Groundcover Management Systems Influence Soil Microbial Community Composition in an Apple Orchard

Abstract

An apple (Malus domestica cv. Empire on M9/MM111 rootstock) orchard groundcover management systems (GMSs) study has been underway since 1992 in Ithaca, N.Y. Four GMS treatments are applied each year in 2-m wide tree-row strips: Pre-emergence herbicides (Pre-H: diuron + norflurazon + glyphosate); Post-emergence herbicide (Post-H: glyphosate); mowed-sod (Grass); and composted hardwood bark mulch (Mulch) treatment. The soil (silty clay loam) physical and chemical conditions have been monitored continuously. In May and Sept. 2003, we sampled topsoil beneath trees in each GMS and used PCR-DGGE combined with sequencing to characterize soil microbial community composition. Mulch had more culturable soil bacteria than the Pre-H treatment. Soil in Grass plots had the most culturable soil fungi. Soil microbial respiration rates were higher in Mulch than Grass and herbicide GMSs. Surface vegetation in the Grass and Post-H plots strongly influenced soil bacterial community composition. In Principal Component Analyses, Post-H and Grass treatments comprised one variance cluster, and Pre-H and Mulch treatments another. The soil fungal community was less diverse (fewer DGGE bands) than the bacterial community, and was less affected by GMS. Treatments with more surface vegetation (Post-H and Grass) also had more free-living and phytonematodes than Pre-H and Mulch. A total of 47 clones from 12 DGGE bands yielded 31 unique DNA sequences. Of these, 15 were novel sequences with no matches in the GenBank (NCBI) database. Another 10 (27 clones) could be matched with known fungal species at 96-100% identity. The primer pair used, ITS1F/ITS2, amplified a considerable number of Basidiomycetes and Ascomycetes, but there was no amplification for Zygomycetes and Oomycetes.