Plant pathogen forensics: capabilities, needs, and recommendations

The activity of leaf extracts, fractions, and isolated compounds from Ptaeroxylon obliquum against nine phytopathogenic fungi and the nematode Meloidogyne incognita

Phytopathogenic fungi and nematodes cause great losses in economically important crops and food production especially in developing countries. To minimize the use of fungicides and nematicides, researchers have concentrated on the use of natural products for crop disease prevention or control. The aim of the study was to investigate the antifungal activity of Ptaeroxylon obliquum leaf extracts, fractions, and isolated compounds (obliquumol and a mixture of lupeol and β-amyrin) and nematocidal activity of fractions (hexane, chloroform and 30% water in methanol and the isolated compounds) on Meloidogyne incognita. Nine phytopathogenic fungi (Aspergillus niger, A. parasiticus, Colletotrichum gloeosporioides, Fusarium oxysporum, Penicillium digitatum, P. expansum, P. italicum, P. janthinellum, and Rhizoctonia solani) were used for testing and nematocidal activity was determined on motility of plant parasitic nematode Meloidogyne incognita race 2 juveniles. Serial microdilution test was utilized to determine the minimum inhibitory concentration (MIC) of each sample against the fungus. Motility tests was done on the second-stage juveniles (J2s) of M. incognita. The most susceptible phytopathogenic fungal species to the acetone crude leaf extracts were A. niger, C. gloeosporioides and P. digitatum with MIC of 80 μg/ml which is considered pharmacological significant. Rhizoctonia solani was the most susceptible fungus against obliquumol and, lupeol and β-amyrin mixture with MIC values of 8 μg/ml and 16 μg/ml respectively. Lupeol & β-amyrin mixture had good activity on juvenile motility at high concentrations used which was significantly high (p ≤ 0.05) after 24 h, further incubation resulted in temporary paralysis at lower concentrations. Fractions and obliquumol showed good activity after 48 h, stable paralysis was observed up to 72 h. The extracts and isolated compounds may be useful as fungicides if the in vitro results can be confirmed under field conditions at levels not toxic to beneficial soil organisms.

Lipid mediated plant immunity in susceptible and tolerant soybean cultivars in response to Phytophthora sojae colonization and infection

BACKGROUND

Soybean is one of the most cultivated crops globally and a staple food for much of the world's population. The annual global crop losses due to infection by Phytophthora sojae is currently estimated at $20B USD, yet we have limited understanding of the role of lipid mediators in the adaptative strategies used by the host plant to limit infection. Since root is the initial site of this infection, we examined the infection process in soybean root infected with Phytophthora sojae using scanning electron microscopy to observe the changes in root morphology and a multi-modal lipidomics approach to investigate how soybean cultivars remodel their lipid mediators to successfully limit infection by Phytophthora sojae.

RESULTS

The results reveal the presence of elevated biogenic crystals and more severe damaged cells in the root morphology of the infected susceptible cultivar compared to the infected tolerant cultivars. Furthermore, induced accumulation of stigmasterol was observed in the susceptible cultivar whereas, induced accumulation of phospholipids and glycerolipids occurred in tolerant cultivar.

CONCLUSION

The altered lipidome reported in this study suggest diacylglycerol and phosphatidic acid mediated lipid signalling impacting phytosterol anabolism appears to be a strategy used by tolerant soybean cultivars to successfully limit infection and colonization by Phytophthora sojae.

Chemical Composition of Essential Oils from Eight Tunisian Eucalyptus Species and Their Antifungal and Herbicidal Activities

Eucalyptus species are known to produce metabolites such as essential oils (EOs) that play an important role in the control of weeds, pests and phytopathogenic fungi. The aims of this study were as follows: (i) to determine the chemical composition of the EOs derived from eight Eucalyptus species growing in Tunisia, and (ii) to study their possible antifungal and herbicidal activities. EOs were obtained by hydrodistillation from the dried leaves of eight Eucalyptus species, namely, E. angulosa, E. cladocalyx, E. diversicolor, E. microcoryx, E. ovata, E. resinifera, E. saligna and E. sargentii, and the determination of their composition was achieved by GC and GC-MS. The EOs' antifungal activities were tested against four Fusarium strains, and the EOs' herbicidal properties were evaluated on the germination and seedling growth of three annual weeds (Trifolium campestre, Lolium rigidum and Sinapis arvensis) and three cultivated crop species (Lepidium sativum, Raphanus sativus and Triticum durum). The EO yields ranged between 0.12 and 1.32%. The most abundant components found were eucalyptol, α-pinene, p-cymene, trans-pinocarveol, α-terpineol and globulol. All EOs showed significant antifungal activity against the four phytopathogenic Fusarium strains. E. cladocalyx EO exhibited the highest level of antifungal activity, and the greatest inhibition of seed germination was obtained even at lowest concentrations used. These findings suggested that E. resinifera, E. ovata and E. cladocalyx EOs could have applications in agriculture as possible biopesticides, as Fusarium antagonists and as bioherbicides.

Management of mung bean leaf spot disease caused by Phoma herbarum through Penicillium janczewskii metabolites mediated by MAPK signaling cascade

Vigna radiata L., an imperative legume crop of Pakistan, faces hordes of damage due to fungi; infecting host tissues by the appressorium. The use of natural compounds is an innovative concern to manage mung-bean fungal diseases. The bioactive secondary metabolites of Penicillium species are well documented for their strong fungi-static ability against many pathogens. Presently, one-month-old aqueous culture filtrates of Penicillium janczewskii, P. digitatum, P. verrucosum, P. crustosum, and P. oxalicum were evaluated to check the antagonistic effect of different dilutions (0, 10, 20, … and 60%). There was a significant reduction of around 7-38%, 46-57%, 46-58%, 27-68%, and 21-51% in Phoma herbarum dry biomass production due to P. janczewskii, P. digitatum, P. verrucosum, P. crustosum, and P. oxalicum, respectively. Inhibition constants determined by a regression equation demonstrated the most significant inhibition by P. janczewskii. Finally, using real-time reverse transcription PCR (qPCR) the effect of P. Janczewskii metabolites was determined on the transcript level of StSTE12 gene involved in the development and penetration of appressorium. The expression pattern of the StSTE12 gene was determined by percent Knockdown (%KD) expression that was found to be decreased i.e. 51.47, 43.22, 40.67, 38.01, 35.97, and 33.41% for P. herbarum with an increase in metabolites concentrations viz., 10, 20, 30, 40, 50 and 60% metabolites, respectively. In silico studies were conducted to analyze the role of Ste12 a transcriptional factor in the MAPK signaling pathway. The present study concludes a strong fungicidal potential of Penicillium species against P. herbarum. Further studies to isolate the effective fungicidal constituents of Penicillium species through GCMS analysis and determination of their role in signaling pathways are requisite.

Forensic botany: who?, how?, where?, when?

