The root system of woody perennial crops exists in an extremely complex environment. We as horticulturists and problem solvers need to improve our understanding of the role of the interactions of soil microrganisms, soil media, and the root rhizosphere. It is for this purpose that several ASHS Working Groups—Rootstocks and Compound Genetics, Citrus Crops, Mycorrhiza, Pomology, Nursery Crops, and Viticulture and Small Fruits—have combined to help sponsor this symposium. Plant pathologists and soil microbiologists were invited to elucidate on the impact of pathogenic and beneficial soil bacteria, fungi, and nematodes. As brought out by authors in the following papers, practices employed in managing horticultural crops often discourage the development of plant growth-stimulating microorganisms. Such practices as fumigation and high application rates of fertilizers can alter the composition of the rhizosphere. Conversely, the bacteria, fungi, and nematodes can also alter the rhizospheres by producing substances such as antibodies and toxic metabolites. In citrus, mycorrhizae can alter the nutrient balances, which can indirectly suppress pathogenic fungi.