Plant pathogen forensics: capabilities, needs, and recommendations

Population-Sequencing as a Biomarker for Sample Characterization

Sequencing is accepted as the “gold” standard for genetic analysis and continues to be used as a validation and reference tool. The idea of using sequence analysis directly for sample characterization has been met with skepticism. However, herein, utility of direct use of sequencing to identify multiple genomes present in samples is presented and reviewed. All samples and “pure” isolates are populations of genomes. Population-Sequencing is the use of probabilistic matching tools in combination with large volumes of sequence information to identify genomes present, based on DNA analysis across entire genomes to determine genome assignments, to calculate confidence scores of major and minor genome content. Accurate genome identification from mixtures without culture purification steps can achieve phylogenetic classification by direct analysis of millions of DNA fragments. Genome sequencing data of mixtures can function as biomarkers for use to interrogate genetic content of samples and to establish a sample profile, inclusive of major and minor genome components, drill down to identify rare SNP and mutation events, compare relatedness of genetic content between samples, profile-to-profile, and provide a probabilistic or statistical scoring confidence for sample characterization and attribution. The application of Population-Sequencing will facilitate sample characterization and genome identification strategies.

A Support Vector Machine based method to distinguish proteobacterial proteins from eukaryotic plant proteins

Background

Members of the phylum Proteobacteria are most prominent among bacteria causing plant diseases that result in a diminution of the quantity and quality of food produced by agriculture. To ameliorate these losses, there is a need to identify infections in early stages. Recent developments in next generation nucleic acid sequencing and mass spectrometry open the door to screening plants by the sequences of their macromolecules. Such an approach requires the ability to recognize the organismal origin of unknown DNA or peptide fragments. There are many ways to approach this problem but none have emerged as the best protocol. Here we attempt a systematic way to determine organismal origins of peptides by using a machine learning algorithm. The algorithm that we implement is a Support Vector Machine (SVM).

Result

The amino acid compositions of proteobacterial proteins were found to be different from those of plant proteins. We developed an SVM model based on amino acid and dipeptide compositions to distinguish between a proteobacterial protein and a plant protein. The amino acid composition (AAC) based SVM model had an accuracy of 92.44% with 0.85 Matthews correlation coefficient (MCC) while the dipeptide composition (DC) based SVM model had a maximum accuracy of 94.67% and 0.89 MCC. We also developed SVM models based on a hybrid approach (AAC and DC), which gave a maximum accuracy 94.86% and a 0.90 MCC. The models were tested on unseen or untrained datasets to assess their validity.

Conclusion

The results indicate that the SVM based on the AAC and DC hybrid approach can be used to distinguish proteobacterial from plant protein sequences.

Antifungal activity of plant extracts against Colletotrichum lagenarium, the causal agent of anthracnose in cucumber

BACKGROUND

Colletotrichum lagenarium is an important plant-pathogenic fungus that causes anthracnose of cucumber, a disease that is widespread under both greenhouse and field cultivation. To find a promising method for the control of this disease, extracts of eight plants from China were screened in the study presented here.

RESULTS

The results showed that the extract of Cinnamomum camphora (L.) Presl had significantly greater inhibitory activity against C. lagenarium than the other seven plant extracts tested in vitro. At 5 days after inoculation in a potted seedling experiment, C. camphora extract demonstrated 95% control of C. lagenarium at a concentration of 16 mg mL⁻¹, and the MIC₅₀ was 2.596 mg mL⁻¹. Microscopic observation showed that this extract had a significant impact on the morphology of the fungus, leading to shorter hyphae that were more branched; this observation was associated with the inhibition of mycelial growth. Stability assays revealed that the extract was relatively stable at 80 °C, under acidic conditions and when exposed to light and short periods of UV radiation.

CONCLUSION

These results demonstrated that the extract from C. camphora could be used as a potent phytochemical fungicide.

