W4147: Managing Plant Microbe Interactions in Soil to Promote Sustainable Agriculture

(Multistate Research Project)

Status: Inactive/Terminating

W4147: Managing Plant Microbe Interactions in Soil to Promote Sustainable Agriculture

Duration: 10/01/2018 to 09/30/2023

Administrative Advisor(s):

NIFA Reps:

Non-Technical Summary

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, increasing costs of such petroleum-based inputs and regulatory requirements

  • Lack of development of pathogen resistance to biological control organisms

  • Lower regulatory costs of registration

  • Faster reentry times after application

  • 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

  • Management of diseases in natural ecosystems

  • Improve plant productivity via controlling biotic and abiotic stress

  • Adaptation to climate change, as pathogen distributions shift

  • Increased N use efficiency and reduced N and P contamination of waterways and oceans 

Demand for biopesticides has continued to expand dramatically in the last five to ten years. In the 5 years since our last proposal, the global market for biopesticides has doubled from $1.5 billion to $3 billion US (Biopesticide Industry Alliance, 2017). The Biopesticide Industry Alliance, established in 2001, had 31 member companies in 2006, 65 members in 2012 and now has over 120 members. The International Biocontrol Manufacturer’s Association had 130 companies marketing microbial biocontrol agents in 2012. But now there are approximately 230 biopesticide manufacturers (not including China and India) with about 98 of those in the Americas and 91 in Europe. This segment of the industry is expected to grow between 15% and 20% annually (http://www.ibma-global.org). This growth has been driven by expanding organic markets as well as increased public sensitivity to the risks and hazards of chemical pesticides. From 2008 to 2012, 15 microbial active ingredients have been registered by EPA. From 2012 to 2017, six Bacillus spp., two Trichoderma spp., one Streptomyces sp., one Pseudomonas sp. and one Muscodor sp. have entered the EPA regulatory process (EPA Biopesticide Workplans 2012-2017). 

     In the last 5 years, there has also been a concerted effort by larger companies to acquire and purchase smaller companies or their products, and increase their investment in this field.  For example, Bayer CropScience bought Agraquest, acquiring Serenade and other Bacillus products. At present, Bayer is still marketing legacy biocontrol agents, including those from Gustafson and others (Kodiak), AgroGeen (Bacillus firmus) and Prophyta (MeloCon). However, in their West Sacramento, CA facility, they are investing millions of dollars in discovery and characterizing new biocontrol agents. Other recent acquisitions have been Prophyta, a German company, by Bayer.  Syngenta acquired Pasteuria BioSciences. Monsanto has entered into a partnership with Novozyme.  Most recently, Bayer will be acquiring Monsanto.

 The other more recent development is next-generation sequencing technologies, also known as high-throughput sequencing. This technology is presently being utilized by our members. Companies are engaging in microbiome research, and using this as a tool to discover new products. These include startup companies such as Agbiome (supported by Syngenta and Genective), Bioconsortia, and Indigo.  Monsanto has also invested millions in conducting microbiome studies on the hundreds of test plots for variety development.   

This proposed research fits one of the REE Action Plan Goals- 

Goal 1. Sustainable Intensification of Agriculture Production.  Subgoal 1B.  Crop and Animal Health.  

Two actionable items fit in perfectly with this project and are also shared by ARS and NIFA-

  1. Develop and extend effective, affordable, and environmentally-sound integrated control strategies to reduce losses caused by diseases, pests, and weeds, including early detection, identification, monitoring, and implementing biologically-based and area-wide strategies to manage key native and invasive species and postharvest pests.

      2.  Optimize integrated pest management practices for production crops by developing knowledge and tools for            cultural methods, biological control, and host plant resistance management tactics. 

Why a Multi-State, Multi-Disciplinary Approach?

As 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-3147 project 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 40 researchers in this multistate project collaborate with additional scientists 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. This group is also at the forefront of research in soil health, and in understanding the complex interactions among the soil microbiota which provide benefits to the plant. In addition, because of the Great Recession and strained state and now federal budgets, the number of faculty and researchers in plant protection has been significantly reduced. Because of this reduction in resources and human capital, it is more important than ever to gain synergy by leveraging resources with a multi-state group.


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.

    • 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.

    • In a survey on various crops in 35 US states nematode-caused yield losses were estimated between 5 to 25% (Koenning et al. 1999).

    • Projected worldwide crop production losses as a result of nematodes infestation were estimated at 14.6% in tropics and subtropics whereas in the developed temperate countries, it was estimated as 8.8% (Nicol et al. 2011).

    • Monetary losses due to soilborne diseases in the U.S. are estimated to exceed $4 billion per year, and losses due to parasitic nematodes exceed $100 billion per year world wide. In soybeans alone, all diseases combined caused losses of $15 billion from 2000-2007.

    • Detailed studies on the wheat crops in the Pacific Northwest had documented loss of up to 36% due to Pythium, Fusarium, Rhizoctonia, and Pratylenchus.

    • 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 fifteen years, including Phytophthora ramorum, cause of sudden oak death and the potato cyst nematode, Globodera pallida in Idaho. New invasive species such as Phytophthora tenticulata, have decimated native ecosystems in California. In natural ecosystems, once they become established, these pathogens cannot be easily managed.

    • In the last few years, citrus greening (Huanglongbing disease) has decimated the citrus industry of Florida, and recently it has been spread to Texas and into California. Plant nutrition and root health are important factors in this disease. 

    • Laurel wilt, caused by Raffaelea lauricola and vectored by exotic ambrosia beetles, threatens the native laurels of the East Coast and the avocado industry in Florida and California.

    • Boxwood blight, caused by Cylindrocladium buxicola, discovered in the US in 2011, has become endemic in 10 states.

    • Wheat blast is a new disease in South America (Brazil) caused by a strain of the pathogen Magnaporthe oryzae. It has recently been detected in Bangladesh, but is not yet present in the United States.

    • Macrophomina and Fusarium wilt in strawberries have become new problems, because of the loss of methyl bromide.

    • Dickeya dianthicola was reported as a newly emerged pathogen causing blackleg and soft rot of potatoes in the Northeastern United States in 2015 and resulting in significant economic losses.

    • Changing climate will result in more plant stress, drought conditions, salinity or in some cases a wetter climate, which will predispose plants to more disease.

 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 effects 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 there are still a few critical use exemptions for the U.S. A potential alternative, methyl iodide, was recently (2012) withdrawn from the U.S. market. Telone (1,3-dichloropropene), widely used as a pre-plant soil fumigant- nematicide in potato production, has reduced supply and restrictions by township quotas, application times and methods. Larger buffers and restriction zones are needed for many pesticides. Soil fumigants are major contributors to volatile organic compounds affecting air quality, especially in the Central and Imperial Valley of California. Development of fungicide resistance continues to be a problem with the newer generation of low impact fungicides with specific modes of action, such as the strobilurins. 

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 impaired. 

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 synthetic pesticides. This has been evident by the rapid growth of the organic food industry. In 2016, there were 5.1 million acres in organic production (USDA Organic Survey), almost double the acreage from 2008. The total farm gate value of organic products in 2016 was $7.5 billion, compared to $3.5 billion in 2011 (NASS). Total sales were $43 billion last year, up 8.4% from the previous year, representing 5.3% of total retail food sales in the U.S (Organic Trade Association). Several other trends have accelerated since our last renewal. Organic food is now available from large retailers such as Walmart, Whole Foods, Kroger Co and others. Amazon has recently acquired Whole Foods, which may result in further expansion of the organic market. There is an increasing “locovore” movement where people want locally-grown, usually organic food, from farmer’s markets, CSA (community supported agriculture) or community gardens. USDA has initiated a BioPreferred® Program for labeling certified biobased products and for encouraging their use by federal agencies. This labeling will tell the consumer the percent of biobased ingredients in a product. 

