This project evaluated two of the newer discovery platforms, proteomics and metabolomics, for effectiveness in the identification of functional biomarkers that differentiate closely related bacterial pathovars. Diagnostics based on functional molecules linked to pathogenicity overcome the limitations of many diagnostics based on anonymous, plasmid-borne or incidental targets. Selected biomarkers were adapted to reliable, high throughput, rapid turn-around diagnostics for the model organisms.

Research outcomes:

This project has demonstrated the effectiveness of proteomics and metabolomics, two novel approaches that identify functional molecules, to discover biomarkers that differentiate closely related bacteria.

Novel diagnostic targets have been identified and validated that differentiate organisms to the levels of specificity required, but not previously available.

Novel diagnostics will translate to improved incursion response because their greater specificity and reliability reduce turn around time.

New specialist capacity and partnerships developed.

Research implications:

This project has delivered positive results in terms of scientific resources and human capacity. The finding that these platforms can fast-track the identification of biomarkers with new specificities, and at the level required, can inform investment decisions for the PBCRC in future.

New diagnostic technologies have been developed that will be incorporated into the National Diagnostic Protocol (NDP) and could be adapted to delivery through a range of other platforms. This provides security to industry and those responsible for surveillance and disease management programs. Extensive data has been generated that is yet to be mined, but is likely to deliver further tests in future, without significant further investment.

Significant specialist capacity in bacteriology has been fostered both nationally and internationally, through recruitment and professional development, which will benefit Australia’s plant industries through local expertise and trusted ‘off-shore intelligence’.

Acknowledgements:

Gary Kong and the CRC NPB Board for funding a ‘blue sky’ project.

Leanne Bringolf for excellent technical assistance.

Aneesha Deanensen for initial technical work at SABC.

Platforms to differentiate exotic pathovars of plant bacteria - Final Report [13]

The project aims to determine the potential risks associated with climate change for key wheat pathogens; wheat using stripe rust, crown rot and Barley yellow dwarf virus and its aphid vector.  The research approach is three-fold:

1. Modelling the effects of increasing temperature on the biology and distribution of pests and diseases and vectors e.g. the bird cherry oat aphid, Rhopalosiphum padi
2. Collecting real-time data on host-pathogen/pest interactions from field experiments using wheat grown under elevated CO2, and
3. Developing adaptation plans for government and industry based on the above data to mitigate any increased risks posed by climate change to biosecurity of wheat crops.

What is the biosecurity problem?

Climate change is clearly recognised as a major threat to agricultural systems. The expected increase in temperature, atmospheric CO2, heavy and unseasonal rains, increased humidity, drought and cyclones, are likely to affect crops, pests and diseases and host pathogen interactions. However, the extent to which climate change will affect emergency pests and pathogens and their hosts is not clearly understood. A review of the impacts of climate change on plant biosecurity (Aurambout et al. 2006) indicated a need to document pest and disease responses to climate change and incorporate them into our management and contingency planning. To respond to future climates, changes to industry practices and government policies may be required. This project will identify the potential risks associated with climate change and plant biosecurity.  Adaptation plans will be developed around these risks to inform industry practice and policy.

The main outputs of this project are to:

• provide new knowledge on the effects of elevated atmospheric CO2 on key wheat diseases, and
• develop a series of tools to inform industry and government to enhance our contingency planning to include the influence of climate change on biosecurity

Who will be the end-users of this research?

• Biosecurity policy and decision makers e.g. BA, OCCPO, PHA, state biosecurity agencies,
• PHA - data and tools will enhance threat categorisation and industry biosecurity plans
• OCCPO - data and tools may be used in incursion responses
• Industry - to adjust management strategies and biosecurity plans and increase their level of preparedness for climate change

This is a screenshot output from the Asian citrus psyllid - citrus growth model using the IPPC A1Fi climate change scenario with a Google Earth application. The ground overlay represents daily spatial variation in the population of adult psyllids displayed sequentially in an animation of 365 frames for the year 1990. The graphics depict temporal variations in the population of the Asian citrus psyllid and increasing temperature for the years 1990, 2030 and 2070 for a specific location. A total of 11,330 graphics can be accessed in the interface (one graph for each 50 km, two-grid cell on which the model was run) providing Australian coverage can be accessed in the interface (one graph for each 50km two-grid cell on which the model was run) providing Australian coverage.

  [21]

The CRCNPB would like to thank Asia-Pacific Network for Global Change Research for their contribution to this project.

This project will provide alternative eradication strategies for emergency plant pest incursions on perennial crops. It will also reduce economic costs and social impact from emergency plant pest eradication measures. The viticulture industry has been selected as an initial pilot with a focus on developing alternative pruning techniques to remove the emergency plant pest but allow enough residual plant material to ensure rapid grapevine regeneration.

What is the biosecurity problem?

The current strategy to eradicate an emergency plant pest is based partly on the removal of whole affected plants, followed by burning and burial. However, this practice incurs significant costs to industry and the community when perennial species are involved. Alternative strategies need to be developed that meet eradication goals while reducing the economic and social impact.

