Dietary Analysis of Marine Fish Species: Enhancing the Detection of Prey-Specific DNA Sequences via High-Throughput Sequencing Using Blocking Primers

Abstract

Dietary studies of fish can enhance our understanding of predator-prey interactions and provide important insights into complex marine food webs. In this study, we performed dietary analyses of three commercially important fish species in South China: Acanthopagrus latus, Pampus argenteus, and Scomberomorus commerson. Two distinct fragments of the mitochondrial cytochrome c oxidase I (mtCOI) gene, a small (130 bp) and large (300 bp) amplicon, were amplified from the DNA extracted from the gut contents in the presence of blocking primers designed to inhibit the amplification of predator-specific DNA. The amplicons from each predator species were tagged with a unique indexing bar code and sequenced using the Illumina MiSeq platform. Our results showed that the three fish species consumed a wide variety of prey, including jellyfish, copepods, crustaceans, and fish. Seasonal variations in prey composition and species-selective predation were observed. Our approach of combining next-generation sequencing with blocking primers greatly enhanced the speed and resolution of the dietary analyses in marine fishes and could provide novel insights into marine ecosystems.