In vivo monitoring of obligate biotrophic pathogen growth by kinetic PCR

The plant kingdom is constantly challenged by a battery of evolving pathogens. New species or races of pathogens are discovered on crops that were initially bred for disease resistance, and globalization is facilitating the movement of exotic pests. Among these pests, obligate biotrophic parasites make up some of the most damaging groups and have been particularly challenging to study. Here we demonstrate the utility of kinetic PCR (kPCR) (real-time PCR, quantitative PCR) to assess the growth of poplar rust, caused by Melampsora species, by quantification of pathogen DNA. kPCR allowed the construction of reliable growth curves from inoculation through the final stages of uredinial maturation, as well as pathogen monitoring before symptoms become visible. Growth parameters, such as latency period, generation time in logarithmic growth, and the increase in DNA mass at saturation, were compared in compatible, incompatible, and nonhost interactions. Pathogen growth was monitored in different applications dealing with plant pathology, such as host and pathogen diversity and transgenic crop improvement. Finally, the capacity of kPCR to differentiate pathogens in the same sample has broad molecular ecology applications for dynamically monitoring the growth of fungi in their environments or in mixed populations or to measure the efficacy of pest control strategies.     

Molecular detection of Puccinia horiana in Chrysanthemum x morifolium through conventional and real-time PCR

Puccinia horiana Henn. is a quarantine organism and one of the most important fungal pathogens of Chrysanthemum x morifolium cultivars grown for cut flower or potted plant production (florist's chrysanthemum) in several regions of the world. Highly specific primer pairs were identified for conventional, nested, and real-time PCR detection of P. horiana based on the specific and sensitive PCR amplification of selected regions in the internal transcribed spacers (ITS1 and ITS2) of the nuclear ribosomal DNA (rDNA). Using these different PCR versions, 10 pg, 10 fg, and 5 fg genomic DNA could be detected, respectively. When using cloned target DNA as template, the detection limits were 5000, 50, and 5 target copies, respectively. These detection limits were not affected by a background of chrysanthemum plant DNA. The DNA extraction method was optimized to maximize the recoverability of the pathogen from infected plant tissue. A CTAB extraction protocol or a selection of commercial DNA extraction methods allowed the use of 10 ng total (plant+pathogen) DNA without interference of PCR inhibitors. Due to the specificity of the primers, SYBR Green I technology enabled reliable real time PCR signal detection. However, an efficient TaqMan probe is available. The lowest proportion of infected plant material that could still be detected when mixed with healthy plant material was 0.001%. The real-time PCR assay could detect as few as eight pure P. horiana basidiospores, demonstrating the potential of the technique for aerial detection of the pathogen. The amount of P. horiana DNA in plant tissue was determined at various time points after basidiospore inoculation. Using the real-time PCR protocol, it was possible to detect the pathogen immediately after the inoculation period, even though the accumulation of pathogen DNA was most pronounced near the end of the latent period. The detection system proved to be accurate and sensitive and could help not only in pathogen diagnosis but also in pathogen monitoring and disease forecasting systems.     

Evaluation of the Siemens VERSANT® CT/GC DNA 1.0 assay (kPCR) for detection of Chlamydia trachomatis and Neisseria gonorrhoeae

The Siemens VERSANT kPCR system is an automated system which combines extraction of nucleic acids from 96 samples with subsequent real-time PCR. The VERSANT CT/GC DNA 1.0 (kPCR) assay detects Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (GC) in a multiplex real-time PCR on this system. We compared this assay with the BD ProbeTe™ ET System (PT) and the Roche Cobas Amplicor (CA). Three different sets of samples were tested in the kPCR: PT pre-treated samples, prospectively collected urine samples during routine CT/GC testing and urine samples obtained in a blinded fashion by an external lab facility. Agreement of kPCR with the comparator tests was > 0.99 for sample set I and complete agreement was observed for sample set II and III. The kPCR assay demonstrated to be an easy to use robust diagnostic platform. A few modifications to the manufacturer's instructions are recommended to intercept false positivity. We advise to retest samples with Cq values above 35 cycles at least one time and we suggest checking the amplification curves.     