Organically-grown crops require non-synthetic methods for management of diseases, and organic growers are seeking scientifically-based disease management methods.

A 2015 survey by the Organic Farming Research Foundation (OFRF) identified disease management and soil health as one of the top five research priorities. 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, as well as many carbamate and organophosphate nematicides (1). Soilborne pathogens are well adapted to soil conditions, and once established are very difficult to eliminate. A classic example of a disease shift with the loss of methyl bromide has been the increased incidence of Fusarium wilt and charcoal rot of strawberries (Macrophomina) in California, which were not major problems 10 years ago. Even if chemical products are available, they are often too expensive to be economically practical. However, for many pathogens, chemical remedies 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 in the US and in Europe. This has resulted in grower's reluctance to adopt such technology as consumer boycott could be devastating, especially in small or specialty crop markets. These concerns, 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-3147 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. 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-3147. Today the EPA lists more than 40 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. Within the last few years, several new products containing Trichoderma and Bacillus have been released.  However, most of these products are for seed and seedling diseases. W-3147 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. Members of the former NC-125 have joined our group, extending expertise to important field crops, including soybean, corn, and alfalfa.  We have also had many members join from the southern and lower Midwest of the US since the last renewal, including those from MS, NH, ME, OK, MD, DE, and NJ. 

Continued Interest in Biological Control.

Interest and enthusiasm about biocontrol continues within the science of plant pathology. Since 2012, over 3,804 peer-reviewed articles have been published on biological control of plant pathogens (Web of Science, October 2017). During this same time, 10,360 papers were published on the subject of soil health. Much of this research is based on understanding how soil physical and chemical properties influence plant performance, but soil health must be studied in the context of microbiomes and how these affect plant diseases. This will be focus of the new project. Combined with the increasing resistance in parts of the world to transgenic plants, it appears that the W-3147 regional project is both very timely and successful. Commercial interest has also increased substantially, as outlined above. A new biocontrol agent, developed by one of our members, Barry Jacobsen (MT), was just registered in 2017 by EPA as a biological plant activator and is now marketed as LifeGard by Certis.  The active ingredient is a species of Bacillus mycoides that has been shown to induce resistance. This is just one example of the products that have been developed by this project over the last 40 years. 

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-3147 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 nematicides, fungicides and soil 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-3147 regional project has excelled and will continue to depend on during the next five years. 

Relationship of this project with other funding opportunities and national goals.

This project fits the goals of numerous other NIFA and USDA initiatives.  But the need for this project has become even greater in the last few years, given changes in funding priorities. The panel on Biologically-Based Pest Management was eliminated in 2004, leaving many biocontrol researchers with reduced or eliminated funding, and this research has not been funded by other programs. Although NIFA has now shifted away from the CAP grants, there are fewer grants. NSF and AFRI Foundational grants that specifically fund this type of research have a low success rate. This multistate project will fill a niche for research, networking, and outreach in the field of biological control of soilborne plant pathogens and soil health.


Related, Current and Previous Work

The Phytobiome 

In the past 40 years, biological control has been a major emphasis of the project, along with development of cultural methods, soil amendments and rotations, cover crops, suppressive soils, and other methods to enhance soil health. However, with the development of next-generation sequencing (high-throughput sequencing) methods that debuted about 10 years ago, we now have a new tool to examine the microbial communities and identify components important for soil health. The first technology was pyrosequencing (454) and has now been replaced by Illumina MiSeq and HiSeq as the most cost-effective methods. Like all technologies, these methods have limitations but are constantly being optimized.  Most studies are amplicon based, with PCR using 16S RNA primers for bacteria and ITS primers for fungi.  In addition, there has been a groundswell of research on the phytobiome.  The phytobiome consists of plants, their environment, and their associated communities of organisms. Interactions within phytobiomes are dynamic and profoundly affect plant and agroecosystem health, which in turn impacts soil fertility, crop yields, and food quality and safety.  It is the networks of interactions among plants, their environment, and complex communities of organism that profoundly influence plant and agroecosystem health and productivity (www.phytobiomes.org)

A new journal was launched in 2017 called Phytobiomes, and one of our members (Borneman) is a senior editor. The Phytobiome Initiative was launched about 3 years ago, and several of our members are a part of that effort, as members of the American Phytopathological Society. This initiative is stimulating research support and collaborations among the scientific community. We believe that the Phytobiome and more specificaly the rhizobiome is the key to understanding how soilborne pathogens can be managed. There has also been a proliferation of new companies funded by millions of dollars of venture capital, to capitalize on using the microbiome in agriculture to find new biological agents, much like the efforts of the 1980s.  These include companies such as AgBiome, Indigo Agriculture, and Bioconsortia.

Over the past several years, a number of members of the W-3147 project have been involved in microbiome research. Researchers at ARS-WA and WA have used these techniques to identify suppression to Rhizoctonia bare-patch (75) and to compare communities in the soil and rhizosphere of long-term no-till and conventional tilled wheat plots, both fungi and bacteria (74, 53).  Recently, they have shown the minimal effects of glyphosate on bacterial and fungal communities (64), a paper with a large impact because of the recent interest in this herbicide, the most widely used in the world. They have shown how biosolids, processed sewage sludge, can shift fungal communities in the soil and dust. (63)  They compared the communities of arbuscular-mycorrhizal in organic vs conventionally grown irrigated onions (24). Researchers in MN have pioneered the studies of the ecology of Streptomyces and their role in suppression of plant diseases (61, 66, 15). 

Researchers at WA are also working on the rhizosphere microbiome of the bioenergy crop switchgrass to understand the interplay between plant physiology and microbial nitrogen fixation / nitrogen cycling (9). They are also working on understanding the ecology, evolution, and genomics of nitrogen-fixing bacteria, both free-living (27, 42, 43) and symbiotic (50, 51). 

Researchers in CA have examined the bacteria and fungi in roots of citrus trees that exhibit tolerance to Huanglongbing disease in Florida. These trees have been termed survivor trees, and they are found in groves where most of the other trees are very unhealthy. Since the trees in such groves are clonal, the cause of this tolerance is likely not genetic. They posit that the cause of this phenotype is the citrus microbiome (16). In their research, they have identified numerous microorganisms that negatively correlate with disease ratings, which may prove to be useful biological control agents. One example is the discovery of several phylotypes of mycorrhizal fungi, which are known to provide phosphorus to plants, and citrus trees with Huanglongbing have been shown to be deficient in phosphorus. 

Researchers at Pullman, WA examined communities of native yeasts and non-yeast fungi on wine grape berries for two consecutive seasons, and found that vineyard location was a major factor in community composition (Wang et al. unpublished). 

Researchers in Maine have worked on soil microbial communities that regulate and zoosporic germination and infection of Phytophthora erythroseptica. They found some specific signal molecules only function above a concentration threshold (21,22). 

We think our group is well positioned to make further advances in this rapidly expanding field. 

