Predictive Management of Soil Microbial Communities using Defined Amendments to Enhance Production in Organic Cropping Systems

Non-Technical Summary: Numerous studies have attempted to develop soilborne disease control and fertility management programs that are compatible with organic crop production systems. Often times, plant-derived or manure-based amendments have been the foundation of such programs. However, in the majority of instances the potential of such a strategy has not been realized due to a lack of understanding of functional mechanisms resulting in an inability to utilize organic amendments with predictable outcomes. Our objective is to garner a greater capacity to manage and predict development of native soil biology-mediated processes that contribute to disease suppression and nitrogen availability in organic crop production systems. This will entail formulation and optimization of brassicaceous seed meal amendments, and evaluation of these materials in advanced on-farm research as a novel disease control and soil fertility management program. This is a pivotal management issue in light of the desire to employ the multitude of resources native to organic ecosystems as a biologically-sustainable disease control option, realization of the complexity of microbial systems and the myriad ways they impact other organisms, and need to identify more cost-effective nitrogen sources while minimizing loss from organic production systems. Our study system has the advantage of pairing a well-characterized overall effect with a microbial community for which we have considerable background information, including demonstrated mechanisms for how soil biology and the amendment are contributing to the overall effect. As many of the focal microorganisms, both deleterious and beneficial, are common in agricultural soils, results will be relevant across a diversity of crop production systems. <P> Approach: Studies will be conducted to assess the capacity of brassicaceous seed meal particle size to enhance populations of resident microbial antagonists, suppress soilborne pathogens and enhance growth of apple in replant orchard soils. Impact on plant beneficial populations (e.g. Streptomyces spp.) and the target soilborne pathogens will be determined using culture-based approaches and real-time quantitative PCR. Effect of particle size on emission of active chemistries resulting from hydrolysis of glucosinolates from Brassica juncea (BjSM)seed meal will be determined by gas chromatography. Studies will clarify the plausible roles of soil biology and chemistry in the brassicaceous seed meal (BSM)-induced suppression of a group of fungi/oomycetes that in concert contribute to apple replant disease. Seed meal will be applied to native and pasteurized orchard soils, infested with inoculum of the individual target pathogens, and planted to apple. Significant reduction in root infection attained with BSM amendment in a pasteurized soil system would suggest a role for glucosinolate hydrolysis products or other chemical factors in disease suppression. Alternatively, disease control realized in a native soil system, but not in the same soil pasteurized prior to pathogen introduction, would be suggestive of soil biology having a significant role in disease suppression. The latter has been documented in the suppression of R. solani in response to B. napus seed meal amendment. Sensitivity of individual fungal/oomycete isolates to the volatile allyl isothiocyanate (AITC) produced in (BjSM)amended soils will be assessed. Preliminary experiments suggest that modification of the fungal community resident to the soil system contributes to the seed meal induced suppression of root rot incited by Pythium spp. Thus, changes in structure of fungal communities in seed meal amended orchard soils will be monitored using culture-based methods and DNA-array analysis. Specific taxa which respond positively to seed meal amendment in a manner that is temporally linked to the initiation of Pythium suppression will be assayed for the capacity to provide disease control. We will explore the effectiveness of host tolerance in conjunction with a novel composite brassicaceous seed meal formulation for control of replant disease and do so at field sites possessing all components of the pathogen complex. Studies will evaluate the efficacy of seed meal amendments made in the autumn prior to planting and in the spring of planting. Nematodes play an important role in nutrient cycling, estimated to contribute approximately 20% of mineralized N in integrated farming systems. The nematicidal activity of certain isothiocyanates, including AITC generated by BjSM, suggests that certain BSMs could negatively impact this community and alter N availability. The effect of individual BSMs and the composite seed meal on nematode population dynamics will be determined over time. The nematode community diversity will be ascertained using T-RFLP analysis and quantitative attributes of the population will be determined using standard isolation methods.