Suppressive soils have been identified as soils that can inhibit the growth of naturally occurring soil-borne diseases. These soils contain microbial communities that are capable of suppressing or controlling disease-causing organisms, including fungi (e.g. Fusarium virguliforme (cause of sudden death syndrome, SDS), Macrophomina phaseolina (cause of charcoal rot), Phytophthora root rot (Phytophthora sojae) and nematodes (e.g., soybean cyst nematode, Heterodera glycines). How the native soil microbial communities reduce disease is not known. Knowledge of factors that contribute to and support these beneficial microbial communities is also unknown.

One example of this natural improvement in soil microbial community reducing disease was demonstrated in our previous research (Sassenrath et al., 2017, 2019; sponsored by the Kansas Soybean Commission) that demonstrated that a high-glucosinolate mustard (Brassica juncea) reduced fungal populations that caused charcoal rot in soil and in soybean plants. The research proposed here builds on those results by exploring the interaction between soil health and disease pressure. Management practices will be tested in field studies to determine the impact on soil health, fungal pathogen presence, and soybean growth and yield.

Impact of soil health on soybean disease.
Crop plants that are disease hosts increase the number of disease-causing organisms in the soil. We have previously shown the increase in colony forming units (CFU) of M. phaseolina in the soil after soybean production (Sassenrath et al., 2019). Other factors reduce soil-borne disease, include high-glucosinolate mustard as a cover crop (Sassenrath et al., 2017, 2019) and increasing the soil temperature (e.g., "solarization"). Use of animal manures greatly increases the diversity of the soil microbial community, and beneficial microorganisms in particular. In addition to improving the soil nutrient balance, manure may contribute to reduced disease pressure (Graham et al., 2014) and soybean cyst nematode populations (Bao et al., 2013). Background information on soil temperature and moisture will be collected continuously throughout the growing season using Hobo Temperature and Moisture sensors installed in each treatment. These sensors are purchased with funds from complimentary grant programs.

Measuring the impact of soybean health on soybean diseases.
Management practices to alter the soil community structure will be implemented in replicated research plots at the Southeast Research and Extension Center fields in Parsons, KS. Treatments will include two treatments that are likely to increase disease (soybeans and corn stubble, both hosts of disease organisms), three treatments that are likely to decrease disease (brassica cover crop, animal manure, and solarization), and a fallow control. We will also be testing different soybean cultivars from MG 3.5 – 4.9 with different susceptibilities to disease. The soybean variety test plots at Ottawa will also be sampled to measure differences in plant and soil disease for MG 3.5 and MG 4.9. Additional test sites include sixteen fields at production farmers in eastern Kansas.

Testing will include several cultivars of soybeans with noted sensitivity to charcoal rot and sudden death (disease susceptibility: 9 = excellent; 1 = poor.):
Cultivar Maturity Group SCN Resistance Source Phytophthora resistance gene Sudden Death Syndrome Susceptibility Charcoal Rot Susceptibility
P35T15E 3.5 P188788 1k 5 4
P38454E 3.8 P188788 1a 7 8
P42T31E 4.2 P188788 - 5 4
P45T88E 4.5 P188788 ^1k 6 8
P49T74E 4.9 P188788 ^1c, ^1k 5 4
Phytophthora resistance gene: 1a: Provides resistance to races 1, 2, 10, 11, 13-18, 24, 26, 27, 31, 32 & 36. 1c: Provides resistance to races 1-3, 6-11, 13, 15, 17, 21, 23, 24, 26, 28-30, 32, 34, 36. 1k: Provides resistance to races 1-11, 13-15, 17, 18, 21-24, 26, 36, 37. (-) no specific gene for resistance

Soils will be sampled at three times during the season to determine: soil nutrients, soil community structure, and pathogen populations. Soils will be sampled prior to implementation of treatments (early March), mid-season (late June-July) and after harvesting soybeans (Sept. – Oct.). Final soybean yield will be collected.

