Tasmanian Institute of Agricultural Research

Pathogen biology and dispersal: The primary fungal species associated with red root-rot is Ganoderma philippii as determined by DNA analysis of isolates from diseased roots and from the association of fruiting bodies of this species with expanding patches of dead trees in Indonesian plantations.
Monitoring the manner of spread of the fungus has begun with the establishment of 15 semi-permanent survey plots at 4 sites and collection of fungal fruiting bodies from more than 16 additional sites. The first 6-monthly survey plot monitoring has also been completed.
Isolations have been made from fruiting bodies and infected root material to allow verification of their pathogenicity, to assess their clonality and pathogen dispersal and also to gauge the potential of non-pathogenic fungi collected to act as biological control agents against Ganoderma. Preliminary results support the pathogenicity of G. philippii against Acacia mangium and infrastructure is in place to carry out more rigorous tests.

Risk assessment: The same survey plots used to assess pathogen dispersal also form the backbone of the project's assessment of the role of environmental factors in determining root-rot incidence and severity.

Management options: Work has already begun on seeking out a suitable biological control from among the native fungi of Indonesia and a number of candidate organisms have already been trialled in the laboratory. One particularly promising organism with activity against two major pathogens of Acacia mangium is currently being formally identified.
In investigating alternative management solutions, observations made in Indonesia by RAPP, a project partner at a trial established by the Centre for International Forest Research (CIFOR), that removal of harvest residues reduces root rot incidence, are to be tested by imposition of an experimental burning treatment on selected survey sites.

Training and Travel: Indonesian scientists from project partner, the Indonesian Forestry Research and Development Agency (FORDA), have received training in Hobart in fungal DNA diagnostic methods and the FORDA laboratory in Jogjakarta now has the capacity to molecularly identify fungal isolates eliminating the necessity to send cultures to Australia. Training in morphological fungal identification has also been given to Indonesian project staff in Indonesia and infrastructure items have been identified without which the development of morphological diagnostic skills in project partners will be hampered.
Travel for the project has included fieldwork in Indonesia in September 2006 (Inception meeting / workshop), November 2006 (plot establishment and monitoring), February 2007 (plot establishment and monitoring) and May 2007 (first 6-monthly monitoring). Geoff Pegg and Michelle Grose from the Queensland Department of Primary industries (Forests) spent time in Hobart for project meetings and fieldwork comparing decay in urban systems with hoop pine and Acacia plantations. Hobart staff have also travelled to Queensland to assist Pegg and Gross in establishing plots in hoop pine plantations based on the survey system established in Indonesia. Indonesian staff have also travelled to Hobart for a period of training in fungal molecular biology.

Extension and adoption: The project has also enhanced the degree of communication between Research and Development arms of the partner forestry companies by fostering cooperation on a shared challenge that will benefit the village, out-grower, mill and associated communities in which they operate, as well as potentially enhancing the sustainability of their tree-growing.