Composition and Antipathogenic Activities of the Twig Essential Oil of Chamaecyparis formosensis from Taiwan

In this study, antipathogenic activities of the twig essential oil and its constituents from Chamaecyparis formosensis Matsum were evaluated in vitro against six plant pathogenic fungi. The essential oil from the fresh twigs was isolated using hydrodistillation in a Clevenger-type apparatus, and characterized by GC-FID and GC-MS. Twenty-five compounds were identified, representing 98.9% of the oil. The main components were β-eudesmol (25.1%), τ-muurolol (21.6%), elemol (15.0%), totarol (14.9%), and α-cadinol (12.4%). The twig oil (500 μg/mL) showed growth inhibitory activity against the phytopathogenic fungi, Fusarium oxysporum, Pestalotiopsis funereal, and Ganoderma austral, with antifungal indices of 92.7%, 71.1%, and 87.7%, respectively. In addition, the oil suppressed totally the growth of Rhizoctonia solani, Colletotrichum gloeosporioides, and Fusarium solani. In order to ascertain the source compounds of these antipathogenic activities, the main components were individually evaluated. τ-Muurolol and α-cadinol exhibited excellent activity against F. oxysporum, R. solani, C. gloeosporioides, and F. solani, with IC50< 50 μg/mL. These compounds also efficiently inhibited the mycelial growths of P. funereal and G. austral. Thus, α-cadinol and τ-muurolol could be considered as potential natural fungicides for controlling fungal pathogens and worth.

Method: a single nucleotide polymorphism genotyping method for Wheat streak mosaic virus

BACKGROUND

The September 11, 2001 attacks on the World Trade Center and the Pentagon increased the concern about the potential for terrorist attacks on many vulnerable sectors of the US, including agriculture. The concentrated nature of crops, easily obtainable biological agents, and highly detrimental impacts make agroterrorism a potential threat. Although procedures for an effective criminal investigation and attribution following such an attack are available, important enhancements are still needed, one of which is the capability for fine discrimination among pathogen strains. The purpose of this study was to develop a molecular typing assay for use in a forensic investigation, using Wheat streak mosaic virus (WSMV) as a model plant virus.

METHOD

This genotyping technique utilizes single base primer extension to generate a genetic fingerprint. Fifteen single nucleotide polymorphisms (SNPs) within the coat protein and helper component-protease genes were selected as the genetic markers for this assay. Assay optimization and sensitivity testing was conducted using synthetic targets. WSMV strains and field isolates were collected from regions around the world and used to evaluate the assay for discrimination. The assay specificity was tested against a panel of near-neighbors consisting of genetic and environmental near-neighbors.

RESULT

Each WSMV strain or field isolate tested produced a unique SNP fingerprint, with the exception of three isolates collected within the same geographic location that produced indistinguishable fingerprints. The results were consistent among replicates, demonstrating the reproducibility of the assay. No SNP fingerprints were generated from organisms included in the near-neighbor panel, suggesting the assay is specific for WSMV. Using synthetic targets, a complete profile could be generated from as low as 7.15 fmoles of cDNA.

CONCLUSION

The molecular typing method presented is one tool that could be incorporated into the forensic science tool box after a thorough validation study. This method incorporates molecular biology techniques that are already well established in research and diagnostic laboratories, allowing for an easy introduction of this method into existing laboratories.

KEYWORDS

single nucleotide polymorphisms, genotyping, plant pathology, viruses, microbial forensics, Single base primer extension, SNaPshot Multiplex Kit.

New grower-friendly methods for plant pathogen monitoring

Accurate plant disease diagnoses and rapid detection and identification of plant pathogens are of utmost importance for controlling plant diseases and mitigating the economic losses they incur. Technological advances have increasingly simplified the tools available for the identification of pathogens to the extent that, in some cases, this can be done directly by growers and producers themselves. Commercially available immunoprinting kits and lateral flow devices (LFDs) for detection of selected plant pathogens are among the first tools of what can be considered grower-friendly pathogen monitoring methods. Research efforts, spurned on by point-of-care needs in the medical field, are paving the way for the further development of on-the-spot diagnostics and multiplex technologies in plant pathology. Grower-friendly methods need to be practical, robust, readily available, and cost-effective. Such methods are not restricted to on-the-spot testing but extend to laboratory services, which are sometimes more practicable for growers, extension agents, regulators, and other users of diagnostic tests.