Identification of New Biocontrol Agents 

As mentioned in previous sections, the field of biological control of soilborne pathogens continues to expand. There are 22 active ingredients with Trichoderma, 28 with Pseudomonas, and over 40 with Bacillus. In terms of registered products, there are 8 with Trichoderma, 6 with Pseudomonas, and 21 with Bacillus (npic.orst.edu/nppo).  This subject continues to generate a significant amount of research (45, 12, 28, 49, 25, 77, 60). These references are just in the last four years.  One area that has drawn more attention is the field of endophytes (10,59). 

W-3147 members have been instrumental in discovering many of these new biocontrol agents, including strains of Pseudomonas fluorescens with superior colonizing ability (Q8R1-96) (54), diacetylphoroglucinol-producing strains of P. fluorescens (55), Trichoderma atroviride 901C (33); Pseudomonas aureofaciens AB254 (29); and Dactylella oviparasitica (46) for control of cyst nematodes. From 2012 to present, the list of biocontrol agents discovered by members continues to grow. Most notable is the product LifeGard WG, registered and marketed in 2017 by Certis USA as a biological activator, containing Bacillus mycoides. This was developed by B. Jacobsen (MT). Table 1 in the appendix shows the complete list of all the biocontrol systems and pathogens that our project is working on. From this list, W-3147 member are moving beyond the usual three biocontrol agents (Trichoderma, Bacillus, and Pseudomonas) and doing research on Lysobacter, Burkholderia, Brevibacillus, Paenobacillus, Chryseobacterium, Bradyrhizobium, Flavobacterium, Dactylella, Streptomyces, and Pochonia. 

Researchers at Pullman, WA showed that specific native yeasts of grape inhibit growth of Botrytis cinerea in vitro and on the grape berry (Wang et al., submitted). In collaboration, ARS-WA and U Washington, Seattle showed that endophytes of poplar and willow inhibited growth of soilborne fungal pathogens of wheat in vitro (23). This group also initiated research with new poplar endophytes that have in vitro activity against R. solani (S.L. Doty and P. Okubara, unpublished). 

Disease Suppressive Soils and Plant Protecting Microorganisms

Over the last 25 years there have been surprising and exciting discoveries for natural methods to suppress or eliminate pathogens, and/or protect plants. Intensive studies of disease suppressive soils have led to the development of new methods of analysis (17, 8, 7, 3) and new insights into the nature of soilborne disease suppression (69,20). The most interesting direction has been the use of microbiome research to describe these complex communities. Members of W-3147 are recognized as leaders in this area, as evidenced by an invited review article titled “Disease Suppressive Soils: New Insights from the Soil Microbiome” which was published in Phytopathology in 2017 (65).  In this paper, Schlatter, Weller, Thomashow and Kinkel, all members of W-3147, speculate on the future of research in this area, show three case studies (take-all, Rhizoctonia, and Streptomycetes) and construct a series of testable hypotheses. Many of the advances in the study of suppressive soils have been made by members of W-3147. This includes the first identification of new bacterial genera associated with Rhizoctonia decline in North America (75), the role of complex communities of phenazine producing Pseudomonas spp. (47), and the role of actinomycetes in suppression by glucosinolate biofumigation (13, 14, 31, 32). Such advances indicate that active management of soil microbial communities can be an effective approach to develop natural suppression of soilborne diseases and improve crop productivity (31). 

CA researchers (Becker, Borneman) have performed numerous studies demonstrating that Dactylella oviparasitica is the causal agent of a Heterodera schachtii suppressive soil at UC Riverside Agricultural Operations, and it also is a very effective biological control agent (8, 71). Expanding this work, these researchers determined that indigenous populations of Dactylella oviparasitica in sugar beet fields located in the Imperial Valley (CA) were also able to dramatically suppress H. schachtii populations (70). 

ME researchers (Hao and students) has studied a naturally occurring disease suppressive soil against potato common scab caused by Streptomyces spp. (35, 58). They have found that after years of monocropping of potato, disease suppression was established, and several antagonistic bacteria were responsible for the suppressiveness. These bacteria include fluorescent Pseudomonas spp., Bacillus spp., Lysobacter spp., and non-pathogenic Streptomyces spp. From these beneficial organisms, they isolated, characterized, and patented one bacterium Bacillus velezensis (formerly B. amyloliquefaciens) that has a potential for commercialization (36, 37). 

A root-knot nematode suppressive soil was identified and investigated by CA researchers (Becker, Borneman). The soil was chosen for its abilities to biologically suppress a M. incognita population on two different crops under greenhouse conditions (4). Three Pochonia chlamydosporia var. chlamydosporia strains were isolated from the M. incognita-suppressive soil, and then genetically characterized with multiple Pochonia-selective typing methods based on analysis of ß-tubulin, rRNA internal transcribed spacer (ITS), rRNA small subunit (SSU), and enterobacterial repetitive intergenic consensus (ERIC) PCR (72). 

Generally speaking, there are two approaches to actively managing crop-associated microbial communities. The first approach is to develop disease suppressive soils through manipulation of carbon inputs.  This involves adjusting the types and timing of organic inputs, such as cover crops, animal manures, composts, compost teas, and crop sequencing.  The second approach involves inoculation with disease suppressive microorganisms.  These disease suppressive organisms may be identified using a microbiome approach, and then developed as effective and low-cost inocula.  Members of W-3147 have done research with both approaches.   

In some cases biocontrol agents are not able to prevent the infective stage of a pathogen from attacking the host seedling and consequent damage. For example, second-stage juveniles of root-knot nematodes hatch and quickly invade susceptible roots before effective microbial metabolites can be sufficiently produced. Seed coating with Streptomyces metabolites (abamectin) and microbial biocontrol organisms can mitigate early attack through the nematicidal activity of the biorational while the biologicals deliver a second punch against the female and/or eggs (2). 

Methods that transform resident microbial communities in a manner which induces natural soil disease suppression have potential as components of environmentally sustainable systems for management of soilborne plant pathogens to reduce the need for pesticides.

 Mechanisms of Disease Control

Biological control agents express a variety of mechanisms that are responsible for pathogen inhibition. Therefore, if we are to maximize the effectiveness of any biocontrol agent, we must understand the function of the mechanism in the biocontrol agent’s lifestyle. Known mechanisms by which biocontrol organisms reduce disease include:

  • Induction of plant resistance mechanisms and regulation of gene expression

  • Antibiotic and toxin production.

  • Cell-wall degrading and lytic enzymes.

  • Siderophore production.

  • Biosurfactant production

  • Mycoparasitism

  • Shifts in microbial communities

  • Alleviation of ROS effects or toxicities

  • Mycoviruses- in soybean on Fusarium

  • Sex pheromone used to disrupt spore germination

  • New mechanisms and chemistries are being discovered by genomic analysis. 

Members of the W-3147 project have been involved in research on all of these mechanisms. They were pioneers in understanding the genetic and biochemical pathways for production of phloroglucinol and phenazine, (48, 34), the regulation of phenazine production (30), the role of phloroglucinol producers in suppressive soils (56) and the in situ detection and quantification of antifungal compounds produced by biocontrol agents in the soil and rhizosphere (67). Researchers in NE identified a number of antibiotics and lytic enzymes produced by Lysobacter, as well as the cellular mechanisms that regulate their biosynthesis (18, 68, 78). One antibiotic, HSAF, was shown to be an important mechanism in the biocontrol of fungal and nematode pathogens (26, 76). Bacillus velezensis BAC03 produces the antibiotic polypeptide LCI, plant growth promoting chemicals including indole-3-acetic acid, 1-aminocyclopropane-1-carboxylate deaminase, and volatile organic compounds such as acetoin and 2,3-butanediol (37, 38). 

