Managing Disease by Managing Soils

Organic Agriculture March 21, 2010|Print

eOrganic author:

Darin Eastburn, Crop Sciences, University of Illinois

This article provides an overview of general and specific disease suppression that results from biological and physical characteristics of the soil that can be influenced by farming practices suitable for use on organic farms. Management practices that can increase disease suppressive properties of soils include the addition of organic amendments, use of good sanitation practices, and crop rotation. A research example is included.

Suppressive Soils, General and Specific Suppression

A disease suppressive soil is one in which the level of disease that develops on plants grown in that soil is less than that which develops on plants grown in other soils under similar conditions. However, almost all soils have some disease suppressive properties, so the phenomenon of disease suppressive soil should be thought of on a continuum of low to high levels of suppression, rather than thinking of soils as being either disease suppressive or conducive. In many cases the disease suppressive nature of a soil is the result of the presence and activity of the microorganisms in the soil. Bacteria, fungi, and soilborne fauna can all act to change the suppressiveness of a soil. If a soil is sterilized and then infested with a plant pathogen, the amount of disease that occurs on plants grown in that soil will usually be much greater than the amount of disease that occurs on plants grown in the same but non-sterilized, pathogen-infested soil.

The type of cropping system and additions of organic matter to the soil have been shown to have an effect on the severity of soilborne diseases. Additions of organic matter can result in increased microbial activity and shifts in microbial community structures. Organic matter amendments, in the form of preceding crop residues, cover crop residues, or direct organic matter applications, have been shown to affect levels of both root and foliar diseases in several crops, and the 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 has been found to be associated with increased microbial activity resulting from the influx of carbon and nitrogen supplied by the incorporated organic matter. Specific cropping systems have been shown to alter the associated soil microbial communities, and in some cases the population levels of known biological control agents have been enhanced.

Two types of disease suppression, general and specific, have been hypothesized. With general suppression the reduced disease levels are thought to be the result of a non-specific increase in the activity of the microbial community. In this case it is the increase in activity of the microbial community as a whole that is important, rather than changes in the activity of a few specific antagonistic organisms. The competition for resources and production of anti-microbial substances reduces the ability of pathogens to grow and infect, resulting in lower disease levels. Specific suppression, on the other hand, is thought to result from the increase in populations of certain microorganisms that are antagonistic to specific plant pathogens. The microorganisms may respond to the presence of the pathogen, such as with an organism that is a parasite of the pathogen; or they may result from the presence of a particular plant species which supplies nutrients necessary for the antagonist populations to increase to the point where they inhibit the pathogen.

Organic Matter Amendments and the Development of Disease Suppressive Soils

One strategy that has received a lot of attention for its potential to increase 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. 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. Several mechanisms have been identified as contributing to disease suppression following the addition of organic matter. These include the stimulation of non-pathogenic microorganisms that inhibit or kill the pathogens through competition or parasitism, the release of compounds that are toxic to the pathogens, and the stimulation of the host plant’s disease defense system.

Not all organic matter amendments produce the same results. An amendment that works well in one situation may not work at all in another. The type of organic matter being added can have an effect on its ability to affect disease suppressiveness. Green manures and fresh animal manures may contain more nutrients, such as nitrogen or available carbohydrates, that can stimulate the growth of soilborne organisms when compared to composted organic matter; and freshly composted organic matter may result in greater changes to soil communities than fully mature composts, which add little available nutrients. Some materials, such as composted hardwood bark, may contain compounds that inhibit pathogens under some conditions.

Some organic amendments are thought to work primarily by altering the structure of the microbial communities in the soil or by changing the physical and chemical properties of the soil. A study on the effects of organic amendments on potato early dying disease found that higher levels of soil organic matter following additions of organic residues were associated with lower disease levels, with the speculation that the disease reductions were due to increased nutrient holding capacity of the soil, increased water infiltration, and decreased soil crusting. Several studies have shown a reduction in disease associated with increases in general levels of soilborne fungi and bacteria following the addition of organic matter, such as the addition of chicken litter or the incorporation of certain cover crops. In some cases the disease reductions were tied to increases in specific organisms such as the bacterium Pseudomonas putida, or several species of the biological control fungus Trichoderma spp.

