Research on Soilborne Pathogens of Cereals in Australia:

ATrip Report by Richard Smiley

February 21, 1999

I travelled to Australia for two weeks during February 1999. The purpose was to attend a plant pathology conference and review recent research on root and crown diseases of wheat and barley in South Australia and southern Queensland. This trip was intended to expand and update findings during a similar trip to Western Australia and South Australia during October 1997. In contrast to the earlier trip, the entire focus of this trip was on new knowledge and approachs that could be used directly in an expanded and refocused cereals pathology program at Pendleton. At Adelaide alone there are perhaps 50 scientists who work specifically on some aspect of disease control for cereals. There are others who work on insects, weeds, agonomy, genetics and breeding, product quality, economics, and other facets of the cereals industry.

The first week in Adelaide was devoted to visits at the South Australian Research and Development Institute (SARDI), Commonwealth Scientific and Industrial Research Organization (CSIRO), and University of Adelaide-Waite Campus (UA). Two days were spent with scientists at the Department of Primary Industries' (DPI) Leslie Research Institute at Toowoomba, Queensland; this facility was named the Wheat Research Institute until it was reorganized in 1998. I was among five foreign delegates to the First Australasian Soilborne Disease Symposium, which was attended by 150 root-disease scientists. A high percentage (65%) of the papers were of direct interest to root disease research on cereals and rotation crops in the PNW. A synopsis of observations and findings is presented. For background and supplemental information regarding the topics and institutions, please refer to the 1997 trip report.

Specific objectives for the trip included the following:

1. Determine the status for applying molecular diagnostics to soilborne pathogens and cereal diseases.

2. Examine methods for quantitative relationships between yield and quantification of pathogens.

3. Determine the progress for SARDI's new soil testing program that includes root disease predictions.

4. Lay the groundwork for sending CBARC's new plant pathologist to Adelaide for orientation and training in the application of molecular biology principals to remote and traditional labs.

5. Examine the intricacies involved in procedures for detecting resistance and tolerance to Fusarium foot rot in field studies and greenhouse seedling tests.

6. Seek advice on method to determine if root lesion nematode is causing economic damage in Oregon.

7. Lay the groundwork for importing seed of Australian wheat varieties with the best and worst resistance and tolerance to Fusarium foot rot, cereal cyst nematode and root lesion nematode, for use in establishing guidelines and relative traits for varieties available in the Pacific Northwest.

8. Re-kindle the preparation of a manuscript describing research on resistance of wheat to Rhizoctonia root rot, as studied at Moro and Pendleton by Pamela Zwer and myself prior to her departure.

1. Commercialization of molecular probes for disease diagnosis, and their application to SARDI's newly revised soil testing service.

In 1998 SARDI offered the world's first commercial root disease prediction and advisory service based on molecular plant disease diagnostic protocols applied to soil samples collected for fertilizer recommendations. I last visited in 1997, as they were preparing to embark on this effort. The following is a synopsis of findings and possible applications to agriculture in Oregon.

A. In 1997 SARDI scientists predicted they would use DNA tests to predict the risk from three diseases in 5,000 soil samples submitted for fertilizer testing during 1998. The diseases included were take-all, Rhizoctonia root rot, and cereal cyst nematode. In fact, they processed 2,000 samples and found it necessary to discontinue the test for cyst nematode. They were pleased with the performance of tests for predicting take-all and Rhizoctonia root rot.

B. They encountered problems with the accuracy of the cereal cyst nematode test during the first year because of errors in soils that had very high organic matter contents, which were not evaluated during development stages for the test. This was unexpected but is understandable; these refinements are commonly necessary when any test is expanded to include a much broader set of conditions than previously examined. SARDI and CSIRO-Canberra redesigned the probe and extraction process during 1997 and introduced the improved version into tests scheduled for 1999 (year 2).