Plants are a good source of biological forensic evidence; this is due to their ubiquity, their ability to collect reference material, and their sensitivity to environmental changes. However, in many countries, botanical evidence is recognised as being scientifically. Botanical evidence is not mostly used for perpertration, instead it tends to serve as circumstantial evidence. Plant materials constitute the basis, among others, for linking a suspect or object to a crime scene or a victim, confirming or not confirming an alibi, determining the post-mortem interval, and determining the origin of food/object. Forensic botany entails field work, knowledge of plants, understanding ecosystem processes, and a basis understaning of geoscience. In this study, experiments with mammal cadavers were conducted to determine the occurence of an event. The simplest criterion characterising botanical evidence is its size. Therefore, macroremains include whole plants or their larger fragments (e.g. tree bark, leaves, seeds, prickles, and thorns), whereas microscopic evidence includes palynomorphs (spores and pollen grains), diatoms, and tissues. Botanical methods allow for an analysis to be repeated multiple times and the test material is easy to collect in the field. Forensic botany can be supplemented with molecular analyses, which, although specific and sensitive, still require validation.

CRISPR/Cas9 technology as an innovative approach to enhancing the phytoremediation: Concepts and implications

Phytoremediation is currently an active field of research focusing chiefly on identifying and characterizing novel and high chelation action super-accumulators. In the last few years, molecular tools have been widely exploited to understand better metal absorption, translocation, cation, and tolerance mechanisms in plants. Recently more advanced CRISPR-Cas9 genome engineering technology is also employed to enhance detoxification efficiency. Further, advances in molecular science will trigger the understanding of adaptive phytoremediation ability plant production in current global warming conditions. The enhanced abilities of nucleases for genome modification can improve plant repair capabilities by modifying the genome, thereby achieving a sustainable ecosystem. The purpose of this manuscript focuses on biotechnology's fundamental principles and application to promote climate-resistant metal plants, especially the CRISPR-Cas9 genome editing system for enhancing the phytoremediation of harmful contamination and pollutants.

Biosynthesized silver nanoparticles using Polygonatum geminiflorum efficiently control fusarium wilt disease of tomato

Nanomaterials are gaining tremendous potential as emerging antimicrobials in the quest to find resistance-free alternatives of chemical pesticides. In this study, stable silver nanoparticles were synthesized using the aqueous extract of medicinal plant species Polygonatum geminiflorum, and their morphological features were evaluated by transmission electron microscopy, X-ray diffraction spectroscopy and energy dispersive X-ray analysis. In vitro Antifungal activity of the synthesized silver nanoparticles (AgNPs) and P. geminiflorum extract (PE) either alone or in combination (PE-AgNPs) against Fusarium oxysporum was evaluated using disc-diffusion and well-diffusion methods. In planta assay of the same treatments against Fusarium wilt diseases of tomato was evaluated by foliar spray method. Moreover, plant extract was evaluated for the quantitative investigation of antioxidant activity, phenolics and flavonoids by spectroscopic and HPLC techniques. Phytochemical analysis indicated the presence of total phenolic and flavonoid contents as 48.32 mg ± 1.54 mg GAE/g and 57.08 mg ± 1.36 mg QE/g, respectively. The DPPH radical scavenging of leaf extract was found to be 88.23% ± 0.87%. Besides, the HPLC phenolic profile showed the presence of 15 bioactive phenolic compounds. Characterization of nanoparticles revealed the size ranging from 8 nm to 34 nm with average crystallite size of 27 nm. The FTIR analysis revealed important functional groups that were responsible for the reduction and stabilization of AgNPs. In the in vitro assays, 100 μg/ml of AgNPs and AgNPs-PE strongly inhibited Fusarium oxysporum. The same treatments tested against Fusarium sprayed on tomato plants in controlled environment exhibited nearly 100% plant survival with no observable phytotoxicity. These finding provide a simple baseline to control Fusarium wilt using silver nano bio-control agents without affecting the crop health.

Green Synthesis of Silver Nanoparticles Using Euphorbia wallichii Leaf Extract: Its Antibacterial Action against Citrus Canker Causal Agent and Antioxidant Potential

Biologically synthesized silver nanoparticles are emerging as attractive alternatives to chemical pesticides due to the ease of their synthesis, safety and antimicrobial activities in lower possible concentrations. In the present study, we have synthesized silver nanoparticles (AgNPs) using the aqueous extract of the medicinal plant Euphorbia wallichii and tested them against the plant pathogenic bacterium Xanthomonas axonopodis, the causative agent of citrus canker, via an in vitro experiment. The synthesized silver nanoparticles were characterized by techniques such as UV-Vis spectroscopy, Fourier transform infrared spectroscopy, energy-dispersive X-ray spectroscopy, X-ray diffraction analysis and transmission electron microscopy. Moreover, the plant species were investigated for phenolics, flavonoids and antioxidant activity. The antioxidant potential of the extract was determined against a DPPH radical. The extract was also evaluated for phenolic compounds using the HPLC technique. The results confirmed the synthesis of centered cubic, spherical-shaped and crystalline nanoparticles by employing standard characterization techniques. A qualitative and quantitative phytochemical analysis revealed the presence of phenolics (41.52 mg GAE/g), flavonoids (14.2 mg QE/g) and other metabolites of medicinal importance. Different concentrations (1000 µg/mL to 15.62 µg/mL—2 fold dilutions) of AgNPs and plant extract (PE) alone, and both in combination (AgNPs-PE), exhibited a differential inhibition of X. axanopodis in a high throughput antibacterial assay. Overall, AgNPs-PE was superior in terms of displaying significant antibacterial activity, followed by AgNPs alone. An appreciable antioxidant potential was recorded as well. The observed antibacterial and antioxidant potential may be attributed to eight phenolic compounds identified in the extract. The Euphorbia wallichii leaf-extract-induced synthesized AgNPs exhibited strong antibacterial activity against X. axanopodis, which could be exploited as effective alternative preparations against citrus canker in planta in a controlled environment. In addition, as a good source of phenolic compounds, the plant could be further exploited for potent antioxidants.

Biotransformation of Waste Bile Acids: A New Possible Sustainable Approach to Anti-Fungal Molecules for Crop Plant Bioprotection?

Phytopathogenic fungi are among the main causes of productivity losses in agriculture. To date, synthetic chemical pesticides, such as hydroxyanilides, anilinopyrimidines and azole derivatives, represent the main treatment tools for crop plant defence. However, the large and uncontrolled use of these substances has evidenced several side effects, namely the resistance to treatments, environmental damage and human health risks. The general trend is to replace chemicals with natural molecules in order to reduce these side effects. Moreover, the valorisation of agri-food industry by-products through biotransformation processes represents a sustainable alternative to chemical synthesis in several sectors. This research is aimed at comparing the anti-phytopathogenic activity of waste bovine and porcine bile with secosteroids obtained by biotransformation of bile acids with Rhodococcus strains. The ultimate goal is to apply these natural products on food crops affected by phytopathogenic fungi.

