Measurement of copepod predation on nauplii using qPCR of the cytochrome oxidase I gene

A method to directly measure predation rates by older stage copepods upon copepod nauplii using species-specific primers for the mitochondrial cytochrome oxidase subunit one gene (mtCOI) and real-time quantitative PCR (qPCR) was developed. The general approach is to determine the mtCOI gene copy number of an individual prey organism and the copy number of the same gene in the stomachs of predatory copepods collected in the field. From the knowledge of DNA disappearance rates in the stomachs, ingestion rates can be calculated. In October 2006, laboratory experiments were carried out with Acartia tonsa N1 and N2 as prey and adult female Centropages typicus as predator. The copepods were collected in Narragansett Bay, USA. A. tonsa mtCOI copy numbers copepod⁻¹ were determined for stages N1–C1 and for adults. A. tonsa DNA was detectable in the guts of the predators for as long as 3 h. Exponential rates of decline in prey DNA from the stomachs of the predators are similar to those measured for gut pigments. Because of the very small amount of DNA in an individual N1 or N2 nauplius, procedures were developed to maximize the quantitative extraction and recovery of DNA and to increase the sensitivity of the method. Two quite divergent haplotypes of A. tonsa were found in Narragansett Bay, which required separate qPCR primers; one was present in summer (July) and the other in fall and winter (October and February). With modification, the methods in this study can likely be applied to a range of predator–prey systems.