C. They found that designing molecular probes for specific pathogens constitutes only 10% of the effort for introducing realistic disease prediction systems into the real world; other components involve development of calibration curves that include weather and cropping variables needed to interpret the disease threat associated with a specific DNA level detected in soil.

D. During year two of the disease predictive testing service SARDI is adding molecular tests for two species of root lesion nematodes, to make a total of four diseases that will be screened on about 5,000 soil samples. During year three they hope to add a test for Fusarium crown rot (called Fusarium foot rot or dryland foot rot in the PNW).

E. SARDI and CSIRO are selling marketing rights for the new cereal cyst nematode and root lesion nematode probes to Rhône-Poulenc, who is not yet ready to distribute them. This is likely to delay our access to these probes in Oregon.

F. SARDI determined that the precision of the disease prediction tests requires that soils be sampled more precisely than is currently practiced for fertilizer testing. New field sampling systems (topography, soil type, etc.) are being researched to modify the soil testing program so it achieves more accuracy for the combined fertilizer and disease-risk recommendations. A special sampling may be required for Fusarium crown rot because most inoculum for this disease is in the stem tissue.

G. SARDI's disease prediction service had first year experiences spanning the spectrum from success to failure. Most disease predictive tests were acceptably accurate with respect to what was ultimately experienced on the fields tested. There were some wrecks when the disease threat was predicted to be low and farmers used that information to cut expenses, only to be zapped by heavy root disease damage they didn't expect. But compared to the wrecks, there were far more examples of growers who were able to use the disease predictions to decide that they could sustain increased risk by quickly changing plans by inserting one more wheat crop into the rotation (rather than a less economic break crop) and therefore improve overall farm income. It worked well for most farms.

H. In 1997 SARDI anticipated the possibility that the service would be opened up to individual farmers after several years. This is no longer planned. SARDI is isolating their testing service for exclusive use by fertilizer company and extension agronomists. They are doing this because it became apparent that accurate interpretation of results is complex. Use of improper interpretations to make management decisions for individual fields was considered an unacceptable legal liability for the lab. SARDI therefore conducted an elaborate training (certification) program for everyone in a position to oversee the collection of soil samples and interpretation of results. Only certified users have access to the test results. I received a copy of their new training manual for certifying advisory agronomists.

I. SARDI is currently developing an alliance with six soil testing labs that handle 300,000 soil samples each year. The alliance will allow the labs to sell the additional cereal root disease prediction service once a few more of the testing and standardization procedures are refined at Adelaide.

2. Repeated observations and/or comments (from all locations visited).

A. Most Australian scientists now rate small grain varieties for tolerance as well as resistance to root diseases. They find the two processes to be very distinct and not genetically linked. Breeders and pathologists now make independent selections for both resistance and tolerance. They employ germplasm for both processes in a strategic manner to achieve the greatest value for the cropping system. Resistance and tolerance ratings are published each year in their variety selection brochure.

B. There are acceptable to excellent sources of resistance and tolerance available for cereal cyst nematode, root lesion nematode, and Fusarium crown rot, but not Rhizoctonia root rot or take-all.

C. It was stated repeatedly that during the past decade there have been no known cases of severe take-all or cereal cyst nematode. They began offering predictive bioassays for these diseases 10 years ago, began to release varieties with resistance and tolerance to cyst nematode, and advocated crop rotations to control take-all.

D. I spent a lot of time gleaning as much new information as possible about procedures they use to screen varieties for resistance and tolerance in the greenhouse and field. Everywhere I looked I found the details for published methods to be incomplete. The success of a test is in its detail, and it was often necessary to talk directly with technicians who do the screening to determine exactly how they do it.

E. Australians appear to be abandoning their recent push for on-farm testing. They believe the wasted effort and expense is too great to justify continuation. They are going back to scientist-operated field research to regain the highest efficiency for the investment, at the expense of the public relations value.

3. Fusarium crown rot and Common root rot.

A. Scientists at SARDI and DPI agreed to send seed of their crown rot resistant and tolerant wheat cultivars to assist us in determining the level of economic damage these fungi are causing in our crops.

