Under the WTO there is increasing pressure on countries to comply with agreed sanitary and phytosanitary standards (SPS) to satisfy trading partners and to access markets. Such SPS conditions apply equally to developed and developing countries, however the latter often lack the expertise, infrastructure and organisational processes required to meet such standards. Together, these elements form the Plant Health System of a country and serve both its trading activities and crop protection needs.

Plant pest diagnostics is at the heart of any Plant Health System and countries that do not have the ability to identify its pests cannot satisfy the requisite SPS conditions for trade. Nor can they protect against the incursions of pests or manage the pests that damage crops. The lack of a Plant Health System is then a huge impediment to economic growth for developing countries.

Research outcomes:

We designed training activities and implemented a workshop program to improve the capability and capacity of plant pest diagnostics in Thailand. The program focussed on current technologies to provide Thailand with fundamental systems and processes that will provide greater efficiencies in diagnostics and which can be expanded across the Thai Plant Health system. The program focussed on providing molecular identification, traditional taxonomy, digital knowledge systems and remote microscopy which led to the following outcomes.

• A Molecular diagnostic laboratory was established in Thailand and staff were embedded in Australian laboratories to learn up-to-date molecular techniques and work practices. The high level of skill attained by Thai scientists was demonstrated in their ability to routinely perform molecular techniques in their own lab, to train their own staff in molecular techniques and to develop diagnostic protocols and optimise existing tests for their own purposes. The focus of this training was on trade sensitive pest groups, such as citrus canker, Huanglongbing, viruses, nematodes, fruitfly and seed-borne bacterial pathogens, to give a good grounding in molecular identification.
• The discovery of new fungal pathogens and the documentation of known pests during the course of this project indicates that staff were able to apply taxonomic principles as well as molecular techniques to verify pest identification. Digital technologies such as advanced image capture techniques and web-based information systems were introduced to Thai scientists so that they could document their diagnostic information and share it over the internet to provide a valuable source of diagnostic information. The Thailand Biosecurity website was established for this purpose.
• Image capture hardware and software were provided together with intensive training and user guides so that high quality images of pests could be obtained for the website. A special laboratory was established by Plant Quarantine for this equipment and for training staff in image capture techniques and use of the website.
• Microscope hardware for remote diagnostics was installed in Bangkok, Chiang Saen, a quarantine port on the northern border with Laos and Myanmar, and at Laem Chiang, the major sea port. A dedicated lab was established in Bangkok for the equipment and remote microscope (RM) operations, as well as for training staff. Post Quarantine (PQ) has plans to establish nine more RM at key border ports to manage the identification of pest interceptions. These systems will be installed according to our specifications.
• An additional use of the RM equipment is that it can be used to remotely train staff in pest identification. RM interactions with experts in Australia were conducted during the course of the project for this purpose.

Research implications:

The current project has provided both skills and lab infrastructure that improve the ability of Thai Post Quarantine PQ to identify and respond to pest threats more efficiently. There is strong support for these new developments from the Thai PQ managers (because of trade implications) and a good prospect that they will continue to develop their expertise and lab infrastructure into the future.

Acknowledgements:

This project was co-ordinated by the Cooperative Research Centre for National Plant Biosecurity in collaboration with its partners, including the CSIRO, Department of Primary Industries and Fisheries Queensland, the Department of Primary Industries Victoria and the NSW Department of Primary Industries.

Thanks also to Dr Ken Walker of the Museum of Victoria who supported training for Thai scientists as well as the development of the Thailand Biosecurity website.

The uses of plant disease and insect collections are numerous but most importantly for taxonomic research and comparative biology. From a biosecurity perspective, these collections allow the development of specimen-based pest lists that are critical for resolving quarantine issues related to agricultural trade. Typically, plant disease and insect specimens are stored in a way that helps preserve the organisms' morphology but not necessarily their DNA. In the age of genomics, DNA sequencing has become one of the most important tools for identifying organisms and for biodiversity studies.

Research outcomes:

The major outcome of this project was the development of the Biosecurity Bank, a national reference collection of DNA samples from plant pathogens. In building the framework for the Biosecurity Bank, the existing Queensland Primary Industries and Fisheries Plant Disease Herbarium database was modified to include new fields for the archiving of information relating to DNA samples and clones. Using this database, it is now possible to link DNA samples to voucher specimens to facilitate taxonomic verification at a later date.

A new web site, www.biosecuritybank.com, was also developed to provide a portal to the DNA collection for the general scientific community to allow searches for samples of interest. The domain has been registered and the site is now live and hosted by Southern Cross University.

A method for storing DNA at room temperature was evaluated but unfortunately, this method did not preserve the DNA as well as storage in a freezer and therefore the latter has been adopted for maintenance of the collection.

Work has begun to populate the Biosecurity Bank with samples and so far 36 samples have been added including those from pathogens that cause citrus canker, tomato leaf curl and Panama disease.

Research implications:

Plant disease herbariums are reference collections of microorganisms (plant pathogens) that cause disease on crops, weeds and native plant species. Specimens held in these collections are important for taxonomic and biodiversity research but also are very important for biosecurity as they allow the development of specimen-based pest lists that are needed for resolving quarantine issues associated with agricultural trade.

Pressed plant specimens are the most common type of specimen held in plant disease herbariums, and provide a good record of the pathogen’s morphology. However,  as previously stated this method of storage is sub-optimal for preserving DNA.