Molecular Inversion Probe: A New Tool for Highly Specific Detection of Plant Pathogens

Highly specific detection methods, capable of reliably identifying plant pathogens are crucial in plant disease management strategies to reduce losses in agriculture by preventing the spread of diseases. We describe a novel molecular inversion probe (MIP) assay that can be potentially developed into a robust multiplex platform to detect and identify plant pathogens. A MIP has been designed for the plant pathogenic fungus Fusarium oxysporum f.sp. conglutinans and the proof of concept for the efficiency of this technology is provided. We demonstrate that this methodology can detect as little as 2.5 ng of pathogen DNA and is highly specific, being able to accurately differentiate Fusarium oxysporum f.sp. conglutinans from other fungal pathogens such as Botrytis cinerea and even pathogens of the same species such as Fusarium oxysporum f.sp. lycopersici. The MIP assay was able to detect the presence of the pathogen in infected Arabidopsis thaliana plants as soon as the tissues contained minimal amounts of pathogen. MIP methods are intrinsically highly multiplexable and future development of specific MIPs could lead to the establishment of a diagnostic method that could potentially screen infected plants for hundreds of pathogens in a single assay.     

Biotechnology offers revolution to fish health management

Biotechnology has many applications in fish health management. The application of monoclonal antibodies (mAbs) provides a rapid means of pathogen identification; antibodies to immunoglobulins from different fish species can be used to monitor the host response following vaccination; and mAbs also have the potential for screening broodstock for previous exposure to pathogens. Luminex technology exemplifies a novel antibody-based method that can be applied to both pathogen detection and vaccine development. Molecular technologies, such as the polymerase chain reaction (PCR), real time PCR and nucleic acid sequence-based amplification (NASBA), have enabled detection, identification and quantification of extremely low levels of aquatic pathogens, and microarray technologies offer a new dimension to multiplex screening for pathogens and host response. Recombinant DNA technology permits large-scale, low-cost vaccine production, moreover DNA vaccination, proteomics, adjuvant design and oral vaccine delivery will undoubtedly foster the development of effective fish vaccines in the future.     

Rapid Detection of Phytophthora nicotianae in Infected Tobacco Tissues and Soil Samples Based on Its Ypt1 Gene

This paper describes the development of a polymerase chain reaction (PCR) assay for the detection of Phytophthora nicotianae , the causal agent of Phytophthora blight of tobacco and other plants. The PCR primers were designed based on a Ras-related protein ( Ypt 1) gene, and 115 isolates representing 26 species of Phytophthora and 29 fungal species of plant pathogens were used to test the specificity of the primers. PCR amplification with species-specific (Pn) primers resulted in a product of 389 bp only from isolates of P. nicotianae . The detection sensitivity with Pn primers was 1 ng of genomic DNA. Using Ypt 1F/ Ypt 1R as first-round amplification primers, followed by a second round using the primer pair Pn1/Pn2, a nested PCR procedure was developed, which increased the detection sensitivity 100-fold to 10 pg. PCR with the Pn primers could also be used to detect P. nicotianae from naturally infected tobacco tissues and soil. The PCR-based methods developed here could simplify both plant disease diagnosis and pathogen monitoring as well as guide plant disease management.     

An ecological framework for understanding the roles of Epichloë endophytes on plant defenses against fungal diseases