ARS-WA and researchers at Justus Liebig University, Giessen Germany found that a commercial Allium-based bio-pesticide had a broad range of activity against various foliar and soilborne pathogens. Poplar endophytes showed initial inhibition but appear to recover and grow on higher concentrations of the bio-pesticide (79). Mechanisms for endophyte inhibition of soilborne fungal pathogens, including those of strawberry, and for endophyte recovery from bio-pesticides will be explored. 

    These examples serve to illustrate the point that every biocontrol agent-plant pathogen-host crop system requires special insight on how best to utilize the biocontrol agent to maximize disease control. This maximization of biocontrol will be different for different regions of the United States. 

     In summary, research related to the objectives outlined above is in progress throughout the world. However, the lack of broad acceptance of biocontrol agents reflects two major obstacles. First is the complexity of the ecological systems in which the biocontrol agents must operate. Second is the current mindset of growers that biocontrol is expensive and inconsistent. To overcome both hurdles, we must better understand the factors that influence the efficacy of biocontrol agents once released in the field in order to begin to manipulate the system as a whole and maximize the benefits of biocontrol and its contribution to sustainable agriculture. 

Differentiation from other regional workgroups in the area of plant pathology 

   NCERA-137 is a Multistate Research Coordinating Committee and Information Exchange Group, but it only deals with soybean diseases. Currently only one other regional workgroup is working in this area. In their last project, S-1053, they had two objectives.  The first was to look at the genetic diversity of the pathogen and antagonistic microbes.  The second objective was more general, to look at the effect of management practices (chemical, cultural and biological) on the microbial community. Previous versions of this project (S-1028 and SDC348) were focused more on testing a common set of biocontrol across the South on vegetable and agronomic crops. None of these objectives overlapped with the objectives of W-3147. W-3147 covered a broader range of agriculture, including nursery, perennial, turfgrass and ornamental crops which were not covered by S-1053. W-3147 has a strong nematology component. But the largest difference is in the approach- our objectives cover everything from basic discovery to testing, development, and application of the technology. In addition, we have a strong record of outreach and extension in our project.

  There is also a geographical separation-  S-1053 worked on crops in the South, and W-3147 on crops in the West, Midwest and Northeast.  Soybean and corn were the only potential overlap.

 However, the S-1053 project expired in Sept, 2017.  They have submitted a preliminary application for a new proposal, with the objectives almost identical to the old project. However, they have not submitted the full proposal, so we can only address the objectives.

S-1053 objectives

Objective 1. Evaluate the biology and diversity of soilborne pathogens, associated and antagonistic microorganisms, and environmental conditions in the context of the whole-system phytobiome. This objective includes traditional, metagenomics, and spatial/temporal methodologies to understand microbial community dynamics that determine soilborne disease incidence and severity on economically important crops in the U.S.

Objective 2. Evaluate the efficacy of soil-borne disease management strategies (chemical, biorational/biological, cultural) and characterize the associations among microbial community profile, soil physicochemical properties, environmental factors and disease suppression. 

Objective 1 has a more descriptive approach- to describe and evaluate the biology and diversity of the pathogen and phytobiome. Our approach is more directed- it goes beyond simply describing the phytobiome, but uses the phytobiome as a tool to pull out microbes, to understand how these function in suppression, disease control and soil health, and how to manipulate the cultural systems to favor this suppression.

In summary, even though we will both be using new techniques to examine the phytobiome, there is no major overlap between the goals and objective of the two projects.


  1. To discover, identify, and characterize microbes, biological control agents, biorational compounds, pathogen-suppressive microbiomes, as well as cultural practices and organic amendments that reduce plant diseases and damage caused by soilborne plant pathogens and improve plant health.
  2. To determine how microbial populations function to suppress disease and how plants and the environment relate to this function.
  3. Develop, assess, and promote sustainable management strategies and practices for soilborne pathogens that are IPM-based and are compatible with soil health management
  4. Provide outreach, education, extension and technology transfer to growers, stakeholders, students and other scientists.


