Current projects of the Environmental Genomics and Systems Biology Research Group

Massive detection of tomato brown rugose fruit virus by high-throughput sequencing (ToViPoRe)

Tomato plants affected by Tomato Brown Rugose Fruit Virus. — Infected tomato plants. (Source: Salvatore Davina, Heike Scholz-Döbelin, https://gd.eppo.int)

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

Close-up of sliced onions with clear signs of decay, displaying browned edges and a mushy texture against a dark background. — Decaying layers like this can show up both in home grown and store purchased bulbs affected by the Enterobacter bulb disease 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

A collection of petri dishes, each containing varying stages of fungal growth, mostly grayish-white in color, organized in rows against a dark background. — Effect of UV-C Exposure on Botrytis spores.
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.