Plants harbor a wide diversity of microorganisms in their tissues. Some of them have a long co-evolutionary history with their hosts, likely playing a pivotal role in regulating the plant interaction with other microbes such as pathogens. Some cool-season grasses are symbiotic with Epichloë fungal endophytes that grow symptomless and systemically in aboveground tissues. Among the many benefits that have been ascribed to endophytes, their role in mediating plant interactions with pathogens has been scarcely developed. Here, we explored the effects of Epichloë fungal endophytes on the interaction of host grasses with fungal pathogens. We made a meta-analysis that covered a total of 18 host grass species, 11 fungal endophyte species, and 22 fungal pathogen species. We observed endophyte-mediated negative effects on pathogens in vitro and in planta. Endophyte negative effects on pathogens were apparent not only in laboratory but also in greenhouse and field experiments. Epichloë fungal endophytes had negative effects on pathogen growth and spores' germination. On living plants, endophytes reduced both severity and incidence of the disease as well as colonization and subsequent infection of seeds. Symbiosis with endophytes showed an inhibitory effect on debilitator and killer pathogens, but not on castrators, and this effect did not differ among biotrophic or necrotrophic lifestyles. We found that this protection can be direct through the production of fungistatic compounds, the competition for a common resource, or the induction of plant defenses, and indirect associated with endophyte-generated changes in the abiotic or the biotic environment. Several mechanisms operate simultaneously and contribute differentially to the reduction of disease within grass populations.     

Beneficial endophytic microorganisms of Brassica – A review

Brassica species display enormous diversity and subsequently provide the widest assortment of products used by man from a single plant genus. Many species are important for agriculture, horticulture, in bioremediation, as medicines, soil conditioners, composting crops, and in the production of edible and industrial oils such as liquid fuels and lubricants. Many wild Brassica relatives possess a number of useful agronomic traits, including beneficial microbial endophytes that could be incorporated into breeding programs. Endophytes of Brassica, and/or their metabolites, have been demonstrated to improve and promote plant growth; increase yield; reduce disease symptoms caused by plant pathogens; reduce herbivory from insect pests; remove contaminants from soil; improve plant performance under extreme conditions of temperature and water availability; solubilise phosphate and contribute assimilable nitrogen to their hosts. Brassica napus (oilseed rape) and Brassica oleracea var. botrytis (broccoli and cauliflower) are the most economically important species of Brassica worldwide. These commercial crops are attacked by a wide range of pathogens and insect pests that are responsible for millions of dollars in lost revenue, with current control options offering little mitigation. No alternative control products are available for the Brassica industry, although it has been well documented in the literature that the use of endophytic microorganisms can offer beneficial traits to their host plants, including pest and disease resistance. The aim of this review is to describe the literature concerning beneficial microbial endophytes and their prospects to enhance or provide additional traits to their Brassica host species.     

Genetic Mechanisms of Host–Pathogen Interactions for Charcoal Rot in Soybean

Soybean is a leading agronomic crop and contributes to food and agricultural security with expanding production areas in diverse regions around the world. Although soybean is challenged by several diseases and pests and progress has been made in understanding and managing some of these pathogens and pests, charcoal rot, incited by the soil-borne fungal pathogen Macrophomina phaseolina, has received little attention. M. phaseolina has a broad host range and is capable of attacking and infecting several groups of plant species, including soybean. Charcoal rot symptoms on soybean appear more commonly during hot and dry weather conditions, and are associated with drought stress. In recent years, it has become more important to develop management strategies to control charcoal rot in soybean fields. Understanding the genetics of this pathogen as well as its interactions with plant hosts will help in developing effective control and management strategies. The biology of M. phaseolina, its genetics, and plant–fungal relationships are reviewed herein. In addition, a discussion of potential opportunities utilizing modern tools to enhance genetic resistance against charcoal rot is also presented.     

Development of a multiplex PCR assay for simultaneous detection of Theileria annulata,Babesia bovis and Anaplasma marginale in cattle