Antifungal potential, chemical composition of Chlorella vulgaris and SEM analysis of morphological changes in Fusarium oxysporum

In pursuit of an environmentally benign fungicide alternative, the current study explored the antifungal activity of Chlorella vulgaris extracts against six plant pathogenic fungi (in vitro). The well diffusion agar method was used to investigate the growth inhibition of Fusarium oxysporum, Fusarium sp., Fusarium solani, A. flavus, A. niger, and A. alternata using the three C. vulgaris extracts viz. methanol (CvME), acetone (CvAE), and diethyl ether (CvDE). Different concentrations of CvDE were also investigated against F. oxysporum. The morphological modifications in F. oxysporum treated with CvDE (5 mg/kg) were studied using SEM and the chemical composition of CvDE was also determined by GC–MS analysis. All extracts, with the exception of A. alternata, were found to be effective in inhibiting the growth of plant pathogenic fungi. The CvDE extract, followed by CvME and CvAE, was found to be efficient against tested fungi. The CvDE was most effective against F. oxysporum with a 73.3% growth inhibition. The effects of various CvDE concentrations on F. oxysporum were found to be dosage dependent. The SEM micrograph revealed that CvDE-treated F. oxysporum had substantially less conidia than the control. The CvDE treatment damaged the mycelial structure as well. Major chemical components detected in CvDE were Heptaldehyde (15.7%), Octadecenoic acid, methyl ester (12.6%), Hexadecanoic acid (12%), 3-Decyn-2-Ol (10.98%), (E)-3,7,11,15-tetramethylhexadec-2-ene (9.76%), heptadecane-1,2,3,4,5-pentol (8.7%), Docosane, 4-methyl (7.28%).

Split down the middle: studying arbuscular mycorrhizal and ectomycorrhizal symbioses using split-root assays

Most land plants symbiotically interact with soil-borne fungi to ensure nutrient acquisition and tolerance to various environmental stressors. Among these symbioses, arbuscular mycorrhizal and ectomycorrhizal associations can be found in a large proportion of plants, including many crops. Split-root assays are widely used in plant research to study local and systemic signaling responses triggered by local treatments, including nutrient availability, interaction with soil microbes, or abiotic stresses. However, split-root approaches have only been occasionally used to tackle these questions with regard to mycorrhizal symbioses. This review compiles and discusses split-root assays developed to study arbuscular mycorrhizal and ectomycorrhizal symbioses, with a particular emphasis on colonization by multiple beneficial symbionts, systemic resistance induced by mycorrhizal fungi, water and nutrient transport from fungi to colonized plants, and host photosynthate allocation from the host to fungal symbionts. In addition, we highlight how the use of split-root assays could result in a better understanding of mycorrhizal symbioses, particularly for a broader range of essential nutrients, and for multipartite interactions.

Selective Toxicity of Secondary Metabolites from the Entomopathogenic Bacterium Photorhabdus luminescens sonorensis against Selected Plant Parasitic Nematodes of the Tylenchina Suborder

Entomopathogenic Photorhabdus bacteria (Enterobacteriaceae: Gamma-proteobacteria), the natural symbionts of Heterorhabditis nematodes, are a rich source for the discovery of biologically active secondary metabolites (SMs). This study describes the isolation of three nematicidal SMs from in vitro culture supernatants of the Arizona-native Photorhabdus luminescenssonorensis strain Caborca by bioactivity-guided fractionation. Nuclear magnetic resonance spectroscopy and comparison to authentic synthetic standards identified these bioactive metabolites as trans-cinnamic acid (t-CA), (4E)-5-phenylpent-4-enoic acid (PPA), and indole. PPA and t-CA displayed potent, concentration-dependent nematicidal activities against the root-knot nematode (Meloidogyne incognita) and the citrus nematode (Tylenchulus semipenetrans), two economically and globally important plant parasitic nematodes (PPNs) that are ubiquitous in the United States. Southwest. Indole showed potent, concentration-dependent nematistatic activity by inducing the temporary rigid paralysis of the same targeted nematodes. While paralysis was persistent in the presence of indole, the nematodes recovered upon removal of the compound. All three SMs were found to be selective against the tested PPNs, exerting little effects on non-target species such as the bacteria-feeding nematode Caenorhabditis elegans or the entomopathogenic nematodes Steinernema carpocapsae, Heterorhabditis bacteriophora, and Hymenocallis sonorensis. Moreover, none of these SMs showed cytotoxicity against normal or neoplastic human cells. The combination of t-CA + PPA + indole had a synergistic nematicidal effect on both targeted PPNs. Two-component mixtures prepared from these SMs revealed complex, compound-, and nematode species-dependent interactions. These results justify further investigations into the chemical ecology of Photorhabdus SMs, and recommend t-CA, PPA and indole, alone or in combinations, as lead compounds for the development of selective and environmentally benign nematicides against the tested PPNs.

IMPORTANCE Two phenylpropanoid and one alkaloid secondary metabolites were isolated and identified from culture filtrates of Photorhabdus l. sonorensis strain Caborca. The three identified metabolites showed selective nematicidal and/or nematistatic activities against two important plant parasitic nematodes, the root-knot nematode (Meloidogyne incognita) and the citrus nematode (Tylenchulus semipenetrans). The mixture of all three metabolites had a synergistic nematicidal effect on both targeted nematodes, while other combinations showed compound- and nematode-dependent interactions.

Design, synthesis and antifungal mechanism of novel acetophenone derivatives containing 1, 3, 4-thiadiazole-2-thioethers

Plant pathogenic fungi could cause significant losses to agricultural productions. To discover new pesticides with novel structures and unique mechanisms of action, a series of novel acetophenone derivatives containing 1,3,4-thiadiazole-2-thioethers...

Agricultural Crop Security: Exploring US Federal Readiness and Response Capabilities

A large-scale agroterrorism attack on the United States would likely have severe economic and social consequences. In particular, the destruction of crops with pests or pathogens could cause substantial damage to food, economic, and social stability, with relatively little health risk to the perpetrators. The tools of engineering biology could enable a well-trained, nefarious actor to amplify their desired impacts through the development of disease-intensifying traits. In the United States, plant health emergencies are handled first at the local and state levels, then escalated to include the support and leadership of the US Department of Agriculture (USDA) and other federal agencies. We used publicly available documents and interviews across government, academia, and industry to explore the strategic and tactical approaches of the US federal government to detect and respond to plant agroterrorism. In this article, we discuss the agroterrorism preparedness and response capabilities at 3 levels of federal response: (1) within the Plant Protection and Quarantine program of the Animal and Plant Health Inspection Service at the USDA, (2) between USDA components, and (3) between federal agencies. We outline the approaches currently taken and identify opportunities to strengthen these approaches.

De Novo Design of Antimicrobial Peptides With a Special Charge Pattern and Their Application in Combating Plant Pathogens

Plant diseases are important issues in agriculture, and the development of effective and environment-friendly means of disease control is crucial and highly desired. Antimicrobial peptides (AMPs) are known as potential alternatives to chemical pesticides because of their potent broad-spectrum antimicrobial activity and because they have no risk, or have only a low risk, of developing chemical-resistant pathogens. In this study, we designed a series of amphipathic helical peptides with different spatial distributions of positive charges and found that the peptides that had a special sequence pattern "BBHBBHHBBH" ("B" for basic residue and "H" for hydrophobic residue) displayed excellent bactericidal and fungicidal activities in a wide range of economically important plant pathogens. The peptides with higher helical propensity had lower antimicrobial activity. When we modified the peptides with a long acyl chain at their N-terminus, their plant protection effect improved. Our application of the fatty acyl-modified peptides on the leaves of tomato and Arabidopsis plants lessened the infection caused by Pectobacterium carotovorum subsp. carotovorum and Botrytis cinerea. Our study provides important insights on the development of more potent novel AMPs for plant protection.

