ACHILLES - Fire Applied Genomics to Develop Innovative Control Products: Identify and exploit the pathogen Achilles heel(s) as control targets (Feuerbrandforschungsprojekt)

• Forschungsstelle: BLW
• Projektnummer: 11.15_1
• Projekttitel Englisch: ACHILLES - Fire Applied Genomics to Develop Innovative Control Products: Identify and exploit the pathogen Achilles heel(s) as control targets (Feuerbrandforschungsprojekt)

Schlüsselwörter (Deutsch)

Feuerbrand, Achilles, Pflanzenkrankheiten, Screening-Ansatz, Pflanzenschutzkontrollmaßnahme, Krankheitserreger, biologische Bekämpfung, Genomik, Epidemiologie, Biosensoren

Schlüsselwörter (Englisch)

Fire blight, Achilles, plant diseases, screening approach, phytosanitary control measure, pathogen, biocontrol, genomics, epidemiology, biosensors

Schlüsselwörter (Französisch)

Feu bactérien, Achilles, maladies des plantes, approche de dépistage, mesure phytosanitaire de contrôle, agent pathogène, lutte biologique, génomique, épidémiologie, biosenseurs

Kurzbeschreibung (Englisch)

Fire blight has been the major threat to pome fruit production globally since it was first described, and one of the most intensively studied plant diseases over the past 100 years. Despite considerable efforts by major international phytopathology laboratories, it remains today a bane to apple and pear growers worldwide.
Recently, Swiss research delivered a major breakthrough in fire blight research with the complete genome sequencing of the fire blight pathogen and of its most promising biocontrol agents (Smits et al. 2010a,b).

This work is positioned to identify and sharpen biocontrol ‘arrows’ that can improve the efficacy and reliability of fire blight control as an alternative to antibiotics. The project builds upon prior BLW projects and apply genomics in order to deliver practical solutions to fire blight. Three modules link pathogen and biocontrol agent genomics with the purpose to bring long-term, major advancement of fire blight research, as well as short-term results with translation into streamlined discovery and optimization of commercial alternatives to antibiotics.

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• Projektbeschreibung [PDF] 205 kB

Methoden (Englisch)

Module 1: Pathogen
- RNA seq transcriptomics performed on apple flowers just prior to infection, to identify all pathogens expressed
- Proteomics performed on the same flower samples to identify which expressed genes are processed into functional proteins
- Genes identified as critical will be used to construct reporter-gene biosensors
- Pathogen biosensors applied to develop a streamlined screening process
- Applied genomics analyzed to identify plant defense determinants

Module 2: Biocontrol
- RNAseq transcriptomics and proteomics used to identify genes actually expressed in flowers
- Molecular markers designed for genes critical for biocontrol
- Molecular markers applied to streamline the isolation of Swiss biocontrol agents
- Reporter-gene biosensors constructed for biocontrol agents to monitor expression of critical genes under any condition

Module 3: Systems Biology - Epidemiology
- Results from modules 1 and 2 integrated into epidemiology study of the pathogen and biocontrol agents in orchards
- Molecular tools adapted and applied to monitor pathogen behavior directly in orchards

Projektziele (Englisch)

The global objective of the project is to deliver practical solutions to fight against fire blight.

More precisely, the project is intended:
- To streamline screening of new control compounds
- To optimize application and formulation conditions that improve activity
- To improve phytosanitary control measures
- To ensure durability of host resistance

Publikationen / Ergebnisse (Englisch)

Modul 1a - Pathogen genomics and diversity
Significance of the acquired knowledge for an improved fire blight management
Comparative genomics enabled the development of biomarker-based tests for detection of E. amylovora  and epidemiological studies. A new test (LAMP) is now available, which allows detection of low numbers of E. amylovora in the field within 15 min. The performance of this test regarding sensitivity, specificity, speed and simplicity is equivalent or greater than real-time PCR (TaqMan), immunoassays (e.g., AgriStrip®) and plating. Its practical utility needs to be assessed by implementation into routine testing. Using the VNTR-based method, specific E. amylovora strains can now be detected. This method is beneficial for epidemiological studies at different geographic levels and allows tracking of fire blight spread. The knowledge gained in such studies will be important for prevention of further dissemination of the disease.

Modul 1b - Pathogen and host transcriptomics
Significance of the acquired knowledge for an improved fire blight management
Transcriptome analysis of both E. amylovora and apple identified genes that are expressed
during the infection process. The identified virulence genes of E. amylovora may serve as new
marker genes and biosensors could be developed to monitor their expression in planta and to
screen new fire blight products with a suppressive activity.
In the apple genome, pathogen resistance and general stress response were up-regulated.
Genes involved in the specific response to E. amylovora could be identified by comparing
transcriptomes of apple challenged with different bacteria. The results gained in these studies
could be used to improve resistance breeding.

Modul 2a - Pantoea genomics and diversity
Significance of the acquired knowledge for an improved fire blight management
Antibiotic biosynthesis clusters of Pantoea with impact on the biocontrol efficacy were identified. The results are prerequisites for the development of the molecular markers in Module 2b.

Modul 2b - Molecular markers
Significance of the acquired knowledge for an improved fire blight management
Molecular markers were used to develop tools for tracking and detection of biocontrol strains and clarify misidentification of Pantoea spp. The environmental behavior of biocontrol strains after their release can now be studied, which helps to optimize application rate and timing to get sufficient efficacy against the pathogen. The available methods identifying biocontrol determinants (e.g., antibiotic synthesis clusters) facilitate isolation of new biocontrol strains with high potential. Finally, Pantoea spp. can reliably be identified to avoid wrong classification.

Modul 2c: QS-mutants and Pantoea transcriptomics
Significance of the acquired knowledge for an improved fire blight management
Analysis of the transcriptome data of P. agglomerans E325 is ongoing. The results will give insight into QS-controlled processes of the fire blight antagonist. Genes important for biocontrol activity could be identified and used in follow-up projects to construct additional biosensors to improve the biocontrol efficacy (see Module 2d).

Modul 2d: Biosensors
Significance of the acquired knowledge for an improved fire blight management
A biosensor is now available, which enables quantification of antibiotic-production in P. agglomerans  E325 under different conditions. Optimal conditions can be evaluated and results implemented into the formulation of the biocontrol strain to achieve highest efficacy against E. amylovora.
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Zugehörige Dokumente

• Final Report ACHILLES 2014 [PDF] 3'929 kB