Tropical theileriosis, bovine babesiosis and anaplasmosis are tick-borne protozoan diseases that impose serious constraints on the health and productivity of domestic cattle in tropical and sub-tropical regions of the world. A common feature of these diseases is that, following recovery from primary infection, animals become persistent carriers of the pathogen and continue to play a critical role in disease epidemiology, acting as reservoirs of infection. This study describes development and evaluation of multiplex and single PCR assays for simultaneous detection of Theileria annulata, Babesia bovis and Anaplasma marginale in cattle. Following in silico screening for candidate target genes representing each of the pathogens, an optimised multiplex PCR assay was established using three primer sets, cytob1, MAR1bB2 and bovar2A, for amplification of genomic DNA of T. annulata, A. marginale and B. bovis respectively. The designed primer sets were found to be species-specific, generating amplicons of 312, 265 and 166 base pairs, respectively and were deemed suitable for the development of a multiplex assay. The sensitivity of each primer pair was evaluated using serial dilutions of parasite DNA, while specificity was confirmed by testing for amplification from DNA of different stocks of each pathogen and other Theileria, Babesia and Anaplasma species. Additionally, DNA preparations derived from field samples were used to evaluate the utility of the single and multiplex PCRs for determination of infection status. The multiplex PCR was found to detect each pathogen species with the same level of sensitivity, irrespective of whether its DNA was amplified in isolation or together with DNA representing the other pathogens. Moreover, single and multiplex PCRs were able to detect each species with equal sensitivity in serially diluted DNA representing mixtures of T. annulata, B. bovis and A. marginale, and no evidence of non-specific amplification from non-target species was observed. Validation that the multiplex PCR efficiently detects single and mixed infections from field samples was demonstrated. The developed assay represents a simple and efficient diagnostic for co-detection of tropical theileriosis, bovine babesiosis and anaplasmosis, and may be a valuable tool for epidemiological studies aimed at assessing the burden of multiple infection with tick-borne pathogens and improving control of the associated diseases in endemic regions.     

The Impact of Plant Enemies Shows a Phylogenetic Signal

The host ranges of plant pathogens and herbivores are phylogenetically constrained, so that closely related plant species are more likely to share pests and pathogens. Here we conducted a reanalysis of data from published experimental studies to test whether the severity of host-enemy interactions follows a similar phylogenetic signal. The impact of herbivores and pathogens on their host plants declined steadily with phylogenetic distance from the most severely affected focal hosts. The steepness of this phylogenetic signal was similar to that previously measured for binary-response host ranges. Enemy behavior and development showed similar, but weaker phylogenetic signal, with oviposition and growth rates declining with evolutionary distance from optimal hosts. Phylogenetic distance is an informative surrogate for estimating the likely impacts of a pest or pathogen on potential plant hosts, and may be particularly useful in early assessing risk from emergent plant pests, where critical decisions must be made with incomplete host records.     

Waterborne Pathogen Detection by Use of Oligonucleotide-Based Microarrays

A small-oligonucleotide microarray prototype was designed with probes specific for the universal 16S rRNA and cpn60 genes of several pathogens that are usually encountered in wastewaters. In addition to these two targets, wecE-specific oligonucleotide probes were included in the microarray to enhance its discriminating power within the Enterobacteriaceae family. Universal PCR primers were used to amplify variable regions of 16S rRNA, cpn60, and wecE genes directly in Escherichia coli and Salmonella enterica serovar Typhimurium genomic DNA mixtures (binary); E. coli, S. enterica serovar Typhimurium, and Yersinia enterocolitica genomic DNA mixtures (ternary); or wastewater total DNA. Amplified products were fluorescently labeled and hybridized on the prototype chip. The detection sensitivity for S. enterica serovar Typhimurium was estimated to be on the order of 0.1% (10⁴ S. enterica genomes) of the total DNA for the combination of PCR followed by microarray hybridization. The sensitivity of the prototype could be increased by hybridizing amplicons generated by PCR targeting genes specific for a bacterial subgroup, such as wecE genes, instead of universal taxonomic amplicons. However, there was evidence of PCR bias affecting the detection limits of a given pathogen as increasing amounts of a different pathogen were spiked into the test samples. These results demonstrate the feasibility of using DNA microarrays in the detection of waterborne pathogens within mixed populations but also raise the problem of PCR bias in such experiments.     