The Soil Management Assessment Framework has identified five factors that are indicative of soil microbial activity. SMAF has been adopted by the NRCS as an indicator of soil health. These factors include: organic carbon, nitrogen, active carbon, wet aggregate stability, and soil respiration. These factors give an indication of the activity of the soil microbiome, though they do not measure the microbes directly. Total microbial biomass and the ratio of fungi to bacteria have also been shown to be related to disease suppression in soils.

Soil nutrients are important for growth of both microbes and plants. These will be measured at the K-State Soil Testing Lab, and include: pH, total organic matter, N, P, K, total organic carbon, total N, NO3-N, NH4-N, along with key micronutrients S, Ca, Mg, and Na. Wet aggregate stability will be measured using the soil volumetric aggregate stability test (VAST) from Solvita. Soil respiration will be measured with the CO2 Burst Test by Solvita. In addition, we will quantitate the disease presence of Macrophomina in soil and plants at three time points during the growing season (prior to planting, mid-season, and at harvest) by measuring CFUs.

This past year, we tested total soil microbial biomass and fungal:bacterial ratio with the MicroBIOMETER system. Unfortunately, results were not clear, and the test was disappointing. An examination of other potential disease organisms would be possible through PCR tests with disease-specific primers. This test would give a qualitative measure of disease presence and, in addition to Macrophomina, and allow detection of Fusarium, Phytophthora, Phomopsis, and Pythium. This analysis is expensive and beyond the scope of this proposal. We have submitted a funding request to SARE to pursue this research. We will continue to explore methods and funding sources to measure and quantitate total soil microbial biomass and fungal:bacterial ratios, and detection of disease organisms as an indication of “soil health”.

M. phaseolina populations will be determined by counting the number of colony-forming units (CFUs). Charcoal rot disease severity will be measured by randomly selecting ten plants per plot at the R7-R8 growth stage for root and stem severity ratings. The plants will be scored by splitting the stem and taproot of each plant and rating the degree of gray discoloration and microsclerotia in the vascular and cortical tissues on a scale of 1-5. M. phaseolina root populations will be estimated by grinding the split roots after the severity evaluation. The ground plant tissue and soil samples will be plated on microbiological media and incubated. CFUs of M. phaseolina will be counted and transformed to CFUs per gram of root tissue or gram of soil.

Identification of management practices, including cover crops, residue management, and animal manures, for use in biocontrol of soil-borne diseases and development of guidelines for economical management practices will assist producers in controlling fungal diseases in soybean. The impact of fungicide use on yield and net return will be determined, and guidelines developed. The interaction between soil health and fungal pressure will be assessed and alternative methods of improving soil health for optimal soybean production, yield components, and net return developed. The economic impact of management choices will assist producers in choosing economically viable production systems.
This research is a component of a project exploring the mechanisms defining how soil health impacts crop production and plant disease. The research team has developed a proposal to leverage KSC funding with national funding through SARE. That research will focus on development of the DNA technology to identify and quantify disease organizations. If funded, that research will contribute to this research by expanding our knowledge of specific disease organisms and quantities under different conditions. This research is exploring the interactions between soil health and crop performance, developing alternative methods to control crop diseases and establish naturally disease-suppressive soils through cultural practices.

Updated January 15, 2025:
Soil-borne diseases severely impact agronomic production, reducing the yield and quality of crops. Our research is designed to identify the modes of infection of disease organisms, and develop and implement alternative methods to manage these disease organisms. The research examines the soil microbiome, presence and abundance of disease organisms, and changes in the soil biology with alternative management practices.

We collected soybean samples from various locations in southeast Kansas and identified common diseases including charcoal rot, soybean cyst nematode, and Phytophthora root rot, while assessing soil health and soybean productivity. Soilborne fungal pathogens reduce yield and quality of the major crops grown in Kansas. M. phaseolina, the organism that causes charcoal rot, infects more than 500 plant species, including soybeans and sorghum. It caused total losses of approximately 220 Mbu in soybean production between 2010-2014. Fusarium spp. cause fungal diseases in multiple crops including wheat, corn, and cotton; in 2015, an estimated 3.4% yield loss in wheat occurred in eastern Kansas due to Fusarium infection.

