W2147: Managing Plant Microbe Interactions in Soil to Promote Sustainable Agriculture
Statement of Issues and Justification
The future of sustainable agriculture in the U.S. will increasingly rely on the integration of biotechnology with traditional agricultural practices. Although genetic engineering promises enhanced yields and disease resistance, it is also important to recognize that plants exist in intimate associations with microorganisms, some of which cause plant disease while others protect against disease. Identifying, understanding and utilizing microorganisms or microbial products to control plant disease and enhance crop production are becoming more central parts of sustainable agriculture. Biological control or biologically-based pest management (BBPM) has the potential to control crop diseases while causing no or minimal detrimental environmental impact. For this proposal, we define biological control as the manipulation of microbial populations through cultural, physical or biological means including plant mechanisms. Some of the benefits of utilizing microorganisms include:reduced dependence on chemical pesticides, which is important because of expanding demand for organic produce and increasing costs of such petroleum-based inputs;
lack of development of pathogen resistance to biological control organisms, important due to the observed increase in resistance to many chemical controls;
more selective action against pathogens and not against beneficial organisms;
biodegradability of microbial pesticides and the by-products of their manufacture;
reduced danger to humans or animals;
improvement of soil quality and health;
increased food safety;
long term solutions for management of soilborne pathogens;
management of diseases in natural ecosystems;
During the past project period, W-1147 made major contributions towards our understanding of microbial biological control of plant disease. Such understanding is necessary for expanding the adoption of pest management strategies that employ native and applied biological controls.
Demand for biopesticides has continued to expand dramatically in the last five years, and the biopesticide industry is expected to double or triple in the next five to ten years (International Biocontrol Manufacturer's Association, 2004). This expansion is evidenced by the Biopesticide Industry Alliance, established in 2001, which had 31 member companies in 2006. This growth has been driven by expanding organic markets as well as increased public sensitivity to the risks and hazards of chemical pesticides. To date several dozen commercial biocontrol products and processes have been registered by the EPA, over half of these were registered in the last five years. These include fifteen bacterial and seven fungal products, and three activators of plant defenses (http://www.apsnet.org/online/feature/biocontrol/). However, further research is required to overcome problems related to high-volume production, storage, delivery and formulation of such products. With increased demand for biological options, new active ingredients will need to be identified and characterized. In addition, regulatory agencies are increasingly interested in understanding the mode of action of such novel microbials. Therefore, basic research into the physiology and genetics of biocontrol microbes will continue to be needed. More research is also need on how to use these products with integrated pest management (IPM) programs that have been developed for many crops.
This proposed research fits two of the Strategic Goals for 2007-2012 established by CSREES: Strategic Goal 4: Enhance Protection and Safety of the Nation's Agriculture and Food Supply and Strategic Goal 6: Protect and Enhance the Nation's Natural Resource Base and Environment. These two goals are tied together by biological control and biologically based pest management- by reducing our reliance on fungicides and nematicides to manage disease, the environment is enhanced.
Why a Multi-State, Multi-Disciplinary Approach? Because biological control is the result of complex interactions between the agent, the environment, and the pathogen, this research area must be multi-disciplinary and collaborative. No single research institution has sufficient resources and diversity of expertise to solve the diverse disease problems that might be addressed through the use of biological controls. Many of these pathogens occur in multiple states and a coordinated research effort could provide more cost-effective outcomes. Because the results of our efforts are only now beginning to affect U.S. agriculture and the biopesticide industry, continuation of the W-1147 project for another five years will lead to further improvements in the efficacy and adoption of biological controls in American agriculture. In addition, these biological and cultural control techniques need to be tested under a range of environmental conditions and cropping systems that reflect the diversity of U.S. agriculture. The more than 20 researchers in this multistate project also collaborate with researchers in the U.S. and around the world, providing further impact and cross-fertilization of knowledge, as well as conducting the needed outreach activities for implementation of biocontrol options.
JUSTIFICATION:
Economic Costs Due to Soilborne Plant Pathogens
From 2001-2003, an average of 7% to 15% of the major world crops (wheat, rice, potatoes, maize and soybean) were lost due to diseases caused by fungi and bacteria (41).Yield failures resulting from acute diseases such as vascular wilts, take-all of cereals, Phymatotrichum root rot, Verticillium and Phytophthora may be even more severe and have destroyed entire agriculture industries. Detailed studies on the wheat crops in the Pacific Northwest had documented loss of up to 36% due to Pythium, Fusarium, Rhizoctonia, and Pratylenchus (13,17,54,55).
For root diseases of mature crops, there are few effective and economical post-plant strategies for control.
About 90% of the 2000 major diseases of the principal crops in the US are caused by soilborne plant pathogens (30).