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. 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. Similarly, the incorporation of broccoli residues have been shown to be effective for controlling diseases caused by the soilborne fungi Fusarium oxysporum, Rhizoctonia solani and Verticillium dahliae, and for reducing the soil populations of these pathogens. The decomposition of the broccoli residues results in the release of compounds called glucosinolates which are believed to be responsible for reducing pathogen populations and for shifting the composition of microbial communities resulting in lower disease levels.

Although we usually think of disease suppressive soils as having the ability to suppress soilborne, root-infecting plant diseases, there is also evidence that shows that organic amendments can have an effect on the levels of foliar diseases as well. Soil-incorporated paper mill residues were shown to lower foliar disease levels of cucumbers and snap beans, and cannery waste added to tomato plots resulted in lower levels of bacterial spot on tomato fruit. 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). With systemic acquired resistance, the presence of certain stresses or microorganisms in the root zone are believed to trigger plant defense systems throughout the plant. Thus a change in the root zone results in an increase of disease resistance in the foliage of the plant.

While the studies on the effects of organic matter amendments show promising results for increasing the disease suppressiveness of soils, there are also studies that show little or no disease control following the application of organic matter. In fact, in some circumstances organic matter amendments have been shown to actually increase disease levels. The types of organic matter applied; the physical, chemical, and biological condition of the soil being treated; tillage methods used; and the crops and pathogens present all have an influence on the process. In many cases the large amounts of organic material needed, the amount of time lost to rotational cropping, and the variable levels of effectiveness may make this disease control strategy impractical. This strategy should always be used as part of an integrated pest management approach in which multiple disease management practices are used.

Sanitation

For plant diseases caused by pathogens that survive the off-season (overwinter) in infested crop debris, good sanitation practices can be used to reduce the levels of the pathogen, and thus the levels of disease. Sanitation practices can include removing, burning, or burying infested crop debris. Burying crop debris makes it more difficult for the pathogen to spread to susceptible plants by wind or splashing rain, and it speeds the decomposition of the crop residue. Once the residue decomposes, the pathogens quickly lose viability. This is usually more effective for managing foliar pathogens than it is for soilborne, root-infecting pathogen, as the latter are often well adapted to surviving in the soil for long periods of time. Sanitation also will be more effective if the pathogen does not have an efficient means of long distance dispersal and there is a limited amount of the pathogen in the general area. For example, sanitation would not be an effective method for controlling a number of foliar diseases of corn in the Midwestern United States because so much corn is grown in the area that pathogen inoculum is ubiquitous. Even if the inoculum was eliminated in a field, it would quickly be replaced by inoculum blown in from surrounding fields.

Crop Rotation

As with sanitation, the goal of crop rotation is to reduce disease levels by lowering pathogen populations. Because many pathogens can only survive in or on a soil for a limited time in the absence of a susceptible plant host, planting a field with a non-susceptible host crop for a year or more will lower population levels of some pathogens over time. Usually a two to three year rotation out of a susceptible crop is sufficient to lower pathogen levels to a point where they are not economically damaging. However, longer rotations may be necessary for some diseases.

Crop rotation is not effective for managing all plant pathogens. Some pathogens can survive for many years without a susceptible host crop being present. These pathogens may survive on susceptible weed species, grow on non-living organic matter, or produce long-term resting structures. Rotation also will not be effective against pathogens that do not overwinter locally, but rather survive in other geographic locations and are carried into the area on wind currents or by disease vectors, such as insects.