The role of strigolactones and ethylene in disease caused by Pythium irregulare

Plant hormones play key roles in defence against pathogen attack. Recent work has begun to extend this role to encompass not just the traditional disease/stress hormones, such as ethylene, but also growth‐promoting hormones. Strigolactones (SLs) are the most recently defined group of plant hormones with important roles in plant–microbe interactions, as well as aspects of plant growth and development, although the knowledge of their role in plant–pathogen interactions is extremely limited. The oomycete Pythium irregulare is a poorly controlled pathogen of many crops. Previous work has indicated an important role for ethylene in defence against this oomycete. We examined the role of ethylene and SLs in response to this pathogen in pea (Pisum sativum L.) at the molecular and whole‐plant levels using a set of well‐characterized hormone mutants, including an ethylene‐insensitive ein2 mutant and SL‐deficient and insensitive mutants. We identified a key role for ethylene signalling in specific cell types that reduces pathogen invasion, extending the work carried out in other species. However, we found no evidence that SL biosynthesis or response influences the interaction of pea with P. irregulare or that synthetic SL influences the growth or hyphal branching of the oomycete in vitro. Future work should seek to extend our understanding of the role of SLs in other plant interactions, including with other fungal, bacterial and viral pathogens, nematodes and insect pests.     

Molecular mechanisms underlying host-induced gene silencing

Host-induced gene silencing (HIGS) refers to the silencing of genes in pathogens and pests by expressing homologous double-stranded RNAs (dsRNA) or artificial microRNAs (amiRNAs) in the host plant. The discovery of such trans-kingdom RNA silencing has enabled the development of RNA interference-based approaches for controlling diverse crop pathogens and pests. Although HIGS is a promising strategy, the mechanisms by which these regulatory RNAs translocate from plants to pathogens, and how they induce gene silencing in pathogens, are poorly understood. This lack of understanding has led to large variability in the efficacy of various HIGS treatments. This variability is likely due to multiple factors, such as the ability of the target pathogen or pest to take up and/or process RNA from the host, the specific genes and target sequences selected in the pathogen or pest for silencing, and where, when, and how the dsRNAs or amiRNAs are produced and translocated. In this review, we summarize what is currently known about the molecular mechanisms underlying HIGS, identify key unanswered questions, and explore strategies for improving the efficacy and reproducibility of HIGS treatments in the control of crop diseases.

A review of what is known and unknown about the molecular mechanisms underlying the silencing of pathogen and pest genes via the expression of complementary RNAs in the host plant.     

Population History and Pathways of Spread of the Plant Pathogen Phytophthora plurivora

Human activity has been shown to considerably affect the spread of dangerous pests and pathogens worldwide. Therefore, strict regulations of international trade exist for particularly harmful pathogenic organisms. Phytophthora plurivora, which is not subject to regulations, is a plant pathogen frequently found on a broad range of host species, both in natural and artificial environments. It is supposed to be native to Europe while resident populations are also present in the US. We characterized a hierarchical sample of isolates from Europe and the US and conducted coalescent-, migration, and population genetic analysis of sequence and microsatellite data, to determine the pathways of spread and the demographic history of this pathogen. We found P. plurivora populations to be moderately diverse but not geographically structured. High levels of gene flow were observed within Europe and unidirectional from Europe to the US. Coalescent analyses revealed a signal of a recent expansion of the global P. plurivora population. Our study shows that P. plurivora has most likely been spread around the world by nursery trade of diseased plant material. In particular, P. plurivora was introduced into the US from Europe. International trade has allowed the pathogen to colonize new environments and/or hosts, resulting in population growth.     

