Comparing three types of dietary samples for prey DNA decay in an insect generalist predator

Abstract

The rapidly growing field of molecular diet analysis is becoming increasingly popular among ecologists, especially when investigating methodologically challenging groups, such as invertebrate generalist predators. Prey DNA detection success is known to be affected by multiple factors; however, the type of dietary sample has rarely been considered. Here, we address this knowledge gap by comparing prey DNA detection success from three types of dietary samples. In a controlled feeding experiment, using the carabid beetle Pterostichus melanarius as a model predator, we collected regurgitates, faeces and whole consumers (including their gut contents) at different time points postfeeding. All dietary samples were analysed using multiplex PCR, targeting three different length DNA fragments (128, 332 and 612 bp). Our results show that both the type of dietary sample and the size of the DNA fragment contribute to a significant part of the variation found in the detectability of prey DNA. Specifically, we observed that in both regurgitates and whole consumers, prey DNA was detectable significantly longer for all fragment sizes than for faeces. Based on these observations, we conclude that prey DNA detected from regurgitates and whole consumers DNA extracts are comparable, whereas prey DNA detected from faeces, though still sufficiently reliable for ecological studies, will not be directly comparable to the former. Therefore, regurgitates and faeces constitute a useful, nonlethal source for dietary information that could be applied to field studies in situations when invertebrate predators should not be killed.

Advancing the integration of multi‐marker metabarcoding data in dietary analysis of trophic generalists

“…It is also highly implausible that wheatears are feeding on other parts of these plants such as buds, flowers, or pollen. A more likely explanation may thus be indirect consumption through the stomach contents of animal prey, which may be recovered by molecular markers amplifying small DNA fragments (<200 bp), such as the 18S and trn L markers used in our study (Kamenova et al, ; Sheppard et al, ). Detection of secondary consumption is well documented even through traditional methods (Johnson, Ross, & Smith, ), but it is usually considered as having little importance (Barrett et al, ).…”

“…Reasons for this are unknown, but it may be a consequence of several nonexclusive factors. One possibility is that metabarcoding detects direct consumption of items for periods longer than the defaecation time (Deagle, Chiaradia, McInnes, & Jarman, 2010;Oehm et al, 2011), especially if short amplicons are used (Kamenova et al, 2018). This can explain for instance, why trnL detected the berry-producing Pistacia terebinthus in 11 samples, while the seeds of this plant were detected in a single faecal sample.…”

High-throughput sequencing for community analysis: the promise of DNA barcoding to uncover diversity, relatedness, abundances and interactions in spider communities

“…Also, prey DNA from the predator's guts is often degraded and present at much lower concentrations than the DNA of a single specimen in a bulk community extract. Hence, short PCR amplicons are usually targeted to achieve a complete prey spectrum (Zeale et al 2011;Kamenova et al 2018). Gut content metabarcoding has become increasingly popular and has recently provided numerous novel insights into the trophic ecology of spiders.…”

Metabarcoding for stomach‐content analyses of Pygmy devil ray (Mobula kuhlii cf. eregoodootenkee): Comparing tissue and ethanol preservative‐derived DNA

“…Nonetheless, gut-derived prey DNA is thought to be of better quality than scat-derived prey DNA since digestion is at its initial phase. As one example, Kamenova, Mayer, Coissac, Plantegenest, and Traugott (2017) noted gut DNA was detectable for longer than scat DNA after periods of feeding and starvation in the predatory carabid beetle (Pterostichus melanarius). In fish stomachs, DNA persistence has been recorded ranging between 16 and 24 hr post digestion using mid-throughput sequencing (Carreon-Martinez et al, 2011).…”