Commercial crop production fields with disease pressure were identified. Soil samples were taken and tested for diseases (phytophthora root rot and charcoal rot) and nematodes (soybean cyst nematodes). Soil biological activity was assessed using the Solvita CO2 burst test; soil background nutrient status was also measured. Charcoal rot was identified to be a much more pervasive disease in southeast Kansas than other diseases or SCN.

To better determine conditions that impact disease pressure, we measured the abundance and viability of disease organisms as a function of the environmental conditions within the soil. Environment studies were conducted to explore the linkages between soil conditions and microenvironment (moisture and temperature) on pathogen viability of M. phaseolina. Treatments were implemented in replicated field plots to measure the disease organisms under different environmental conditions in the fields. Treatments included two treatments that are likely to increase disease (soybeans and corn stubble, both hosts of disease organisms), three treatments that are likely to decrease disease (brassica cover crop, animal manure, and solarization), and a fallow control. Temperature sensors were installed in plots and temperatures were recorded continuously. Plastic sheets provide a “solarization” treatment, increasing soil temperature and potentially reducing soil microbes. Corn stubble is a potential source of pathogens, as corn is a host; alternatively, corn stubble provides more carbon for soil microbes, increasing their abundance and potentially reducing pathogens by increasing beneficial microbial populations. Animal manure would also provide a greater carbon source for the microbes, and add additional microbes to the soil, increasing the complexity of the soil microbiome. Interesting differences were observed in the environment within the soil of the different treatments. The plastic sheets raised the temperature more than 10 degrees above the fallow treatment, and temperatures remained elevated at night. Animal manure also raised the day-time temperature, but temperatures decreased at night to that of fallow. Temperatures under corn stubble greatly decreased soil temperatures throughout the day, keeping soil temperatures cooler than air temperatures during both night and day. Soil samples were collected and analyzed for microbial activity. Analysis of soil and plant samples for disease is continuing. We are continuing the analysis to delineate potential causal factors increasing, or decreasing, disease organisms and disease in soybeans, focusing primarily on charcoal rot.

Updated September 24, 2025:
Soil microbes play a critical role in nutrient cycling in the soil. Microbes break down materials, including plant roots and biomass. The breakdown products of this digestion then become available to support the growth of plants. There is a strong symbiotic interaction between plants and microbes in the nutrient cycling of the soil. Plants release carbohydrates that are then taken up by microbes and used for growth and development. In exchange, the plant microbes deliver nutrients and water to plants, including N, P, and K, as well as micronutrients. This symbiosis is at the heart of nutrient cycling in the soil, and essential for optimal plant growth and productivity. The soil microbiome is very responsive to plants, changing even for different varieties of the same crop.

Some soil microbes can also be harmful, such as disease-causing organisms, including fungi (e.g., Fusarium virguliforme (cause of sudden death syndrome, SDS), Macrophomina phaseolina (cause of charcoal rot), Phytophthora root rot (Phytophthora sojae), and nematodes (e.g., soybean cyst nematode, Heterodera glycines)). Diseases reduce the yield and quality of soybeans and other crops in Kansas and throughout the world. Soil-borne diseases are prevalent in crop production fields. Control methods of disease include use of solarization to heat the soil, or chemical fumigation. Some plants have been shown to produce chemicals that act as biofumigants that control or reduce harmful soil microorganisms. These plants can be used to create suppressive soils that inhibit the growth of naturally-occurring soil-borne diseases. Alternative management practices, such as addition of animal manures, have also been used to alter the soil microbiome to improve control of disease organisms. Use of cover crops, such as the high-glucosinolate mustard (Brassica juncea) can reduce fungal populations that caused charcoal rot in both soil and soybean plants. Conversely, some management practices increase disease organisms, such as use of corn stover, which is a host of multiple disease organisms, or tillage.

