Comparative Genomics to Develop a Specific Multiplex PCR Assay for Detection of Clavibacter michiganensis

Clavibacter michiganensis Reframed: The Story of How the Genomics Era Made a New Face for an Old Enemy

OBJECTIVE

Bacterial wilt and canker of tomato caused by the gram-positive corynebacterial species Clavibacter michiganensis is an economically important disease threatening the tomato industry in both open-air and greenhouse productions around the world. The disease occurs in many countries, with a particular importance in regions characterised by high temperature and water scarcity. Management of bacterial canker has been a major problem since its original description in 1909. This is due in part to the seedborne nature of the pathogen, allowing the bacterium to be transmitted over long distances via infected seeds, as well as a lack of effective treatment to clean seeds. Detection of the pathogen from seeds is difficult due to high competition on culture media with diverse members of the seed-associated microbiota. Identification of the pathogen can also be difficult owing to the presence of different colony variants on culture media. In this review, we provide a historical perspective and an updated overview on the aetiology, epidemiology and management strategies of the bacterial canker disease. We also gathered recent molecular findings in the pathogenicity mechanisms and bioecology of C. michiganensis to boost management of the bacterial canker disease in the 21st century tomato industry.

TAXONOMY

Class: Actinobacteria; Order: Micrococcales; Family: Microbacteriaceae; Genus: Clavibacter; Species: Clavibacter michiganensis.

DISEASE SYMPTOMS

Interveinal leaf chlorosis leading to necrotic areas. Canker on stems and lateral branches of the plant. Discolouration of vascular and pith tissues to dark yellow or brown. Small and early ripened fruits or discolouration of the placenta from white to yellow in the interior part of the ripening fruits.

HOST RANGE

Tomato (Solanum lycopersicum) is the main host of the pathogen while natural infection has also been reported on eggplant, pepper and wild nightshade plants.

SYNONYMS (HISTORICAL/NON-PREFERRED SCIENTIFIC NAMES)

Aplanobacter michiganensis; Pseudomonas michiganense; Pseudomonas michiganensis; Bacterium michiganense; Phytomonas michiganensis; Mycobacterium michiganense; Erwinia michiganensis (=michiganense); Corynebacterium michiganense; Corynebacterium michiganense pv. michiganense; Corynebacterium michiganense subsp. michiganense; Clavibacter michiganensis subsp. michiganensis.

MICROBIOLOGICAL PROPERTIES

The bacterium produces domed, round and shiny mucoid colonies on general culture media. Colonies are usually yellow-pigmented, while pink-pigmented strains are occasionally observed. Cells are gram-positive, aerobic, non-motile, non-spore-producing curved rods (coryneform).

DISTRIBUTION

Present in all continents.

PHYTOSANITARY CATEGORIZATION

EPPO A2 List no. 50, EU 2019/2072 RNQP Annex IV. See EPPO (https://gd.eppo.int/taxon/CORBMI/categorization) and CABI (https://www.cabidigitallibrary.org/doi/10.1079/cabicompendium.15338) databases for further country-specific categorisations. EPPO code: CORBMI.

The contribution of beneficial wheat seed fungal communities beyond disease-causing fungi: Advancing heritable mycobiome-based plant breeding

Wheat (Triticum sp.) is a staple cereal crop, providing nearly a fifth of the world's protein and available calories. While fungi associated with wheat plants have been known for centuries, attention to fungi associated with wheat seeds has increased over the last hundred years. Initially, research focused on fungal taxa that cause seed-borne diseases. Seeds act as a physical link between generations and host specialized fungal communities that affect seed dormancy, germination, quality, and disease susceptibility. Interest in beneficial, non-disease-causing fungal taxa associated with seeds has grown since the discovery of Epichloë in fescue, leading to a search for beneficial fungal endophytes in cereal grains. Recent studies of the wheat seed mycobiome have shown that disease, seed development, and temporal variation significantly influence the composition and structure of these fungal communities. This research, primarily descriptive, aims to better understand the wheat seed mycobiome's function in relation to the plant host. A deeper understanding of the wheat seed mycobiome's functionality may offer potential for microbiome-assisted breeding.