<p><strong>METHODS:<strong>&nbsp;</strong></strong></p> <p><strong>Objective 1. To discover, identify,&nbsp;and characterize microbes, biological control agents, biorational compounds,&nbsp;pathogen-suppressive&nbsp;microbiomes, as well as cultural&nbsp;practices and organic&nbsp;amendments that reduce plant diseases and damage caused by soilborne plant&nbsp;pathogens and improve plant health.&nbsp;<br /> </strong></p> <p>&nbsp;A. <strong>Discovering, identifying and characterizing microbes and biocontrol agents. </strong></p> <p>&nbsp;&nbsp;&nbsp;&nbsp; <strong>1. Beneficial Microbes.</strong></p> <p>Within the last few years, there has been an increase in the number of papers on plant endophytes, both bacterial and fungal, which can be identified with next-generation sequencing (2499, 2012-2016, Web of Science). Endophytes have been shown to give benefits to plants, protecting against pathogens and also plant stresses, such as drought and nutrient deficiency. Researchers in WA are exploring mechanisms of action of Salicaceae endophytes using genome sequence data and gene knockout approaches. They are also characterizing the activities and mechanisms of newly-isolated endophytes, with emphasis on soilborne fungal pathogens of cereal production systems. Researchers in WA are also looking at communities of arbuscular mycorrhizal fungi in organic and conventional onion production. Plant growth promoting rhizobacteria (PGPR) has been extensively studied in disease control. Hao (ME) has isolated <em>Bacillus velezensis</em> and patented the strain BAC03 which shows strong disease control against potato common scab and increases plant yield. Researchers at WA are also focused on plant protection through general plant growth promotion as well as through biological nitrogen-fixation. They are using genomics and metabolomics to characterize these interactions, with a focus on both free-living nitrogen fixers as well as the canonical rhizobial symbionts of legumes. They are also characterizing mathematical modeling and synthetic systems to understand the coupling between photosynthetically-fixed carbon and microbial nitrogen-fixation.&nbsp;</p> <p>&nbsp;&nbsp;&nbsp;&nbsp;<strong> 2.&nbsp; Biocontrol Agents. </strong></p> <p>In the past, extensive efforts were made to isolate microorganisms at random from soil and plant material and then identify, through in vitro, greenhouse and field tests, those with potential as biological control agents or plant growth promoters. This strategy tended to yield candidate species that occur in high populations or those that grow quickly in culture. Past members of this project have produced <em>Bacillus</em> (41) and <em>Trichoderma</em> products (19). With the development of high-throughput sequencing and microbiome studies, we can now implicate and identify new fungi and bacteria. But much of the community work is still correlative- certain OTUs are associated with a phenomenon, such as disease suppression. Few studies have isolated, identified and tested candidate organisms, i.e. performing Koch&rsquo;s postulates. Project researchers in WA and CA were among the first to do this (75, 8). The other limitation is that many of the bacteria and fungi that are implicated in a function have been isolated or cultured.&nbsp; This will require new methods of directed isolation.&nbsp; For example, genomic understanding of the organism may provide clues to specific catabolic processes and unique carbon and nitrogen sources that can only be used by the organism.&nbsp; Other novel techniques include the use of isolation chips (5), co-culturing, or manipulation of the environment eg. acid conditions, high CO<sub>2</sub><strong>. Members will continue to search for novel biocontrol agents using more directed methods based on high-throughput sequencing. Members will share protocols, data pipelines, and develop common projects.<strong>&nbsp;<strong>&nbsp;</strong></strong></strong></p> <p><strong><strong>&nbsp;&nbsp;&nbsp;&nbsp; 3. Biorational compounds. </strong></strong></p> <p>Biorational compounds are certain types of materials derived from animals, microorganisms, or plants. They include plant-derived materials, such as extract of <em>Chenopodium ambrosioides,</em> garlic and <em>Eynoutria sachalinensis</em>; and plant-derived oils, such as neem oil and many other essential oils (rosemary oil, soybean oil). Hao (ME) found that the essential oils of oregano and thyme can effectively inhibit <em>Phytophthora capsici</em> and control blight on squash (6). The same products also showed effectiveness in suppressing bacterial pathogens causing blackleg and soft rot of potato (unpublished). The mode of actions of biorational compounds include direct inhibition of pathogens and induced resistance of host plants. The latter is crucial in long-term consideration of disease management. Because these biorational compounds are environmentally safe, they can play important and unique roles in plant disease management, including in the application of organic production where conventional pesticides are not permitted, as well as greenhouses where the controlled conditions favor enhancing the efficacy of these products. In addition, the application of biorational products can be extended to postharvest and foodborne pathogens. Members will continue to explore the potential application in different disease management strategies (ME, NE).&nbsp;</p> <p><strong>B. Pathogen suppressive microbiomes.&nbsp;</strong>&nbsp;&nbsp;</p> <p>Naturally suppressive soils have been long studied for clues to how microbes suppress soilborne pathogens and environmental factors that enable them to function. Armed with such knowledge, it may be possible to develop effective and sustainable pest management strategies through the application of the organisms and through agronomic practices that influence their populations.&nbsp; Our project, over the past 20 years, has studied many suppressive systems, such as suppression to take-all, <em>Rhizoctonia</em>, <em>Macrophomina phaseolina,</em> <em>Streptomyces </em>and suppression to the sugar beet cyst nematode. These were recently highlighted in a Feature Article in Phytopathology written by members of W-3147 (65).&nbsp; But what is new is the ability to use next-generation sequencing to gain new insights into the role of communities and consortia in suppression. The past work has focused on identifying one microbe or group of closely related microbes, and then demonstrating their effect using a type of Koch&rsquo;s postulates.&nbsp; Experiments implicate or correlate the organism with disease reduction, the organism is isolated and tested in the greenhouse or controlled conditions against the pathogen to show biocontrol activity. Members of W-3147 have been one of the few groups that have successfully done this. &nbsp;For example, Paulitz (ARS-WA) identified bacterial taxa in the Sphingobacteria (<em>Flavobacterium</em> and <em>Chryseobacterium</em>) and Oxalobacteriaceae that may be involved in suppression of Rhizoctonia bare patch of wheat. They tested isolates of <em>Chryseobacterium</em><em> soldanellicola</em> and showed they could suppress Rhizoctonia in the greenhouse. Weller (ARS-WA) identified unique communities of phenazine-producing <em>Pseudomonas </em>in arid wheat producing areas, extending across hundreds of square kilometers of the Pacific Northwest.&nbsp; These have been widely tested in the greenhouse and in the field as seed treatments. &nbsp;Becker and Borneman (UCR) are extending their studies of a <em>Dactylella oviparasitica</em>-based <em>Heterodera schachtii</em> suppressive soil at UCR to use cropping schemes to manipulate populations of indigenous <em>D. oviparasitica</em> in sugar beet fields in the Imperial Valley (CA). The purpose of this work is to enable growers to be able to create and maintain <em>H. schachtii</em> suppressive soils for sugar beet production. In addition, Becker and Borneman (UCR) are collaborating with Paulitz (WA-ARS) and Adesemoye (NE) to adapt this <em>D. oviparasitica</em>-based cropping-scheme strategy to create and maintain suppressive soils targeting the cereal cyst and soybean cyst nematodes, respectively. Hao (ME) has worked on naturally occurring soil that is suppressive to potato common scab. He has identified fluorescent <em>Pseududomonas</em>, <em>Lysobacteria,</em> <em>Bacillus</em>, and non-pathogenic <em>Streptomyces</em> spp. as the top contributors of disease suppression.</p> <p>However, little is known about how larger groups or consortia function in disease suppressiveness. One line of research has focused on making synthetic microbial consortia and testing them in model systems such as Arabidopsis. Core microbiomes are identified, and combinations are tested. However, because our group is more oriented to practical applications, we will focus on describing and characterizing entire microbiomes. To this end, some of our members (WA-ARS, KS-KSU) have begun to describe the core rhizosphere microbiome of wheat in disease suppressive soils, under long-term no-till (which can promote suppression). Network analysis has provided a powerful tool to see interactions that are not evident by just analyzing the abundance of OTUs. Members of WA-ARS have begun to use these tools in describing how herbicides such as glyphosate and fertilization may have subtle effects on microbial communities (52, 62, 63, 64). <strong>W-3147 members are on the cutting edge of soil and root microbiome research, which will provide a powerful tool for understanding how natural disease suppression occurs and give clues to cultural methods that can be used to enhance this under real grower conditions. One major advantage of investigating microorganisms associated with suppressive soils is that these organisms have demonstrated the ability to function in production agricultural systems. We can study both fungal and bacterial communities, and even nematode communities. This can lead to the development of more sustainable and effective strategies to manage soilborne pathogens and enhance soil health.&nbsp;</strong></p> <p><strong><strong>C.&nbsp; Examining cultural practices and organic amendments that influence soilborne pathogens</strong>. </strong></p> <p>Members of W-3147 have been at the forefront of understanding the effects of soil management practices on the incidence and damage of root diseases. This is the most cost effective and feasible method of translating our research to real-life grower conditions. Can we develop suppressive soils or stimulate host resistance by manipulating crop rotations or by incorporating cover crops or green manures? Can we reduce crop damage by timing of herbicide application? Can we reduce inoculum in soil by solarization or anaerobic soil disinfestation?