Suppression of Soybean Diseases Through the Use of Cover Crops

Project Overview

Project Type: Research and Education
Funds awarded in 2010: $174,823.00
Projected End Date: 12/31/2013
Region: North Central
State: Illinois
Project Coordinator:
Dr. Darin Eastburn
University of Illinois

Annual Reports


  • Agronomic: canola, rapeseed, rye, soybeans


  • Crop Production: cover crops
  • Education and Training: extension, on-farm/ranch research, participatory research, workshop
  • Pest Management: biological control, cultural control, integrated pest management, mulching - vegetative
  • Soil Management: green manures, organic matter, soil microbiology


    The impacts of fall cover crops on diseases in spring planted soybeans were conducted at 6 locations in Illinois. Soybean stand establishment was highest in rye plots inoculated with Rhizoctonia solani, as compared to the fallow plots, and Rhizoctonia root severity rot was lowest in the rye plots. Counts of soybean cyst nematodes were reduced in rye and rape plots at several locations. Greenhouse assays of field soils showed reductions of Rhizoctonia root rot and sudden death syndrome in rye and rape soils. No differences in other pathogens or microbial communities were detected among soils from the cover crop treatments.


    Context, Background, Rationale, and Need

    Diseases of soybean annually cause significant reductions in soybean yields as a result of disruption of root and vascular function, loss of photosynthetic area, and direct degradation of the beans. Important soybean diseases in the Midwestern US include those caused by plant pathogenic fungi, nematodes, bacteria, and viruses. Some seed/seedling diseases are managed through the application of seed protectant fungicides, and foliar fungicides are often applied in southern soybean growing regions of the US to combat foliar diseases such as frogeye leaf spot and more recently Asian soybean rust. Soilborne diseases such as sudden death syndrome (SDS), charcoal rot, Rhizoctonia rot, Sclerotinia rot (white mold), and Phytophthora rot can be particularly problematic, as they are very widespread and difficult to manage.

    Most commercial soybean growers in the Midwest rely on only three disease management strategies instead of a toolbox of integrated pest management (IPM) practices. These three limited strategies are crop rotation, disease resistant varieties, and, more recently, seed treatment and foliar fungicides. Crop rotation is only useful for pathogens that overwinter in the field, as opposed to those carried into the field from other locations, and the corn/soybean rotation is often not long enough to adequately reduce soilborne pathogen populations. Repeated use of host resistance genes, without other disease management strategies, induces changes in pathogen populations, allowing them eventually to overcome host resistance. In addition, there are no resistant cultivars available for many of the important soybean diseases, and recent increased use of fungicides is raising concern about the development of fungicide resistance within pathogen populations. Developing alternative soybean disease management tactics would contribute to NCR-SARE’s outcomes and impact sustainable agriculture in the NCR by increasing yield and yield stability, reducing input costs, fostering the use of IPM practices, and helping prevent the development of pathogen resistance.

    Crop and cover crop residues, or direct organic matter applications, have affected the level of root and foliar diseases in high value crops, such as lettuce, snap bean, and bell peppers, as well as for crops such as peanut and soybean. Research in 2006 in Southern IL showed that foliar symptoms of SDS and population densities of soybean cyst nematode (SCN) were reduced dramatically following rapeseed cover or green manure crops compared to the non-cover crop control. In addition, a study looking at organic transition strategies showed that specific rotation sequences and the application of certain types of organic matter lowered disease levels over time by enhancement of naturally present disease suppressive microorganisms, inhibition of pathogen activities, and stimulation of host defense mechanisms. Understanding the impact of cover crops on soil microbial populations and root system development could help develop better disease management strategies. Characterization of microbial communities may lead to the discovery of specific disease suppressive microorganisms and to an understanding of community profiles associated with disease suppressive conditions. The selected cover crops are simple to adapt for conventional farmers, as their emergence and large seed size makes planting easy. In addition, canola could provide an option for farmers who decided to grow it in a double crop system for oilseed or forage uses, rather than for the green manure benefits. Demonstrating that cover crop residues can lower disease severity levels would provide soybean farmers with a disease management tool that has the added benefits of increasing soil organic matter content, enhancing nutrient and water holding capabilities, and reducing soil erosion.

    Constraints on using cover crops include the economics of their use, concerns about integration with current corn/soybean rotations, and a lack of understanding and incorrect perceptions by farmers. Cover crops are more likely to be used in organic agricultural production.  However, results from this project could help alleviate many misunderstandings and incorrect perceptions by conventional producers, as well. Understanding the impact of cover crop residues on pathogenic organisms and disease processes will enhance our knowledge and aid in the development of sustainable disease management strategies for soilborne and foliar soybean diseases.

