Fungi are a major biosecurity concern because they cause a wide variety of plant diseases that threaten agricultural productivity, market access, and natural ecosystems. The surveillance of fungal pathogens is an essential part of Australia’s biosecurity efforts. However, airborne fungal spores are especially challenging to monitor due to the small size of the spores, their wind-driven dispersal over long distances, and the low concentration of the spores relative to the vast volume of the air that can carry them.
A spore trap is a device designed to capture spores from the air for subsequent analysis. When deployed in the field, a spore trap can be used to monitor the abundance and diversity of fungal pathogens that are present in the surrounding environment. Existing research has developed a variety of designs for spore traps, ranging from low-cost passive devices through to sophisticated high-volume automatic samplers.
These traps have been used for many years in studying the epidemiology of plant diseases. However, there has been less effort directed towards the efficient and effective application of spore traps for biosecurity surveillance. Significant questions remain about the optimal design of the traps, when and where to deploy them, the limits of detection, whether certain taxa are more or less likely to be detected, and the sensitivity of the design to various operational and weather conditions.
If a device is to be used for biosecurity, then there needs to be robust scientific evidence about its ability to reliably determine the presence or absence of the pathogen in airborne biota.
Aim: The project aims to improve our understanding of how to use spore traps for biosecurity. The project will explore a variety of trap designs and investigate the best way to deploy them. Ultimately, the project will work towards ground-truthing the effectiveness of the trap itself as well as the effectiveness of a surveillance system consisting of a network of traps. The project will contribute towards the evidence base needed to support the real-world deployment of a spore-trap based biosecurity surveillance program.
Meet the PhD student for this project
Shiron Thalagala
“My name is Shiron Thalagala, and I hold a Bachelor’s degree in Production Engineering and a master’s degree in Electromechanical Engineering. I am passionate about developing mechatronic systems and applying machine learning for systems control. Currently, I am pursuing a PhD titled where I am developing an advanced fungal spore monitoring system. My research combines electronics, mechanical design, and computational fluid dynamics (CFD), while also integrating machine learning and computer vision to detect and analyse fungal spores. The ultimate goal of my work is to strengthen the Australian biosecurity industry by providing reliable surveillance tools against potential fungal pathogens.
Outside of research, I enjoy running, meditation, and yoga.”
Supervisors and advisors
Associate Professor Bronson Philippa, James Cook University.
Dr Rohan Kimber, Dr Nicole Thompson, Dr Daniele Giblot-Ducray, Dr Kelly Hill, South Australian Research and Development Institute (SARDI).
Approach
The project will include a combination of the following activities.
- Review existing research on spore traps, the various trap designs that have been reported, and previous research about their use in surveillance systems, with a particular focus on the potential uses for biosecurity.
- Design or refine new traps, including innovative electrical or mechanical aspects, depending upon the student’s interest. Potential approaches include the development of low-cost electronics or capture techniques within the trap and/or optimising the mechanical design using computational fluid dynamics and wind tunnel testing.
- Use the experimental data to develop models using machine learning or other methods to support the optimal placement of traps to capture the most information, considering local weather conditions, seasonal variation, the availability of host plants, topography or landscape scale dynamics and logistical constraints in the deployment strategy.
- Extend trap design applications to examine mobile (moving) trapping across landscapes, especially in context of responsive surveillance for biosecurity.
- Develop methods to assess the accuracy of spore trap surveillance and apply these to build an evidence base to inform surveillance efforts across Australia.
Want to know more? Email shiron.thalagala@my.jcu.edu.au.