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Apple (Malu ×domestica) replant disease (ARD) is a soil-borne disease syndrome of complex etiology that occurs worldwide when establishing new orchards in old fruit-growing sites. Methyl bromide (MB) has been an effective soil fumigant to control ARD, but safer alternatives to MB are needed. We evaluated soil microbial communities, tree growth, and fruit yield for three pre-plant soil treatments (compost amendment, soil treatment with a broad-spectrum fumigant, and untreated controls), and five clonal rootstocks (M7, M26, CG6210, CG30, and G16), in an apple replant site at Ithaca, N.Y. Molecular fingerprinting (PCR-DGGE) techniques were used to study soil microbial community composition of root-zone soil of the different soil treatments and rootstocks. Tree caliper, shoot growth, and yield were measured annually from 2002–04. Among the five rootstocks we compared, trees on CG6210 had the most growth and yield, while trees on M26 had the least growth and yield. Soil treatments altered soil microbial communities during the year after pre-plant treatments, and each treatment was associated with distinct microbial groups in hierarchical cluster analyses. However, those differences among fungal and bacterial communities diminished during the second year after planting, and soil fungal communities equilibrated faster than bacterial communities. Pre-plant soil treatments altered bulk-soil microbial community composition, but those shifts in soil microbial communities had no obvious correlation with tree performance. Rootstock genotypes were the dominant factor in tree performance after 3 years of observations, and different rootstocks were associated with characteristic bacterial, pseudomonad, fungal, and oomycetes communities in root-zone soil.

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.