Project advances are presented in line with the project's four overarching objectives:
Pathogen identity, biology and dispersal
A number of other species have been identified fruiting or associated with root rot disease in Acacia mangium including three Phellinus / Inonotus species and five Ganoderma species. Thus there is a diversity of potentially pathogenic species present on all areas surveyed. This has enabled us to alert industry to the need to test proposed management solutions against as wide a range of potential pathogens as possible.
Somatic incompatibility testing has been commenced in Yogyakarta, Indonesia. These tests show if fungal isolates collected from different trees or sites belong to the same individual allowing us to draw conclusions about the dispersal mechanism and management of the fungi in question. The project culture collection to be used for these experiments is now in excess of 2800 databased, spatially referenced isolates.
Pathogen spread is being monitored on a system of 24 semi-permanent plots on six sites across Indonesia and Northern Australia representing a broad range of site conditions and vegetation histories. All Indonesian sites have now been monitored at least twice and 4 of the 5 Indonesian sites have now been monitored three times. This is providing information on disease progression in Acacia mangium at an unprecedented level of detail which will underpin disease modelling for the remainder of the project.
Risk assessment
The value of various above-ground variables for detecting the below-ground presence of root rot on a tree has been assessed.
For individual trees, though there is a tendency for living trees with root rot to show poorer crown condition, if an individual tree has good crown condition this does not mean that root rot is not present on its roots. In fact, most living trees with root rot have healthy crowns.
Our ability to predict the disease status of a tree is markedly improved by the use of a new index developed to integrate not only the health of the individual tree but also the health of its nearest neighbours
Preliminary models have been developed (using the index mentioned above) to link the number of dead trees in root rot infected areas to the total, underlying level of infection / inoculum potential on a range of sites.
Collaboration with the ACIAR project (FST/2004/058: Realising genetic gains in Indonesian and Australian plantations through water and nutrient management) will underpin the parameterisation, validation and delivery of the model developed.
Management options
Experiments have been set up on one of the 5 Indonesian sites mapped for root rot disease to examine effectiveness of inter-rotation stump removal and remediation burns.on the spatial and temporal development of root rot disease in the subsequent crop.
Biological controls are being investigated:
The putative biological control targeted by one of our industry partners has been identified molecularly to genus and morphological identification to species is now underway.
Indigenous Indonesian fungi with antifungal and wood decomposing activity have been discovered through the project and are currently being laboratory tested to discern if these abilities could allow them to inhibit or out-compete the pathogens on dead wood.
Training, cooperation, extension and adoption
Preparations are underway for two Indonesian collaborating scientists to visit Australia to develop their skills in risk assessment and biological control.
Collaboration and cooperation in data management has been enhanced through the development of a project website including members only online-access to project data and planning tools.
Molecular training in Hobart and Yogyakarta has meant that routine molecular identification of fungal isolates can be undertaken in the Yogyakarta FORDA laboratory.
We have recommended that Industry partners integrate mechanised planting-hole preparation and biological control application and higher cost management solutions including stem injection of systemic fungicides or plant growth promoters (such as phosphite or Biosil) on high value assets such as seed orchards.
We are also investigating the relationship between root rot in Acacia mangium and the performance of Eucalyptus pellita planted on ex A. mangium lands, as the use of E. pellita as an alternative crop has been proposed as one possible management solution to the root rot problems in A. mangium. Our research into pathogens and pathogenicity is helping to assess the feasibility of this.

Project advances are presented in line with the project's four overarching objectives:
Pathogen identity, biology and dispersal
We have uncovered some of the diversity of fungi associated with root rot in Eucalyptus pellita (and clones of E. pellita hybrids) planted as an alternative species on ex Acacia mangium land. Ganoderma philippii and Ganoderma mastoporum have both been recovered from areas where both the previous acacia and the current eucalypt crop suffered high losses from root rot. The project's work in developing diagnostic capacity is also now being utilised by industry partners for the conclusive identification of isolates used in pathogenicity testing or as potential biological controls.
Pathogenicity tests are underway at the FORDA laboratories in Yogyakarta to provide definitive assessments of the pathogenicity of Ganoderma philippii against Acacia mangium, Eucalyptus pellita and Alstonia solaris. Because of the molecular identification work, isolates with a confirmed identity have been offered to industry partners to enable them to test new genetic material against the range of possibly pathogenic fungi encountered on their concessions rather than only a limited range of pathogens.
We are preparing to make the final monitoring of our 24 semi-permanent plots and have carried out somatic incompatibility tests on isolates from these plots. The data suggests that root to root contact is the predominant form of pathogen spread within disease gaps while different gaps appear to be the result of spore dispersal at some stage rather than the fragmentation of a very large clone. Observations have also been made in Queensland indicating the importance of cryptic resupinate fruiting bodies in spore production leading to the spread of Phellinus noxius.
Risk assessment
A risk assessment tool has been developed using data on disease incidence on the concessions of our project partners. This tool currently provides a low, medium or high risk rating to sites based on age, rotation, soil type, slope and GPS coordinates. Refinement and validation is to be supported by additional data from project partners. The relationship between risk, incidence and rate of spread is still being investigated. Work is continuing to provide effective root rot control solutions for those sites determined to have high risk because merely identifying risk does not constitute management of risk.
Ground penetrating radar has been used for the first time in the Indonesian pulpwood industry to assess root structure and the implications of this for disease spread. Assessments were made to assess root structure in areas with differing silvicultural treatments and different tree species. Analysis of this data is continuing.
Management options
Field trials have been carried out and monitoring of their effectiveness is continuing. Options for biological control scale-up and application have been discussed between Australian commercial producers and Indonesian project partners - these would reduce the logistical problems of this method of control. Additional potential biological control agents have been isolated from areas of low root rot incidence including a species of Phlebiopsis an effective stump treatment biological control used against the Northern Hemisphere root rot caused by Heterobasidion annosum. Tests for antagonism to major pathogen species are underway for this and other species isolated by the project.
Training, cooperation, extension and adoption
A collaborative research / training visit to Australia was made by Indonesian scientists Dr. A. Gafur & Mr. H. Indrayadi. This facilitated training and discussion on risk and distribution modelling, remote sensing, development, application and industrial scale-up of biological control production, disease monitoring and mapping, Integration of GIS and site data with disease mapping and enabled the development of the project's risk assessment tool.
Postgraduate training of three John Allwright Postgraduates, Luci Agustini, Purnamila Sulistyawati (MSc) and Istiana Prihatini (PhD) continuing and making good progress. The students projects cover areas including molecular and field diagnostics, morphological mycology, host physiological responses, forest health surveillance and possibilities for early disease detection.
The project team assisted in organising and participated in a PSLP AusAID Workshop in Yogyakarta "Disease Management Strategies in Plantations", running practical sessions in: Disease monitoring techniques and strategies, morphological mycology and molecular diagnostics.

