Culture-Based Assessment of Microbial Communities in Soil Suppressive to Potato Common Scab

Meng, Q. X., Yin, J. F., Rosenzweig, N., Douches, D., and Hao, J. J. 2012. Culture-based assessment of microbial communities in soil suppressive to potato common scab. Plant Dis. 96:712-717. A field in East Lansing, MI, showed a decline of potato common scab compared with an adjacent potato field. To confirm that the decline was due to biological factors, the soil was assayed. In the greenhouse, putative common-scab-suppressive soil (SS) was either treated with various temperatures or mixed with autoclaved SS at various ratios. Pathogenic Streptomyces scabies was incorporated into the treated soil at 106 CFU/cm3 of soil, followed by planting of either potato or radish. Disease severity was negatively correlated with the percentage of SS in the mixture and positively correlated with temperature above 60°C. The soil was screened for four groups of potential antagonists (general bacteria, streptomycetes, fluorescent pseudomonads, and bacilli) pairing in culture with S. scabies. The frequency of antagonistic bacteria in SS was higher than common-scab-conducive soil (CS) in all four groups but only pseudomonads and streptomycetes were significantly higher. The population of pathogenic Streptomyces spp. in the rhizosphere of CS was significantly higher than SS. Dilution plating of CS and SS samples showed no clear trends or differences in populations of total fungi, total bacteria, streptomycetes, fluorescent pseudomonads, and bacilli but terminal restriction fragment polymorphism analysis revealed two distinct microbial communities were present in SS and CS. Potato common scab (PCS) is caused by Streptomyces spp. Since its first report in North America in the late 19th century, the disease has been found worldwide wherever potato is grown. Streptomyces spp. are persistent soil inhabitants that survive saprotrophically in soil for long periods in the absence of hosts. Usually, the disease affects tuber quality by resulting in superficial, raised, or pitted lesions on the periderm (19,20). In some cases, potato yield can be reduced due to severe infection. PCS threatens the $3.5 billion potato industry (NASS, 2010) due to lack of effective control methods (9). Management of PCS is difficult. Scab-resistant cultivars are the ultimate goal but current commercial varieties have only partial resistance or tolerance (35). The only widely used chemical, pentachloronitrobenzene (5), has been withheld in the United States recently by the Environmental Protection Agency (EPA) due to its carcinogenicity and nondegradability in soil (EPA website). Increasing irrigation intensity and lowering soil pH are partially effective in reducing the disease severity but lower pH may also result in yield reduction (9). Cultural practices, such as organic soil amendments, green manures, and crop rotation, have been shown to reduce PCS by improving the beneficial soil microbial community (12,37). Naturally occurring disease-suppressive soils provide a valuable resource for studying beneficial microbial communities (2). A number of soils have been reported as suppressive against plant diseases, including Fusarium wilt (Fusarium oxysporum), damping-off (Pythium spp.), root rot (Rhizoctonia solani), take-all (Gaeumannomuces graminis var. tritici), and PCS (Streptomyces scabies) (7,10,13,36). In the 1950s, Menzies observed that PCS disease severity was almost zero in a field after many years of potato monoculture in central Washington, and the suppressiveness was biological (24). Decline of common scab with potato monoculture was also identified in fields at Grand Rapids and Becker, MN (14,16). In these systems, nonpathogenic Streptomyces spp. are believed to play a major role in disease suppressiveness (15,17). Elucidating the mechanisms for suppressiveness may help to improve soil health through manipulating the microbial communities. In recent years, the authors have observed a decline in PCS in a potato field near the campus of Michigan State University, East Lansing, and decided to evaluate the soil microbial communities implicated in the disease suppressiveness of these fields. Knowing the specific soil profile of suppressive soil may help us to improve soil health by adding various amendments. Various techniques are available to enumerate, identify, and culture microorganisms, such as selective media-based methods (32) and molecular approaches surveying the entire microbial community present in a soil (33). The main objectives of this work were to determine whether the soil was suppressive to PCS, characterize the structure of microbial communities likely contributing to the disease suppressiveness, and culture specific beneficial microorganisms or microbial communities that can be reestablished to control common scab. A preliminary report has been published (23). A related study using pyrosequencing to characterize soil microbial communities will be reported separately (29). Materials and Methods Field history and soil properties. A field (N42°43.014′, W84°27.972′) near the campus of Michigan State University in East Lansing has been cultivated with potato consecutively for more than 25 years. This field, designated as the scab-suppressive (SS) field, was used as a scab nursery for potato variety evaluation. Because the disease declined gradually over several years, the varietal test was moved to a new field (N42°42.937′, W84°27.975′) in 2005, designated as the scab-conducive soil (CS) field, in the same area, separated by a distance of 200 m. This field showed higher disease pressure of PCS according to disease ratings from the past 5 years. Soil samples collected from SS and CS fields were analyzed for physical and chemical properties at the Michigan State University’s Soil and Plant Nutrient Laboratories using different methods for each element as recommended for the NorthCentral Region. The soil type from both SS and CS fields is loamy sand (Table 1). Corresponding author: J. Hao, E-mail: [email protected] Accepted for publication 27 November 2011. http://dx.doi.org/10.1094 / PDIS-05-11-0441 © 2012 The American Phytopathological Society