The Microbe: The Basics of Structure, Morphology, and Physiology as They Relate to Microbial Characterization and Attribution

This chapter is meant to (1) review classical methods used to characterize and classify microbes and (2) introduce new molecular methods used in microbial characterization. The fundamental composition of microbes is discussed as well as their importance in classification of microbes into genus and species. Classical microbiological methods in general seek to define the common features of specific bacterial groups as a means of classification and identification of microbes. Thus, the focus was to describe the common features which discriminated closely related groups of organisms. In contrast, the newer molecular methods often seek to expand the classification of microbes not only as a means to organize microbial phylogeny but also to differentiate signatures between microbes identified within a species in greater detail. Molecular biology tools are used both as an adjunct to established methods and as replacement for classical methods for detection, discrimination, or identification of bacterial and viral species.

Use of media and public-domain Internet sources for detection and assessment of plant health threats

Event-based biosurveillance is a recognized approach to early warning and situational awareness of emerging health threats. In this study, we build upon previous human and animal health work to develop a new approach to plant pest and pathogen surveillance. We show that monitoring public domain electronic media for indications and warning of epidemics and associated social disruption can provide information about the emergence and progression of plant pest infestation or disease outbreak. The approach is illustrated using a case study, which describes a plant pest and pathogen epidemic in China and Vietnam from February 2006 to December 2007, and the role of ducks in contributing to zoonotic virus spread in birds and humans. This approach could be used as a complementary method to traditional plant pest and pathogen surveillance to aid global and national plant protection officials and political leaders in early detection and timely response to significant biological threats to plant health, economic vitality, and social stability. This study documents the inter-relatedness of health in human, animal, and plant populations and emphasizes the importance of plant health surveillance.

Phytotoxic and antifungal metabolites from Curvularia sp. FH01 isolated from the gut of Atractomorpha sinensis

Two main phytotoxic and antifungal phthalic acid butyl isobutyl ester (1) and radicinin (2) were isolated from the culture of Curvularia sp. FH01, a fungus residing in the Atractomorpha sinensis gut. The structures of isolated metabolites were established on the basis of spectral analysis. Metabolites 1 and 2 exhibited significant phytotoxic activity against the radical growth of Echinochloa crusgalli with their IC(50) values of 61.9 and 5.9 μg/mL, respectively, which were comparable to that 2,4-dichlorophenoxyacetic acid (2.0 μg/mL) used as a positive control. The antifungal test results showed that compound 2 possessed strong antifungal activity against Magnaporthe grisea (IC(50)=16.3 μg/mL) and Valsa mali (IC(50)=18.2 μg/mL). The findings of the present study suggest that bioactive properties of the fungus FH01 can be attributed to its major components, phthalic acid butyl isobutyl ester and radicinin, and both agents have a potential to be used as herbicide and fungicide.

Xylella fastidiosa: a model for analyzing agricultural biosecurity

The threat to national security posed by the hostile release of human pathogens has been extensively documented. However, conclusions regarding the menace that plant pests and pathogens pose to the national economy and food supply are less developed. Here we present a risk analysis for the arrival and spread of foreign plant pathogens into the U.S. agricultural system. Xylella fastidiosa Citrus Variegated Chlorosis strain, an exotic plant pathogenic bacterium listed as a regulated biological agent under the Agricultural Bioterrorism Protection Act of 2002, serves as a model to evaluate the threat that plant diseases pose to crops and agriculture-dependent industries. We assess the nation's capacity to detect, contain, and manage newly introduced plant pathogens, exposing areas that need improvement and limitations of the system. This analysis provides a framework for understanding the risk that exotic plant diseases pose to U.S. agricultural biosecurity and a reference to continue preparing for the possible arrival of these threats.

Antifungal activity of the essential oil of Illicium verum fruit and its main component trans-anethole

In order to identify natural products for plant disease control, the essential oil of star anise (Illicium verum Hook. f.) fruit was investigated for its antifungal activity on plant pathogenic fungi. The fruit essential oil obtained by hydro-distillation was analyzed for its chemical composition by gas chromatography (GC) and gas chromatography-mass spectrometry (GC-MS). trans-Anethole (89.5%), 2-(1-cyclopentenyl)-furan (0.9%) and cis-anethole (0.7%) were found to be the main components among 22 identified compounds, which accounted for 94.6% of the total oil. The antifungal activity of the oil and its main component trans-anethole against plant pathogenic fungi were determined. Both the essential oil and trans-anethole exhibited strong inhibitory effect against all test fungi indicating that most of the observed antifungal properties was due to the presence of trans-anethole in the oil, which could be developed as natural fungicides for plant disease control in fruit and vegetable preservation.

