Current projects of the Environmental Genomics and Systems Biology Research Group
Massive detection of tomato brown rugose fruit virus by high-throughput sequencing (ToViPoRe)
Swiss agriculture is under pressure from the highly contagious Tomato Brown Rugose Fruit Virus (ToBRFV). The virus affects tomatoes and peppers, leading to severe crop losses and significant economic damage. It spreads mainly through tools or plant material and is further distributed via global trade in seeds and seedlings. Since 2021, the virus has been repeatedly detected in imported plants in Switzerland.
Swiss tomato producers are therefore calling for improved diagnostic tests, as current methods are unsuitable for large-scale testing. A research project funded by the Federal Office for Agriculture aims to develop a fast, specific, and cost-effective molecular test and to combine it with high-throughput sequencing. This would allow for the detection of the virus and related pathogens while enabling the simultaneous analysis of multiple samples.
Collaborating with stakeholders from research and practice, the initiative is breaking new ground in plant pathogen diagnostics, with the potential to revolutionize future detection methods.
Project duration: 02/2023-01/2025
Project partners: Bundesamt für Landwirtschaft BLW, Agroscope, Landwirtschaftliche Zentrum Liebegg, Bioreba AG
EBDOmics – Comparative genomics of Enterobacter spp. causing bulb decay of onions
Enterobacter bulb disease of onions (EBDO) is caused by members of the Enterobacter cloacae complex, a diverse group of Enterobacter species found in both clinical isolates and the environment. Despite its long-standing recognition, systematic studies on the taxonomy of these isolates and the virulence factors specific to plant pathogens are lacking.
The project aims to determine the position of EBDO isolates within the Enterobacter genus using modern taxonomic and phylogenomic methods. Isolates will be collected and tested for their ability to cause EBDO (WP1). The genomes of plant-pathogenic isolates will be sequenced to clarify their taxonomic placement (WP2). Pan-genome analyses of plant-pathogenic and clinical isolates will identify pathogenicity factors and assess their role in onion disease (WP3).
Based on the genomic data, LAMP-based diagnostic tests will be developed to enable early detection of plant-pathogenic isolates in the field (WP4). The project provides valuable insights into distinguishing plant-pathogenic, environmental, and clinical isolates, aiding the prevention and management of EBDO. Additionally, it contributes to understanding the role as an opportunistic human pathogen of the E. cloacae complex.
Projektlaufzeit: 01/2022-04/2025
Project partners: University of Pretoria; University of the Witwatersrand; University of Venda; University of Limpopo
Contracting body: Swiss National Science Foundation / Project Nr. 204333
Efficacy of Far-UV-C and development of a rapid test for Botrytis resistance
The spores are eliminated after just 60–120 seconds of UV-C exposure.
The Environmental Genomics and Systems Biology research group at ZHAW is conducting additional studies alongside the Federal Office for Agriculture (FOAG) project, "Non-chemical treatment of strawberry seedlings against Botrytis cinerea". The project includes several modules. One focuses on identifying UV-C wavelengths that are more effective and safer to use (far-UV-C). Unlike conventional UV-C, far-UV-C cannot penetrate human tissue. This module tests the effect of far-UV-C on various pathogens and determines its efficacy. Another module, "Rapid Test Development," involves creating a molecular rapid test to detect Botrytis resistance to botryticides.
List of projects
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Sepsis-Associated Microorganisms in Brazilian Ambulatories (SAMBA) (SAMBA)
Fifty-six cases of bloodstream infections caused by contaminated total parenteral nutrition were recorded between November 2013 and July 2014 in four Brazilian states resulting in 15 deaths. One of the bacteria involved, albeit repeatedly causing similar outbreaks, is habitually misidentified in…
completed, 01/2016 - 12/2016
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Silent pathway awakening to discover novel antibacterial compounds from actinomycetes
There is a tremendous need for novel antibiotics due to the global resistance crisis. Actinomycetes are the most important sources of secondary metabolites. They provide an enormous potential to discover novel antibiotics.