In developing the Biosecurity Bank, the Australian scientific community is now provided with a reference collection of DNA samples from plant pathogens, which could potentially be used in all types of research projects, from the development of molecular diagnostic assays to ‘gene-mining’ for biologically-active compounds. To provide even greater assurance of the origin of the DNA, samples will be linked to voucher specimens held in Australian plant disease herbariums. 

Acknowledgements:

Funding from the Office the Chief Plant Protection Officer, Australian Department of Agriculture, Fisheries and Forestry, is gratefully acknowledged.

The objective of this project is to produce an inventory of Australian Epiphyas species which, combined with host plant information and reliable identification tools for caterpillars (molecular) and adults (molecular and morphological), will expand our knowledge of the genus, address the concerns of our agricultural trading partners and remove the threat of unjustified quarantine measures.

What is the biosecurity problem?

Epiphyas is a large genus of Australian moths. The light-brown apple moth (Epiphyas postvittana) is a native pest that attacks various horticultural crops. The larvae of Epiphyas caryotis, E. liadelpha, E. pulla and E. xylodes are also known to feed on cultivars in a variety of plant families and are difficult to distinguish from their relative - the light-brown apple moth.

The main outputs of this project are to:

In addition to providing the tools for Epiphyas pest species identification, the revision will inform the management of Australia's biodiversity by providing a sound taxonomic base for all future research involving Australia's indigenous Epiphyas species and their native habitats.

Who will be the end-users of this research?

Agricultural Departments, Quarantine Services, Lepidopterists, Ecologists and other managers of Australia's biodiversity and plant biosecurity.

(Left & middle) ~ Brindabella woodland (ACT); Epiphyas caryotis (male).
(Right top & bottom) ~ molecular + morphological identification tools.

This project is developing a mix of digital technologies designed to provide the building blocks of future diagnostic information systems. The Plant Biosecurity Toolbox™ and the Biosecurity Bank are web-based tools which provide users with specific diagnostic information to assist them identify the plant pest or disease. The Plant Biosecurity Toolbox™ can be accessed through PaDIL* and hopefully in the future users will also be able to access the Biosecurity Bank through this portal.
 

In addition, a Remote Microscope Network allows species experts to view and identify specimens in real time via a microscope and internet connection. This tool facilitates access to experts both nationally and internationally to support fast and inexpensive diagnostics. Current nodes of the network include most states of Australia, New Zealand, Indonesia and some south-east Asian countries.
 

What is the biosecurity problem?

The frenetic increase in the pace of people movement and international trade puts added pressures on our borders and a greater need to quickly identify potential harmful pests and diseases. Through retirement of skilled diagnosticians and a low-level of uptake to study these disciplines, we are seeing a decline in our human capital. It is essential that alternative strategies are developed to support quick and accurate diagnostics in an increasingly resource poor environment.

The main outputs of this project are to:

• develop a standard diagnostic information template in collaboration with staff involved in plant biosecurity diagnostics
• audit diagnostic information relating to harmful pest and diseases to populate the template and identify gaps in diagnostic information, and 
• provide a web-based portal to access diagnostic information.

Who will be the end-users of this research?

Users will range from inspectors in our ports and borders to field-based crop protection officers, to taxonomists and experts in labs. This may include farmers, consultants, policy makers, regulators or just simply members of the public. Users may be national or international. These tools engage a wide audience and provide information at a number levels – from taxonomy and general biology to risk analysis and detailed molecular tests.

What this means for future diagnostics

Viewed independently, the tools present the user with a simple pathway to solve a diagnostic problem and in so doing, perform the useful biosecurity function of pest identification. Wider access and use of the tools will be enhanced through the application of better digital technologies, such as personal digital assistants, wireless networks, portable remote microscopes, dedicated web portals and organised networks of facilities with agreed standards and processes.

Beyond this primary function, people interact with the tools to create an instantaneous log of pest specimens, their prevalence and locations which can then be picked up by analytical databases such as the Atlas of Living Australia that will aggregate and draw on these tools and data to provide a deeper understanding of trends. In this sense, these tools provide the materials for future heuristic models of analysis.

*PaDIL is a partnership between the Department of Agriculture, Fisheries and Forestry, Department of Agriculture and Food Western Australia, Plant Health Australia, Museum Victoria, Queensland University of Technology and the Cooperative Research Centre for National Plant Biosecurity.

Through a web-based remote microscope system, this project will improve the responsiveness to potential incursions by reducing delays in diagnosis, particularly in remote areas. This technology will provide national and international real-time microscope links between experts and non-experts. Diagnostic centres will be linked via web-based communication, for example, through an access portal located on the Diagnostic Database website see CRC27012. 

What is the biosecurity problem?

Currently, biological specimens requiring identification are mailed to taxonomic experts for determination. This may take several days and delay diagnosis and any response to deal with potential incursions.

The main output of this project is to:

• evaluate the effectiveness and practicalities of using web-based microscopes in the field, linked to plant laboratories supported by user-friendly software, to dramatically reduce the time required for expert taxonomic identification of emergency plant pests.

Who will be the end-users of this research?

The system will be used by biosecurity researchers (expert-to-expert) and operational staff (expert-to-non-expert) who will have the opportunity to access the remote microscope network via central hubs.