Australia's avocado orchards remain largely free from exotic pests and diseases that affect production in the Americas, Chile, and Asia Pacific regions. However, maintaining this requires proactive monitoring and biosecurity management to detect and respond quickly to any potential pest incursions. Traditional methods for detecting pests and diseases often rely on visual inspection or laboratory testing of symptomatic plants. These approaches can miss early-stage infections or require expertise to identify problems before they spread. By the time visual symptoms appear, significant damage may have already occurred, making control more difficult and expensive.

eDNA offers a revolutionary approach to pest and disease monitoring. Hort Innovation invested in developing eDNA technologies for the rapid detection and identification of priority pests for the avocado industry. EnviroDNA developed field and lab-based testing techniques to improve the ability of the avocado industry, and those undertaking surveillance activities, to quickly and accurately identify pest incursion threats in a cost-effective manner.
 

EnviroDNA evaluated practical and scalable sampling methods to collect eDNA from various sources relevant to pests including swabbing of plant surfaces, washing of plant/fruit surfaces to collect and concentrate eDNA, air sampling, direct collection of soil and roots/rhizosphere to detect soil-borne diseases, and insect traps. Initial trials to validate and refine sampling methodology were done in Victoria, at a wildlife reserve and local orchard, before we conducted larger trials in Australia's major avocado-growing regions. These locations represent the majority of Australian avocado production, with Queensland contributing 53% and Western Australia 32% of national output. 

We evaluated multiple genetic markers (DNA barcodes) to detect and identify insects, animals, fungi, plants, and other microorganisms from environmental samples. We also tested an existing assay designed to detect Phytophthora, a harmful pathogen that causes root rot in avocado trees and developed and validated new assays to detect the causative agent of brown root rot (Phellinus noxius / Pyrrhoderma noxium). 
 

Results

Overall, across all production locations and sampling approaches, almost 20,000 detections of more than 1250 distinct fungi and arthropod taxa were obtained. These included many priority pathogen/pest families, with methods found to be particularly sensitive for fungi. The methodologies developed provide the Australian avocado industry with enhanced surveillance capabilities, supporting continued growth while protecting against future biosecurity threats. 

Impact

• Validated broad-spectrum surveillance eDNA sampling methods. We developed cost-effective active and passive eDNA sampling methods that require minimal technical expertise and equipment. This included both targeted surface swabbing for arthropod detection and passive air sampling. We also tested root and soil sampling that yielded the highest diversity of fungi species. This project developed methods that can be utilised by the avocado industry for future eDNA monitoring.
• Developed targeted assays for differentiation of brown root rot and Phytophthora root rot. These tests aid in the early detection of these pathogens. We assessed the efficacy of an existing targeted assay for Phytopthora species and developed two new assays to detect brown root rot (Phellinus noxius = Pyrrhoderma noxium). We successfully detected P. noxium and Phytopthora from soil, root and wipes collected from the base of both healthy and unhealthy (visually) trees from farms in North QLD. Targeted assays can help confirm which pathogen is present without waiting for visible symptoms. This avoids misdiagnosis when symptoms overlap and gives growers a head start to remove or isolate infected stock.

This project has been funded by Hort Innovation using the avocado research and development levy and funds from the Australian Government. For more information on the fund and strategic levy investment visit horticulture.com.au.

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