Modern agricultural systems can benefit from the application of concepts and models from applied ecology. When understood, multitrophic interactions among plants, pests, diseases and their natural enemies can be exploited to increase crop production and reduce undesirable environmental impacts. Although the understanding of subterranean ecology is rudimentary compared to the perspective aboveground, technologies today vastly reduce traditional obstacles to studying cryptic communities. Here we emphasize advantages to integrating as much as possible the use of these methods in order to leverage the information gained from studying communities of soil organisms. PCR–based approaches to identify and quantify species (real time qPCR and new generation sequencing) greatly expand the ability to investigate food web interactions because there is less need for wide taxonomic expertise within research programs. Improved methods to capture and measure volatiles in the soil atmosphere in situ make it possible to detect and study chemical cues that are critical to communication across trophic levels. The application of SADIE to directly assess rather than infer spatial patterns in belowground agroecosystems has improved the ability to characterize relationships between organisms in space and time. We review selected methodology and use of these tools and describe some of the ways they were integrated to study soil food webs in Florida citrus orchards with the goal of developing new biocontrol approaches.

The geospatial patterns of four species of native entomopathogenic nematodes in Florida were previously shown to be related to soil properties that affect soil water potential. Here we compared the responses to water potential of 3rd stage, infective juvenile (IJ) Steinernema sp. (Sx) and S. diaprepesi (Sd) in controlled conditions. The two species were selected because they are closely related (S. glaseri-group), but tend to occupy different habitats. In columns of sandy soil with moisture gradients ranging from field capacity (6% w:w) to saturated (18%), Sx migrated toward wetter soil whereas Sd migrated toward drier soil. Survival of two isolates each of Sx and Sd for seven days in the absence of food was greatest at 18% and 6% soil moisture, respectively. After three cycles of migration through soil to infect insect larvae 10 cm distant, Sd dominated EPN communities when soil columns were maintained at 6% moisture, whereas Sx was dominant in soil maintained at 18% moisture. When rehydrated after 24 h on filter paper at 90% RH, 50% of Sd survived compared to no Sx. Two isolates of Sd also survived better than two isolates of Sx during up to 24 h in a hypertonic solution (30% glycerol). The behavioral responses of both species to water potential and osmotic gradients were consistent with surveys in which Sx was recovered only from flatwoods ecoregions with shallow water tables and poorly drained soils, whereas Sd most frequently inhabited the central ridge ecoregion comprising well-drained soils and deeper water tables. Comparative proteomic analysis revealed differential expression of proteins involved in thermo-sensation (guanylyl cyclase and F13E6-4) and mechano-sensation and movement (paramyosin, Actin 3, LET-99, CCT-2), depending on whether Sd was in soil at 6% or 18% moisture. Proteins involved in metabolism, lectin detoxification, gene regulation and cell division also differed between the two conditions. Our data suggest the plausibility of modifying soil moisture conditions in flatwoods orchards in ways that favor more desirable (effective) EPN species. Similarly, these particular behavioral traits are likely to be useful in guiding the selection or engineering of EPN species for use in different ecoregions.