Quassinoids with Inhibitory Activities against Plant Fungal Pathogens from Picrasma javanica

A bioactivity-guided study on the leaves of Picrasma javanica led to the isolation of 19 quassinoids, including 13 new compounds. The structures of the new compounds were elucidated by a combination of spectroscopic data analysis, X-ray crystallography studies, and electronic circular dichroism (ECD) data interpretation. Compounds 1-7 are rare examples of quassinoids with a keto carbonyl group at C-12. The biological activities of 11 of the more abundant isolates were evaluated against five phytopathogenic fungi in vitro, and several of them including 6 and 15 showed moderate inhibitory effects that were comparative to those of the positive control, carbendazim. In addition, the preliminary structure-activity relationships (SARs) of these quassinoids were also investigated.

Biosensor Technologies for Early Detection and Quantification of Plant Pathogens

Plant pathogens are a major reason of reduced crop productivity and may lead to a shortage of food for both human and animal consumption. Although chemical control remains the main method to reduce foliar fungal disease incidence, frequent use can lead to loss of susceptibility in the fungal population. Furthermore, over-spraying can cause environmental contamination and poses a heavy financial burden on growers. To prevent or control disease epidemics, it is important for growers to be able to detect causal pathogen accurately, sensitively, and rapidly, so that the best practice disease management strategies can be chosen and enacted. To reach this goal, many culture-dependent, biochemical, and molecular methods have been developed for plant pathogen detection. However, these methods lack accuracy, specificity, reliability, and rapidity, and they are generally not suitable for in-situ analysis. Accordingly, there is strong interest in developing biosensing systems for early and accurate pathogen detection. There is also great scope to translate innovative nanoparticle-based biosensor approaches developed initially for human disease diagnostics for early detection of plant disease-causing pathogens. In this review, we compare conventional methods used in plant disease diagnostics with new sensing technologies in particular with deeper focus on electrochemical and optical biosensors that may be applied for plant pathogen detection and management. In addition, we discuss challenges facing biosensors and new capability the technology provides to informing disease management strategies.

Allopatric Plant Pathogen Population Divergence following Disease Emergence

Within the landscape of globally distributed pathogens, populations differentiate via both adaptive and nonadaptive forces. Individual populations are likely to show unique trends of genetic diversity, host-pathogen interaction, and ecological adaptation. In plant pathogens, allopatric divergence may occur particularly rapidly within simplified agricultural monoculture landscapes. As such, the study of plant pathogen populations in monocultures can highlight the distinct evolutionary mechanisms that lead to local genetic differentiation. Xylella fastidiosa is a plant pathogen known to infect and damage multiple monocultures worldwide. One subspecies, Xylella fastidiosa subsp. fastidiosa, was first introduced to the United States ∼150 years ago, where it was found to infect and cause disease in grapevines (Pierce's disease of grapevines, or PD). Here, we studied PD-causing subsp. fastidiosa populations, with an emphasis on those found in the United States. Our study shows that following their establishment in the United States, PD-causing strains likely split into populations on the East and West Coasts. This diversification has occurred via both changes in gene content (gene gain/loss events) and variations in nucleotide sequence (mutation and recombination). In addition, we reinforce the notion that PD-causing populations within the United States acted as the source for subsequent subsp. fastidiosa outbreaks in Europe and Asia.IMPORTANCE Compared to natural environments, the reduced diversity of monoculture agricultural landscapes can lead bacterial plant pathogens to quickly adapt to local biological and ecological conditions. Because of this, accidental introductions of microbial pathogens into naive regions represents a significant economic and environmental threat. Xylella fastidiosa is a plant pathogen with an expanding host and geographic range due to multiple intra- and intercontinental introductions. X. fastidiosa subsp. fastidiosa infects and causes disease in grapevines (Pierce's disease of grapevines [PD]). This study focused on PD-causing X. fastidiosa populations, particularly those found in the United States but also invasions into Taiwan and Spain. The analysis shows that PD-causing X. fastidiosa has diversified via multiple cooccurring evolutionary forces acting at an intra- and interpopulation level. This analysis enables a better understanding of the mechanisms leading to the local adaptation of X. fastidiosa and how a plant pathogen diverges allopatrically after multiple and sequential introduction events.

Recent advances in bio-chemical, molecular and physiological aspects of membrane lipid derivatives in plant pathology

Plant pathogens pose a significant threat to the food industry and food security accounting for 10-40% crop losses annually on a global scale. Economic losses from plant diseases are estimated at $300B for major food crops and are associated with reduced food availability and accessibility and also high food costs. Although strategies exist to reduce the impact of diseases in plants, many of these introduce harmful chemicals to our food chain. Therefore, it is important to understand and utilize plants' immune systems to control plant pathogens to enable more sustainable agriculture. Lipids are core components of cell membranes and as such are part of the first line of defense against pathogen attack. Recent developments in omics technologies have advanced our understanding of how plant membrane lipid biosynthesis, remodelling and/or signalling modulate plant responses to infection. Currently, there is limited information available in the scientific literature concerning lipid signalling targets and their biochemical and physiological consequences in response to plant pathogens. This review focusses on the functions of membrane lipid derivatives and their involvement in plant responses to pathogens as biotic stressors. We describe major plant defense systems including systemic-acquired resistance, basal resistance, hypersensitivity and the gene-for-gene concept in this context.

Forest Tree Associated Bacterial Diffusible and Volatile Organic Compounds against Various Phytopathogenic Fungi

Plant growth-promoting rhizobacteria (PGPR) can potentially be used as an alternative strategy to control plant diseases. In this study, strain ST-TJ4 isolated from the rhizosphere soil of a healthy poplar was found to have a strong antifungal activity against 11 phytopathogenic fungi in agriculture and forestry. Strain ST-TJ4 was identified as Pseudomonas sp. based on 16S rRNA-encoding gene sequences. The bacterium can produce siderophores, cellulase, and protease, and has genes involved in the synthesis of phenazine, 1-phenazinecarboxylic acid, pyrrolnitrin, and hydrogen cyanide. Additionally, the volatile compounds released by strain ST-TJ4 can inhibit the mycelial growth of plant pathogenic fungi more than diffusible substances can. Based on volatile compound profiles of strain ST-TJ4 obtained from headspace collection and GC-MS/MS analysis, 1-undecene was identified. In summary, the results suggested that Pseudomonas sp. ST-TJ4 can be used as a biocontrol agent for various plant diseases caused by phytopathogenic fungi.

