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Type: Journal article
Title: Earthworm primers for DNA-based gut content analysis and their cross-reactivity in a multi-species system
Author: Admassu, Belayneh
Juen, Anita
Schmid, Michael
Citation: Soil Biology & Biochemistry, 2006; 38 (6):1308-1315
Publisher: Pergamon-Elsevier Science
Issue Date: 2006
ISSN: 0038-0717
School/Discipline: School of Agriculture, Food and Wine : Agricultural and Animal Science
Statement of
Belayneh Admassu, Anita Juen and Michael Traugott
Abstract: Specific primers can be used in polymerase chain reactions (PCR) to amplify prey DNA from the gut content of generalist predators at high specificity and sensitivity. A prerequisite for applying this approach to field studies, however, is to confirm that primers are actually targeting specific prey species or prey groups and do not produce false positive results by amplifying DNA either from predator species or from the wide range of potential alternative prey found under natural conditions. Here, we report on a new group-specific primer pair for earthworms designed from cytochrome oxidase c subunit 1 (COI) sequences of 11 earthworm species found in Central Europe that can be used to detect consumption of earthworms by invertebrate predators. Besides inter-specific also considerable intra-specific variation was found for COI sequences among most of the earthworm species. We, therefore, combined a universal forward primer with an earthworm-specific reverse primer which amplified a 523 bp product from all 11 species tested. Earthworm DNA amplification was also successful in the presence of excess DNA of a predator species. The primer pair was tested against 82 non-target invertebrate species commonly found in the same habitats, including potential prey for generalist predators and predators themselves. The earthworm primer was highly specific: only one of the non-target species showed a product of similar length as the earthworms, whereas PCR with 12 non-target species produced amplicons whose length differed from that of earthworms. We conclude that the new primer will be a useful tool to investigate the role earthworms play as a food resource in soil food-webs. Moreover, we suggest that future studies utilizing DNA-based approaches for prey detection should select non-target species for cross-reactivity tests according to their abundance and importance rather than choosing representatives of taxonomic units; this will help validate the results achieved using species- or group-specific primers and guarantee their meaningful ecological interpretation.
Keywords: Soil food-web; Lumbricidae; Soil biodiversity; Diagnostic PCR; Specificity test
RMID: 0020063694
DOI: 10.1016/j.soilbio.2005.08.019
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Appears in Collections:Agriculture, Food and Wine publications

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