You are here: Home >


Plant nematology as a discipline is in a state of depletion in Australia at present, yet nematode pathogens cause losses of at least $450 million per annum in Australia and US$120 billion each year in crop losses worldwide.

There are some serious emergency nematode pathogens, such as the potato cyst-nematodes (Globodera rostochiensis, G. pallida), and stem nematodes (Ditylenchus dipsaci), and their presence is a quarantine issue and a non-tariff barrier to trade. In the past three years several additional species of root-lesion nematode (Pratylenchus spp) have been found in Western Australia (WA). The cereal cyst nematode (Heterodera avenae) is now known to be much more widely spread in WA than previously thought. The root-knot nematode Meloidogyne fallax has recently been detected in WA, and related species such as M. artiellia are serious problems in chickpeas grown in the Mediterranean region where new germplasm is often collected for Australian crop improvement. Climate modelling also indicates that many nematode pests of Mediterranean, sub-tropical and tropical regions would survive well if introduced into Australia. 

What is the biosecurity problem?

In order to improve Australian biosecurity against new incursions of nematode pathogens, it is essential to conduct a risk analysis, to assess potential agricultural and horticultural zones at risk.
There is also a need to have improved technologies available to detect, identify and eliminate exotic plant parasitic nematodes. This will enable potential new incursions to be predicted, controlled, and a thorough knowledge of nematode issues will also promote Australian trade and market access through high quality evidence-based support of phytosanitary issues and regulations.

The main outputs of this project were to:

  • train an individual to the PhD level in plant parasitic nematode biology, risk assessment and taxonomy
  • train an individual to the PhD level in classical and molecular diagnostics of plant nematode pathogens
  • develop and validate new high throughput nematode diagnostic techniques for surveying and monitoring the presence of nematode pathogens
  • provide a trained individual with expertise and understanding of plant biosecurity issues, who can take on a leadership role in this area of biosecurity of soil-borne pathogens, and
  • develop a faster detection techniques such as MALDI-TOF MS

Who are the end-users of this research?

Personnel without nematode knowledge, Australian Quarantine Inspection Services officers and the agricultural industry in general.

The Estonian translation of this page is available here. 


Matthew Tan
Student CRC60044: Nematode taxonomy - PhD

Read More


Professor Michael Jones (Murdoch University) and Dr Vivien Vanstone (Department of Agriculture and Food, Western Australia)
Supervising Institution
Murdoch University
August 2009 - June 2010


Diagnosing karnal bunt

Karnal bunt is disease of wheat caused by the fungus Tilletia indica and was first discovered in northern India in 1930.

Thai scientists visit the nation's capital

Due to the increased movement of people and agricultural

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.


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.


Dr Gary Kong
Project Leader CRC20093: Increasing diagnostic capacity in Thailand

Read More


January 2008 - November 2010
$579,436 (cash and in-kind)



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.

CRC60038: Picture strip

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


Ms Bobbie Hitchcock
Student CRC60038: Epiphyas Revision - PhD

Read More


Dr. Marianne Horak (CSIRO Entomology / ANIC), Dr. Andrew Mitchell (DPI NSW), Prof. Mike Crisp and Dr. John Trueman (ANU)
Supervising Institution
Australian National University
July 2007- June 2010


This project focuses on development of nanosensor technology and software for detection of human, animal and plant pathogens that are highly significant biosecurity threats to public health and agriculture in Australia. The project is a collaboration between the CRC for National Plant Biosecurity (CRCNPB), Nanomics BioSystems, the Australian Biosecurity CRC for Emerging Infectious Disease (AB-CRC) and the Queensland Department of Primary Industries and Fisheries.

The technology comprises ceramic beads (OptoPlexTM beads) on which biomolecular interactions (either DNA or protein-based) are detected, screened, analysed and reported. The technology will be optimised for generic detection devices and, potentially, hand-held devices for use in medical practices, ports and/or farms.

What is the biosecurity problem?

