Fungal biological control agents against plant pathogens, especially those in soil, operate within physically, biologically, and spatially complex systems by means of a variety of trophic and nontrophic interspecific interactions. However, the biocontrol agents themselves are also subject to the same types of interactions, which may reduce or in some cases enhance their efficacy against target plant pathogens. Characterization of these ecologically complex systems is challenging, but a number of tools are available to help unravel this complexity. Several of these tools are described here, including the use of molecular biology to generate biocontrol agents with useful marker genes and then to quantify these agents in natural systems, epifluorescence and confocal laser scanning microscopy to observe their presence and activity in situ, and spatial statistics and computer simulation modeling to evaluate and predict these activities in heterogeneous soil habitats. 1. Introduction Reduction of chemical pesticide usage, including chemicals for control of soilborne plant pathogens, is widely recognized as a desirable goal for agriculture and forestry. Many traditional chemical means of disease control (e.g., methyl bromide and certain fungicides) are being or have been phased out due to economic considerations and/or mandate. Application of fungi and bacteria as microbial antagonists of plant pathogens offers prospects of environmentally benign pest control. A wide range of fungi have shown potential as agents for biological control of soilborne phytopathogens, and this review will focus on these fungal biocontrol agents. Unlike gnotobiotic systems, soil is characterized by a multitude of both trophic (food webs) and nontrophic (e.g., mutualism, commensalism, neutralism, amensalism, antagonism, and competition) interspecific relationships [1]. The distinction between trophic and nontrophic relationships is somewhat arbitrary, since it focuses only on “what an organism eats and what eats it.” Parasitism typically is categorized as a trophic interaction, since a parasite derives nutrition from its host, whereas mutualism is generally considered a nontrophic interaction. Nonetheless, in an alternate taxonomy of interspecific relationships, mutualism and parasitism are often considered to be part of a continuum [2, 3]. Biocontrol microbes that are applied to seeds or soil prior to planting may colonize the spermosphere and/or rhizosphere of seedlings and thus may be present at or near infection courts of soilborne pathogens. There, biocontrol agents may
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