B. My observations and discussions at SARDI and DPI lead me to think that we may be erring in some of our visual ratings for Fusarium foot rot. Common root rot may confuse this process in some locations.

C. Our program at Pendleton was further advanced than SARDI's for adapting and applying molecular probes for identifying Fusarium species. They were developing a probe similiar to the unpublished one we found by simply contacting colleagues via email, acquiring the appropriate description, and then hiring a commercial service in Texas to manufacture the probe to specifications. SARDI wasn't aware of the existence for two of the Fusarium probes we are using. Within two hours following our conversation they placed an email order for these probes. They agreed to check one of them for a potential error we think we detected. They will communicate the results of the accuracy evaluation in about one month.

D. At DPI, the pathologist found that he needed a plot drill with a dual-cone and custom opener to properly screen varieties for tolerance and resistance to Fusarium crown rot under field conditions. The drill places inoculum in soil in a band above the seed. I took a photograph of the opener.

E. Wildermuth convinced me that my program on Fusarium foot rot will require much more emphasis on bundle sampling, bundle storage, and evaluations of basal stems during the winter. We have been trying to avoid this type of manual rating because it requires much more labor and would also require a more strict limit on our ability to provide diagnostic support services for other scientists. I took photographs of their bundle storage room.

F. A custom-designed water bath at DPI is used to screen for resistance and tolerance to crown rot. Precise root temperatures are required. Two baths in his greenhouse cost $7,000 each. I took photos.

G. The pathologist at DPI found a direct relationship between depth of crown formation and resistance to crown rot. This is a genetically controlled process. We have not examined our varieties in the PNW.

H. Chickpeas rotated with wheat in Queensland dramatically reduced Fusarium crown rot and increased wheat yields to levels equal with fumigated soil.

I. Fractal geometry was applied to microscopic surface ruggedness of soil particles to describe relationships between crown rot and "soil wetness duration". Analagous to leaf wetness duration for foliar diseases, this process provides an improved way to relate cumulative soil wetness and temperature to crown rot incidence and severity. Infection did not occur if soil water potentials were either too high or too low. This will be applied to crown rot predictive (risk assessment) systems.

J. Sydney University will fax two graduate student theses of importance to our program. I also became aware of several publications I was not familiar with, and several new manuscripts were given to me.

4. Root lesion nematode.

A. A nematologist and a wheat breeder at UA offered to send seed of resistant and tolerant cultivars to assist in determining whether lesion nematodes are causing economic damage in our crops. They also agreed to test some of our varieties if I will send the seed. They also gave me copies of several unpublished manuscripts.

B. On the basis of my observations during this and the trip in 1997, I think we may be wrong in some of our visual ratings of root pruning caused by Rhizoctonia root rot and Pythium root rot. Root lesion nematode is present in at least some PNW wheat fields and may be causing confusion in this process. Pratylenchus species are migratory endoparasites that are very difficult to detect. The nematologist at DPI emphasized that we can't rely on root staining or visual techniques to determine if lesion nematodes are contributing to the damage -- we have to sort this out with extractions to be sure what is happening.

C. Nematologists at SARDI, UA, and DPI provided guidance on methods for using Temik and specific crop rotations and sequences of tolerant and intolerant wheat varieties to determine if root lesion nematode is causing economic damage in our area. One nematologist uses a gun powder dispensor for reloading shotgun shells to meter known volumes of Temik into a covered cone on the plot drill. The dispenser is mounted above the cone and eliminates the need for the drill operator to handle this toxic material.

D. Nematologists at SARDI, UA, and DPI gave me guidance on methods used to extract and enumerate lesion nematodes. They also demonstrated several self-watering systems for greenhouse benches. I took photographs.

E. I evaluated options for obtaining the new molecular probes for detecting Pratylenchus thornei and P. neglectus in soil. Commercial agreements between SARDI, CSIRO, and Rhône-Poulenc are likely to delay my access and prevent a no-cost transfer.