                Diseases of soybean regularly cause significant reductions in yield, leading to substantial economic losses. Although yield losses are difficult to measure precisely, one survey-based study estimated that in one year the most common diseases of soybean resulted in a loss of 14,993,800 metric tons worldwide, and 4,962,600 metric tons in the US alone (54, 55). Many of the most important diseases are soilborne, including charcoal rot, Phytophthora rot, Rhizoctonia rot, root knot, soybean cyst nematode, and sudden death syndrome. A few of these diseases are partially managed with disease resistant varieties (10, 17, 32, 33, 45) or crop rotation (33). However, the development of additional management strategies would reduce annual yield losses from these of diseases.

    One strategy that could be effective against a broad array of diseases is the induction of disease suppressive soil. A disease suppressive soil is one in which the incidence or severity of a disease on plants growing in that soil is less than what one would see on a plant growing in a conducive soil with a similar pathogen population(3). However, disease suppression is not a qualitative trait, meaning that soils are either suppressive or not. Rather disease suppression is a quantitative characteristic, with all soils falling along a gradient of levels from highly conducive to highly suppressive. Most natural field soils have some degree of natural disease suppression. In many cases the suppression is the result of the activities of microorganisms in the soil. This can be demonstrated by comparing the level of disease that develops on plants growing in natural field soil with the disease level that develops in that same soil after it has been sterilized (21, 41). Most of the time the level of disease developing on plants growing in the sterilized soil will be significantly higher than the level seen on plants growing in the natural, non-sterilized soil.

                There are many mechanisms that may contribute to the soil suppression of plant diseases, including non-pathogenic microorganisms competing with pathogens for nutrients or infection sites, direct parasitism of plant pathogens by antagonistic organisms, and stimulation of a plants ability to resist disease, a phenomenon known as induced systemic resistance. It has been shown that the level of disease suppression of a soil can be altered by changing environmental conditions, which in turn alter the structure and activity of the microbial community in the soil (5, 26).

                One strategy that has received a lot of attention for its potential to elevate the disease suppressiveness of a soil is addition of organic matter. A number of studies have shown that disease levels are reduced following the incorporation of organic matter into the soil (12, 46). However, a survey of the plant pathology literature quickly shows that this is a complex phenomenon, and that simply adding organic matter to a soil will not necessarily lower the amount of diseases that develop on plants grown in these amended soils. Not all organic matter amendments produce the same results, and an amendment that works well in one situation may not work at all in another. Where, when, and how well the addition of organic matter increases disease suppressiveness depends, in part, on the mechanism involved in changing the level of suppression (46).

    Organic matter amendments to soil, in the form of residues of the preceding crop, cover crop residues, or direct organic matter applications, have been shown to affect levels of root and foliar diseases in several crops (9, 12, 20, 47). Suppression of soilborne plant pathogens has been observed following additions of certain types of organic matter to soils. In some cases, the mechanism of suppression in these systems was associated with increased microbial activity resulting from the influx of carbon and nitrogen supplied by the incorporated organic matter (42, 43). In a process termed general suppression, it is believed that these organisms compete for nutrients and sites of colonization/infection. There can also be an enhancement of specific suppression, in which there is increased activity of one or a few organisms that directly parasitize, antagonize, or inhibit certain plant pathogens. Specific cropping systems have been shown to alter the associated soil microbial communities (8, 18), and in some cases the population levels of known biological control agents have been enhanced (6).

    Certain types of organic matter have been investigated for their ability to release toxic compounds that inhibit or kill soilborne plant pathogens. The incorporation of Sudangrass cover crops has been shown to reduce nematode and fungal diseases of lettuce and potatoes (1, 9, 40, 49). The fact that Sudangrass was able to lower disease levels while equivalent amounts of other types of organic matter were not, and that incorporating two-month old Sudangrass provided better control than three-month old Sudangrass, lends support to the hypothesis that compounds called cyanoglucosides, released by the decomposing grass tissues, are toxic to the pathogens in the soil. Recently, broccoli residues have been shown to effectively control diseases caused by the soilborne fungi Fusarium oxysporum, Rhizoctonia solani, Verticillium dahliae, and others by reducing populations of these pathogens in soil (7, 9, 13, 20, 27, 35, 49). In this case, it is believed that compounds called glucosinolates, released by the decomposing broccoli tissues, are responsible for reductions in pathogen populations. Other pathogen inhibitory chemicals released during the decomposition of organic matter are thought to include ammonia, nitrous acids, alcohols, and aldehydes.