A host shift as the origin of tomato bacterial canker caused by Clavibacter michiganensis

The Actinomycetota (formerly Actinobacteria) genus Clavibacter includes phytopathogens with devasting effects in several crops. Clavibacter michiganensis, the causal agent of tomato bacterial canker, is the most notorious species of the genus. Yet, its origin and natural reservoirs remain elusive, and its populations show pathogenicity profiles with unpredictable plant disease outcomes. Here, we generate and analyse a decade-long genomic dataset of Clavibacter from wild and commercial tomato cultivars, providing evolutionary insights that directed phenotypic characterization. Our phylogeny situates the last common ancestor of C. michiganensis next to Clavibacter isolates from grasses rather than to the sole strain we could isolate from wild tomatoes. Pathogenicity profiling of C. michiganensis isolates, together with C. phaseoli and C. californiensis as sister taxa and the wild tomato strain, was found to be congruent with the proposed phylogenetic relationships. We then identified gene enrichment after the evolutionary event, leading to the appearance of the C. michiganesis clade, including known pathogenicity factors but also hitherto unnoticed genes with the ability to encode adaptive traits for a pathogenic lifestyle. The holistic perspective provided by our evolutionary analyses hints towards a host shift event as the origin of C. michiganensis as a tomato pathogen and the existence of pathogenic genes that remain to be characterized.

A New Multiplex TaqMan qPCR for Precise Detection and Quantification of Clavibacter michiganensis in Seeds and Plant Tissue

Bacterial canker of tomato caused by Clavibacter michiganensis (Cm) is one of the most devastating bacterial diseases affecting the tomato industry worldwide. As the result of Cm colonization of the xylem, the susceptible host shows typical symptoms of wilt, marginal leaf necrosis, stem cankers, and ultimately plant death. However, what makes Cm an even more dangerous pathogen is its ability to infect seeds and plants without causing symptoms. Unfortunately, there are no resistant cultivars or effective chemical or biological control methods available to growers against Cm. Its control relies heavily on prevention. The implementation of a rapid and accurate detection tool is imperative to monitor the presence of Cm and prevent its spread. In this study, we developed a specific and sensitive multiplex TaqMan qPCR assay to detect Cm and distinguish it from related bacterial species that affect tomato plants. Two Cm chromosomal virulence-related genes, rhuM and tomA, were used as specific targets. The plant internal control tubulin alpha-3 was included in each of the multiplexes to improve the reliability of the assay. Specificity was evaluated with 37 bacterial strains including other Clavibacter spp. and related and unrelated bacterial pathogens from different geographic locations affecting a wide variety of hosts. Results showed that the assay is able to discriminate Cm strains from other related bacteria. The assay was validated on tissue and seed samples following artificial infection, and all tested samples accurately detected the presence of Cm. The tool described here is highly specific, sensitive, and reliable for the detection of Cm and allows the quantification of Cm in seeds, roots, stems, and leaves. The diagnostic assay can also be adapted for multiple purposes such as seed certification programs, surveillance, biosafety, the effectiveness of control methods, border protection, and epidemiological studies.[Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

A one-step multiplex PCR assay for the detection and differentiation of four species of Clarireedia causing dollar spot on turfgrass

BACKGROUND

Dollar spot (DS) is one of the most destructive and economically important diseases of cool- and warm-season turfgrasses worldwide. A total of six species causing DS disease in the genus Clarireedia have been described, and four of them have been reported to be distributed countrywide in China. Identification of different species of Clarireedia is a prerequisite for the effective management of DS disease.

RESULTS

Here we report a novel polymerase chain reaction (PCR)-based method for the detection and differentiation of the four species of Clarireedia associated with DS on turfgrass in China: C. jacksonii, C. paspali, C. monteithiana and C. hainanense. Species-specific genes were identified for each species by comparative genomics analysis. Four primer pairs were designed and mixed to amplify species-specific PCR fragments with differential sizes for the four species of Clarireedia in a single multiplex PCR assay. No PCR products were generated from the DNA templates of other common fungal pathogens associated with multiple turfgrass diseases. The multiplex PCR method developed can be used for the rapid and accurate detection and differentiation of the four species of Clarireedia from pure cultures as well as from infected turfgrass blades with DS symptoms.

