Effectiveness of TaqMan probes for detection of fish eggs and larvae in the stomach contents of a teleost predator

Abstract

Experiments were conducted on the ability of TaqMan molecular probes to detect plaice Pleuronectes platessa DNA from eggs, and cod Gadus morhua DNA from eggs and larvae following ingestion by a teleost predator, whiting Merlangius merlangus. Estimated half-life detection rate (T50) for eggs was 31 h, and 26 h for larvae, with some positive detections occurring even after visual inspection indicated complete gut clearance. Because TaqMan probes are taxon specific, the results presented demonstrate that this technique can provide a means of rapid and unambiguous detection of predation by teleosts on fish eggs and larvae.

Reliability of qPCR for quantitative gut content estimation in the circumglobally abundant pelagic tunicate Dolioletta gegenbauri (Tunicata, Thaliacea)

“…Although initially we hypothesized that the digestion of prey DNA would be less than that of algal pigments because of the greater stability of DNA compared to photosynthetic pigments (chlorophyll a), these studies indicated that, at least in copepods, prey DNA digestion was significant. Similar results have been reported in other studies with copepods (Durbin et al, 2012), other marine crustaceans (Tobe et al, 2010) and a wide variety of other marine and terrestrial predators (Bowen and Iverson, 2013;Hunter et al, 2012;Weber and Lundgren, 2009). However, it is difficult to predict based on first principles whether prey digestion will be a significant impediment to the quantification for specific predators.…”

Identification of marine fish egg predators using molecular probes

“…Dependent on development stage and temperature, the TaqMan probe has a T90 (the length of time after ingestion that target DNA can be detected in > 90% of the predators tested) of between 4 and 5 h (Albaina et al 2010, Hunter et al 2012 Unfortunately, we are not aware of any studies which provide data on how rapidly this can occur so the 2 h limit we used, whilst somewhat arbitrary, seemed a reasonable compromise between allowing full sorting and sampling of the catch and this risk. For sprat and herring, more than 85% of individuals tested positive, regardless of the time of day of sampling, supporting high detection efficiency for the assay and suggesting that degradation of target DNA was not a major problem.…”

“…It is usually recommended to use tows that are as short as possible to minimise this problem. However, the molecular approach to stomach content analysis may be less sensitive to this problem, since the TaqMan probe has been shown to be capable of detecting residual prey DNA, even when there are no remaining visible signs (Hunter et al 2012). The opposite problem, that other organisms might consume regurgitated material whilst in the trawl or plankton nets, leading to over-estimation of feeding rates, cannot be dismissed entirely, although for the trawl it is likely that regurgitated material would be rapidly flushed out of the net during towing because of the mesh size of the cod-end.…”

“…Given the extreme sensitivity of these methods, stringent efforts are also needed to control cross-contamination during field sampling (Symondson 2002, Passmore et al 2006. In previous papers we described the development of a TaqMan probe for plaice DNA, demonstrated its specificity and described the effects of digestion by crustacean and teleost predators on detection efficiency (Albaina et al 2010, Hunter et al 2012). Here we describe the first application of this method to study predation of plaice eggs (and larvae) in the field.…”

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

“…Greenstone et al, 2013). To estimate the digestion time effects we considered previously published results (Albaina et al, 2010;Hunter et al, 2012), combined with an experiment for macrozooplankton performed onboard during the campaign. An extra MIK haul was carried out (46°N, 2.42°W; Fig.…”