5. Rhizoctonia root rot.

A. A molecular biologist at SARDI will send their molecular probes for Rhizoctonia solani AG-8 and AG-3. A student is also developing probes for AG-2-1 and AG-2-2 but they are not yet operational.

B. One molecular biologist considers molecular probes appropriate for identifying these fungi in cultures, roots and soil, but doubts that DNA in soil can be a meaningful predictor of Rhizoctonia root rot in commercial fields. That opinion is based on the fact that the fungus is so saprophytic in soil that even a small amount of DNA can lead to great crop damage if the rotation and tillage are favorable to the pathogen. In contrast, a very large amount of DNA can have minimal impact if farming systems are set up to manage the fungus. Further study is needed.

C. A pathologist at SARDI showed me improved techniques for preserving Rhizoctonia cultures, thereby improving the stability and viability of these fungal pathogens in the laboratory.

D. Pamela Zwer and I re-initiated the preparation of a paper on resistance of winter wheat to Rhizoctonia root rot in the PNW. The work and paper were disrupted by Pamela's departure. Yet the results are now being used or planned as the basis for variety screening in Washington, Oregon and Australia.

6. Take-all.

A. A molecular biologist at CSIRO will send their molecular probe for Gaeumannomyces graminis var. tritici.

B. I learned nothing new about the potential for breeding wheat for resistance to take-all.

C. A SARDI pathologist is working with a newly registered seed treatment fungicide from AgrEvo. It controls take-all much better than Baytan and all other fungicides. Tests are continuing.

D. Detection of take-all inoculum in soil can be greatly improved by screening out specific size segments of organic matter and then testing the organic matter rather than whole soil.

E. A CSIRO pathologist adds sucrose to soil to amplify their ability to detect and quantify soils suppressive to take-all. Other scientists are now adapting this procedure. I had not heard about this technique . It will be useful for quantifying the low level of take-all that occurs in annual wheat and barley plots at Pendleton.

F. Another CSIRO microbiologist showed results of tests in which the biocontrol agent Tk7a provides twice the yield increase achieved with Baytan in crops affected by take-all and sharp eyespot in China and Australia.

G. CSIRO pathologists reported that both dicamba and MCPA increase the severity of take-all in the field.

7. Seed Treatment Screening.

A. When I visited SARDI in 1997 they had just introduced a Aterrace system@ for evaluating tens of thousands of plants for disease and nematode resistance, and for effects of seed treatments against smuts and root rots. The terrace system is proving to be much more cost effective and uniform compared to screening varieties and seed treatments in the field. Manufacturers haven't reduced funding as SARDI shifted from field tests to this artificial system for evaluating seed treatments. Butts is sending me protocols for setting up the system and scoring results. I took photographs.

B. The terrace system is used to screen up to 10,000 plants annually for resistance to cereal cyst nematode. They use a custom computerized handling system to manage the logistics and data. But the computer system is no longer used by staff who handle smaller numbers of plants. For small experiments they have returned to manual scoring sheets and note taking, and manual entering of data into the computer for analysis. The automated computer system has become a huge drain on finances, is too complex for use with reasonable numbers of plants, and will require an extensive upgrade in 1999 to make it Y2K compatible; they must expend the equivalent of the original cost ($40,000) to keep it working in 2000.

8. General comments and observations of importance.

A. Disease decline phenomena may not occur when soils are highly eroded or low in organic matter. I have not heard this before. I have wondered why the phenomenon such as take-all decline sometime fail to appear in our soils. I have therefore considered them to be unpredictable. It seems that disease decline phenomena appear to work best in farming systems that maintain or improve levels of soil organic matter. Suppressiveness to disease is relatively common but suppressiveness to the pathogens is uncommon. Procedures were described for identifying soils suppressive to specific diseases, and scoring suppressiveness relative to a standard reference soil.