Quantifying the relationship between disease severity and the amount of Aphanomyces euteiches detected in roots of alfalfa and pea with a real-time PCR assay

A real-time PCR assay was used to quantify the relationship in alfalfa and pea between disease severity and the amount of Aphanomyces euteiches detected in roots. The study included isolates of race 1 and race 2 of the alfalfa pathovar of A. euteiches and an isolate obtained from diseased pea. Spearman rank correlations between pathogen DNA content and disease severity index (DSI) ratings were positive ( ? 0.57) and significant (P  0.0007) for individual alfalfa plants, bulked alfalfa plant samples, and individual pea plants. In all experiments, significantly more pathogen was detected in susceptible populations than in resistant populations. The results clearly demonstrate that resistance to A. euteiches in both alfalfa and pea is characterized by a reduction in pathogen colonization relative to levels observed for susceptible reactions. The assay was very specific for A. euteiches, producing very linear assays with DNA extracted from pathogen isolates obtained from alfalfa, pea, and bean. Possible applications of the assay in conjunction with other real-time PCR assays specific to other legume pathogens are discussed in relation to simultaneous disease screening for multiple plant pathogens and the study of microbial population dynamics in mixed plant infections.     

The rhizobacterium Arthrobacter agilis produces dimethylhexadecylamine, a compound that inhibits growth of phytopathogenic fungi in vitro

Plant diseases caused by fungal pathogens such as Botrytis cinerea and the oomycete Phytophthora cinnamomi affect agricultural production worldwide. Control of these pests can be done by the use of fungicides such as captan, which may have deleterious effects on human health. This study demonstrates that the rhizobacterium Arthrobacter agilis UMCV2 produces volatile organic compounds that inhibit the growth of B. cinerea in vitro. A single compound from the volatile blends, namely dimethylhexadecylamine (DMHDA), could inhibit the growth of both B. cinerea and P. cinnamomi when supplied to the growth medium in low concentrations. DMHDA also inhibited the growth of beneficial fungi Trichoderma virens and Trichoderma atroviride but at much higher concentrations. DMHDA-related aminolipids containing 4, 8, 10, 12, and 14 carbons in the alkyl chain were tested for their inhibitory effect on the growth of the pathogens. The results show that the most active compound from those tested was dimethyldodecylamine. This effect correlates with a decrease in the number of membrane lipids present in the mycelium of the pathogen including eicosanoic acid, (Z)-9-hexadecenoic acid, methyl ester, and (Z)-9-octadecenoic acid, methyl ester. Strawberry leaflets treated with DMHDA were not injured by the compound. These data indicate that DMHDA and related compounds, which can be produced by microorganisms may effectively inhibit the proliferation of certain plant pathogens.     

Minor effects of two elicitors of insect and pathogen resistance on volatile emissions and parasitism of Spodoptera frugiperda in Mexican maize fields

Synthetic elicitors can be used to induce resistance in plants against pathogens and arthropod herbivores. Such compounds may also change the emission of herbivore-induced plant volatiles, which serve as important cues for parasitic wasps to locate their hosts. Therefore, the use of elicitors in the field may affect biological control of insect pests. To test this, we treated maize seedlings growing in a subtropical field in Mexico with methyl jasmonate (MeJA), an elicitor of defense responses against many insects, and benzo-(1,2,3)-thiadiazole-7-carbothioic acid S-methyl ester (BTH), an elicitor of resistance against certain pathogens. Volatile emission, herbivore infestation, pathogen infection, and plant performance (growth and grain yield) of treated and untreated maize plants were measured. Application of BTH slightly reduced volatile emission in maize, while MeJA increased the emission compared to control treatments. Despite the apparent changes in volatile emissions, the elicitor application did not consistently affect infestation by Spodoptera frugiperda larvae, the main insect pest found on the maize seedlings, and had only marginal effects on parasitism rates. Similarly, there were no treatment effects on infestation by other herbivores and pathogens. Results for the six replications that stretched over one summer and one winter season were highly variable, with parasitism rates and the species composition of the parasitoids differing significantly between seasons. This variability, as well as the severe biotic and abiotic stresses on young seedlings might explain why we measured only slight effects of elicitor application on pest incidence and biological control in this specific field study. Indeed, an additional field experiment under milder and more standardized conditions revealed that BTH induced significant resistance against Bipolaris maydis, a major pathogen in the experimental maize fields. Similar affects can be expected for herbivory and parasitism rates.