Forest biosecurity faces significant challenges in surveillance and diagnostics of invasive pests and pathogens due to vast, diverse ecosystems that complicate monitoring efforts. Climate change exacerbates these challenges, altering pest and pathogen distributions and behaviours. International trade and travel further increase the risk of introducing invasive species into novel environments, where existing surveillance and diagnostic tools struggle to keep pace with the scale and complexity of assessing the potential biosecurity threats.
Improved approaches to assessing risk and the subsequent response to forest pests/pathogens is needed given challenges of scale and limited resources. Exploring invasion biology through genomic-based approaches can assist us to better understand the processes of invasion of exotic pests through time and space, and compliment surveillance and diagnostic efforts.
This project is supported by Forest and Wood Products Australia, with direct investment by their grower members.
Aim: The project will use novel genomic and metagenomic methods to study the invasion biology and history of well-established exotic forestry pests and pathogens to investigate how populations have changed post-incursion. This will enable better risk assessment and monitoring of future novel incursions, improving Australia’s overall surveillance and diagnostic systems.
Meet the PhD student for this project
Sylvia Jepkemboi
Sylvia is working on transformational molecular approaches for forest pests and pathogens, which will use novel genomic and metagenomic methods to study the invasion biology and history of well-established exotic forestry pests and pathogens to investigate how populations have changed post-incursion.
This will enable better risk assessment and monitoring of future novel incursions, improving Australia’s surveillance and diagnostic systems.
When not studying, Sylvia enjoys exploring nature, singing in choirs and watching movies.
Supervisors and advisors
Professor Dianne Gleeson, University of Canberra.
Senior Research Fellow Alejandro Trujillo-Gonzales, University of Canberra.
Dr Angus Carnegie, NSW Department of Primary Industries and Regional Development.
Dr Conrad Trollip, NSW Department of Primary Industries and Regional Development.
Approach
This project will use the economically important pine bark beetles and their fungal associates as a model system, with a particular focus on Ips grandicollis and its associated blue-stain fungi (Yousuf et al. 2014; Carnegie et al. 2019; Carnegie and Nahrung, 2019; Trollip et al. 2021).
These biological systems have been particularly challenging to study historically due to the cryptic nature of insect-fungus interactions, environmental factors that influence their lifecycles, and variation in their ability to spread across ecosystems, altogether, making downstream analyses and predictive modelling difficult (Hulcr et al. 2020).
Novel molecular tools can be leveraged to study invasions using a more holistic approach (Six, 2013), allowing us to not only characterise the insects and their fungal associates simultaneously, but also to uncover deeper genetic signatures that may shed light on various evolutionary factors and biological processes within these pest-pathogen invasion systems (Zepeda Mendoza et al. 2023; McGaughran et al. 2023).
Molecular methods may include but are not limited to:
- Targeted DNA enrichment (e.g., insect mitochondria) and shotgun sequencing.
- Genome-skimming approaches (0.1× and 1× coverage) for cost-effective development of genome-based tools.
- Metagenomic analysis of microbial (fungal) associates
- Single-cell sequencing of individual beetles
- Utilizing ‘omic data sets for genotype–environment associations in parallel with gradient forest analysis to iteratively partition climatic variables and adaptive genetic variation
Research objectives:
- Compare different metagenomic approaches (standard shotgun vs low-coverage skimming vs mitochondrial enrichment (centrifugation) to study Ips grandicollis populations. Can this same data be used to study fungal associates?
- Explore single-cell sequencing as an approach to recover metagenomic assembled genomes (MAGS) of fungal associates from a beetle sample – compared to datasets above? Which metagenomic approach allows accurate assessment of core fungal associates and insect populations?
- Population dynamics and invasion history of Ips grandicollis – sampled from across Australian mainland and if possible, native range retrospectively in herbaria.
- Population dynamics and invasion history of fungal associates.
Questions? Questions about this project can be directed to Sarah Adams, Chief Operating Officer, at plantbiosecurity@anu.edu.au or +61 459 341 281.