completed, 08/2019 - 01/2021
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CarbonATE - microbiological methanation
Development of an enzymatic CO2-capture strategy for an optimised microbiological methanation
completed, 03/2019 - 12/2022
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Turf Pathogen Screening System using Loop Mediated Isothermal Amplification
The objective is the development of a real-time pathogen screening system for a group of global relevant turf grass diseases using loop mediated isothermal amplification, LAMP technology. From a turf sample, DNA isolated and amplified using LAMP. Pathogen occurrence in the sample will be detected…
completed, 12/2021 - 12/2023
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XhortOMICs: Diagnostic and epidemiological tools for the Xanthomonas hortorum species-level clade based on OMICs technologies
Despite its recent re-emergence and increased prevalence in many countries, the research on Xanthomonas hortorum species-level clade members has been very limited until now. It is thus important to have an increased knowledge thereof to be able to react to its increasing occurrence. Therefore, the…
completed, 04/2018 - 06/2022
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Development of a fast and exact method for R. solanacearum detection in Swiss surface water samples
The broad-host range plant pathogen Ralstonia solanacearum is a treat for Swiss agriculture and therefore classified as quarantine organism. The current detection methods are, however, cumbersome. Testing surface water at strategic sites, especially downstream of locations where potential host…
completed, 03/2018 - 03/2020
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LAMP Diagnostic in Ornamentals
completed, 11/2018 - 12/2020
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DROPSA – Strategies to develop effective, innovative and practical approaches to protect major European fruit crops from pests and pathogens
The DROPSA consortium will create new knowledge and understanding of the damage and losses of fruit crops resulting from pests and pathogens, with a specific focus on the new and emerging threats due to Drosophila suzukii and quarantine pathogens Pseudomonas syringae, Xanthomonas fragariae and X.…
completed, 10/2013 - 02/2018
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In-depth molecular analysis of stool and water samples collected in Kampala, Uganda
A novel approach, combining next-generation sequencing and comparison to custom databases is being tested to assess the impact of wastewater use in agriculture in the city of Kampala, Uganda. The overarching goal of this project is to bring epidemiological studies, classically targeting only one or…
completed, 05/2013 - 04/2017
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High-throughput proteomics of Thiodictyon synthrophicum strain Cad16T
Our goal is to elucidate the proteome of Thiodictyon synthrophicum, a purpur sulphur Gram-negative bacterium, by a shotgun/bottom-up nanoUHPLC-MS/MS approach to better understand its role in the Cadagno Lake ecosystem.
completed, 09/2013 - 12/2018
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Comparative genomics to untangle insect pathogenicity in plant-associated pseudomonads
We study the genomes of an array of plant-beneficial pseudomonads using a comparative genomics approach. The aim is to define the potential of the different isolates as insect pathogens and as plant beneficials.
completed, 11/2016 - 12/2019
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EBDOmics – Comparative genomics of Enterobacter spp. causing Bulb Decay of Onions
Enterobacter bulb disease of onions (EBDO) is caused by members of the Enterobacter cloacae complex. This includes a diverse group of Enterobacter species that occur as clinical isolates and in the environment. Although EBDO has been known for several years, no systematic study has been conducted on…
ongoing, 01/2022 - 02/2026
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Bioprospecting and genomics of actinobacteria isolated from the Marchica lagoon (ActinOmics)
The massive and excessive use of antibiotics in medicine has led to the emergence and spread of multi-resistant pathogens, rendering treatment with the usual antibiotics ineffective. Added to this phenomenon of antibiotic resistance is the emergence of new infectious diseases, often zoonotic, in…
ongoing, 09/2023 - 09/2025
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Development of a pathogen screening system for all globally relevant turf grass diseases
The objective is the development of a near real-time pathogen screening system for all globally relevant turf grass diseases using PCR-ELISA technology against a prepared array of disease specific oligonucleotide probes.
completed, 03/2012 - 03/2018
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Loop-mediated isothermal amplification for real-time pathogen screening in soil
The aim of this project is to develop a real-time pathogen screening system for important soil pathogens using loop-mediated isothermal amplification (LAMP) technology. The process will involve the isolation and amplification of DNA from plant, seed or soil samples. A key challenge will be to…
ongoing, 11/2024 - 12/2026
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Long-term conservation of Arctic char (Salvelinus umbla) in Lake Zurich
In order to ensure a stable population of Arctic char in Lake Zurich in the long term, existing measures (fish stocking and artificial spawning grounds) are being evaluated and optimised. The aim is to make recommendations for terminating useless measures, optimising moderate ones and expanding…
ongoing, 05/2024 - 03/2030
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New Atlas of Mammals of Switzerland and Liechtenstein
completed, 07/2015 - 12/2021
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MALDI-TOF MS for microorganism identification: from pattern recognition towards marker based approaches
In collaboration with Mabritec AG, we have developed a database of an unprecedented nature, the PAPMID (putative assigned protein masses for identification database). Based on over 12,000 sequences of bacterial genomes, it contains the molecular masses of the ribosomal proteins of these…
ongoing, 05/2013 - 12/2029
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Comparative genomics of the plant pathogen Xanthomonas arboricola pv. pruni and related xanthomonads
Xanthomonas arboricola pv. pruni (Xap) causes bacterial spot and canker on a wide range of Prunus spp. (e.g., apricot, peach, plum, al-mond, cherry). Outbreaks on stone fruits can result in severe economic losses to fruit quality and yield, branch/tree dieback, and orchard devastation. Xap is…
ongoing, 05/2013 - 12/2029
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MinION2FixID: fast and reliable legume root nodule bacteria identification using nanopore sequencing technology
Rhizobia are bacterial symbionts associated with legumes that are of paramount importance for the fixation of atmospheric nitrogen in the soil. The success of this process (and ultimately the performance of the plant) depends on the type of root nodule bacteria, which should be adequate to each…
completed, 07/2018 - 06/2019