A Research Example

An organic transition study - Illinois

In a study at the University of Illinois, done in collaboration with the Illinois Natural History Survey, researchers evaluated the effects of several different strategies for transitioning from a conventional agricultural system to a certified organic system on plant diseases. The study has involved the establishment of three cropping intensity systems: a 3 year pasture (grass/legume) system, a cash grain (corn, soybeans, wheat) system, and a vegetable (tomato, crucifer, squash) system. In addition, three organic amendment treatments (cover crops only, cover crops plus animal manure amendment, and cover crops plus compost amendments) were applied to each of the three cropping systems over the three year transition period. In the first year following the transition period, tomatoes and peppers were planted in all the plots as assay crops, and in the second year following the transition period all plots were planted to soybeans as an assay crop (Fig. 1). The assay crops allowed the direct comparison of the effects of the various cropping system and organic amendment treatments.

The effects of the cropping systems and organic matter amendments on plant disease levels were evaluated in two ways. First, the types and levels of diseases that developed on the various crops in each of the cropping/amendment systems were evaluated throughout the three year transition period, and on the assay crops in the two year period following the transition. Second, soil samples were collected from each of the treatment plots periodically throughout the course of the study. These soil samples were used in greenhouse bio-assays to measure the levels of disease suppressiveness of the soils in the treatment plots.

Differences in disease levels resulting from the treatments were observed for some diseases on some crops in the field plots. Levels of leaf rust on pasture grass (Fig. 2) and common rust on corn (Fig. 3) were higher in plots receiving manure amendments during the transition period. In the first year following the transition some diseases of tomato were found to be affected by both the previous crop and the amendment treatments, with the lowest disease levels in the pasture plots and those plots receiving either compost or manure. In the greenhouse bioassays, a general increase in disease suppressiveness was observed in the soils from all plots over the course of the study. However, no differences in suppression were detected as a result of the cropping system or amendment treatments.

This graph demonstrates the biological nature of disease suppressiveness of field soils. The information in this graph was gathered in a greenhouse bioassay in which soil from field plots undergoing transition to organic production was inoculated with the sudden death syndrome pathogen, a disease of soybeans. That soil was then planted with a susceptible variety of soybean and evaluated it for symptom development, in this case, percent root discoloration as a result of infection. When the soil was autoclaved or sterilized and then inoculated, there was a relatively high level of root discoloration. In soils that were not autoclaved and therefore contained the microorganisms that were present in the field, there was a much lower level of root discoloration, a much lower level of disease. As expected, in the negative control, where no pathogen was added to the soil, we saw very little root discoloration. This shows that if soil is autoclaved or sterilized, destroying the soil's microorganisms, the amount of disease that develops goes up. If those microorganisms are present, as is the case in the non-autoclaved soil, then the amount of disease that develops is suppressed.
Figure 1. This graph demonstrates the biological nature of disease suppressiveness of field soils. The information in this graph was gathered in a greenhouse bioassay in which soil from field plots undergoing transition to organic production was inoculated with the sudden death syndrome pathogen, a disease of soybeans. That soil was then planted with a susceptible variety of soybean and evaluated it for symptom development, in this case, percent root discoloration as a result of infection. When the soil was autoclaved or sterilized and then inoculated, there was a relatively high level of root discoloration. In soils that were not autoclaved and therefore contained the microorganisms that were present in the field, there was a much lower level of root discoloration, a much lower level of disease. As expected, in the negative control, where no pathogen was added to the soil, we saw very little root discoloration. This shows that if soil is autoclaved or sterilized, destroying the soil's microorganisms, the amount of disease that develops goes up. If those microorganisms are present, as is the case in the non-autoclaved soil, then the amount of disease that develops is suppressed. Figure credit: Darin Eastburn, University of Illinois.

