Molecular detection of plaice remains in the stomachs of potential predators on a flatfish nursery ground

Abstract

Stomach contents of potential predators from a flatfish nursery ground on the Scottish west coast were examined visually and probed using a TaqMan real-time PCR based assay designed to detect plaice Pleuronectes platessa DNA. Stomachs from 1137 brown shrimp Crangon crangon, along with a lesser number of shore crab Carcinus maenas, grey gurnard Eutrigla gurnardus and Gobiidae were analysed. Overall 45% of shrimp tested positive for plaice DNA, a proportion considerably higher than in stomachs containing visually identifiable flatfish remains. When scaled to the population level, predation by shrimp generated an estimated mortality of 9% d . The discrepancy between mortality estimates based on molecular and catch-curve analysis might be due to sampling being conducted at low water between dusk and dawn, which would concentrate predators and prey at times coincident with peaks of shrimp feeding. In addition, the sensitivity of the TaqMan assay could have led to some over-estimation because non-fatal interactions may also have been detected, e.g. shrimp are known to nibble the fins of flatfish, that might result in a positive TaqMan result but not necessarily in mortality for the fish. The percentage of shrimp testing positive for presence of plaice DNA in their stomachs was also related to plaice density in a positive, linear manner. For less abundant predators, stomachs of 6% of shore crabs, 40% of gurnards and 11% of large gobies also tested positive.

A real-time PCR assay to estimate invertebrate and fish predation on anchovy eggs in the Bay of Biscay

“…Assay sensibility was also tested against a series of E. encrasicolus DNA dilutions including both muscle tissue and single eggs. DNA extractions and real-time PCR settings for assay validation were based in those established by Albaina et al (2010Albaina et al ( , 2012. DNA was extracted using a modified salt extraction protocol (Aljanabi and Martinez, 1997).…”

“…Due to the absence of anchovy larvae counts, daily mortality due to macrozooplankton predation was then computed as the fraction of anchovy eggs eaten in the last 24 h (Eqs. (1) and (2); adapted from Albaina et al, 2012). Both prey and predator abundances were transformed to abundances per unit area.…”

“…Fox et al, 2005Fox et al, , 2008Minegishi et al, 2009). Examples of real-time PCR application to characterize marine animals diet include copepods (Nejstgaard et al, 2008;Troedsson et al, 2009;Durbin et al, 2008Durbin et al, , 2011, decapods (Töbe et al, 2010;Albaina et al, 2010Albaina et al, , 2012Cleary et al, 2012;Redd et al, 2014), fishes Fox et al, 2012;Baerwald et al, 2012) and mammals (Bowles et al, 2011).…”

Ten real‐time PCR assays for detection of fish predation at the community level in the San Francisco Estuary–Delta

“…They can detect prey composed of soft tissue, such as eggs and larvae (Symondson ; Albaina et al . , ; Fox et al . ) as well as prey that have been digested and are no longer phenotypically identifiable.…”

“…DNA-based methods for diet analysis offer several advantages over the visual identification methods that are often used in predation studies (Sheppard & Harwood 2005;Carreon-Martinez & Heath 2010). They can detect prey composed of soft tissue, such as eggs and larvae (Symondson 2002;Albaina et al 2010Albaina et al , 2012Fox et al 2012) as well as prey that have been digested and are no longer phenotypically identifiable. When thoroughly validated, TaqMan qPCR assays are specific enough to reliably identify species without additional confirmation such as sequencing or cloning, offering a faster turnover time than other DNA-based methods.…”