PCR-DHPLC assay for the identification of predator-prey interactions
2012 (English)In: Journal of Plankton Research, ISSN 0142-7873, E-ISSN 1464-3774, Vol. 34, no 4, 277-285 p.Article in journal (Refereed) Published
Denaturing high-performance liquid chromatography (DHPLC) is a relatively new method for separating amplicons in a mixture, and was recently developed for parasite detection in the blue crab Callinectes sapidus. That assay used a peptide nucleic acid (PNA) PCR hybridization blocking probe (PNAPCRDHPLC) to decrease the generic PCR bias of dominant templates (the host) in the mixture prior to separation on the DHPLC column, thus enhancing the less abundant parasite DNA. The same assay and rational can be used to investigate predatorprey interactions. However, in ecosystem studies with many predatorprey relationships, development of specific PNA-blocking probes for each predator would be too laborious. Here, we have developed a PCRDHPLC assay excluding the dominant predator amplicons in a first DHPLC run, followed by re-amplification of the non-predator retention volumes and further separation and characterization in a second DHPLC run. This assay generated data on the specific trophic interactions between the calanoid copepod Limnocalanus macrurus and its prey from a seasonal sampling programme. The assay provides an efficient way for an unbiased screening of predatorprey relationships, and although developed for L. macrurus in this study, the approach has wide applicability for any predatorprey interaction.
Place, publisher, year, edition, pages
Oxford: Oxford University Press, 2012. Vol. 34, no 4, 277-285 p.
trophic interaction, biodiversity, feeding, zooplankton, 18S rDNA
Oceanography, Hydrology, Water Resources Biological Sciences
IdentifiersURN: urn:nbn:se:umu:diva-53925DOI: 10.1093/plankt/fbr110ISI: 000301360800002OAI: oai:DiVA.org:umu-53925DiVA: diva2:515271