Group‐specific polymerase chain reaction for DNA‐based analysis of species diversity and identity in dietary samples

Abstract

Unique DNA sequences are present in all species and can be used as biomarkers for the detection of cells from that species. These DNA sequences can most easily be detected using the polymerase chain reaction (PCR), which allows very small quantities of target DNA sequence to be amplified even when the target is mixed with large amounts of nontarget DNA. PCR amplification of DNA markers that are present in a wide range of species has proven very useful for studies of species diversity in environmental samples. The taxonomic range of species to be identified from environmental samples may often need to be restricted to simplify downstream analyses and to ensure that less abundant sequences are amplified. Group-specific PCR primer sets are one means of specifying the range of taxa that produce an amplicon in a PCR. We have developed a range of group-specific PCR primers for studying the prey diversity found in predator stomach contents and scats. These primers, their design and their application to studying prey diversity and identity in predator diet are described.

Qualitative assessment of the diet of European eel larvae in the Sargasso Sea resolved by DNA barcoding

“…The nearest relatives of the Streptophyta sequences included not only marine sequences but also genes from higher plants, suggesting potential contamination. However, reports of similar sequences from whale faeces (Jarman et al 2004) and guts of lobster larvae (Suzuki et al 2006) indicate that they represent hitherto unknown organisms in marine plankton. Similarly, some of the fungal sequences were related to sequences obtained from marine plankton.…”

Faeces of generalist predators as ‘biodiversity capsules’: A new tool for biodiversity assessment in remote and inaccessible habitats

“…Although this is not an issue for species with highly specialised diets (Rougerie et al, 2011), this is particularly limiting for generalist predators that feed on a variety of prey species. Until recently, such mixed DNA samples could be analysed only after the development of large panels of species-specific primers (Jarman et al, 2004) used in complex multiplex PCRs (Harper et al, 2005;King et al, 2011) or cloning analyses (Zeale et al, 2011).…”

Extreme food webs: Foraging strategies and diets of scavenging amphipods from the ocean’s deepest 5 kilometers

“…These approaches include (1) stable isotope ratios and fatty acid signatures as biomarkers of assimilated food (Hobson and Welch 1992;Graeve et al 2001;Nyssen et al 2002), and (2) the nascent approach of using universal polymerase chain reaction (PCR) primers to amplify and sequence the DNA from gut contents to identify ingested organisms (Blankenship and Yayanos 2005). Consumed organisms that are digested beyond visually identifiable remains can still leave residual DNA in the digestive tract (Duplessis et al 2004;Jarman et al 2004). Recently, it was shown that this dietary DNA can be amplified with highly conserved primers and sequenced (see Blankenship and Yayanos 2005).…”