Abstract
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 next 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.
Highlights
Challenges for modern agriculture include producing enough food while simultaneously reducing negative impacts on the environment and using our resources in sustainable ways
By identifying organisms that contribute to the complex multitrophic interactions in the soil it becomes possible to infer the existence of underlying processes, such as intraspecific and interspecific interactions among organisms or responses to environmental heterogeneity (Perry and Dixon, 2002; Ings et al, 2009)
Research on plant volatile organic compounds (VOCs) produced after insect herbivory has been dominated by studies aboveground, probably due to methodological constraints related to subterranean investigations
Summary
Challenges for modern agriculture include producing enough food while simultaneously reducing negative impacts on the environment and using our resources in sustainable ways. The main advantage of TRFLP with respect the DGGE/TGGE technique is the opportunity to compare data from different runs, whereas cryptic bands and intraspecific variation make the comparison of results between gels difficult (Nunan et al, 2005; Pompanon et al, 2012); an important advantage of DGGE is the ability to excise and sequence gel fragments In addition to these methods, conventional PCR-based methods have been proposed to study belowground predator-prey interactions (Read et al, 2006; Waldner et al, 2013; Wallinger et al, 2013) including protocols for multiplexing (Harper et al, 2005; Eitzinger and Traugott, 2011). As in aboveground systems, the use of qPCR and NGS are replacing these previous techniques
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