S-Nitroso-Proteome Revealed in Stomatal Guard Cell Response to Flg22

Nitric oxide (NO) plays an important role in stomata closure induced by environmental stimuli including pathogens. During pathogen challenge, nitric oxide (NO) acts as a second messenger in guard cell signaling networks to activate downstream responses leading to stomata closure. One means by which NO’s action is achieved is through the posttranslational modification of cysteine residue(s) of target proteins. Although the roles of NO have been well studied in plant tissues and seedlings, far less is known about NO signaling and, more specifically, protein S-nitrosylation (SNO) in stomatal guard cells. In this study, using iodoTMTRAQ quantitative proteomics technology, we analyzed changes in protein SNO modification in guard cells of reference plant Arabidopsis thaliana in response to flg22, an elicitor-active peptide derived from bacterial flagellin. A total of 41 SNO-modified peptides corresponding to 35 proteins were identified. The proteins cover a wide range of functions, including energy metabolism, transport, stress response, photosynthesis, and cell–cell communication. This study creates the first inventory of previously unknown NO responsive proteins in guard cell immune responses and establishes a foundation for future research toward understanding the molecular mechanisms and regulatory roles of SNO in stomata immunity against bacterial pathogens.

An insight into the mechanism of antifungal activity of biogenic nanoparticles than their chemical counterparts

Herein, we describe the enhanced antifungal activity of silver nanoparticles biosynthesized by cell free filtrate of Trichoderma viride (MTCC 5661) in comparison to chemically synthesized silver nanoparticles (CSNP) of similar shape and size. Biosynthesized silver nanoparticles (BSNP) enhanced the reduction in dry weight by 20 and 48.8% of fungal pathogens Fusarium oxysporum and Alternaria brassicicola respectively in comparison to their chemical counterparts (CSNP). Nitroblue tetrazolium and Propidium iodide staining demonstrated the higher generation of superoxide radicals lead to higher death in BSNP treated fungus in comparison to CSNP. Scanning electron microscopy of A. brassicicola revealed the osmotic imbalance and membrane disintegrity to be major cause for fungal cell death after treatment with BSNP. To gain an insight into the mechanistic aspect of enhanced fungal cell death after treatment of BSNP in comparison to CSNP, stress responses and real time PCR analysis was carried out with A. brassicicola. It revealed that generation of ROS, downregulation of antioxidant machinery and oxidative enzymes, disruption of osmotic balance and cellular integrity, and loss of virulence are the mechanisms employed by BSNP which establishes them as superior antifungal agent than their chemical counterparts. With increasing drug resistance and ubiquitous presence of fungal pathogens in plant kingdom, BSNP bears the candidature for new generation of antifungal agent.

Detection of Clavibacter michiganensis subsp. michiganensis Assisted by Micro-Raman Spectroscopy under Laboratory Conditions

Clavibacter michiganensis subsp. michiganesis (Cmm) is a quarantine-worthy pest in México. The implementation and validation of new technologies is necessary to reduce the time for bacterial detection in laboratory conditions and Raman spectroscopy is an ambitious technology that has all of the features needed to characterize and identify bacteria. Under controlled conditions a contagion process was induced with Cmm, the disease epidemiology was monitored. Micro-Raman spectroscopy (532 nm λ laser) technique was evaluated its performance at assisting on Cmm detection through its characteristic Raman spectrum fingerprint. Our experiment was conducted with tomato plants in a completely randomized block experimental design (13 plants × 4 rows). The Cmm infection was confirmed by 16S rDNA and plants showed symptoms from 48 to 72 h after inoculation, the evolution of the incidence and severity on plant population varied over time and it kept an aggregated spatial pattern. The contagion process reached 79% just 24 days after the epidemic was induced. Micro-Raman spectroscopy proved its speed, efficiency and usefulness as a non-destructive method for the preliminary detection of Cmm. Carotenoid specific bands with wavelengths at 1146 and 1510 cm-1 were the distinguishable markers. Chemometric analyses showed the best performance by the implementation of PCA-LDA supervised classification algorithms applied over Raman spectrum data with 100% of performance in metrics of classifiers (sensitivity, specificity, accuracy, negative and positive predictive value) that allowed us to differentiate Cmm from other endophytic bacteria (Bacillus and Pantoea). The unsupervised KMeans algorithm showed good performance (100, 96, 98, 91 y 100%, respectively).

Essential Oil of Achillea ligustica (Asteraceae) as an Antifungal Agent against Phytopathogenic Fungi

The essential oil from the inflorescences of Ligurian yarrow ( Achillea ligustica All., Asteraceae) naturalized in Central Italy was investigated in order to evaluate the antifungal activity against five phytopathogenic fungi. The composition of the essential oil characterized by GC-FID and GC-MS, revealed linalool (24.8%), viridiflorol (9.6%), β-pinene (6.4%), 1,8-cineole (5.8%) and terpinen-4-ol (5.3%) as the major constituents. The antifungal activity was evaluated by the in vitro disc agar diffusion test and Agar vapor assay on 5 microbial strains. The essential oil showed a good antifungal activity against all fungal strains, being a valid candidate in the fight against plant pathogens that harm many traditional crops. The possible incorporation of this essential oil into antifungal preparations with a low environmental impact is hypothesized.

Hyperspectral Sensors and Imaging Technologies in Phytopathology: State of the Art

Plant disease detection represents a tremendous challenge for research and practical applications. Visual assessment by human raters is time-consuming, expensive, and error prone. Disease rating and plant protection need new and innovative techniques to address forthcoming challenges and trends in agricultural production that require more precision than ever before. Within this context, hyperspectral sensors and imaging techniques-intrinsically tied to efficient data analysis approaches-have shown an enormous potential to provide new insights into plant-pathogen interactions and for the detection of plant diseases. This article provides an overview of hyperspectral sensors and imaging technologies for assessing compatible and incompatible plant-pathogen interactions. Within the progress of digital technologies, the vision, which is increasingly discussed in the society and industry, includes smart and intuitive solutions for assessing plant features in plant phenotyping or for making decisions on plant protection measures in the context of precision agriculture.

Transcriptomic Profiling Suggests That Promysalin Alters the Metabolic Flux, Motility, and Iron Regulation in Pseudomonas putida KT2440

Promysalin, a secondary metabolite produced by P. putida RW10S1, is a narrow-spectrum antibiotic that targets P. aeruginosa over other Pseudomonas spp. P. putida KT2440, a nonproducing strain, displays increased swarming motility and decreased pyoverdine production in the presence of exogenous promysalin. Herein, proteomic and transcriptomic experiments were used to provide insight about how promysalin elicits responses in PPKT2440 and rationalize its species selectivity. RNA-sequencing results suggest that promysalin affects PPKT2440 by (1) increasing swarming in a flagella-independent manner; (2) causing cells to behave as if they were experiencing an iron-deficient environment, and (3) shifting metabolism away from glucose conversion to pyruvate via the Entner-Doudoroff pathway. These findings highlight nature's ability to develop small molecules with specific targets, resulting in exquisite selectivity.

