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ChitinOMix: A multidisciplinary project to understand the effect of chitin soil amendment on the plant response, natural microbial community and the fate of human pathogenic bacteria

English title ChitinOMix: A multidisciplinary project to understand the effect of chitin soil amendment on the plant response, natural microbial community and the fate of human pathogenic bacteria
Applicant Pothier Joël F.
Number 189340
Funding scheme Project funding
Research institution Zürcher Hochschule für Angewandte Wissenschaften
Institution of higher education Zurich University of Applied Sciences - ZHAW
Main discipline Agricultural and Forestry Sciences
Start/End 01.08.2020 - 31.07.2024
Approved amount 697'093.00
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All Disciplines (5)

Discipline
Agricultural and Forestry Sciences
Environmental Research
Ecology
Molecular Biology
Experimental Microbiology

Keywords (11)

suppressive effect; chitin; soil amendment; OMICS approaches; preharvest; Salmonella; phyllosphere; lettuce; rhizosphere; Arabidopsis; human pathogens

Lay Summary (French)

Lead
La consommation de fruits et de légumes est considérée comme importante pour une alimentation saine et équilibrée et est reconnue comme source significative de vitamines et de fibres. Les autorités encouragent la consommation de produits végétaux frais, mais la sécurité alimentaire des fruits et légumes frais reste une préoccupation majeure. Il est désormais largement admis que bactéries pathogènes pour l’homme peuvent survivre sur les plantes. L’amendement des sols avec de la chitine s’est avéré prometteur pour améliorer la qualité des sols, la croissance et la résistance des plantes. L’objectif de ce projet est de mieux comprendre les mécanismes de suppression des agents pathogènes suite à l’amendement des sols avec de la chitine afin de proposer une alternative pour réduire le risque de contamination des produits frais avant la récolte, l’étape de production la plus importante pour réduire le risque pour la santé humaine.
Lay summary

Ce projet du SNF-FWO se concentre sur la recherche et la consolidation des facteurs causaux de l’effet suppresseur en utilisant des approches OMICs innovantes et ambitieuses (par exemple la métagénomique, le dual RNA-seq combiné à la métabolomique) en combinaison avec de la microbiologies classique reposant sur des étapes de culture ou bien encore avec l’étude de mutants de la plante. Salmonella a été choisis comme bactérie modèle étant donné le nombre élevé de foyers liés aux produits frais. La laitue a été retenue comme modèle de plante comestible car il s’agit d’une culture sensible étant donné les conditions humides favorables existant entre les feuilles de la plante. Des expériences seront également réalisées sur la plante modèle Arabidopsis afin de comparer nos résultats avec les connaissances fondamentales concernant le système d’immunité de la plante.

Direct link to Lay Summary Last update: 28.07.2020

Lay Summary (English)

Lead
The consumption of fruit and vegetables are considered as important for a healthy and balanced diet and recognized as a significant source of vitamins and fibre. Authorities encourage the consumption of fresh plant produce, but food safety of fresh fruits and vegetables continues to be a major concern. By now it is a well-accepted fact that human pathogenic can survive in plants. Soil amendment with chitin has been shown to be promising for improving soil quality, plant growth, and plant resilience. The suppressive effect on human pathogens in the phyllosphere was only recently described. The objective of this project is thus to gain a deeper understanding of the mechanisms behind pathogen suppression in order to offer an alternative to reduce the contamination risk of fresh produce during preharvest, the most important production step to reduce the human health risk.
Lay summary
This SNSF-FWO project will focus on finding and consolidating the causal factors of the suppressive effect of soil amendment with chitin by using innovative and challenging OMICS approaches (e.g. shotgun metagenomics, dual RNA-seq combined with metabolomics) in combination with classical culture dependent microbiology and plant mutant studies. Salmonella is chosen as model pathogen, given the high number of outbreaks related to fresh produce. Lettuce is chosen as a model for an edible crop, it is a susceptible crop given the conducive wet conditions between the leaves of the plant. Secondly, experiments will also be performed on the plant model Arabidopsis in order to compare our results with the known fundamental knowledge regarding the plant immunity system.
Direct link to Lay Summary Last update: 28.07.2020

Responsible applicant and co-applicants

Employees

Associated projects

Number Title Start Funding scheme
182625 Encoding, regulation and decoding of early plant receptor kinase signaling 01.01.2019 Project funding

Abstract

Vegetable consumption is considered important for a healthy diet. Authorities encourage the consumption of fresh plant produce, but its food safety continues to be a major concern. It is an accepted fact that human pathogenic bacteria including Salmonella enterica, are able to survive in plants. Chitin is the second most abundant biopolymer in nature after cellulose. Soil amendment with chitin has been shown to be promising for improving soil quality, plant growth, and plant resilience. A suppressive effect on human pathogens in the phyllosphere was only recently described. The objective of ChitinOMix is to gain a deeper understanding of the mechanisms behind pathogen suppression in order to offer an alternative to reduce the contamination risk of fresh produce during preharvest, the most important production step to reduce the human health risk. This project will focus on finding and consolidating the causal factors of the suppressive effect by using innovative and challenging OMICS approaches (e.g. shotgun metagenomics, dual RNA-seq combined with metabolomics) in combination with classical culture dependent microbiology and plant mutant studies. Salmonella is chosen as model pathogen, given the high number of outbreaks related to fresh produce. Lettuce is chosen as model for an edible crop. Secondly, experiments will be performed on the plant model Arabidopsis in order to compare our results with the known fundamental knowledge regarding the plant immunity system.
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