Ground cover and organic nutrient management practices altering the denitrifier community in an organic apple orchard soil

Project Overview

Project Type: Graduate Student
Funds awarded in 2013: $11,000.00
Projected End Date: 12/31/2015
Grant Recipient: University of Arkansas
Region: Southern
State: Arkansas
Graduate Student:
Major Professor:
Dr. Mary Savin
University of Arkansas

Annual Reports


  • Fruits: apples, general tree fruits


  • Crop Production: nutrient cycling, organic fertilizers
  • Natural Resources/Environment: biodiversity
  • Production Systems: organic agriculture, transitioning to organic
  • Soil Management: nutrient mineralization, organic matter, soil analysis, soil microbiology, soil quality/health


    Molecular analysis complemented investigation of the long-term changes in microbial communities and soil nutrients of an organic apple orchard receiving annual additions of ground cover and fertilizer treatments. Seven years of compost and wood chip applications resulted in the greatest soil organic matter (OM), and richest and most diverse denitrifier communities. However, dissolved organic carbon, OM, microbial biomass, and range-weighted richness of denitrifiers revealed different interactions among fertilizers and ground cover combinations. It is necessary to understand how those interactions affect the soil microbial community to properly manage for decomposition and nutrient cycling and to build soil quality.


    The purpose of this project is to provide organic fruit growers in the mid-southern U.S. useful information about how ground cover and organic fertilizer management practices affect N availability by understanding the impacts of practices on the microbial community and soil health. Microbial activity and the soil nutrient cycling services microbes provide play a significant role in healthy soil functioning. Excess NO3- can be leached out of the soil profile to groundwater or reduced to nitric oxide (NO), nitrous oxide (N2O), or dinitrogen (N2) during denitrification. Determining how repeated annual applications of ground covers and organic fertilizers have changed the denitrifier community will provide insight into the fate of N and ultimately the sustainability of these treatments.

    Traditional analyses of samples collected beginning 2007 (organic matter (OM), size of N pools, microbial biomass, and enzyme activities) indicate that while microbial biomass and soil OM have increased from years of additions, treatments are differentiating in terms of dissolved organic C (DOC) and inorganic N. These analyses do not provide insight into the microbial community composition and thus provide an incomplete picture. Molecular techniques provide another tool and approach to open the “black box of microbial ecology” which will allow for unraveling of mechanisms responsible for processes underlying varying conditions. There is potential for denitrification to occur, especially in the treatments receiving compost (increased microbial biomass, organic C, and nitrate (NO3-) concentrations) and in other ground covers, depending on the nutrient source.

    Denitrification is a multiple-step pathway that ultimately reduces NO3- to N2, by nitrate, nitrite, nitric oxide, and nitrous oxide reductases (Zumpft, 1997). Genes code for the enzymes that catalyze these reductions. To gain insight into the community diversity and the relative contribution of organisms to this functional potential, denitrification genes can be analyzed. In this study, we were able to successfully target nirK coding for the nitrite reductase to better understand the community diversity and potential to contribute to terrestrial N loss. The nirK gene is a gene in the denitrification pathway that has been shown to work well in environmental samples using denaturant gradient gel electrophoresis (DGGE) (Throbäck et al., 2004).

    Project objectives:

    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.

    Any opinions, findings, conclusions, or recommendations expressed in this publication are those of the author(s) and do not necessarily reflect the view of the U.S. Department of Agriculture or SARE.