The central role of plant secondary metabolites (PSMs) in mediating the ecological interactions between plants and other organisms is both well known and well studied, particularly in the case of the defensive responses of plants against attack by herbivores or pathogens (Dangl & Jones, 2001; Kessler & Baldwin, 2002). Furthermore, because plants face many simultaneous threats (Maleck & Dietrich, 1999; Paul et al., 2000), the chemical changes within plants in response to one attacking organism can influence the behaviour and performance of many others (Thaler et al., 2002; Biere et al., 2004). Thus, chemically mediated plant-based interactions have significant consequences for individual species, ecological communities and ecosystem function, so gaining an in-depth understanding of the chemical basis of these interactions is vital for ecologists (van der Putten, 2003; Dicke, 2006; Schuman & Baldwin, Chapter 15; Dicke et al., Chapter 16).
Recent advances in ecological genomics have demonstrated the complexity of plant responses to biotic challenges at the molecular level: hundreds of genes are now known to be up- or down-regulated in response to herbivore or pathogen attack (Zheng & Dicke, 2008). This has been of great benefit in understanding the molecular basis of plant defence, but microarray data alone cannot unravel the complexity and variability in plant responses, many of which are specific to particular types of natural enemy, and/or vary according to environmental conditions (Kant & Baldwin, 2007). Genomic analysis needs to be supported by manipulative experiments which assess all the metabolic responses of plants to environmental challenges as well as the molecular ones – so-called metabolomic approaches. Metabolomics is the systematic analysis of the set of metabolites synthesised by an organism at a particular ‘snapshot’ in time and can be described as providing the link between genotypes and phenotypes (Fiehn, 2002; Macel et al., 2010). Assuming that this set of metabolites reflects the interactions the plant is having with its abiotic and biotic environment, chemical ecologists can use this technique to study the mechanisms underpinning these interactions (Bundy et al., 2009), including those between plants and other organisms such as herbivores and pathogens (Allwood et al., 2008).