Rapid eradication of bacterial phytopathogens by atmospheric pressure glow discharge generated in contact with a flowing liquid cathode

Diseases caused by phytopathogenic bacteria are responsible for significant economic losses, and these bacteria spread through diverse pathways including waterways and industrial wastes. It is therefore of high interest to develop potent methods for their eradication. Here, antibacterial properties of direct current atmospheric pressure glow discharge (dc-APGD) generated in contact with flowing bacterial suspensions were examined against five species of phytopathogens. Complete eradication of Clavibacter michiganensis subsp. sepedonicus, Dickeya solani, and Xanthomonas campestris pv. campestris from suspensions of OD₆₀₀  ≈ 0.1 was observed, while there was at least 3.43 logarithmic reduction in population densities of Pectobacterium atrosepticum and Pectobacterium carotovorum subsp. carotovorum. Analysis of plasma-chemical parameters of the dc-APGD system revealed its high rotational temperatures of 2,300 ± 100 K and 4,200 ± 200 K, as measured from N₂ and OH molecular bands, respectively, electron temperature of 6,050 ± 400 K, vibrational temperature of 4000 ± 300 K, and high electron number density of 1.1 × 10¹⁵  cm^-1 . In addition, plasma treatment led to formation of numerous reactive species and states in the treated liquid, including reactive nitrogen and oxygen species such as NO_x , NH, H₂ O₂ , O₂ , O, and OH. Further examination revealed that bactericidal activity of dc-APGD was primarily due to presence of these reactive species as well as to UVA, UVB, and UVC irradiation generated by the dc-APGD source. Plasma treatment also resulted in an increase in temperature (from 24.2 to 40.2 °C) and pH (from 6.0 to 10.8) of bacterial suspensions, although these changes had minor effects on cell viability. All results suggest that the newly developed dc-APGD-based system can be successfully implemented as a simple, rapid, efficient, and cost-effective disinfection method for liquids originating from different industrial and agricultural settings.

Exploitation of microbial forensics and nanotechnology for the monitoring of emerging pathogens

Emerging infectious diseases remain among the leading causes of global mortality. Traditional laboratory diagnostic approaches designed to detect and track infectious disease agents provide a framework for surveillance of bio threats. However, surveillance and outbreak investigations using such time-consuming approaches for early detection of pathogens remain the major pitfall. Hence, reasonable real-time surveillance systems to anticipate threats to public health and environment are critical for identifying specific aetiologies and preventing the global spread of infectious disease. The current review discusses the growing need for monitoring and surveillance of pathogens with the same zeal and approach as adopted by microbial forensics laboratories, and further strengthening it by integrating with the innovative nanotechnology for rapid detection of microbial pathogens. Such innovative diagnostics platforms will help to track pathogens from high risk areas and environment by pre-emptive approach that will minimize damages. The various scenarios with the examples are discussed where the high risk associated human pathogens in particular were successfully detected using various nanotechnology approaches with potential future prospects in the field of microbial forensics.

Synthetic biology approach for plant protection using dsRNA

Pathogens induce severe damages on cultivated plants and represent a serious threat to global food security. Emerging strategies for crop protection involve the external treatment of plants with double-stranded (ds)RNA to trigger RNA interference. However, applying this technology in greenhouses and fields depends on dsRNA quality, stability and efficient large-scale production. Using components of the bacteriophage phi6, we engineered a stable and accurate in vivo dsRNA production system in Pseudomonas syringae bacteria. Unlike other in vitro or in vivo dsRNA production systems that rely on DNA transcription and postsynthetic alignment of single-stranded RNA molecules, the phi6 system is based on the replication of dsRNA by an RNA-dependent RNA polymerase, thus allowing production of high-quality, long dsRNA molecules. The phi6 replication complex was reprogrammed to multiply dsRNA sequences homologous to tobacco mosaic virus (TMV) by replacing the coding regions within two of the three phi6 genome segments with TMV sequences and introduction of these constructs into P. syringae together with the third phi6 segment, which encodes the components of the phi6 replication complex. The stable production of TMV dsRNA was achieved by combining all the three phi6 genome segments and by maintaining the natural dsRNA sizes and sequence elements required for efficient replication and packaging of the segments. The produced TMV-derived dsRNAs inhibited TMV propagation when applied to infected Nicotiana benthamiana plants. The established dsRNA production system enables the broad application of dsRNA molecules as an efficient, highly flexible, nontransgenic and environmentally friendly approach for protecting crops against viruses and other pathogens.

Diffusible and Volatile Antifungal Compounds Produced by an Antagonistic Bacillus velezensis G341 against Various Phytopathogenic Fungi

The aim of this study was to identify volatile and agar-diffusible antifungal metabolites produced by Bacillus sp. G341 with strong antifungal activity against various phytopathogenic fungi. Strain G341 isolated from four-year-old roots of Korean ginseng with rot symptoms was identified as Bacillus velezensis based on 16S rDNA and gyrA sequences. Strain G341 inhibited mycelial growth of all phytopathogenic fungi tested. In vivo experiment results revealed that n-butanol extract of fermentation broth effectively controlled the development of rice sheath blight, tomato gray mold, tomato late blight, wheat leaf rust, barley powdery mildew, and red pepper anthracnose. Two antifungal compounds were isolated from strain G341 and identified as bacillomycin L and fengycin A by MS/MS analysis. Moreover, volatile compounds emitted from strain G341 were found to be able to inhibit mycelial growth of various phytopathogenic fungi. Based on volatile compound profiles of strain G341 obtained through headspace collection and analysis on GC-MS, dimethylsulfoxide, 1-butanol, and 3-hydroxy-2-butanone (acetoin) were identified. Taken together, these results suggest that B. valezensis G341 can be used as a biocontrol agent for various plant diseases caused by phytopathogenic fungi.

THE USE OF PLANTS TO PROTECT PLANTS AND FOOD AGAINST FUNGAL PATHOGENS: A REVIEW

Background:

Plant fungal pathogens play a crucial role in the profitability, quality and quantity of plant production. These phytopathogens are persistent in avoiding plant defences causing diseases and quality losses around the world that amount to billions of US dollars annually. To control the scourge of plant fungal diseases, farmers have used fungicides to manage the damage of plant pathogenic fungi. Drawbacks such as development of resistance and environmental toxicity associated with these chemicals have motivated researchers and cultivators to investigate other possibilities.

Materials and Methods:

Several databases were accessed to determine work done on protecting plants against plant fungal pathogens with plant extracts using search terms “plant fungal pathogen”, “plant extracts” and “phytopathogens”. Proposals are made on the best extractants and bioassay techniques to be used.

Results:

In addition to chemical fungicides, biological agents have been used to deal with plant fungal diseases. There are many examples where plant extracts or plant derived compounds have been used as commercial deterrents of fungi on a large scale in agricultural and horticultural setups. One advantage of this approach is that plant extracts usually contain more than one antifungal compound. Consequently the development of resistance of pathogens may be lower if the different compounds affect a different metabolic process. Plants cultivated using plants extracts may also be marketed as organically produced. Many papers have been published on effective antimicrobial compounds present in plant extracts focusing on applications in human health. More research is required to develop suitable, sustainable, effective, cheaper botanical products that can be used to help overcome the scourge of plant fungal diseases.