CONCLUSION

The study developed a one-step multiplex PCR assay for the detection and differentiation of four species of Clarireedia causing DS on turfgrass in China, which will have important implications for DS management in China and worldwide. © 2022 Society of Chemical Industry.

Advances in the Characterization of the Mechanism Underlying Bacterial Canker Development and Tomato Plant Resistance

Bacterial canker caused by the Gram-positive actinobacterium Clavibacter michiganensis is one of the most serious bacterial diseases of tomatoes, responsible for 10–100% yield losses worldwide. The pathogen can systemically colonize tomato vascular bundles, leading to wilting, cankers, bird’s eye lesions, and plant death. Bactericidal agents are insufficient for managing this disease, because the pathogen can rapidly migrate through the vascular system of plants and induce systemic symptoms. Therefore, the use of resistant cultivars is necessary for controlling this disease. We herein summarize the pathogenicity of C. michiganensis in tomato plants and the molecular basis of bacterial canker pathogenesis. Moreover, advances in the characterization of resistance to this pathogen in tomatoes are introduced, and the status of genetics-based research is described. Finally, we propose potential future research on tomato canker resistance. More specifically, there is a need for a thorough analysis of the host–pathogen interaction, the accelerated identification and annotation of resistance genes and molecular mechanisms, the diversification of resistance resources or exhibiting broad-spectrum disease resistance, and the production of novel and effective agents for control or prevention. This review provides researchers with the relevant information for breeding tomato cultivars resistant to bacterial cankers.

Bacterial Canker of Tomato: Revisiting a Global and Economically Damaging Seedborne Pathogen

The gram-positive actinobacterium Clavibacter michiganensis is the causal agent of bacterial canker of tomato, an economically impactful disease with a worldwide distribution. This seedborne pathogen systemically colonizes tomato xylem leading to unilateral leaflet wilt, marginal leaf necrosis, stem and petiole cankers, and plant death. Additionally, splash dispersal of the bacterium onto fruit exteriors causes bird's-eye lesions, which are characterized as necrotic centers surrounded by white halos. The pathogen can colonize developing seeds systemically through xylem and through penetration of fruit tissues from the exterior. There are currently no commercially available resistant cultivars, and bactericidal sprays have limited efficacy for managing the disease once the pathogen is in the vascular system. In this review, we summarize research on epidemiology, host colonization, the bacterial genetics underlying virulence, and management of bacterial canker. Finally, we highlight important areas of research into this pathosystem that have the potential to generate new strategies for prevention and mitigation of bacterial canker.

Improved multiplex TaqMan qPCR assay with universal internal control offers reliable and accurate detection of Clavibacter michiganensis

AIM

Clavibacter michiganensis (Cm) is a seed-borne plant pathogen that significantly reduces tomato production worldwide. Due to repeated outbreaks and rapid spread of the disease, seeds/transplants need to be certified free of the pathogen before planting. To this end, we developed a multiplex TaqMan qPCR assay that can accurately detect Cm in infected samples.

METHODS AND RESULTS

A specific region of Cm (clvG gene) was selected for primer design using comparative genomics approach. A fully synthetic universal internal control (UIC) was also designed to detect PCR inhibitors and false-negative results in qPCRs. The Cm primers can be used alone or in a triplex TaqMan qPCR assay with UIC and previously described Clavibacter primers. The assay was specific for Cm and detected up to 10 fg of Cm DNA in sensitivity and spiked assays. Addition of the UIC did not change the specificity or sensitivity of the multiplex TaqMan qPCR assay.

CONCLUSION

The triplex TaqMan qPCR provides a specific and sensitive diagnostic assay for Cm.

SIGNIFICANCE AND IMPACT OF THE STUDY

This assay can be used for biosecurity surveillance, routine diagnostics, estimating bacterial titres in infected material and for epidemiological studies. The UIC is fully synthetic, efficiently amplified and multiplex compatible with any other qPCR assay.