Chemical compositions, antifungal and antioxidant activities of essential oil and various extracts of Melodorum fruticosum L. flowers

This research presents the chemical composition antifungal and antioxidant activities of essential oils and various extracts from Melodorum fruticosum flowers. The essential oil composition of M. fruticosum flowers were investigated by GC-MS with 88 identified volatile constituents. Phenyl butanone, linalool, benzyl alcohol, alpha-cadinol, globulol and viridiflorol were found to be the major components, respectively. The dichloromethane extract played a major role as a remarkable fungicide according to their inhibition action against all tested pathogens followed by hexane extract, essential oil and methanol extract, respectively, along with their respective MIC values ranging from 125 to 1000 microg/ml. The dichloromethane extracts were also evaluated to be superior to all extracts tested with an IC(50) value of 87.6 microg/ml whereas other extracts showed their IC(50) values ranging from 100.13 to 194.50 microg/ml.

Population genetic analysis infers migration pathways of Phytophthora ramorum in US nurseries

Recently introduced, exotic plant pathogens may exhibit low genetic diversity and be limited to clonal reproduction. However, rapidly mutating molecular markers such as microsatellites can reveal genetic variation within these populations and be used to model putative migration patterns. Phytophthora ramorum is the exotic pathogen, discovered in the late 1990s, that is responsible for sudden oak death in California forests and ramorum blight of common ornamentals. The nursery trade has moved this pathogen from source populations on the West Coast to locations across the United States, thus risking introduction to other native forests. We examined the genetic diversity of P. ramorum in United States nurseries by microsatellite genotyping 279 isolates collected from 19 states between 2004 and 2007. Of the three known P. ramorum clonal lineages, the most common and genetically diverse lineage in the sample was NA1. Two eastward migration pathways were revealed in the clustering of NA1 isolates into two groups, one containing isolates from Connecticut, Oregon, and Washington and the other isolates from California and the remaining states. This finding is consistent with trace forward analyses conducted by the US Department of Agriculture's Animal and Plant Health Inspection Service. At the same time, genetic diversities in several states equaled those observed in California, Oregon, and Washington and two-thirds of multilocus genotypes exhibited limited geographic distributions, indicating that mutation was common during or subsequent to migration. Together, these data suggest that migration, rapid mutation, and genetic drift all play a role in structuring the genetic diversity of P. ramorum in US nurseries. This work demonstrates that fast-evolving genetic markers can be used to examine the evolutionary processes acting on recently introduced pathogens and to infer their putative migration patterns, thus showing promise for the application of forensics to plant pathogens.

Antifungal activity of nettle (Urtica dioica L.), colocynth (Citrullus colocynthis L. Schrad), oleander (Nerium oleander L.) and konar (Ziziphus spina-christi L.) extracts on plants pathogenic fungi

Anti-mycotic activity of the ethanol extracts from Nettle (Urtica dioica L.), Colocynth (Citrullus colocynthis L. Schrad), Konar (Ziziphus spina-christi L.) and Oleander (Nerium oleander L.) floral parts were screened in vitro against four important plant pathogenic fungi viz.; Alternaria alternate, Fusarium oxysporum, Fusarium solani and Rizoctonia solani using agar dilution bioassay. Extracts showed antifungal activity against all the tested fungi. Among the plants, Nettle and Colocynth were the most effective against A. alternate and R. solani while Oleander possesses the best inhibition on F. oxysporum and F. solani. Konar was the most effective extract by reducing the growth of Rizoctonia solani than other fungi. These results showed that extracts could be considered suitable alternatives to chemical additives for the control of fungal diseases in plants.

Antifungal, phytotoxic and insecticidal properties of essential oil isolated from Turkish Origanum acutidens and its three components, carvacrol, thymol and p-cymene

