolia tested positive most often from wild lands. Of the 118,410 samples isolated onto PARP media, 0.8% was identified as P. ramorum. Of 115,056 samples tested by ELISA, 5.9% tested positive for Phytophthora spp. Of the 6,520 samples tested by PCR, 12.4% tested positive for P. ramorum. The false-negative, positive, and internal control failure rates of the assays are discussed. After removing the seasonal effect of sampling strategy, isolation of the pathogen into culture was found to be seasonally dependent whereas detectability by PCR and ELISA was not. To our knowledge, this is the first evaluation of a regulatory testing program for a plant pathogen on this scale using standardized assays.

Detection, Diversity, and Population Dynamics of Waterborne Phytophthora ramorum Populations

Sudden oak death, the tree disease caused by Phytophthora ramorum, has significant environmental and economic impacts on natural forests on the U.S. west coast, plantations in the United Kingdom, and in the worldwide nursery trade. Stream baiting is vital for monitoring and early detection of the pathogen in high-risk areas and is performed routinely; however, little is known about the nature of water-borne P. ramorum populations. Two drainages in an infested California forest were monitored intensively using stream-baiting for 2 years between 2009 and 2011. Pathogen presence was determined both by isolation and polymerase chain reaction (PCR) from symptomatic bait leaves. Isolates were analyzed using simple sequence repeats to study population dynamics and genetic structure through time. Isolation was successful primarily only during spring conditions, while PCR extended the period of pathogen detection to most of the year. Water populations were extremely diverse, and changed between seasons and years. A few abundant genotypes dominated the water during conditions considered optimal for aerial populations, and matched those dominant in aerial populations. Temporal patterns of genotypic diversification and evenness were identical among aerial, soil, and water populations, indicating that all three substrates are part of the same epidemiological cycle, strongly influenced by rainfall and sporulation on leaves. However, there was structuring between substrates, likely arising due to reduced selection pressure in the water. Additionally, water populations showed wholesale mixing of genotypes without the evident spatial autocorrelation present in leaf and soil populations.

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.

Molecular Detection and Quantification of Pythium Species: Evolving Taxonomy, New Tools, and Challenges

The genus Pythium is one of the most important groups of soilborne plant pathogens, present in almost every agricultural soil and attacking the roots of thousands of hosts, reducing crop yield and quality. Most species are generalists, necrotrophic pathogens that infect young juvenile tissue. In fact, Cook and Veseth have called Pythium the "common cold" of wheat, because of its chronic nature and ubiquitous distribution. Where Pythium spp. are the cause of seedling damping-off or emergence reduction, the causal agent can easily be identified based on symptoms and culturing. In more mature plants, however, infection by Pythium spp. is more difficult to diagnose, because of the nonspecific symptoms that could have abiotic causes such as nutrient deficiencies or be due to other root rotting pathogens. Molecular methods that can accurately identify and quantify this important group are needed for disease diagnosis and management recommendations and to better understand the epidemiology and ecology of this important group. The purpose of this article is to outline the current state-of-the-art in the detection and quantification of this important genus. In addition, we will introduce the reader to new changes in the taxonomy of this group.

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.

A universal microarray detection method for identification of multiple Phytophthora spp. using padlock probes

The genus Phytophthora consists of many species that cause important diseases in ornamental, agronomic, and forest ecosystems worldwide. Molecular methods have been developed for detection and identification of one or several species of Phytophthora in single or multiplex reactions. In this article, we describe a padlock probe (PLP)-based multiplex method of detection and identification for many Phytophthora spp. simultaneously. A generic TaqMan polymerase chain reaction assay, which detects all known Phytophthora spp., is conducted first, followed by a species-specific PLP ligation. A 96-well-based microarray platform with colorimetric readout is used to detect and identify the different Phytophthora spp. PLPs are long oligonucleotides containing target complementary sequence regions at both their 5' and 3' ends which can be ligated on the target into a circular molecule. The ligation is point mutation specific; therefore, closely related sequences can be differentiated. This circular molecule can then be detected on a microarray. We developed 23 PLPs to economically important Phytophthora spp. based upon internal transcribed spacer-1 sequence differences between individual Phytophthora spp. Tests on genomic DNA of many Phytophthora isolates and DNA from environmental samples showed the specificity and utility of PLPs for Phytophthora diagnostics.

Development of a lab-on-a-chip device for diagnosis of plant pathogens

A lab-on-a-chip system for rapid nucleic acid-based analysis was developed that can be applied for diagnosis of selected Phytophthora species as a first example for use in plant pathology. All necessary polymerase chain reaction process (PCR) and hybridization steps can be performed consecutively within a single chip consisting of two components, an inflexible and a flexible one, with integrated microchannels and microchambers. Data from the microarray is collected from a simple electrical measurement that is based on elementary silver deposition by enzymatical catalyzation. Temperatures in the PCR and in the hybridization zone are managed by two independent Peltier elements. The chip will be integrated in a compact portable system with a pump and power supply for use on site. The specificity of the lab-on-a-chip system could be demonstrated for the tested five Phytophthora species. The two Pythium species gave signals below the threshold. The results of the electrical detection of the microarray correspond to the values obtained with the control method (optical grey scale analysis).