A project initiation and planning meeting was held in Nha Trang in August 2009, where all project participants attended and discussed implementation of the project. Following the project planning meeting, the first of a planned series of annual Regional Aquafeed Forums was held at the University of NhaTrang.
Follow-up visits by Dr Brett Glencross and Dr David Smith have taken place in November 2009 and March 2010, respectively, to address any arising concerns of the project partner participants.
During the November 2009 visit Dr Glencross was joined by a leading Australian feed extrusion consultant to begin the planning process for a series of training workshops to be held in Vietnam in 2010 and 2011. This opportunity was also used to provide direct extrusion advice on processing and feed formulation to Vietnamese feed companies.
Consistent with the project objectives, protocols have been developed for a series of information gathering exercises:
- Socioeconomic surveys of marine-fish, Mudcrab and Spiny Lobster farmers to understand the real and perceived limitations to the adoption of pelleted feeds.
- Feed mill survey to characterize the feed production industry and raw material options available locally in Vietnam
- Production survey and sample collections to underpin the development of growth models for each of the project core species (Asian seabass, Cobia, Grouper - Epinephelus coioidies and E. fuscoguttatus, Mudcrab and Spiny Lobster).
The protocols have been developed by the leader of the socio-economics component of the project (Dr Elizabeth Petersen) in close consultation with each of the collaborating partner country institutes. These protocols/survey forms have then been translated from English into Vietnamese by the lead institution (Mr Dinh Van Trung).
Progress in Vietnam in implementing these surveys has been delayed due to the late signoff of the project, but began in May 2010.
Work has begun on each of the components of the project that have been earmarked activity in Australia:
- To identify barriers to feed technology uptake by aquaculture sectors
- To define the protein and energy digestibility of suite of locally available and/or key raw materials
- To explore mechanistic elements of fish nutritional modelling systems
Several fish farmers and feed manufacturers have already been canvassed regarding the issues affecting fishmeal replacement technology in Australia for the production of diets for marine species. The outcomes of this survey will be used to guide the research priorities to address the issues that are most pertinent to each sector.
Two experiments have been conducted already to evaluate the nutrient and energy digestibilities of a suite of raw materials. The acquisition of digestibility data for these ingredients was identified as being highly desirable by the feed production sector in Australia during discussions with the Project Leader. These studies have also been used to add additional data and strength to NIRS calibrations so as to be able to use NIRS to estimate protein and energy digestibility of both ingredients and feeds.
The basis for a mechanistic model, that represents actual discrete biochemical processes in fish, is in the process of being constructed. This component of the project will require a range of empirical experiments to measure critical growth parameters of barramundi . The first of these experiments is due to begin in late 2010.

The project was approved during the period of the previous report, and implementation has progressed quite rapidly, especially since June 2010. All deadlines to date for specific activities have been substantially or fully met, and substantial progress has been made on a number that are not due until later in the project. Specifically, Value Chain Analyses have been completed and design of new chains is well advanced, and those aspects that can be implemented at an early stage are in progress eg gaining cooperation and inputs/actions by entrepreneurs. Research priorities for field experimentation have been identified, sites selected, partner activity commenced and the experiments will be planted in May-June 2011. Sociological work - interviews, meetings and workshops as planned have been completed, data analysis is well advanced and reports are being prepared. A number of conference papers have been published or submitted (awaiting acceptance), and training for one project participant is to be undertaken in late 2011. Initial Geographic Information Systems work has been completed.