Molecular detection of algal prey in copepod guts and fecal pellets

Abstract

The ability to obtain information about feeding selectivity and rates in situ for key organisms such as copepods and other zooplankton is vital for understanding the mechanisms structuring marine ecosystems. Copepods feed on a wide range of prey, and there are presently no methods available to directly quantify zooplankton feeding on all different prey types in situ. Therefore, the development of a new nonintrusive direct method is necessary to gain a better understanding of the trophic interactions in aquatic ecosystems. Molecular methods based on the polymerase chain reaction have recently become an important tool to study predation by arthropods, particularly insects. Here we present the first results of successful molecular detection of a specific prey consumed by calanoid copepods from gut and fecal material. Using the calanoid copepod species Calanus finmarchicus consuming the haptophyte alga Emiliania huxleyi as a model system, 18S ribosomal DNA originating from E. huxleyi was unambiguously detected in whole DNA extracts from copepods and from their fecal pellets. The results also suggest that prey DNA may be quantified for determination of prey-specific zooplankton feeding rates. However, significantly more research under controlled laboratory and field conditions will be required to achieve these objectives. We hypothesize that molecular methods will become an important tool with the potential to quantify undisturbed trophic interactions between individual predators and all their prey in the complex natural plankton.

Identification of marine fish egg predators using molecular probes

“…In order to improve the chances of successful detection it is usual to target relatively short nucleotide sequences, since prey DNA be comes fragmented during digestion in the predator gut. Examples of successful applications include Rosel & Kocher (2002), who described a polymerase-chain reaction (PCR) assay to detect cod larvae in mackerel Scomber scomber stomachs, and Nejstgaard et al (2003) and Vestheim et al (2005) who used similar assays for identifying prey in copepod faecal pellets. Applications using cloning or pyro-sequencing to identify multiple prey taxa in clude studies on the diets of seals (Deagle et al 2009) and lobster larvae (Suzuki et al 2008).…”

Feeding selectivity of bivalve larvae on natural plankton assemblages in the Western English Channel

“…As part of this study, we performed molecular analysis of gut content of bivalve larvae following the bottle incubations, and where there were sufficient larvae, on the gut content of larvae taken directly from the field. Recent studies have used DNA-based techniques for dietary analysis including PCR amplification of 18S genes from the gut content of zooplankton (Nejstgaard et al 2003;Troedsson et al 2007;Nejstgaard et al 2008;Troedsson et al 2009;Durbin et al 2012), including meroplanktonic larvae (Maloy et al 2009;Riemann et al 2010;Fileman et al 2014). If the gut content of the predator can first be removed to reduce coamplification of host DNA, then general or universal primers designed to conserved regions (Holland et al 1991) targeting the 18S gene can be used.…”

“…Each monthly data point is based on the mean of all samples taken in that month over the whole 22-year time series barcoding and to experimentally determine their feeding selectivity in the natural plankton assemblage over a seasonal cycle. Due to the methodology problems with studying feeding in zooplankton (Bamstedt et al 2000;Nejstgaard et al 2001Nejstgaard et al , 2003, we used molecular methods alongside traditional bottle incubations to increase the resolution of identification of ingested prey and compare feeding in the field with that under experimental conditions.…”

Molecular identification of the invasive cladoceranCercopagis pengoi(Cladocera: Onychopoda) in stomachs of predators

“…When dietary information is particularly difficult to obtain by other means, DNA-based methods have been successfully used to identify prey species via species-or groupspecific polymerase chain reaction (PCR) assays (Symondson, 2002;Jarman et al, 2004;Harper et al, 2005); the develop-ment and application of such methods for studying trophic interactions in aquatic ecosystems has been limited, however (but see Nejstgaard et al, 2003). A molecular method for identification of C. pengoi in predator stomach content is proposed here.…”