</p> <p>The following are some specific questions that will be addressed by W-3147 members.</p> <p>-what is the dynamics of fungal succession (pathogens and saprophytes) in roots killed by glyphosate? What fungi eventually displace the pathogens and make greenbridge management effective (ARS-WA)?&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</p> <p>-how does Anaerobic Soil Disinfestion reduce pathogen inoculum and alter the microbiome of soil, which could reduce the pathogen recolonization? What are the best organic substrates to use in controlling strawberry diseases (ARS-WA)?</p> <p>&nbsp;-how do Brassica seed meal amendments alter the microbiome and pathogen spectrum involved in apple replant and nematodes on vegetables (ARS-WA, CA)?</p> <p>&nbsp;-how does soil fumigation influence the communities of beneficial arbuscular mycorrhizal fungi in onion production (WA) and potato (ME)?</p> <p>&nbsp;-can soil health be accurately assessed and measured to help growers make management decisions (NY)?</p> <p>&nbsp;-can long-term no-till practices in wheat shift fungal communities to be more suppressive to <em>Rhizoctonia </em>(ARS-WA)?</p> <p>&nbsp;- how is the soil microbiome and soil community (fungi, bacteria, Oomycetes) changed by soil solarization and biosolarization (OR)?</p> <p>&nbsp;-how do different agricultural practices (cultivars grown, growing substrates) influence performance and activity of the different types of biopesticides (fungal, bacterial, metabolites) (NH)?</p> <p>&nbsp;- how does crop rotation change the soil microbial profile that favors the control of pink rot of potato (<em>Phytophthora erythroseptica</em>) and nematodes on vegetables (ME and CA)?&nbsp;</p> <p><strong>Objective 2. To determine how microbial populations function to suppress disease and how plants and the environment relate to this function.</strong></p> <p>The previous objective is focused on describing, identifying and understanding the complex of microbes that function in plant health. This objective focuses on the question of HOW? How do these microbes function in plant/microbe interactions? This research is more basic and lab based. But understanding function is important to know how environmental conditions will affect the microbes, how the pathogen will respond and adapt, and explain some of the inconsistency that may occur.</p> <p>The following is a short list of the mechanisms of primary interest and the microbial systems in which they will be investigated</p> <p><strong>Secondary metabolite production, lytic enzymes and novel compounds.-</strong>Researchers at ARS-WA have been conducting a long-term experiment, under irrigated and non-irrigated conditions. Under irrigated conditions, the <em>Pseudomonas </em>population shifts to phloroglucinol-producers, but under dryland conditions, the population reverts to phenazine producers. How do these two antifungal compounds influence the soil microbiome? Researchers from NJ are looking at novel lipopeptides produced by endophytic <em>Bacillus</em> in grasses, and their role in protecting them from soilborne pathogens. They are also looking at how endophytes enhance the ability of roots to take up organic forms of N and enhance plant growth. Researchers at NE working with <em>Lysobacter</em> discovered a novel antibiotic (HSAF) and lytic enzymes to be biocontrol mechanisms against fungi and bacteria.</p> <p><strong>Pathogen and microbe signaling</strong>- Researchers at ME are studying signaling molecules that regulate the zoosporic germination and infection of <em>Phytophthora erythroseptica.</em> This will help us to understand how the pathogen behaves in the natural environment.</p> <p><strong>Biofilm production</strong>- has been shown to be important in the survival of phenazine producing <em>Pseudomonas</em> in dryland wheat production under very arid conditions. Researchers at ARS-WA are investigating the role with biofilm minus mutants and using electron microscopy to view micro colonies in situ on roots. They are also looking at how phenazines function in electron transport and Fe uptake in the rhizosphere under low O<sub>2 </sub>conditions in biofilms.</p> <p><strong>Enzyme production-</strong> Researchers at NE are examining lytic enzymes produced by <em>Lysobacter</em> spp. including glucanases and chitinases.</p> <p><strong>Host resistance-</strong> Researchers at NE will analyze induced resistance signaling pathways activated in different plants by the biocontrol bacterium <em>Lysobacter</em>. Researchers at ARS-WA are mapping resistance genes to Fusarium crown rot and using markers to identify <em>Cre </em>genes for resistance to cereal cyst nematode. Researchers NY are looking at mechanisms of resistance genes to <em>Phytophthora capcici</em> in peppers.</p> <p><strong>Population biology and distribution of virulence and avirulence genes-</strong> how do populations of vegetable pathogens such as <em>Phytophthora</em> and <em>Sclerotinia</em> vary over time and with different cropping systems (NY)? Researchers at CA-UCR are looking at the breaking of the Mi resistance gene to <em>Meloidogyne</em> in tomatoes. &nbsp;</p> <p><strong>Objective 3. Develop, assess, and promote sustainable strategies and practices to manage soilborne plant pathogens that are&nbsp;IPM-based and are compatible with organic and soil health management practices. </strong></p> <p>Intensive production of crops has contributed to gradual deterioration of soil health, resulting in reduced yield and profitability. Characteristics of deteriorated soils include crusting, compaction, low content of organic matter, the increased incidence and damage of root diseases caused by soilborne pathogens, and the prevalence of other pests. In addition, it is well documented that damage due to diseases caused by soilborne pathogens is greater in poor quality and unhealthy soils. Thus, there has been an increasing interest in addressing soil health constraints in a holistic, sustainable, and environmentally compatible manner. Among the long-term management practices promoted to maintain and/or improve soil health status are various reduced tillage systems, more diverse crop rotations, numerous cover crops, green manures and the application of composts. All these soil and crop management practices have profound direct and indirect effects on the populations and disease potential of soilborne pathogens as well as on the diversity and dynamics of the soil microbial communities. The increased implementation of soil health management practices, specifically reduced tillage systems, are impacting many of our current recommendations and strategies for controlling plant pathogens. Thus, there is a great opportunity and a challenge for scientists associated with W-3147 to become involved in the multi-disciplinary investigations dealing with soil health management to assure the development and implementation of programs that are also suppressive to soilborne pathogens and plant diseases in general.</p> <p>This objective covers the applied aspect of the project. How do we demonstrate, evaluate and promote a workable, realistic tool that growers can use for long- sustainable disease management? This first involves field testing under real conditions. Almost all of our members have been involved in this (ARS-WA, CA-R, MD, MI, MN, MS, MT, NE, NJ, NM, NY, OR, and WA). This may involve soil management practices like incorporation of cover crops and organic amendments, applying microbials to the seed, greenhouse mix or directly to the soil; or enhancing suppression by crop rotation. Plant genetics are also part of the equation. Recent research has focused on how different cultivars may support a different root microbiome and thus enhance suppression of pathogens. But it also involves assessment of the impacts on soil health through microbiome research using high-throughput sequencing and also the impacts on the pathogen. This is done with recent advances in identification and quantification of pathogens and beneficials with real-time quantitative PCR, loop-mediated isothermal amplification, and smart chip based real time PCR (Wafergen). In other words, many of the findings in Objective 1 and 2 will be applied to this objective. &nbsp;&nbsp;&nbsp;&nbsp;</p> <p>Much of this research is conducted on grower fields and research stations, and thus involves interactions with growers as part of our extension effort (Objective 4, outlined in OUTREACH). Growers like to see demonstrations before they will adopt new technologies. Thus, the applied part is crucial. The successful completion of this objective will contribute to greater root health (reducing damage caused by soilborne pathogens), improving soil health and productivity, and reducing environmental risks; thus leading to a more sustainable and resilient agrosystem.&nbsp;</p> <p>Below are a few examples of the type of research that will be conducted</p> <p>Continue testing soil solarization in field production nurseries, organic vegetables, and berry crops (OR).&nbsp;</p> <p>Understand how efficacy of soil solarization is affected by soil moisture and solarization duration (OR).&nbsp;</p> <p>Compare soil solarization vs. biosolarization (=solarization following incorporation of a cover crop) under aerobic vs. anaerobic conditions (OR).&nbsp;</p> <p>Studies on plant cultivar and growing media and interactions with biocontrol agents in pre-commercial facilities (NH)</p> <p>Develop models to predict efficacy of soil solarization for management of diseases caused by <em>Fusarium oxysporum</em>, <em>Agrobacterium tumefaciens,</em> <em>Pythium</em> spp.,<em> Phytophthora</em> spp. (OR)</p> <p>Screen for resistance for cereal cyst nematode on wheat in field and greenhouse trials (ARS-WA)</p> <p>Sample sugar beet fields for levels of <em>Dactylella ovaparasitica</em> to establish risk models (CA).</p> <p>Test mustard seed meals and other treatments for control of root knot nematode in organic carrot and tomato production (CA)</p> <p>Evaluate the effects of combining biostimulants with biopesticides and determine if these effects are additive or synergistic (NH)</p> <p>Evaluation of compatible biocontrol agents and fungicides (NE)</p> <p>Integration of cover crops and biocontrol agents (NE)</p> <p>Field and greenhouse testing of <em>Burkholderia</em> and <em>Bacillus</em> on soybean and corn (NE)</p> <p><strong>Objective 4. Provide outreach, education, extension and technology transfer to growers, stakeholders, students and other scientists.&nbsp;&nbsp;&nbsp;&nbsp; This is covered in the OUTREACH section.&nbsp;</strong></p>