The main outputs of this project are to:

• conduct due diligence on current eradication strategies using responses to citrus canker, fireblight and banana freckle as case studies
• develop a research and development model system that features identification of endemic pathogens with similar biology and epidemiology to high priority target emergency plant pests and a system for the validation of eradication strategies in countries where the emergency plant pest is endemic
• develop novel alternative strategies that meet eradication goals while minimising negative economic and social impact.
• implement novel research strategies on key exotic diseases in partnership with leading international laboratories.

Who will be the end-users of this research?

Contact with industry through grower workshops and meetings throughout the project will provide important feedback on the practicality and economic advantage of proposed alternative eradication strategies. The development of strategies will be undertaken in consultation with relevant regulatory authorities. Plant Health Australia will be engaged to gain an understanding of the possible implications of the new drastic pruning strategy in the context of PLANTPLAN.

This project evaluated current surveillance systems for EPPs using Bayesian statistical methods and identifed other sources of data that could be used to complement existing surveillance programs. It  also evaluated specific surveillance methods and tests such as visual inspection by field and quality assurance staff and diagnostic tests used in the identification of plant pathogens.

What is the biosecurity problem?

Under the Agreement on the Application of Sanitary and Phytosanitary Measures (SPS agreement) countries are no longer allowed to restrict imports of plant products for non-scientifically justifiable reasons and the need to provide valid data supporting the status of plant pathogens of concern is becoming increasingly important.

Current plant pathogen surveillance systems are often focused on targeted surveillance for a specific pathogen and methods are based on 'expert opinion' and historically used tests. These surveillance systems only report on the pest status in a particular time period, effectively a ‘snapshot' and are often expensive to implement due to the large number of samples required to provide sufficient confidence of obtaining an accurate representation of the pest status in a given region or country at that time.

The main outputs of this project were to:

• assess the application of statistical and modeling tools for their evaluation of plant health surveillance systems
• develop methods for identifying different risks in population subgroups based on risk-based analysis
• develop methods for risk-based surveillance design
• statistically evaluate methods and tests currently used in surveillance systems, and
• assess alternative sources of data available that may contribute towards demonstrating disease freedom and early detection of EPPs.

Who are the end-users of this research?

The tools and methodologies developed in this project are most applicable to government departments for use in designing future surveillance programs, assessing current surveillance programs and demonstrating disease freedom for use in the support of market access applications. The tools and methods developed are also applicable for assessing surveillance data supplied by trading partners as part of import applications.

This project will develop tools for plant pathogen recognition to support rapid response to disease threats.

What is the biosecurity problem?

The development of tools for pathogen recognition enabling rapid response has been listed as one of the top issues to improve Australia's preparedness to deal with emerging disease threats.

The main outputs of this project are to:

• develop methodology for DNA detection of airborne pathogens from spore traps using known model systems.
• develop methodology for monitoring exotic and unknown pathogens in spore traps (using community analysis DNA methods such as T-RFLP).
• develop and evaluate alternative eradication strategies for high priority emergency plant pests affecting industries based on perennial species.

Who will be the end-users of this research?

This project will deliver a new PhD graduate trained in plant pathology with specific skills in pathogen detection and monitoring. The graduate will be available for employment within the Australian plant biosecurity system, enhancing Australia's capacity for pathogen recognition and enabling rapid responses to emergency plant pests.

The project will provide improved surveillance tools for rapid, widespread detection of plant pathogens in crops and native vegetation by producing a library of unique spectral signatures that identify specific foliar emergency plant pest pathogens, and detection hardware. Off-the-shelf digital still and video cameras will be re-formatted for a specific pathogen signature, allowing surveillance staff to undertake field assessment with this visual aid. In time, this type of assessment could become the main tool to aid in the declaration of area freedom for emergency plant pest pathogens.

What is the biosecurity problem?

Current ground surveillance by trained staff for emergency plant pest pathogens is inefficient and time-consuming. As a result, this project is the first step in developing hyperspectral camera technology that detects specific signatures in plant leaves for a large number of species.

The main output of this project is to:

• assess the potential of hyperspectral imaging to detect plant pathogens (bacteria, viruses, fungi and phytoplasmas), and
• analyse the cost-benefits of hyperspectral imaging for widespread surveillance of plant pathogens.

Who will be the end-users of this research?

Federal and state agencies involved in on-ground surveillance indicate strong interest in imaging technology for plant pathogen surveillance.

This research project will increase our knowledge about the epidemiology and biology of the exotic plant pathogen Fusarium wilt of banana caused by Fusarium oxysporum f. sp. cubense ‘tropical' race 4 (Foc TR4)

What is the biosecurity problem?

The strain Foc TR4 is already present in Australia (Darwin). However, through quarantine measures the disease has not progressed further than the outer Darwin rural area. Once Foc TR4 is introduced to a new area, establishment and further spread is rapid. Much about how the disease spreads so effectively is unknown. As yet, there are no methods of eradication of this fungus from a banana plantation. Alternative strategies need to be developed and validated that meet control and containment goals while minimising economic and social impact. This is particularly important if Foc TR4 is detected in important banana growing regions of Australia, such as Queensland, which is responsible for 95% of the Australian banana industry.

The main outputs of this project are to:

• increase in our knowledge of the epidemiology of Foc TR4
• Further understand of the infection processes of Foc TR4
• develop methods for containment and control of Foc TR4

Who will be the end-users of this research?

The potential end users of the knowledge acquired in this study includes people in the banana industry as well as people involved with Primary Industries.