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|Title:||Amplification facilitators and multiplex PCR: Tools to overcome PCR-inhibition in DNA-gut-content analysis of soil-living invertebrates|
|Citation:||Soil Biology & Biochemistry, 2006; 38(7):1872-1879|
|Publisher:||Pergamon - Elsevier Science|
|School/Discipline:||School of Agriculture, Food and Wine : Agricultural and Animal Science|
|Anita Juen and Michael Traugott|
|Abstract:||Polymerase chain reaction (PCR) can be used to detect prey within the gut contents of predators and allows specific trophic interactions to be studied among soil-dwelling invertebrates which cannot be examined by other approaches. PCR-inhibitory substances, however, are commonly found in DNA prepared from soil organisms or from biological material contaminated with soil. This can lead to false-negative results and the risk of not detecting trophic connections or of underestimating predation rates in field studies. In the present study, we developed mitochondrial DNA markers to detect Amphimallon solstitiale (Coleoptera: Scarabaeidae) in the gut contents of invertebrate predators. Larvae of A. solstitiale can cause serious damage in grasslands, field crops, and forests by feeding on roots. Adequate methodologies to study predation on these pests are lacking, and their invertebrate predator guild is, therefore, barely known. To test the new molecular markers for prey detection, larvae and eggs of A. solstitiale were fed to Poecilus versicolor larvae (Coleoptera: Carabidae), which are abundant below-ground predators in grassland ecosystems. Unfortunately, even when specific DNA extraction and purification methods were used, DNA extracts from predators were of poor quality and not amplifiable by PCR; this yielded false-negative results and a dramatically lower prey-detection rate. We overcame PCR-inhibition by applying 1.28 μg μl−1 bovine serum albumin to the PCR reaction mix. This enabled us to detect A. solstitiale DNA within fed carabid larvae up to 48 and 40 h post-feeding for 127 and 463 bp sized DNA fragments, respectively. When single A. solstitiale eggs were consumed by the carabid larvae, predation could be verified in 100% of the predators within the first 8 h of digestion; some carabid larvae even tested positive 32 h after feeding. Moreover, by multiplexing primers targeting both prey and predator, we were able to simultaneously screen for prey consumption and check for co-purified PCR inhibitors. Sensitivity in prey detection was not reduced compared to singleplex PCR. We recommend the multiplex approach because it considerably reduces time and costs compared to singleplex assays. We also show that multiplex PCR not only detects specific prey, but also can identify the predator itself. This allows the identification of taxa which are difficult or not identifiable based on morphological characters, such as soil-dwelling predatory beetle larvae.|
|Keywords:||Soil food-web; Predator–prey interactions; Soil pests; Multiplex PCR; PCR-inhibition; White grubs|
|Appears in Collections:||Agriculture, Food and Wine publications|
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