Measurement of Progress and Results


  • Publications- peer reviewed, extension and technical bulletins, meeting proceedings, abstracts, book chapters.
  • Outreach and education materials- grower and extension talks, teaching materials, web-based training modules and certification programs
  • Highly qualified personnel- Trained students, educators and consultants that will serve the agricultural and biocontrol industry.
  • Management recommendations for soilborne diseases- ways of managing soilborne diseases with cultural methods, crop rotation, cover crops, organic amendments, and suppressive soils.
  • Biocontrol products- novel organisms with new modes of action, improved formulations and production systems, quality control assays, and application guidelines.

Outcomes or Projected Impacts

  • Knowledge and understanding of the phytobiome of agricultural systems and the benefits and services they provide to crop productivity
  • Identification of communities and consortia involved in natural suppression of soilborne plant pathogens
  • Reduced use of chemical pesticides and increased use of biologically based products.
  • Reduced damage by soilborne pathogens and increased crop productivity and profitability.
  • Safe, low-cost agricultural products
  • Benefits to growers, consumers, and the environment by making significant progress in producing low cost safe agricultural products.
  • A greater understanding of the basic molecular and biochemical mechanisms will allow a better selection and improvement of existing new strains, and a more rational implementation of these organisms.
  • Knowledge of the genomic and biochemical diversity of microbial communities and biocontrol agents, and how they function in agroecosystems.
  • Understanding how the biocontrol agents interact with the plant and the environment, to predict their limitations and inconsistency in the field.
  • Expanded tool kit of disease management options for both organic and conventional growers, leading to improved agricultural productivity and sustainability.


(2019):(Year 1): Objective 1. Survey soils for suppressive activity against soilborne pathogens. Define and characterize phytobiomes of agriculture systems. Objective 2. Conduct laboratory studies on the mechanisms of action of biocontrol and beneficial microbes (secondary metabolites, antibiotics, lytic enzymes, induced resistance, biofilms, etc). Objective 3. Establish and maintain research and demonstration sites. Test potential management strategies (biological, biorational, cultural, organic amendments, genetic) in field trials. Objective 4. Transmit knowledge and technology to growers and stakeholders. Develop and implement disease management guidelines for organic and conventional producers.

(2020):(Year 2): Objective 1. Survey soils for suppressive activity against soilborne pathogens. Identify causal antagonists or suppressive microbial communities (including fungi) with culture-dependent and/or independent (DNA based) techniques. Define and characterize phytobiomes of agriculture systems. Objective 2. Conduct laboratory studies on the mechanisms of action of biocontrol and beneficial microbes (secondary metabolites, antibiotics, lytic enzymes, induced resistance, biofilms, etc). Objective 3. Test potential management strategies (biological, biorational, cultural, organic amendments, genetic) in field trials. Objective 4. Transmit knowledge and technology to growers and stakeholders. Develop and implement disease management guidelines for organic and conventional producers.

(2021):(Year 3): Objective 1. Survey soils for suppressive activity against soilborne pathogens. Identify causal antagonists or suppressive microbial communities (including fungi) with culture-dependent and/or independent (DNA based) techniques. Define and characterize phytobiomes of agriculture systems. Objective 2. Conduct laboratory studies on the mechanisms of action of biocontrol and beneficial microbes (secondary metabolites, antibiotics, lytic enzymes, induced resistance, biofilms, etc). Objective 3. Test potential management strategies (biological, biorational, cultural, organic amendments, genetic) in field trials. Develop application and management practices. Objective 4. Transmit knowledge and technology to growers and stakeholders. Develop and implement disease management guidelines for organic and conventional producers.

(2022):(Year 4): Objective 1. Characterize how agriculture practices (tillage, rotation, tillage) and beneficial practices organic amendments) drive and shift the phytobiome. Define communities associated with soil health. Objective 2. Conduct laboratory studies on the mechanisms of action of biocontrol and beneficial microbes (secondary metabolites, antibiotics, lytic enzymes, induced resistance, biofilms, etc). Objective 3. Test potential management strategies (biological, biorational, cultural, organic amendments, genetic) in field trials. Develop application and management practices, determine cost-benefits, and foster stakeholder involvement. Objective 4. Transmit knowledge and technology to growers and stakeholders. Develop and implement disease management guidelines for organic and conventional producers.

(2023):(Year 5): Objective 1. Characterize how agriculture practices (tillage, rotation, tillage) and beneficial practices organic amendments) drive and shift the phytobiome. Define communities associated with soil health. Objective 2. Conduct laboratory studies on the mechanisms of action of biocontrol and beneficial microbes (secondary metabolites, antibiotics, lytic enzymes, induced resistance, biofilms, etc). Objective 3. Develop application and management practices, determine cost-benefits, and foster stakeholder involvement. Objective 4. Transmit knowledge and technology to growers and stakeholders. Develop and implement disease management guidelines for organic and conventional producers.

Projected Participation

View Appendix E: Participation

Outreach Plan

This outreach plan is Objective 4 of the proposal, given in detail below. 

  1. Outreach and education to growers: presentations and workshops Over 50% of our members have extension appointments and regularly meet, consult, and teach growers, pest control advisors, industry representatives, as well as with members of the general public. Proposed outreach will be in the form of field days, workshops, grower meetings, and websites. In the last 5 years, our members have given 227 extension talks and published 85 extension bulletins. We publish extension publications, pamphlets and grower manuals, including IPM guides such as the Organic Strawberry Production manual published by UC Press. Our members publish chapters in the disease compendium series of the American Phytopathological Society (APS) Press and results of biocontrol trials are published in Plant Disease Management Reports and Plant Health Instructor. Some specific web-based examples include contributions to the Pacific Northwest Plant Disease Control Handbook, University of California IPM series, UC IPM Crop Management Guidelines (http://www.ipm.ucdavis.edu/PMG/crops-agriculture.html) High Plains IPM Guide, CROPWATCH (cropwatch.unl.edu) and the Annual Integrated Crop and Pest Management Recommendations from Cornell. We provide diagnostic services through the local and National Plant Disease Diagnostic Networks. Members of this project in NY are collaborating with other colleagues in presenting participatory training workshops throughout the NE-Region dealing with the diagnosis, biology and management of soilborne pathogens of vegetable crops and their sustainable management options with funding support from the NE-SARE program. Members also provide training for Certified Crop Advisors and pesticide credits for pesticide applicators. This training increases the level of safety and reduces overuse of fungicides. Members of our project reach large numbers of stakeholders at regional meetings such as the Empire State Producers Expo, Mid-Atlantic Fruit and Vegetable Convention, Pennsylvania Vegetable Growers Association meeting, Great Lakes Expo, Western Disease Conference, Portland, OR, Native Western Plant Conference, Western Forestry Conservation Association, Western Forestry and Conservation Nursery Association and the Intermountain Container Seedling Growers’ Association and Annual Rutgers Turfgrass Symposium, Desert Fall Crop Workshop, Imperial, CA, Annual California Fresh Carrot Research Symposium, Bakersfield, CA, Pitahaya Production Tour and Field Day and Turf & Landscape Day, UC Riverside's AgOps, Annual meetings of Potato Pest management Conference, Maine Potato Research Conference and 2017 Dickeya and Pectobacterium Summit, Sugarbeet Work Group Meeting, Holtville CA, Florida Citrus Processors Association (FCPA) Riverside CA, and Washington Association of Wine and Grape Growers Convention. 