Monetary losses due to soilborne diseases in the U.S. are estimated to exceed $4 billion per year (32), and losses due to parasitic nematodes exceed $100 billion per year world wide (5).
Several of the top 15 restricted, invasive quarantine pathogens listed by APHIS are soil borne, and could represent a biosecurity risk.
New invasive species have been discovered in N. America in the last five years, including Phytophthora ramorum, cause of sudden oak death, the potato cyst nematode, Globodera pallida in Idaho and most recently golden cyst nematode G. rostochiensis in Alberta and Quebec. In Nov. 2007, Phytophthora alnus was discovered in Alaska. This pathogen causes dieback of alders in Europe. Ralstonia solaneacearum race 3 biovar 2 has been periodically detected on geranium cuttings in the US, but has not been detected in the field, and would be a serious pathogen of potatoes. The root knot nematode Meloidogyne mayaguensis was first detected in the U.S. in Florida a few years ago, and could overcome genetic resistance to other root knot species. In natural ecosystems, once they become established, these pathogens cannot be easily managed.
Environmental Costs of Soilborne Plant Pathogens
The cost of soilborne plant pathogens to society and the environment far exceeds the direct costs to growers and consumers. The use of chemical pesticides to control soilborne pathogens has caused significant changes in air and water quality, altered natural ecosystems resulting in direct and indirect affects on wildlife, and caused human health problems. For example, methyl bromide, a fumigant used to control soilborne diseases, has become notorious in recent years for contributing to the depletion of the ozone layer. The planned ban on production and importation of this product has been repeatedly delayed by a lack of cost-effective alternatives, and there remains an intensive search for replacement control methods. This fumigant was to be totally banned by 2005, but critical use exemptions for the U.S. resulted in 2007 usage of 29% of the 1991 levels. Several other chemicals could be removed from the market due to regulatory and public concerns. For example, Nemacur (fenamiphos) was taken off the U.S. market this spring, triggered by a regulatory action. Many of these chemicals are now regulated by cities and towns. Additionally, plants evolved in the presence of microorganisms and are dependent on them in order to carry out many activities necessary for growth and reproduction. Thus, long-term chemical applications may permanently alter the microbial community structure sufficiently such that sustainable agriculture may be impossible.
Society's Expectations
As is readily apparent from reading the popular press, consumers are demanding plentiful low cost but safe food while simultaneously requiring the use of fewer chemical controls. From 2000 to 2005, the number of organic acres in the U.S. increased 128%, to around 4 million acres. In 2005, about 5% of vegetable acreage was organic. In the state of Washington, certified organic vegetable production increased 41% in 2006, and organic fruit production is expected to increase by 54% by 2008. The sale of organic milk reached $1 billion in 2005, up 25% from 2004, which has increased demand for organic feed. Organically-grown crops require non-synthetic methods for management of diseases, and organic growers are seeking scientifically-based disease management methods. Recent national surveys (2004) by the Organic Farming Research Foundation have identified pest and disease problems as a major concern for organic growers. Many of our products are certified as organic with the Organic Materials Review Institute (OMRI). During the last few years, more and more pesticides that control soilborne diseases have been taken off the market or regulated, including methyl bromide. Several soilborne diseases, for example, those caused by Phytophthora, Verticillium, Gaeumannomyces, nematodes, Pythium, Rhizoctonia, Fusarium, Streptomyces and Sclerotinia remain major problems after more than 100 years of study. Soilborne pathogens are well adapted to soil conditions, and once established are very difficult to eliminate. Chemical controls are often too expensive to be economically practical and chemicals effective against many pathogens have yet to be identified. Other approaches with great potential include the development of transgenic crops engineered with resistance genes to several pathogens. However, there is widespread public reluctance to accept these crops as evidenced by protests both here and in Europe. This public concern, combined with the natural ability of pathogens to overcome introduced resistance genes, has frustrated efforts to maximize this approach.
The ultimate goals of this collaborative work of W-1147 are to:
Provide society with a safe, low cost food supply.
Reduce the environmental impact of soilborne disease control on ornamental, bioenergy, fiber and food crop production.
Protect natural ecosystems from invasive species
Development of new industries and products for biologically based disease control
Biological Control and Soil IPM Systems As Attractive Alternatives
Biological control is an attractive approach for the control of soilborne diseases (15,16,25,30,60,61,43,62,63,39,40,33,12,27). Advantages of a biological approach to disease control include a lack of environmental damage, reduced human health risks, lack of resistance development in the pathogen, selectivity in mode of action, lack of activity against most beneficial microorganisms, and improved soil conditions and agricultural sustainability.