The chemical composition of essential oil isolated by hydrodistillation from the aerial parts of Origanum acutidens was analyzed by GC-MS. Carvacrol (87.0%), p-cymene (2.0%), linalool acetate (1.7%), borneol (1.6%) and beta-caryophyllene (1.3%) were found to be as main constituents. Antifungal, phytotoxic and insecticidal activities of the oil and its aromatic monoterpene constituents, carvacrol, p-cymene and thymol were also determined. The antifungal assays showed that O. acutidens oil, carvacrol and thymol completely inhibited mycelial growth of 17 phytopathogenic fungi and their antifungal effects were higher than commercial fungicide, benomyl. However, p-cymene possessed lower antifungal activity. The oil, carvacrol and thymol completely inhibited the seed germination and seedling growth of Amaranthus retroflexus, Chenopodium album and Rumex crispus and also showed a potent phytotoxic effect against these plants. However, p-cymene did not show any phytotoxic effect. Furthermore, O. acutidens oil showed 68.3% and 36.7% mortality against Sitophilus granarius and Tribolium confusum adults, respectively. The findings of the present study suggest that antifungal and herbicidal properties of the oil can be attributed to its major component, carvacrol, and these agents have a potential to be used as fungicide, herbicide as well as insecticide.

Plant-pathogenic bacteria as biological weapons - real threats?

At present, much attention is being given to the potential of plant pathogens, including plant-pathogenic bacteria, as biological weapons/bioterror weapons. These two terms are sometimes used interchangeably and there is need for care in their application. It has been claimed that clandestine introduction of certain plant-pathogenic bacteria could cause such crop losses as to impact so significantly on a national economy and thus constitute a threat to national security. As a separate outcome, it is suggested that they could cause serious public alarm, perhaps constituting a source of terror. Legislation is now in place to regulate selected plant-pathogenic bacteria as potential weapons. However, we consider it highly doubtful that any plant-pathogenic bacterium has the requisite capabilities to justify such a classification. Even if they were so capable, the differentiation of pathogens into a special category with regulations that are even more restrictive than those currently applied in quarantine legislation of most jurisdictions offers no obvious benefit. Moreover, we believe that such regulations are disadvantageous insofar as they limit research on precisely those pathogens most in need of study. Whereas some human and animal pathogens may have potential as biological or bioterror weapons, we conclude that it is unlikely that any plant-pathogenic bacterium realistically falls into this category.

Economic aspects of agricultural and food biosecurity

Concerns about biosecurity in the food system raise a variety of issues about how the system is presently organized, why it might be vulnerable, what we could reasonably do to better secure it, and the costs of doing so. Emphasizing the role of incentives in efficient resource allocation, this article considers economic dimensions of three aspects of the general problem. One is the global problem, or the way biosecurity measures can affect how countries relate to each other and the global consequences that result. Another is how to best manage the immediate aftermath of a realized threat in order to minimize damage. The third is how to seek to prevent realization of the threat. Some policy alternatives are presented.

Genetic diversity of citrus bacterial canker pathogens preserved in herbarium specimens

Citrus bacterial canker (CBC) caused by Xanthomonas axonopodis pv. citri (Xac) was first documented in India and Java in the mid 19th century. Since that time, the known distribution of the disease has steadily increased. Concurrent with the dispersion of the pathogen, the diversity of described strains continues to increase, with novel strains appearing in Saudi Arabia, Iran, and Florida in the last decade. Herbarium specimens of infected plants provide an historical record documenting both the geographic distribution and genetic diversity of the pathogen in the past. However, no method was available to assess the genetic diversity within these herbarium samples. We have developed a method, insertion event scanning (IES), and applied the method to characterize the diversity present within CBC populations documented as herbarium specimens over the past century. IES is based on the specific amplification of junction fragments that define insertion events. The potential for IES in current forensic applications is demonstrated by finding an exact match of pathogen genotypes preserved in herbarium specimens from Japan and Florida, demonstrating the source of the original outbreak of citrus canker in Florida in 1911. IES is a very sensitive technique for differentiating bacterial strains and can be applied to any of the several hundred bacteria for which full genomic sequence data are available.

Resistance to pathogens and host developmental stage: a multifaceted relationship within the plant kingdom

The induction of resistance to disease during plant development is widespread in the plant kingdom. Resistance appears at different stages of host development, varies with plant age or tissue maturity, may be specific or broad-spectrum and is driven by diverse mechanisms, depending on plantpathogen interactions. Studies of these forms of resistance may help us to evaluate more exhaustively the plethora of levels of regulation during development, the variability of the defense potential of developing hosts and may have practical applications, making it possible to reduce pesticide applications. Here, we review the various types of developmental resistance in plants and current knowledge of the molecular and cellular processes involved in their expression. We discuss the implications of these studies, which provide new knowledge from the molecular to the agrosystem level.