B. There is increasing evidence that pathologists are overlooking the nondescript Aminor@ pathogens. As Australian scientists gain control over major pathogens they are still finding meaningful benefits from crop rotations and soil fumigation (chemical or biological fumigants). One example involved a comparison of direct drilling and planting into cultivated soil at 30 sites. Early seedling growth (biomass production) was reduced as much as 64% by direct drilling at two-thirds of the sites. There were no known root diseases present and the biomass reductions appeared to be associated with populations of growth-inhibiting Pseudomonas bacteria.

C. I gained access to additional sources of information, techniques and supplies for biological control studies, although that is not a focus of my program.

D. New molecular probes are being developed for a wide array of pathogens, including some of importance to potential rotation crops in the PNW. Probes continue to become more efficient and less expensive.

E. One soil microbial ecologist strongly advocated the need for pathologists to change from diagnostic service providers to predictive service providers, and to more proactive and efficient delivery of existing knowledge to crop consultants and growers. He stated that the ultimate goal of detection and quantification procedures must be the commercialization of those services to assure that growers get appropriate access it them.

F. Systematic research is required to identify effective biofumigants (natural soil fumigation from a cover crop or an appropriate rotation crop like rapeseed). The correct combination of Brassica species and procedures and timing for incorporation are critical to prevent inaccurate negative results and wasted opportunities. One paper reported 50-fold differences in glucosinolate levels and the degree of GSL toxicity in existing germplasm, and a 20-fold difference in biomass production. Procedures and appropriate controls for systematic research and its' interpretation were presented.

G. Pythium irregulare isn't as simple a pathogen as once thought. This root rotting species has pathotypes that are specifically selected for higher virulence on specific crops. The pathotype most damaging to barley isn't as damaging to wheat. A CSIRO pathologist developed molecular probes to sort out these Pythium pathotypes and thereby improve their ability to examine the host:pathogen relationships on wheat.

9. Some Other Memories.

A. SARDI, CSIRO and DPI scientists are using my research results rather extensively, particularly relating to our work on Rhizoctonia root rot, Fusarium foot rot, physiologic leaf spot, and seedling emergence.

B. One of the molecular biologists at Adelaide stated an interest in applying for one of the positions opening up in my pathology program. I carried the application back to Pendleton and set a schedule for the interview. The scientist developed molecular probes for Rhizoctonia root rot of cereals and several diseases of potato and grapevine. Colleagues of the scientist have developed probes for take-all and cereal cyst nematode. Some of the probes will be delivered and installed in our lab during the interview.

C. The Director of SARDI's Plant Division invited me to formalize my collaboration with their program, so long as there are mutual benefits that can be clearly defined to the Grains Research and Development Corporation. He also strongly endorsed Pamela Zwer's performance and he continues to shift more administrative responsibilities to her.

10. Synopsis and Challenge.

A. There is a wealth of cereal root disease experience concentrated at relatively few (<6) locations in Australia. This concentrated expertise, focus on achievable mission-oriented projects, strong industrial and governmental support, and excellent communications and cooperation among intra- and interstate work groups has allowed the Australians to reach a state-of-the-art at least one or two decades ahead of comparable research on cereal root diseases and soilborne pathogens in the Pacific Northwest or in any specific region anywhere else in North America. In part because of the long distances between Australia and European and North American countries, the Australians welcome meaningful interactions and exchanges with our scientists. Properly fostered, the Australian knowledge and resources can become even more valuable for infusing new efficiencies of thought, process and product into the Oregon small grains industry. The key will be to develop programs with sufficient personnel and focus to properly employ information and processes already available, so that new technologies can be moved efficiently into our farming systems.