                The use of cover crops as a method of disease control has primarily been investigated for high-value crops, such as apple, potato, and strawberry (22, 27, 28, 48, 51). Research in this area is driven, in part, by the reduced availability of chemical control materials, such as methyl bromide, on which production has depended for many years. The cancelation of the registration of methyl bromide lead to a pressing need and several research projects to develop alternatives. However, the principles learned in the studies on high-value crops should be useful in the management of soilborne diseases in crops, such as soybean, where the application of soil fumigants has never been economically feasible, but the pressures from soilborne pathogens are just as great. There have been a few studies looking at the effects of cover crops in soybean systems. For example, an annual ryegrass cover crop was found to reduce population levels of the soybean cyst nematode (14, 30, 39).

                Foliar disease levels also have been shown to be affected by applications of soil organic matter (47), even for diseases caused by pathogens that do not have a soilborne phase in their disease cycles. Possible mechanisms suggested for this type of disease suppression include changes in a plant’s nutrient status and the phenomenon known as systemic acquired resistance (SAR) or induced systemic resistance (ISR)(46, 47, 56). In these systems, it is believed that microorganisms associated with the roots systemically stimulate the plant’s disease defense system, resulting in lower levels of some foliar diseases.

                Use of cover crops or other organic matter soil amendments to foster the development of disease suppressive soils fit well with other sustainable agricultural practices designed to inhibit soil erosion, improve soil structure, and provide habitats for beneficial organisms. The increased soil organic matter levels resulting from cover crops helps improve several soil factors including compaction, water and nutrient holding capacity, friability, and air and water infiltration (11). Cover crops also have been shown to reduce weed populations through several mechanisms including allelopathy and light competition (23, 31, 57). 

                In a study at the University of Illinois, which evaluated different systems for transitioning from conventional to organic agriculture, crop rotation sequences and organic matter amendments were found to have an effect on some of the naturally occurring foliar diseases of some of the crops included in the study, but no effect on the severity of soilborne root diseases was detected in field or greenhouse evaluations (25). In this study, molecular techniques, including ARISA and rtPCT, were used to analyze microbial community structures and their relationship to the cropping system and amendment treatments. In particular, population levels of a specific group of soil inhabiting bacteria, DAPG producing fluorescent Pseudomonas spp., were evaluated and compared with observed levels of disease suppressiveness to determine if such population levels can be used as indicators of soil health and soil suppressiveness to disease (6, 53).

                A 2006 field trial in southern Illinois reveled that SDS was dramatically reduced in soybean plots following rapeseed as a cover or green manure crop when compared to the level of SDS in plots that did not receive a cover crop. The area under the disease progress curve (AUDPC) was significantly reduced from 157.7 in the fallow to 37.1 in the green manure treatment. Previous studies have shown that residues of cruciferous crops, such as broccoli, reduced the inoculum density of soilborne plant pathogens possibly resulting from the release of toxic compounds from the decomposing residues (20, 34, 35, 44). Like broccoli, the incorporation of cover crop residues of canola have been found to reduce the severity of diseases of wheat and potato (15, 24). The inclusion of canola and rapeseed in the proposed study is intended to determine if these cover crops might be especially efficacious in reducing levels of soilborne diseases in soybean.


    SARE has funded various aspects of cover crop research (FS07-218, LNE07-252, FNE07-611, LNE88-005 and 007, FNE08-648, LNC07-276 and 282). Some SARE projects have looked at using cover crops for disease suppression or evaluating soil microbe populations for disease control, mainly on ornamental or vegetable crops. FS07-218 evaluated plant vigor with cover crop mulches, but not specific diseases or microbial populations. SW04-113 looked at cover crops impacting soil populations of nematodes and entomopathogenic fungi, LNE01-150 used compost to control grape diseases, and OS07-035 assessed cover crops on Fusarium wilt in watermelon. None of these projects have evaluated cover crops in large-acreage crops, such as soybean, in relation to disease suppression. This study would be the first to look at effects on diseases in this large acreage crop. 

    Project objectives:

    The primary objective of this project was to have growers, researchers, and extension personnel collaborated in university and on-farm trials in western, central, and southern Illinois to evaluate the efficacy and feasibility of using cover crops for disease suppression in soybeans. As a result, growers and the academic community would increase their knowledge on the use of four cover crops for suppressing soybean diseases and better understand how cover crops can integrate with current production practices. Growers and researchers would share their results at field days and disease management workshops. Results would be reported on websites, in popular-press and scientific publications, and at research and extension meetings. Participating growers would serve as resources to help educate other growers on the usefulness of using cover crops.

    Any opinions, findings, conclusions, or recommendations expressed in this publication are those of the author(s) and do not necessarily reflect the view of the U.S. Department of Agriculture or SARE.