Soil Microbial Community Composition Under Integrated and Organic Apple Systems In a New York Orchard

Terminal-Restriction Fragment Length Polymorphism (T-RFLP), a Polymerase Chain Reaction based method, was used to determine bacterial and fungal soil community composition in an orchard of disease-resistant ‘Liberty’/‘M.9’ apple (Malus × domestica Borkh.) trees during and after the transition from conventional to either integrated (IFP) or organic fruit production (OFP) systems. Sampling occurred in May and August over three years at both the 0-6 and 6-12 cm soil depths. Additional biological, chemical, and physical soil properties were also measured. Composted bark mulch with infrequent herbicide application was used for IFP, and provided effective weed control, while increasing soil organic matter, pH, soil nutrient availability, microbial biomass carbon, and microbial respiration. Mechanical cultivation along with chicken manure compost was used for OFP, and increased soil porosity, decreased aggregate stability, and increased potentially mineralizable nitrogen and total inorganic N. Neither system increased levels of leaf nutrients. The OFP system appeared to be leaching inorganic N through the soil profile. Using the T-RFLP analyses we found that sampling time influenced the soil bacterial communities more than the treatments. However, soil fungal communities in the 0-6 cm depth segregated by treatment, possibly because of increased detritivore presence under the bark mulch. For most measurements, the 6-12 cm depth only showed minimal treatment differences. Soil quality did not improve as much in the OFP system as in the IFP soil during four years at this orchard.