B. It will be a keen challenge to generate the support, understanding, leadership and technical staff necessary to modify existing cereal root disease research and extension programs in Oregon. While daunting, it is imperative that these changes be made to improve the return on investments directed into root disease research. There are opportunities at the present time to move efficiently into new directions for research on root and crown diseases affecting Oregon wheat and barley crops. Thrusts deemed most important are introduction of molecular disease diagnostics, breeding for resistance and/or tolerance to root pathogens, and amplifying the rate of transfer of existing knowledge to growers and their advisors. The greatest difficulties include garnering reasonably long-term financial support, and changing directions without increasing the size of the existing small research staff that currently operates in an environment that fosters research diversity and breadth rather than in-depth focus. It is often easier to make a clean and dramatic change in research direction than to move through a prolonged evolution. The new five-year USDA-ARS cooperative agreement for root disease research provides a stong new impetus to make a bolder move into the fundamental research objectives that will be needed to move cereal root disease management, and yield stability, to a new plateau in Oregon.

List of the Most Important Visits During Smiley's Trip During February 1999

South Australian Research and Development Institute, Adelaide:

Dr. Alan Dubé. Administers the Plant Division, including breeding and pest management sciences.

Dr. Hugh Wallwork. Director of the Pathology Program in Center for Molecular Plant Breeding.

Dr. Dara Melanson. Director of the Molecular Plant Pathology Section. Develops probes.

Dr. Sharyn Taylor. Administers the Nematology Section. Focuses on cereal cyst and lesion nematodes.

Dr. Pamela Zwer. Oat breeder and administers vetch and pea breeding programs.

Dr. Kathy Ophel Keller. Application of molecular disease diagnostics to the soil testing program.

Dr. Alan McKay. Application of molecular disease diagnostics to the soil testing program.

Dr. Dermott Kelly. Coordinates field research for Rhizoctonia root rot.

Dr. Kevin Williams. Develops molecular probes for Fusarium crown rot.

Mr. Mark Butts. Screens seed treatments for take-all, Fusarium crown rot, smuts, and others.

Dr. John Lewis. Screens for resistance to cereal cyst nematode & locates sites for field tests.

Mr. Jerry Dennis. Coordinates screening for resistance and tolerance to Fusarium crown rot.

Commonwealth Scientific and Industrial Research Organization, Adelaide:

Dr. Martin Ryder. Administers Soil Biology Section of the Land and Water Division. Biocontrol.

Dr. Steven Neate. Coordinates research on soils suppressive to take-all and Rhizoctonia root rot.

Dr. Herdina. Develops molecular probes to detect and quantify take-all.

Dr. Suha Jabaji-Hare. Visiting scientist with expertise in molecular probes for Rhizoctonia.

Dr. David Roget. Practices leading to disease control and decline phenomena for cereal root diseases.

Dr. Albert Rovira. Retired administrator of this group. Now a training consultant for extension.

Dr. Steve Barnett. Research on effects of mutations in biological control agents.

University of Adelaide, Waite Campus, Adelaide:

Dr. Vivien Vanstone. Screening for resistance and tolerance to root lesion nematode.

Dr. Tony Rathjun. Wheat breeder.

Victoria Department of Agriculture, Horsham:

Dr. Grant Holloway. Screening crop rotations and wheat varieties for controlling root diseases.

University of Sydney:

Dr. Lester Burgess. Dean of Agriculture. Continues with his research on Fusarium crown rot.

Dr. Percy Wong. Development of biocontrol agents for take-all and Fusarium crown rot.

Leslie Research Institute, Queensland Department of Agriculture, Toowoomba:

Dr. Graham Wildermuth. Resistance and tolerance to Fusarium crown rot and common root rot.

Dr. John Thompson. Resistance and tolerance to root lesion nematode species.

Dr. Bob Dodman. Retired. Edits their APPS Journal. Consults on Fusarium crown rot control.

Dr. Peter Williamson. Research of black point, rusts, tan spot, and other diseases of foliage and heads.

Ms. Nikki Seymour. Nematology research officer for John Thompson.

Dr. Graham Stirling. Biocontrol of plant diseases. Nematology. Located at Moggill, QLD.