Trophic ecology

Understanding the trophic structure of a community is indispensable to understanding the underlying ecosystem in its entirety. Unfortunately, basic information on animal diet is often incomplete or simply missing. This is not a surprise as the assessment of animal diet is rather difficult. Very often direct observation of feeding is not possible. Species are elusive, small, rare or live in regions that are inaccessible. Another issue is variability of diets within species, populations or even between life stages. And to add more complexity to that, diet is dynamic, i.e. it fluctuates with seasons, day time, geography, and ecosystems. 

As usual, our knowledge about diet is far more detailed when it comes to vertebrates, specifically larger predators. However, once the focus shifts toward e.g. the trophic ecology of many arthropod species one quickly finds out that not much is covered by the literature, because it has not yet been studied as a consequence of the difficulties described above. 

For quite some years stable isotope analysis has been used to reconstruct diets, to characterize trophic relationships, to elucidate patterns of resource allocation, and for construction of food webs. Isotopes of a given element differ in the number of neutrons they contain. Everybody might have heard about radioactive isotopes which are those that spontaneously decay into other element isotopes. Stable isotopes are those which do not, but they might be the result of such a decay. Nonradiogenic stable isotopes are most useful for ecological studies, and particularly those of the light elements: H, C, N, O and S, as those are the major constituents of organic materials, and for which there are large relative mass differences between isotopes of the same element. Stable isotope ratios are usually measured using stable isotope mass spectrometry and currently the most commonly used isotopes are δ¹³C and δ¹⁵N. 

Similarly, DNA barcodes have much utility in revealing trophic interactions among organisms and determining diet items although they often can only provide a snapshot of mostly local, present-day interactions. Thus, stable isotope analysis can complement DNA barcoding techniques by adding coarser but more integrated averages of food web structure across space and time. In addition it allows for tracing nutrient fluxes in changing organismal communities. In other words, DNA barcodes allow us to pinpoint the exact composition of a species’ diet while both δ¹³C and δ¹⁵N isotopes can be used to trace the structure (and its change over time) of the underlying food webs, with δ¹⁵N showing enrichment between trophic levels and δ¹³C distinguishing between prey groups. 

A recent study on a particular butterfly group shows how stable isotope analysis and DNA metabarcoding can be combined to better assess diet and trophic position. The family Lycaenidae (Gossamer-winged butterflies) is the second largest of all butterflies (about 6000 species) with various life histories and diets. About 75% of the species in this group are known to associate with ants and these associations can be mutualistic, parasitic, or predatory. In some cases caterpillars produce nutritious secretions from specialized organs to reward ants in exchange for their protection against predators and parasitoids.

However, the larval diets of many lycaenid butterflies remain poorly characterized, likely because the caterpillars are camouflaged, difficult to rear in captivity and often live in inaccessible microhabitats such as flower buds or subterranean ant nests. For many species, no records exist for direct observations of feeding behaviors, leaving researchers to rely on indirect evidence to infer larval diets. One such species is Anthene usamba (previously A. hodsoni), a lycaenid butterfly found in the savannas of eastern Africa.

An earlier study using comparative microbiome analysis showed that adults in contrast to caterpillars were aphytophagous. Now, metabarcoding of caterpillar gut content chloroplast 16S rRNA found a match to the acacia tree (Vachellia drepanolobium) the caterpillars are known to live on. Stable isotope analysis confirmed that Anthene usamba gets most of its carbon directly or indirectly from its host plant, rather than from surrounding grasses. Although the feeding behaviour of the larvae remains unknown it can be clearly stated that they feed on their host tree.

There is a lot that speaks for the complementary use of stable isotope analysis and DNA barcoding in some dietary studies. There are individual limitations to both methods, e.g. analysis of diets with stable isotope analysis requires prior knowledge of the isotopic signatures of potential food sources. They also are not useful when the number of potential food sources exceeds the number of isotopes available. DNA-based methods such as metabarcoding are subject to various biases especially when PCR is involved. They highly depend on well-parameterized reference libraries and it is not possible to quantify individual contributions to complex DNA mixtures especially in a sample with different levels of degradation (here through differential digestion).

As there are so many species for which we have no clue on what they are feeding on it is reassuring to know that there are a number of methods available that can help us to learn more.