Uncovering Trophic Interactions in Arthropod Predators through DNA Shotgun-Sequencing of Gut Contents

Abstract

Characterizing trophic networks is fundamental to many questions in ecology, but this typically requires painstaking efforts, especially to identify the diet of small generalist predators. Several attempts have been devoted to develop suitable molecular tools to determine predatory trophic interactions through gut content analysis, and the challenge has been to achieve simultaneously high taxonomic breadth and resolution. General and practical methods are still needed, preferably independent of PCR amplification of barcodes, to recover a broader range of interactions. Here we applied shotgun-sequencing of the DNA from arthropod predator gut contents, extracted from four common coccinellid and dermapteran predators co-occurring in an agroecosystem in Brazil. By matching unassembled reads against six DNA reference databases obtained from public databases and newly assembled mitogenomes, and filtering for high overlap length and identity, we identified prey and other foreign DNA in the predator guts. Good taxonomic breadth and resolution was achieved (93% of prey identified to species or genus), but with low recovery of matching reads. Two to nine trophic interactions were found for these predators, some of which were only inferred by the presence of parasitoids and components of the microbiome known to be associated with aphid prey. Intraguild predation was also found, including among closely related ladybird species. Uncertainty arises from the lack of comprehensive reference databases and reliance on low numbers of matching reads accentuating the risk of false positives. We discuss caveats and some future prospects that could improve the use of direct DNA shotgun-sequencing to characterize arthropod trophic networks.

Fig 1. Qualitative trophic network for the focal predators using DNA shotgun-sequencing of their gut content.

The focal predators are in black balloons, the prey are in white (extraguild) and grey (intraguild) balloons with black letters and edges, the parasitoids in white balloons with grey edges, in which grey letters are for the known aphid parasitoids, and black letters for other parasitoids. The arrows indicate the flux of biomass, in which black arrows indicate direct predation, and the dashed arrows indicate inferred predation associated with symbionts. The numbers at the origin of each arrow indicate the number of reads supporting the arrow, which for inferred predation is a thesum of the total aphid-specific symbiont reads.