Conclusions:

Scientists who have worked only on using plants to control human and animal fungal pathogens should consider the advantages of focusing on plant fungal pathogens. This approach could not only potentially increase food security for rural farmers, lead to commercial rewards, but it is also much easier to test the efficacy in greenhouse or field experiments. Even if extracts are toxic it may still be useful in the floriculture industry.

Forensic Phytopathology: a Critical Review

Forensic phytopathology is the application of plant pathology to legal or criminal matters. It is an emerging field. The existing literature focuses mainly on potential agricultural bioterrorism threats to the United States. Here we try to take a broader view including agricultural bioterrorism, mycoherbicide applications to eradicate plants used for illegal drugs, civil cases involving charges of sale or movement of diseased plants, and mycotoxins. In several of the examples given the evidence is inconclusive, but the examples are no less interesting for that.

Chemical Composition and Antibacterial Activity of Essential Oils of Tagetes minuta (Asteraceae) against Selected Plant Pathogenic Bacteria

The objective of this study was to determine the chemical composition and antibacterial activity of essential oils (EOs) of Tagetes minuta against three phytopathogenic bacteria Pseudomonas savastanoi pv. phaseolicola, Xanthomonas axonopodis pv. phaseoli, and Xanthomonas axonopodis pv. manihotis. The essential oils were extracted using steam distillation method in a modified Clevenger-type apparatus while antibacterial activity of the EOs was evaluated by disc diffusion method. Gas chromatography coupled to mass spectrometry (GC/MS) was used for analysis of the chemical profile of the EOs. Twenty compounds corresponding to 96% of the total essential oils were identified with 70% and 30% of the identified components being monoterpenes and sesquiterpenes, respectively. The essential oils of T. minuta revealed promising antibacterial activities against the test pathogens with Pseudomonas savastanoi pv. phaseolicola being the most susceptible with mean inhibition zone diameters of 41.83 and 44.83 mm after 24 and 48 hours, respectively. The minimum inhibitory concentrations and minimum bactericidal concentrations of the EOs on the test bacteria were in the ranges of 24-48 mg/mL and 95-190 mg/mL, respectively. These findings provide a scientific basis for the use of T. minuta essential oils as a botanical pesticide for management of phytopathogenic bacteria.

Degradation of Zearalenone by Essential Oils under In vitro Conditions

Essential oils are volatile compounds, extracted from plants, which have a strong odor. These compounds are known for their antibacterial and antifungal properties. However, data concerning degradation of mycotoxins by these metabolites are very limited. The aim of the present study was to investigate the effect of essential oils (cedarwood, cinnamon leaf, cinnamon bark, white grapefruit, pink grapefruit, lemon, eucalyptus, palmarosa, mint, thymic, and rosemary) on zearalenone (ZEA) reduction under various in vitro conditions, including the influence of temperature, pH, incubation time and mycotoxin and essential oil concentrations. The degree of ZEA reduction was determined by HPLC method. It was found that the kind of essential oil influences the effectiveness of toxin level reduction, the highest being observed for lemon, grapefruit, eucalyptus and palmarosa oils, while lavender, thymic and rosemary oils did not degrade the toxin. In addition, the decrease in ZEA content was temperature, pH as well as toxin and essential oil concentration dependent. Generally, higher reduction was observed at higher temperature in a wide range of pH, with clear evidence that the degradation rate increased gradually with time. In some combinations (e.g., palmarosa oil at pH 6 and 4 or 20°C) a toxin degradation rate higher than 99% was observed. It was concluded that some of the tested essential oils may be effective in detoxification of ZEA. We suggested that essential oils should be recognized as an interesting and effective means of ZEA decontamination and/or detoxification.

Deep RNA-Seq profile reveals biodiversity, plant-microbe interactions and a large family of NBS-LRR resistance genes in walnut (Juglans regia) tissues

Deep RNA-Seq profiling, a revolutionary method used for quantifying transcriptional levels, often includes non-specific transcripts from other co-existing organisms in spite of stringent protocols. Using the recently published walnut genome sequence as a filter, we present a broad analysis of the RNA-Seq derived transcriptome profiles obtained from twenty different tissues to extract the biodiversity and possible plant-microbe interactions in the walnut ecosystem in California. Since the residual nature of the transcripts being analyzed does not provide sufficient information to identify the exact strain, inferences made are constrained to the genus level. The presence of the pathogenic oomycete Phytophthora was detected in the root through the presence of a glyceraldehyde-3-phosphate dehydrogenase. Cryptococcus, the causal agent of cryptococcosis, was found in the catkins and vegetative buds, corroborating previous work indicating that the plant surface supported the sexual cycle of this human pathogen. The RNA-Seq profile revealed several species of the endophytic nitrogen fixing Actinobacteria. Another bacterial species implicated in aerobic biodegradation of methyl tert-butyl ether (Methylibium petroleiphilum) is also found in the root. RNA encoding proteins from the pea aphid were found in the leaves and vegetative buds, while a serine protease from mosquito with significant homology to a female reproductive tract protease from Drosophila mojavensis in the vegetative bud suggests egg-laying activities. The comprehensive analysis of RNA-seq data present also unraveled detailed, tissue-specific information of ~400 transcripts encoded by the largest family of resistance (R) genes (NBS-LRR), which possibly rationalizes the resistance of the specific walnut plant to the pathogens detected. Thus, we elucidate the biodiversity and possible plant-microbe interactions in several walnut (Juglans regia) tissues in California using deep RNA-Seq profiling.

Future of portable devices for plant pathogen diagnosis

The demand for rapid and accurate diagnosis of plant diseases has risen in the last decade. On-site diagnosis of single or multiple pathogens using portable devices is the first step in this endeavour. Despite extensive attempts to develop portable devices for pathogen detection, current technologies are still restricted to detecting known pathogens with limited detection accuracy. Developing new detection techniques for rapid and accurate detection of multiple plant pathogens and their associated variants is essential. Recent single DNA sequencing technologies are a promising new avenue for developing future portable devices for plant pathogen detection. In this review, we detail the current progress in portable devices and technologies used for detecting plant pathogens, the current position of emerging sequencing technologies for analysis of plant genomics, and the future of portable devices for rapid pathogen diagnosis.

Evaluating the impacts of stressors of Pseudomonas syringae pathovar tomato on the effectiveness of multi-locus variable number tandem repeat analysis and multi-locus sequence typing in microbial forensic investigations

BACKGROUND

Crops in the USA are vulnerable to natural and criminal threats because of their widespread cultivation and lack of surveillance, and because of implementation of growing practices such as monoculture. To prepare for investigation and attribution of such events, forensic assays, including determination of molecular profiles, are being adapted for use with plant pathogens. The use of multi-locus variable number tandem repeat (VNTR) analysis (MLVA) and multi-locus sequence typing (MLST) in investigations involving plant pathogens may be problematic because the long lag periods between pathogen introduction and discovery of associated disease may provide enough time for evolution to occur in the regions of the genome employed in each assay. Thus, more information on the stability of the loci employed in these methods is needed.