  Presentations at these meetings increase adoption of sustainable agriculture practices.

  1. Online Outreach: A very innovative online outreach tool has been constructed by our members at Cornell University- The Cornell Soil Health Website ((http://soilhealth.cals.cornell.edu/). Growers can send in samples to have soil health status evaluated and to learn of major soil quality constraints that need to be addressed. They are also able to access the Soil Health Manual that contains detailed information on what is measured, what soil processes are impacted and potential remedial practices. Another example is the Online Phytophthora Course: Training for Nursery Growers, developed by members from OR for growers and nursery workers to promote best management practices to eliminate Phytophthora. This free course is available in English and Spanish language versions. Course participants who pass an optional fee-based exam may obtain a certificate of mastery and earn continuing education credits. A new website, Forest Phytophthoras of the World (www.ForestPhytophthoras.org), was recently established to provide science-based information to aid in the understanding and management of the world’s forest Phytophthora species, all of which have a soilborne phase. A companion online journal, Forest Phytophthoras, provides immediate open access to its content on the principle that making research freely available to the public supports a greater global exchange of knowledge. We envision an even greater web presence in the future, making use of webinars and distance education. A member in OR has given webinars on systems approaches for managing Phytophthora in nurseries and water disinfestation techniques through the Water Education Alliance for Horticulture website. She maintains the following web sites: Forest Phytophthoras http://forestphytophthoras.org/, Phytophthora Online Course http://horticulture.oregonstate.edu/content/phytophthora-online-course-training-nursery-growers and Soil Solarization Forecasting Model http://uspest.org/soil/solarize 

    Additionally, a Phytophthora Blight web resource is available http://phytophthora.pppmb.cals.cornell.edu/ to provide information on the identification, biology and management of this devastating disease. As part of a climate change project, a 614- page book was created for growers, "Advances in Dryland Farming in the Inland Pacific Northwest". ARS-WA wrote a chapter and created a 50 minute webinar on Pathogens in Dryland Cereal Systems, presented and archived on Climatewebinars.net 

      3. Outreach to the biocontrol industry and agro-industry. Many of the products developed by our group are
          being marketed by the biocontrol industry. This includes products such as Root Shield and Plant Shield,
          Trichoderma products developed by members in NY and ARS-MD. Another example is a product marketed by
          Certis USA, called LifeGard WP, developed by a member in MT. Our members facilitate this technology transfer
          through patents and other IP protection vehicles with their respective agencies. We will continue our liaisons and
          cooperation with the agroindustry and the Biopesticide Industry Alliance. In addition, members of W-3147
          coordinate the yearly meeting of the Conference on Soilborne Plant Pathogens, which moves around CA, OR, and
          WA. This attracts a large number of industry- especially in the area of biocontrol. For example, last year we had
          representatives from Marrone, Bioconsortia, Dow, Syngenta, Bayer, and Certis. Members are regularly doing
          testing for companies such as Indigo and BASF, Prophyta/Certis, Marrone Bio Innovations, Syngenta,
          Bayer, Natural Industries, Amvac, Monterey/Brandt and EngageAgroUSA, Pathway Biologic, and AdvanSipcan.
          Our members also conduct training for growers to qualify for Pesticide Applicator licenses and Certified Crop
          Advisor certification. 

  1. Training the next generation of biocontrol scientists and practitioners. Almost all of our members have teaching responsibilities, both at the graduate and undergraduate levels. They teach courses in biological control and plant pathology, train students in the lab and supervise graduate students. Many undergraduate students do special or honors projects in our labs. For example, over the last four years, one member (NE) has reached 240 undergrad students in intro plant pathology and over 80 grad students in his distance education grad level course on biocontrol of pests. We train and mentor postdoctoral research associates in our labs and research stations.  Finally, we have extensive international collaborations, and travel to other countries to give seminars, and host international scientists in our labs. An example is collaborations between ARS-WA and China, Turkey, Tunisia, and Morocco. Some of our members (NE) also teach in long-distance web-based courses. Over the past 4 years, project members have supervised 61 undergraduate projects, 40 graduate students and 11 postdocs. This is only a partial count, based on a survey of the members. They also teach formal courses, such as a course at CA-UCR, MCBL 126. This is an undergraduate course on microbiomes, and includes a section on biological control on plant pathogens. 


  1. Public education to general community and grades K-12. Our members participate in science fair judging, Master Gardener Training, 4-H and FAA. Members from ARS WA have taught science modules at grade and middle schools and science summer camps for underrepresented groups on the Colville Indian Reservation, Kalispell Reservation and rural towns such as LaCrosse, WA. NY (Cornell) has a K-12 outreach program to 200 third grade students each year that focuses on the school vegetable garden that we help students run. For example, CA-UCR assisted a high school student perform microbial community analyses by using Illumina sequencing for a STEM science project. NY has a K-12 outreach program to 200 third grade students each year that focuses on the school vegetable garden that we help students run. They also do the Geneva School District Third-Grade Seed Planting and the Geneva Green Thumb Planting Event with the community and home gardens. 


  1. Providing information to policy makers at the local, state and national level. In the past, members of W-3147 were involved in the development of microbial sequencing priorities list assembled by APS and have contributed to materials prepared by the APS Public Policy Board. One of our members is President-Elect of our professional society (APS), and in this capacity will serve on the Public Policy Board which advocates for agricultural sciences funding, training of future scientists, consortia of affiliated professional societies and private industries A member from OR has served on state, regional, and national advisory committee on Phytophthora ramorum and sudden oak death, and led a technical working group on systems approaches for APHIS. In this latter capacity she helped develop a national set of minimum best management practices for producing healthy nursery and greenhouse plants.  


  1. Publishing results in peer-reviewed scientific journals. Finally, we must transmit our findings and results to or peers. W-3147 has an excellent publication record, which will continue. In the last 5 years, we have published 275 peer reviewed publications, 10 book chapters, 14 theses and 83 conference proceedings/abstracts by our members. Members also perform important editorial functions. For example, James Borneman (CA) serves as a senior of the new journal Phytobiomes and Antoon Ploeg (CA) serves as senior editor of Plant Disease. Another member (ARS-WA) was editor-in-chief of American Phytopathological Society Press, which publishes books for a wide audience.


The W-4147 regional research program will be administered by a technical committee consisting of a project leader from each of the participating states. Administrative representative is Laura Lavine, Assistant Dean at Washington State University. Officers of the committee will be the Chairman and Secretary. The Secretary will be elected each year and will advance to Chairman the following year. For 2018-19 the committee officers will be Chairman- Gary Yuen; Secretary: Antoon Ploeg. Meetings will be called each year by the administrative advisor, and a local arrangements coordinator will be determined for each annual meeting. For the last 8 years, these have been held in Riverside, CA. At those meetings research accomplishments will be reviewed and recommendations made for coordination and publication of results. Several new members have been recruited into the project since the last renewal- Maren Friesen (WA), Harsh Bais (DE), Sharon Doty (WA), Gachomo, Emma (CA), Chuanxue Hong (VA), Sarah Pethybridge (NY), Anissa Poleatewich (NH), Gretchen Sassenrath (KS), Tim Widmer (MD) and Tessie Wilkerson (MS).

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