This research tests the hypothesis that improving the overall soil health by supporting healthy soil microbial communities can reduce disease pressure. We are exploring how to create suppressive soils by altering management practices to reduce disease pressure. The research reported here explores the relationship between soil microbial activity and soil nutrients. The research tests the ability of cover crops, animal manure, and solarization to control or reduce charcoal rot in soybean production through improved soil microbial communities.

Replicated plots were established at the Southeast Research and Extension Center in Parsons in the spring, 2024. Plots included: fallow, mustard cover crop, soybean, corn stubble, cow manure, and plastic sheets. Plastic sheets provide a “solarization” treatment, increasing soil temperature and potentially reducing soil microbes. Plastic sheets were placed on plots and held in place with concrete blocks. Corn stubble was spread to about a 2-in. layer. Corn stubble may increase the soil microbial activity by providing more carbon, but is also a host for M. phaseolina, potentially increasing the disease prevalence. Cattle manure was spread to about a 2-in. layer on the plots. Cattle manure adds additional microbes to the soil, increasing the soil microbial diversity and increasing food sources for microbes. The high-glucosinolate mustard, Mighty Mustard Pacific Gold (Johnny’s Selected Seeds, Winslow, ME) was broadcast in plots in early April. The use of a mustard cover crop has been shown to reduce the number of CFUs of M. phaseolina, while soybeans are a host and increase the CFUs of M. phaseolina. Because of poor plant stand in the mustard, seeds were spread at additional times during the growing season. The fallow treatment was left unplanted and served as a control. Five cultivars of soybeans, ranging from MG 3.4 to 4.8, were also planted to test for variation in charcoal rot sensitivity.

Soil samples to a depth of 6 in. were collected at three time periods, in spring prior to implemented treatments, mid-season, and after harvest. Soils were analyzed for nutrients at the K-State Soil testing lab in Manhattan. Soil microbial activity was measured with the 24-hour CO2-burst test (Solvita, Woods End, ME). Disease prevalence was tested at the Plant Pathology lab in Manhattan.

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Differences in microbial activity were observed based on management as determined by soil respiration measured with the Solvita CO2 Burst test (Figure 1). Soybean plots varied from a low of 73.5 to a high of 86.8 ppm, indicative of a medium range in soil microbial activity (Solvita, 2017). The plots with added corn stubble and mustard seed were similar, at 78 and 67 ppm, respectively. The plots with manure were much higher, at 100 ppm. Conversely, the fallow and solarization plots were the lowest, at 52 and 48 ppm, respectively. The corn stubble and manure had much higher microbial activity (note different scale of axis) at 290 and 180 ppm, respectively. This level of activity would be rated high for microbial activity (Solvita, 2017).

Soil microbial activity increased as major and minor soil nutrient levels of increased (Figure 2). This pattern was observed for pH and minor nutrients as well, including sulfur, boron, and calcium (data not shown). Much greater rates of increase in soil microbial activity were observed as soil carbon increased (Figure 3). This was apparent for both total organic carbon and organic matter. Increased soil microbial activity been observed in other studies, and is indicative of the importance of carbon as a food source for microbial growth and production. The only soil nutrient that had a negative impact on soil microbial activity was NH4.

Conclusions

Soil nutrients are essential for plant growth and development. They are also critical for the soil microbes. The role of soil microbes in plant nutrition is important to maintain the nutrient cycle within the soil. A healthy soil microbial community supports crop production. Here, we demonstrate differences in soil microbial activity with management, and the increase in soil microbial activity with increasing soil nutrient levels.

Diseases are primary factors reducing the yield and quality of soybeans in Kansas and throughout the world. Soil-borne diseases are highly prevalent in eastern Kansas crop fields. Certain plants have been shown to produce chemicals that act as biofumigants that control or reduce harmful soil fungi. Animal manures have also been used to alter the soil microbiome to improve control of disease organisms. Our working hypothesis is that improving the overall soil health by supporting healthy soil microbial communities can reduce disease pressure, i.e. creating suppressive soils by altering management practices will reduce disease pressure. This research will explore the relationship between soil health and disease pressure. The research outlined here will test the ability of cover crops, animal manure, and solarization to control charcoal rot in soybean production through improved soil microbial communities.