Figure 2. Leaf rust severity (% leaf area) on pasture grass. This graph shows the effect of amendment treatment on the development of rust on pasture grass in the ley system in 2004. The amendment treatments included non-amended, which only got cover crops; compost-amended plots; and plots that were amended with manure. Plots that had received manure treatments had an elevated level of rust that was significantly higher than the amount of rust seen in the compost treatment and the non-amended treatment. This probably has something to do with the nutritional status of the plant. Having elevated nitrogen levels allows the plant to be a little bit lusher and the pathogen is able to infect that plant more severely.
Figure 2. Leaf rust severity (% leaf area) on pasture grass. This graph shows the effect of amendment treatment on the development of rust on pasture grass in the ley system in 2004. The amendment treatments included non-amended, which only got cover crops; compost-amended plots; and plots that were amended with manure. Plots that had received manure treatments had an elevated level of rust that was significantly higher than the amount of rust seen in the compost treatment and the non-amended treatment. This probably has something to do with the nutritional status of the plant. Having elevated nitrogen levels allows the plant to be a little bit lusher and the pathogen is able to infect that plant more severely. Figure credit: Darin Eastburn, University of Illinois.

Common rust severity (% leaf area) on corn. The effects of three different organic amendment treatments, non-amended plots, compost-amended plots, and plots that were amended with manure on common rust severity in corn were examined in 2005. Elevated levels of common rust on corn were found in the plots receiving manure treatment. As in the case of pasture grass, this probably relates to the nutritional-physiological status of the plants. Plants in the manure-amended plots had higher levels of nitrogen available to them, they grew a little more vigorously, were a little lusher, and were more susceptible to infection by the common rust pathogen.
Figure 3. Common rust severity (% leaf area) on corn. The effects of three different organic amendment treatments, non-amended plots, compost-amended plots, and plots that were amended with manure on common rust severity in corn were examined in 2005. Elevated levels of common rust on corn were found in the plots receiving manure treatment. As in the case of pasture grass, this probably relates to the nutritional-physiological status of the plants. Plants in the manure-amended plots had higher levels of nitrogen available to them, they grew a little more vigorously, were a little lusher, and were more susceptible to infection by the common rust pathogen. Figure credit: Darin Eastburn, University of Illinois.

