Molecular identification of laser-dissected gut contents from hatchery-reared larval cod, Gadus morhua: a new approach to diet analysis

The transition between endogenous and exogenous feeding in hatchery production of fish larvae has long been a bottleneck to increased production. Identification of alternative prey species with a wider array of nutritional profiles is essential for further expansion and diversification within the aquaculture industry. Traditional morphological methods to identify dietary composition are limited. In this study, we present a novel DNA-based methodology for identifying the gut contents of larval fish that is independent of prey retaining identifiable characteristics. Laser capture microdissection is used to collect ingested material for DNA extraction, thus limiting contaminating DNA originating from the larval fish. PCR is then conducted using universal eukaryotic primers that have the potential to detect a wide diversity of prey items. Using this approach, we identified ingested Artemia salina from hatchery-reared Gadus morhua larvae. Differential length amplification PCR was used to evaluate the effects of DNA degradation on the sensitivity of A. salina detection. Although it was possible to detect A. salina with relatively long (626 bp) fragments, targeting smaller fragments (264 bp) resulted in the highest return of prey sequences. This combined LCM and molecular approach to diet analysis could offer a more complete assessment of the diets of naturally feeding larvae.