Chapter Three - Empirically Characterising Trophic Networks: What Emerging DNA-Based Methods, Stable Isotope and Fatty Acid Analyses Can Offer
Introduction
Interest in food webs has increased considerably in recent years, with especially rapid progress being made via the development of new theoretical modelling and numerical simulation tools (e.g. Dobson et al., 2009, Ings et al., 2009, Stouffer, 2010). Although models and simulations have provided important new insights into food web structure and dynamics, it is still essential to validate trophic links empirically with real-world data (Finlay-Doney and Walter, 2012). However, it is often not known what, when and where specific trophic interactions occur in arable ecosystems, as feeding behaviour is affected by both the biotic and abiotic environment, which remains poorly understood. Consequently, our understanding of agricultural food webs is often still too fragmentary to understand fully how the community functions via the application of food web approaches. The current paucity of accurate dietary information is, in part, due to the difficulties of tracking trophic interactions in the field, and the lack of high-throughput techniques to record feeding interactions in communities is a longstanding obstacle for the construction of empirical food webs (Cohen et al., 1993, Memmott, 2009).
These difficulties apply to ecological networks in general (Ings et al., 2009), but they are particularly acute in the agricultural context (Bohan et al., 2013), where the principal actors are typically small, invertebrates with cryptic and complex trophic behaviour, which are difficult to assess using classical techniques such as direct observation or morphological identification of prey remains in gut contents or faeces (Sunderland et al., 2005). In addition, many of the most common taxa in agricultural fields, such as carabid beetles, are opportunistic feeders, consuming a wide range of animal prey and plant material, which makes their diets difficult to characterise fully for any given system (Holland, 2002). Many important consequences of generalist feeding behaviour, such as prey switching or intraguild predation, therefore remain difficult to measure in the field, despite their importance for the structure of food webs and the delivery of ecosystem services, such as pest control (e.g. Finke and Denno, 2004, Wilson and Wolkovich, 2011). Due to these difficulties, the most complex feeding networks measured in arable systems to date have dealt with relatively simple host–parasitoid communities (e.g. Bukovinszky et al., 2008, Tylianakis et al., 2007) or mutualistic, plant–pollinator webs (Burkle and Alarcón, 2011, Memmott, 2009). Although determining and quantifying host–parasitoid interactions is relatively easy, in contrast to assessing what generalist herbivores or carnivores consume, there are still significant methodological hurdles associated with the description of trophic interactions in host–parasitoid communities; for example, discriminating among cryptic interactions, such as multiparasitism and hyperparasitism, is impractical with conventional methods (Gariepy et al., 2008a, Traugott et al., 2008) and requires novel approaches. Another particular problem is that, unlike many aquatic food webs, which tend to be dominated by engulfing, gape-limited consumers (e.g. see Gilljam et al., 2011, Ledger et al., 2013, O'Gorman et al., 2012), agroecosystems have large numbers of fluid-feeding consumers, whose gut contents are unidentifiable using traditional microscopy techniques.
In recent years, significant methodological advances have been made for studying feeding interactions in the field, opening up exciting new perspectives in trophic ecology. Stable isotope and fatty acid (FA) analyses provide new means to elucidate patterns of resource allocation (Boecklen et al., 2011, Ruess and Chamberlain, 2010), while DNA-based techniques allow feeding interactions to be characterised to a high level of taxonomic resolution (Gariepy et al., 2007, Symondson, 2012). These approaches have been reviewed and their potential applications summarised elsewhere (e.g. Gariepy et al., 2007, King et al., 2008, Martínez del Rio et al., 2009, Pompanon et al., 2012, Post, 2002, Ruess and Chamberlain, 2010, Sheppard and Harwood, 2005, Symondson, 2002), yet an integrated overview of the possibilities they offer for describing trophic networks is notable by its absence. Here, we address this gap by comparing DNA-based, stable isotope and FA analyses and providing guidance as to which tools are best suited to address specific questions in agroecosystem food web ecology (Fig. 3.1).
Section snippets
Methodological background
Isoenzyme electrophoresis (e.g. Traugott, 2003, Walton et al., 1990) and monoclonal antibodies (e.g. Hagler and Naranjo, 1994, Symondson et al., 1997) were the most commonly used molecular-based methods to assess invertebrate feeding interactions by targeting prey- and parasitoid-specific proteins during the 1980s and 1990s. While enzyme electrophoresis is relatively cheap and easy to conduct, this technique is often limited by low specificity and sensitivity to identify and detect specific
Methodological background
The principles of stable isotope analysis have been known since the beginning of the twentieth century (Högberg, 1997). In the second half of the century, palaeontologists and plant physiologists in particular adopted this method increasingly to address diverse topics, including characterising the diets of extinct animals and nitrogen-fixing efficiency of plants (deNiro and Epstein, 1978, Gannes et al., 1998). Animal ecologists first began to use the approach in the early 1970s (deNiro and
Methodological background
Fatty acid (FA) analysis is a well-established tool for studying trophic interactions in many different ecosystems. In marine environments the utility of FAs as bottom-up dietary tracers in food webs is reflected in recent reviews on arctic mammals (Thiemann et al., 2008), sea birds (Williams and Buck, 2010), plankton (Perhar et al., 2012) and the benthos (Kelly and Scheibling, 2012). FA use in arable and soil ecology has lagged behind. Starting a decade ago with laboratory investigations of
Which Approach to Choose, How to Start and How to Interpret the Data?
The three different methodological approaches we have outlined have different strengths and weaknesses, which are summarised in Table 3.1. In general terms, the molecular techniques allow identification of highly taxonomically resolved interactions to be identified, which can produce very detailed, complex ecological networks of different types (e.g. host–parasitoid networks, food webs, plant–pollinator networks). Stable isotopes and FAs reflect broad pathways of biomass that is assimilated
Acknowledgements
We thank the editors of this issue, Guy Woodward and Dave Bohan, for their invitation and the encouragement to write this article. Michael J. O. Pocock and another anonymous referee provided helpful comments for improving the manuscript. We are also grateful to Dave Bohan and Guy Woodward for linguistic revision. Julia Seeber was funded by the Austrian Science Fund, project T441 ‘Litter decomposition and humus formation in high alpine soils’.
Glossary
DNA-based techniques
- Blocking primer
- unique primer specifically designed to prevent the amplification of particular DNA sequences. Widely applied in NGS-based diet analysis, to avoid preferential amplification of consumer DNA over DNA from food remains.
- Diagnostic PCR
- a PCR assay which is used to test (dietary/host) samples for the presence of DNA from a specific species or a group of organisms.
- DNA cloning
- process where individual PCR products are inserted into a plasmid to generate many identical copies which can then
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