Polymerase chain reaction as a promising tool for DNA-based diet studies of crustaceans

Abstract

Studying the diet of crustaceans based on the direct visual inspection of the gut contents can be difficult because they can ingest only a portion of the prey and further crush it into very small pieces, making a very few food items identifiable. Here, the usefulness of molecular methods to identify the species present in the gut contents of two crustaceans, the shore crab Carcinus maenas and the brown shrimp Crangon crangon, was tested. Stomach contents were removed, and their total genomic DNA extracted followed by amplification (PCR) with four specific prey mtDNA primers. Since both crustaceans are opportunistic predators, preying upon around 40 different species, the study was restricted to common potential preys in the sampled area, the Minho Estuary (Portugal): the common goby Pomatoschistus microps, the ragworm Hediste diversicolor, the flounder Platichthys flesus and the peppery furrow shell Scrobicularia plana. After testing the most appropriate methodology for DNA extraction and PCR amplification to detect the presence of each potential prey with positive control samples, the same methodology was applied to the stomach content samples. The molecular methods allowed for detection of the presence of P. microps, P. flesus and H. diversicolor in the stomachs of both crustaceans. Therefore, once potential prey and their availability in the system are known, PCR technique can be an alternative tool to overcome some of the limitations of traditional methods in the study of the crustaceans’ diet, even when stomach contents include a great part of ‘detritus’. This study reflects also the need to develop more tools (primers) to improve the assessment of predator–prey interactions in aquatic ecosytems.