Biological control of soilborne plant pathogens has made large strides over the past several years. Much of this success is due to activities of the members of W-1147. Today the EPA lists more than 24 commercial biocontrol agents that are registered and commercially available in North America. Nearly all of them have been registered during the past five to ten years. However, most of these products are for seed and seedling diseases. W-1147 project is unique in emphasizing biological control of root diseases of perennial crops, including tree fruits and turfgrass, which are generally not treatable with chemicals or other methods as well as annual crops (Table 2). Since our last renewal, members of the former NC-125 have joined our group, extending expertise to important field crops, including soybean, corn, and alfalfa.
Interest and enthusiasm about biocontrol continues within the science of plant pathology. Since 2000, over 600 peer-reviewed articles have been published on biological control of plant pathogens (Web of Science, Dec. 2007). In fact, two new journals were launched in the 1990s-the journal Biological Control, which covers both arthropod and microorganism-mediated control methods, and Biocontrol Science and Technology. Combined with the increasing resistance in parts of the world to transgenic plants, it appears that the W-1147 regional project is both very timely and successful. Commercial interest has also increased substantially. In the past five years, over a dozen new companies have been formed that develop and market biopesticides. During that time, the EPA has registered over 100 new active ingredients as biopesticides and expects to see a continuation of such development in the years ahead. Indeed, the industry projects a rapid expansion of biopesticide products and a doubling of sales within the next five years.
In spite of the strides made in biological control research and development, there are many areas that require work before biocontrol will be used extensively. Current areas of research include:
Identification of more effective agents. Workers are isolating potential antagonists from soils where many pathogens originated and testing on a range of pathogens.
New bioinformatics information through the genomic analysis of the biocontrol agents and using microarrays to study gene expression in the plant. For example, P. fluorescens Pf5 and Burkholderia ambifaria AMMD have been sequenced since the last proposal, and P. chlororaphis 30-84, P. fluorescens Q2-87, and Q8r1-96 are currently being sequenced.
Advances in metabolomics and proteomics are also being used to study the biochemical pathways and in-situ detection of antifungal metabolites produced by biocontrol bacteria
Understanding the genetic diversity of pathogens, biocontrol agents and beneficial microbes, using advances in DNA sequencing, such as pyrosequencing.
Identification and characterization of natural disease suppressive soils.
Development of lower cost production, storage, and distribution systems.
Improved quality control assays.
Improved stability of the agent during production, storage and application.
Integration of biocontrol into current agronomic practices.
Identification of parameters affecting efficacy and survival after application.
Understanding the mechanisms of action of control, especially at the molecular and biochemical level.
Mycofumigation-(production of organic antimicrobial volatiles with activity against fungi.bacteria and nematodes)
Investigation of manipulation of cultural parameters that advance biological control (eg. uses of compost, green manures, and rotation crops).
Understanding the role of the plant in biological control (vis-a-vis induced resistance pathways).
Microbial community and plant-microbe interactions with biocontrol agents.
Use of microbial products or metabolites and other biorational approaches, such as compost teas, plant strengtheners, etc.
The promise, public acceptance and environmental benefits of non-chemical management of root diseases continue to make research on this area both timely and of critical importance to the future of U.S. and world agriculture.
Clearly there is much to be done in order to improve biocontrol agents so that they will continue to become major factors in the control of soilborne diseases. Biocontrol agents isolated by participants of W-1147 at ARS-WA, ARS-CA, CA-R, OR, MT, AK, OH, NB and NY have the ability to suppress a wide variety of plant pathogens that cause serious diseases of food, fiber and ornamental crops. The need for "high quality" biocontrol agents has never been more critical because of the pending loss of fungicides and fumigants upon which agriculture has been dependent for the last 50 years. Understanding the complex biological and environmental interactions that must occur for biocontrol to be effective requires the combined efforts of multiple investigators at multiple institutions focusing on different aspects of the problem, from applied to basic research. This logical approach is an area in which the W-1147 regional project has excelled and will continue to depend on during the next five years.
This project also fits the goals of other CSREES initiatives, including the National Integrated Food Safety Initiative of 1998, and other programs, such as Integrated Pest Management (IPM), Integrated Organic Program, Methyl Bromide Transition Program (MTB), Pest Management Alternatives Program (PMAP) and Sustainable Agriculture Research and Education Program (SARE). Other programs with similar goals include Risk Avoidance and Mitigation Program (RAMP), Crops at Risk (CAR), Minor Crop Pest Management (IR-4), Organic Transitions Program (OTP), and the Western Regional IPM Program.
The need for this project has become even greater in the last few years, given the elimination of the NRI program on Biologically-Based Pest Management in 2004 that has left many biocontrol researchers with reduced or eliminated funding, and this research has not been funded by other programs. W-1147 and S-1028 met jointly in Oct. 2006 with the National Program Staff at CSREES in Washington D.C. to discuss this problem and possible solutions.
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