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Soil is a highly heterogeneous environment with many physical and chemical factors that are expected to vary within and across fruit orchards, and many of these factors also drive changes in the soil microbiome. To understand how biogeography influences apple root microbiomes, we characterized the bacterial and archaeal, fungal, nematode, oligochaete, and mycorrhizal communities of the root zone soil (soil adjacent to the tree trunk and expected to be influenced by the plant) across 20 sites that represent the main Michigan apple-producing region. Amplicon sequencing of the 16S rRNA and internal transcribed spacer genes were performed, as well as direct quantification of nematodes, oligochaetes, and mycorrhizal fungi with microscopy. The microbiome community structures were affected by site and rootstock, but not by scion. Microbiomes had taxa typical of soil, including an archaeal taxon affiliated with family Nitrososphaeraceae, bacterial phyla Proteobacteria and Acidobacteria, and fungal phyla Ascomycota and Basidiomycota. While many taxa were detected in all samples and collectively composed 41.55% of the relative abundances, they had average relative abundances each of less than 1%, with no notable dominance. We used network analysis to understand potential for intertrophic interactions, but detected few cross-kingdom associations. Together, these results show the complexity of the apple root zone microbiome and did not identify obvious biotargets that may universally associate with tree health. This suggests that the key attributes of the apple root zone community may be in the community-level functional traits that are shared and distributed across the membership, rather than by its composition.

Biogeography and Diversity of Multi-Trophic Root Zone Microbiomes in Michigan Apple Orchards: Analysis of Rootstock, Scion, and Local Growing Region