A two-step multiplex PCR system identifying Central European fish species

• Main Author: Johannes Oehm
• Format: Article
• Language: English
• Published: Frontiers Media S.A. 2015-12-01
• Series: Frontiers in Marine Science
• Subjects: Europe; molecular identification; freshwater fishes; trophic ecology; multiplex PCR; Piscivory
• Online Access: http://journal.frontiersin.org/Journal/10.3389/conf.FMARS.2015.03.00218/full

The morphological identification of fish samples can be difficult, for example, when dealing with eggs, larvae, tissue samples, or dietary samples of piscivores. Hard parts such as otoliths, chewing pads, pharyngeal bones or scales can enable morphological identification if present. However, species-specific identification is often not possible, especially in species-rich groups like the cyprinids. Here, we present a two-step multiplex PCR system, tailored for rapid, sensitive, and specific molecular detection of Central European fish species. It is composed of six assays, covers 79 fish and lamprey species, and enables the identification of 31 species, six genera, two families, two orders, and two fish family clusters. This novel approach is tailored for samples with bad DNA quality and has been successfully applied to identify fish prey in feces of the Eurasian otter, the Common Kingfisher, as well as feces and regurgitated pellets of cormorants. More than 4,000 dietary samples of the latter were collected within a two-year field study in the Alpine foreland. These samples have already been analyzed cost-effectively with the presented approach thus generating a detailed picture of cormorant diet in relation to fish phenology. The high sensitivity and specificity of the multiplex PCR system makes it also suitable for applications outside the field of trophic ecology such as the identification of juvenile fish, environmental monitoring, or environmental DNA studies.