RESULTS

The MLVA fingerprints and MLST profiles were consistent throughout the experiment, indicating that, using a specific set of primers and conditions, MLVA and MLST typing systems reliably identify P.s. tomato DC3000. This information is essential to forensic investigators in interpreting comparisons between MLVA and MLST typing profiles observed in P.s. tomato isolates.

CONCLUSIONS

Our results indicate that MLVA and MLST typing systems, utilizing the specified primers and conditions, could be employed successfully in forensics investigations involving P.s. tomato. Similar experiments should be conducted in the field and with other high-consequence plant pathogens to ensure that the assays are reliable for pathogens infecting plants in their natural environment and for organisms that may display faster rates of mutation.

Validation of high throughput sequencing and microbial forensics applications

High throughput sequencing (HTS) generates large amounts of high quality sequence data for microbial genomics. The value of HTS for microbial forensics is the speed at which evidence can be collected and the power to characterize microbial-related evidence to solve biocrimes and bioterrorist events. As HTS technologies continue to improve, they provide increasingly powerful sets of tools to support the entire field of microbial forensics. Accurate, credible results allow analysis and interpretation, significantly influencing the course and/or focus of an investigation, and can impact the response of the government to an attack having individual, political, economic or military consequences. Interpretation of the results of microbial forensic analyses relies on understanding the performance and limitations of HTS methods, including analytical processes, assays and data interpretation. The utility of HTS must be defined carefully within established operating conditions and tolerances. Validation is essential in the development and implementation of microbial forensics methods used for formulating investigative leads attribution. HTS strategies vary, requiring guiding principles for HTS system validation. Three initial aspects of HTS, irrespective of chemistry, instrumentation or software are: 1) sample preparation, 2) sequencing, and 3) data analysis. Criteria that should be considered for HTS validation for microbial forensics are presented here. Validation should be defined in terms of specific application and the criteria described here comprise a foundation for investigators to establish, validate and implement HTS as a tool in microbial forensics, enhancing public safety and national security.

Designing an effective microbial forensics program for law enforcement and national security purposes

Forensic capabilities that provide lead information, and investigative, intelligence, prosecution and policy decision support can be invaluable for responding to and resolving bioterrorism events. Attributing biological attacks through scientific and other resources and processes is an important goal, for which science can be instrumental. Some even believe that having effective microbial forensics capabilities along with others can even deter adversaries from using biological weapons. For those nations that do not have such or wish to integrate or upgrade capabilities, thoughtful analysis and consideration of certain design principles will increase the likelihood that success will be attained.

Validation of real-time PCR assays for bioforensic detection of model plant pathogens

The U.S. agricultural sector is vulnerable to intentionally introduced microbial threats because of its wide and open distribution and economic importance. To investigate such events, forensically valid assays for plant pathogen detection are needed. In this work, real-time PCR assays were developed for three model plant pathogens: Pseudomonas syringae pathovar tomato, Xylella fastidiosa, and Wheat streak mosaic virus. Validation included determination of the linearity and range, limit of detection, sensitivity, specificity, and exclusivity of each assay. Additionally, positive control plasmids, distinguishable from native signature by restriction enzyme digestion, were developed to support forensic application of the assays. Each assay displayed linear amplification of target nucleic acid, detected 100 fg or less of target nucleic acid, and was specific to its target pathogen. Results obtained with these model pathogens provide the framework for development and validation of similar assays for other plant pathogens of high consequence.

The Microbial Rosetta Stone Central Agricultural Database: An Information Resource on High-Consequence Plant Pathogens

Microbial pathogens of humans, animals, and plants can serve as potential agents of biowarfare, bioterrorism, and biocrime. Previously, the Microbial Rosetta Stone (MRS) Central database, an easily accessible informational resource tool, was developed to assist law enforcement personnel in the event of a disease investigation by providing key information on pathogens of concern. Although the database already contained information on a few high-profile plant pathogens, the coverage was insufficient considering the large number of plant pathogens that pose a threat, not only to agricultural production but also to natural plant resources such as forests and rangelands. In this project, 100 plant pathogens of high consequence were selected for study, existing literature on these agents was reviewed, and both the sources and key pathogen information provided therein were curated in the new Agricultural Database (AgDB), an accessory to the existing MRS Central Database. Chosen for inclusion in the MRS Central AgDB were plant pathogens having significant potential for damage to U.S. agricultural and natural ecosystems. The selection process included review of several previously developed plant-pathogen threat lists and recommendations from experts within the U.S. plant biosecurity community. Pathogen information was collected by searching a number of relevant literature databases, sites on the World Wide Web, and other resources. For inclusion in the MRS, the information was curated into categories: pathogen taxonomy, nomenclature synonyms, disease symptoms and geographic distribution, plant hosts, insect vectors, detection and diagnostic methods, laboratory and field protocols, sample collection, and epidemiology. The resulting AgDB enhances the MRS Central Database by summarizing and linking key information on high-threat plant diseases and their causal agents to relevant scientific literature and internet resources. The AgDB contains critical, key information on high-consequence plant pathogens, curated in a format that is readily accessible and easily searched. The resource enhances the existing MRS Central Database and provides law enforcement, forensic, and investigative personnel with an additional tool with which to respond to microbial emergencies, particularly those affecting the agricultural and environmental sectors.

Combining field epidemiological information and genetic data to comprehensively reconstruct the invasion history and the microevolution of the sudden oak death agent Phytophthora ramorum (Stramenopila: Oomycetes) in California

Understanding the migration patterns of invasive organisms is of paramount importance to predict and prevent their further spread. Previous attempts at reconstructing the entire history of the sudden oak death (SOD) epidemic in California were limited by: (1) incomplete sampling; (2) the inability to include infestations caused by a single genotype of the pathogen; (3) collapsing of non-spatially contiguous yet genetically similar samples into large meta-samples that confounded the coalescent analyses. Here, we employ an intensive sampling coverage of 832 isolates of Phytopthora ramorum (the causative agent of SOD) from 60 California forests, genotyped at nine microsatellite loci, to reconstruct its invasion. By using age of infestation as a constraint on coalescent analyses, by dividing genetically indistinguishable meta-populations into highly-resolved sets of spatially contiguous populations, and by using Bruvo genetic distances for most analyses, we reconstruct the entire history of the epidemic and convincingly show infected nursery plants are the original source for the entire California epidemic. Results indicate that multiple human-mediated introductions occurred in most counties and that further disease sources were represented by large wild infestations. The study also identifies minor introductions, some of them relatively recent, linked to infected ornamental plants. Finally, using archival isolates collected soon after the discovery of the pathogen in California, we corroborate that the epidemic is likely to have resulted form 3 to 4 core founder individuals evolved from a single genotype. This is probably the most complete reconstruction ever completed for an invasion by an exotic forest pathogen, and the approach here described may be useful for the reconstruction of invasions by any clonally reproducing organism with a relatively limited natural dispersal range.