Biosecurity diagnostic protocols currently depend upon a complicated variety of tests based on a wide range of (often expensive) technological platforms. Each platform requires significant investment in single-use equipment and training. Despite this investment, results can be ambiguous and require multiple (and different) tests to produce a confirmed result for a single pest or pathogen. These factors can lead to delayed diagnoses and subsequent delays in responsiveness to biosecurity threats.

The main outputs of this project are to:

  • develop a new diagnostic platform optimised for generic detection devices and, potentially, hand-held devices for use in medical practices, ports and/or farms.
  • validate diagnostic assays for exotic pests and pathogens.

Who will be the end-users of this research?

The outputs of the project will be used by government/university and industry diagnostic labs and field-based (operational) biosecurity staff such as AQIS/NAQS and state government agencies.


Dr Andrew Geering
Project Leader CRC20030: Nanobead Diagnostic Platform
Phone: 07 3896 9353
Fax: 07 3896 9533

Read More


February 2007 – December 2009
$368,200 (cash and in-kind support)



Diagnostics Research Program Image


Identification: World-class biosecurity capability for early identification of plant biosecurity threats.


A world-class biosecurity capability for early identification of plant biosecurity incursions in Australia through provision of data, expertise and diagnostic technology that is accurate, sensitive, reliable and cost-effective.

Indicators of success


New diagnostic tools to improve responsiveness to plant biosecurity incursion events.


World recognised protocols for rapid identification of harmful pests and diseases are developed and published in international journals.


Databases and new tools to share diagnostic information are standardised.

Protocols for plant biosecurity threats are developed and submitted to the Subcommittee on Plant Health Diagnostic Standards.


Improved diagnostics transferred to end-users to support monitoring and market access activities.


New diagnostic information (services, protocols and expertise) are accessed by end-users via internet systems.

Diagnostics Research Projects

CRC20004: Karnal Bunt DetectionDr Mui-Keng Tan

This project developed an accurate, reliable and internationally recognised DNA-based protocol to detect Karnal bunt. The methodology was validated by laboratories in Australia and overseas and more

CRC20025: Remote MicroscopesDr John La Salle

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 more

CRC20030: Nanobead Diagnostic PlatformDr Andrew Geering
This project focuses on development of nanosensor technology and software for detection of human, animal and plant pathogens that are highly significant biosecurity threats to public health and more
CRC20054: Plant Bacteria PlatformsDr Deborah Hailstones

This project evaluated two of the newer discovery platforms, proteomics and metabolomics, for effectiveness in the identification of functional biomarkers that differentiate closely related more

CRC20055: DNA DatabankDr Andrew Geering

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 more

CRC20057: Phosphine Resistance - Proteomics Peter Campbell

Phosphine is the main fumigant used in Australia to control insect pests in grain storages; both bulk grain handlers and farmers rely on phosphine for the control of insects and more than 80% of more

CRC20080:Phosphine Resistance - MolecularDr David Schlipalius

This project aimed to provide rapid identification of the phosphine resistance status of any individual R. dominica or T. castaneum collected from grain in storage across more

CRC20081: Biosensor-based Detection of Grain PestsDr Alisha Anderson

There is a need to develop technologies that can be used to rapidly detect and quantify pest infestations in bulk grain to assist in the management of these biosecurity threats. This project more

CRC20093: Increasing diagnostic capacity in ThailandDr Gary Kong

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 more

CRC20115: Resolving the Bactrocera dorsalis ComplexDr Anthony Clarke

Flies belonging to the Oriental Fruit Fly species complex, Bactrocera dorsalis, include a number of serious horticultural pest species which are difficult to identify (i.e. B. more

CRC20137: Khapra Beetle Diagnostics

This project established a National Reference Laboratory for Dermestidae, with particular reference to the genus Trogoderma. The laboratory provides molecular and morphological diagnostic more

CRC27012: National Diagnostic DatabaseDr Gary Kong

This project is developing a mix of digital technologies designed to provide the building blocks of future diagnostic information systems. The more


Dr Deborah Hailstones
Program Leader Diagnostics

Phone: 02 4640 6442
Fax: 02 4640 6300

Read More


To undertake research that will provide rapid identification of plant biosecurity threats in order to decrease the cost of eradication and impacts through rapid response.