Ground cover and organic nutrient management practices altering the denitrifier community in an organic apple orchard soil
An assessment of the effects of seven years annual ground cover and nutrient amendments to an organically managed apple orchard soil microbial community is in progress. Analysis of soil nutrient data and examination of the microbial community via molecular techniques from 2007 to 2013 will allow interpretation of the possible treatment effects. Extraction of DNA from 0-10 and 10-30 cm soil samples followed by PCR, qPCR and DGGE will be implemented to gain insight into the size and diversity of the denitrifying community.
1) Determine changes in the soil microbial community composition in response to seven years of annual ground cover and nutrient amendments to an organically managed apple orchard.
2) Determine if different annual ground cover and nutrient amendments result in various lengths of time before treatment effects are detected and differentiated at the 10-30 cm soil depth.
3) Determine if annual ground cover and nutrient amendments to an organically managed apple orchard have altered denitrification potentials.
PCR primers for nirK and nosZ were ordered and obtained for future use. A series of DNA extraction kits were tested and the most efficient kit with the greatest quality and quantity of DNA tested was chosen for extractions (NucleoSpin Soil DNA Extraction Kit, Clontech Inc., Mountain View, CA). DGGE reagents were ordered and received, the system was set up and the procedure was performed to ensure reliable and accurate results with future applications. The graduate student was trained to make polyacrylamide gels and implement DGGE procedures. DNA extractions of 2007 and 2013 soil samples are in progress.
Impacts and Contributions/Outcomes
An experimental organic apple orchard was established in 2006 using SARE funds. The goal was to provide regionally appropriate science to understand sustainable management of an orchard. The ground covers and fertilizers applications were obtained locally and created a new use from “waste” items contributing to the sustainability of the project. A challenge in perennial systems involves determining how orchard soils respond to repeated annual additions of organic nutrient containing materials and decompose and build soil organic matter without promoting N losses. Orchards have been better studied in the northeastern and northwestern U.S., but the soils, climate, and pest pressures are different from those in the south, and producers in the south need regionally appropriate recommendations. Soil is the foundation of a healthy sustainable system, a physically and chemically complex matrix supporting a dynamic biological community. Determining the effects of these treatments on the soil microbial community under the unique regional conditions will provide a clearer picture of the basis of a sustainable system.
University of Arkansas
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