Additional Resources

  • Baysal, F., M.-S. Benitez, M. Kleinhenz, S. A. Miller, and B. B. McSpadden Gardener. 2008. Field management effects on damping-off and early season vigor of crops in a transitional organic cropping system. Phytopathology 98: 562–570. http:/dx.doi.org/10.1094/PHYTO-98-5-0562
  • Benitez, M.-S., F. B. Tustas, D. Rotenberg, M. D. Kleinhenz, J. Cardina, D. Stinner, S. A. Miller, and B. B. McSpadden Gardener. 2007. Multiple statistical approaches of community fingerprint data reveal bacterial populations associated with general disease suppression arising from the application of different organic field management strategies. Soil Biology and Biochemistry 39: 2289–2301. http:/dx.doi.org/10.1016/j.soilbio.2007.03.028
  • Blok, W. J., J. G. Lamers, A. J. Termorshuizen, and G. J. Bollen. 2000. Control of soilborne plant pathogens by incorporating fresh organic amendments followed by tarping. Phytopathology 90: 253–259. http:/dx.doi.org/10.1094/PHYTO.2000.90.3.253
  • Chellemi, D. O. 2002. Nonchemical management of soilborne pests in fresh market vegetable production systems. Phytopathology 92: 1367–1372. http:/dx.doi.org/10.1094/PHYTO.2002.92.12.1367
  • Cunfer, B. M., G. D. Buntin, and D. V. Phillips. 2006. Effect of crop rotation on take-all of wheat in double-cropping systems. Plant Disease 90: 1161–1166. http:/dx.doi.org/10.1094/PD-90-1161
  • Garbeva, P., J. A. van Veen, and J. D. van Elsas. 2004. Microbial diversity in soil: Selection of microbial populations by plant and soil type and implications for disease suppressiveness. Annual Review of Phytopathology 42: 243–270. http:/dx.doi.org/10.1146/annurev.phyto.42.012604.135455
  • Hao, J., K. V. Subbarao, and S. T. Koike. 2003. Effects of broccoli rotation on lettuce drop caused by Sclerotinia minor and on the population density of sclerotia in soil. Plant Disease 87: 159–166. http:/dx.doi.org/10.1094/PDIS.2003.87.2.159
  • Larkin, R. P., and C. W. Honeycutt. 2006. Effects of different 3-year cropping systems on soil microbial communities and Rhizoctonia diseases of potato. Phytopathology 96: 68–79. http:/dx.doi.org/10.1094/PHYTO-96-0068
  • Liu, B., C. Tu, S. Hu, M. Gumpertz, and J. B. Ristaino. 2007. Effect of organic, sustainable, and conventional management strategies in grower fields on soil physical, chemical, and biological factors and the incidence of Southern blight. Applied Soil Ecology 37: 202–214. http:/dx.doi.org/10.1094/PHYTO.2002.92.12.1356
  • Martin, F. N., and C. T. Bull. 2002. Biological approaches for control of root pathogens of strawberry. Phytopathology 92: 1356–1362.
  • Marzano, S. L., and D. M. Eastburn. 2007. Assessment of disease suppression in organic transition farming systems. Phytopathology 97: S71.
  • McKeown, A. W., and J. W. Potter. 2001. Yield of 'Superior' potatoes (Solanum tuberosum) and dynamics of root-lesion nematode (Pratylenchus penetrans) populations following "nematode suppressive" cover crops and fumigation. Phytoprotection 82: 13–23. (Available online at: http://www.phytoprotection.ca/toc.php?id=21) (verified 10 March 2010).
  • Ochiai, N., M. L. Powelson, R. P. Dick, and F. J. Crowe. 2007. Effects of green manure type and amendment rate on Verticillium wilt severity and yield of russet burbank potato. Plant Disease 91: 400–406. http:/dx.doi.org/10.1094/PDIS-91-4-0400
  • Shetty, K. G., K. V. Subbarao, O. C. Huisman, and J. C. Hubbard. 2000. Mechanism of broccoli-mediated Verticillium wilt reduction in cauliflower. Phytopathology 90: 305–310. http:/dx.doi.org/10.1094/PHYTO.2000.90.3.305
  • Stone, A. G., S. J. Scheurell, and H. M. Darby. 2004. Suppression of soilborne diseases in field agricultural systems: organic matter management, cover cropping, and other cultural practices. p. 131–177. In F. Magdoff and R. R. Weil (ed.) Soil organic matter in sustainable agriculture. CRC Press, Boca Raton, FL.
  • Stone, A. G., G. E. Vallad, L. R.  Cooperband, D. Rotenberg, H. M. Darby, R. V. James, W. R. Stevenson, and R. M. Goodman. 2003. Effect of organic amendments on soilborne and foliar diseases in field-grown snap bean and cucumber. Plant Disease 87: 1037–1042. http:/dx.doi.org/10.1094/PDIS.2003.87.9.1037
  • Subbarao, K. V., Z. Kabir, F. N. Martin, and S. T. Koike. 2007. Management of soilborne diseases in strawberry using vegetable rotations. Plant Disease 91: 964–972. http:/dx.doi.org/10.1094/PDIS-91-8-0964
  • Utkhede, R. S., and E. J. Hogue. 1999. Influence of ground cover on development of phytophthora crown and root rot of apple trees. Canadian Journal of Plant Pathology 21: 106–109. http:/dx.doi.org/10.1080/07060669909501199
  • Weller, D. M., J. M. Raaijmakers, B. B. M. Gardener, and L. S. Thomashow. 2002. Microbial populations responsible for specific soil suppressiveness to plant pathogens. Annual Review of Phytopathology 40: 309–348. http:/dx.doi.org/10.1146/annurev.phyto.40.030402.110010
  • Zhang, W., D. Y. Han, W. A. Dick, K. R. Davis, and H. A. J. Hoitink. 1998. Compost and compost water extract-induced systemic acquired resistance in cucumber and arabidopsis. Phytopathology 88: 450–455. http:/dx.doi.org/10.1094/PHYTO.1998.88.5.450

 

This is an eOrganic article and was reviewed for compliance with National Organic Program regulations by members of the eOrganic community. Always check with your organic certification agency before adopting new practices or using new materials. For more information, refer to eOrganic's articles on organic certification.

eOrganic 2848