Let the prey speak: Using PNA clamps to silence predator DNA in marine faecal diet studies
DNA metabarcoding of faeces is a powerful, non-invasive method for assessing predator diets. However, when studying the diet of generalist predators, broad PCR primers are used to amplify the wide range of potential prey species and metabarcoding outputs are often dominated by sequences from the predator. While blocking primers can be used to reduce PCR amplification of predator DNA, they frequently cause partial predator suppression and unintended prey blocking. Peptide nucleic acid (PNA) clamps, offer a promising, underutilised alternative by binding strongly and selectively to predator DNA to block its PCR amplification. In this study we designed and validated a novel PNA clamp targeting the 18S rRNA gene to suppress bird and mammal predator DNA in dietary samples. We tested this clamp on tissue mixtures and faecal samples from three seabird and two seal species across temperate, subantarctic, and Antarctic regions. The PNA clamp substantially increased the proportion of prey reads recovered while maintaining consistent prey community composition across all predator species. Our results demonstrate not only the general effectiveness of PNA clamps over standard blocking primers, but also provide a powerful, broadly applicable new tool to improve the accuracy in DNA diet metabarcoding studies.