Use of Quantitative Real-Time PCR to Unravel Ecological Complexity in a Biological Control System

Biological control of soilborne plant pathogens using beneficial fungi, such as the mycoparasite Trichoderma harzianum, offers the prospect of environmentally benign pest control. However, biocontrol organisms have their own natural enemies; for example the fungivorous nematode Aphelenchoides saprophilus preys on T. harzianum. A trophic cascade occurs when three or more trophic levels are present in a food chain, and consumption of the intermediate species affects biomass or productivity of a lower trophic level; such an interaction in this system might reduce the biocontrol efficacy of T. harzianum. However, the presence of refuges, where intermediate-level species are protected from predation, may reduce the ecological impact of a trophic cascade. Interactions among microscopic organisms in a complex medium such as soil are difficult to observe and quantify. We evaluated the potential of quantitative real-time PCR (qRT-PCR) as a tool to investigate the trophic cascade interaction among T. harzianum, A. saprophilus, and the plant pathogen Sclerotinia sclerotiorum. Results indicate that the mycoparasite colonized and persisted inside structures (sclerotia) of the target plant pathogen, where it was relatively protected from predation compared to the surrounding soil environment. In this way, colonization of sclerotia may provide a refuge that reduces trophic cascade effects in this system. qRT-PCR provided a sensitive method to investigate fungal dynamics over time in this multitrophic system.