A DNA metabarcoding approach for studying reindeer diet – effect of the DNA extraction method
|Theme||1. Environmental protection|
|Session Name||1.11 Reindeer & caribou in the Arctic system: Interactions between environmental, social and biophysical processes|
|Author(s)||Stefaniya Kamenova (CEES, University of Oslo, Norway), Galina Gusarova (Tromsø Museum, University of Tromsø, Norway)|
DNA metabarcoding diet analysis is increasingly used in ecological studies as it is a time-efficient method with the capacity to deliver taxonomically precise assessment of the species consumed by an organism. However, DNA metabarcoding could be also subject to methodological biases, especially during the first steps of DNA handling and extraction. Typically, environmental DNA from dietary samples is extracted using standard commercial kits optimized to yield high quality DNA, while removing PCR inhibitors. However, commercial kits rely on a relatively low amount of starting material, which may be insufficient for tackling the highly diverse composition of diet in many species. Recently, new protocols for the extraction of DNA from large volumes of starting material have been proposed. These protocols consist in desorbing the extracellular DNA bound to particles using saturated phosphate buffer. In this study, we investigate the effects of five DNA extraction protocols and different amounts of starting material on reindeer diet composition. For this, we used a DNA metabarcoding approach and rumen samples collected from free ranging Svalbard reindeers. Extracted DNA was amplified using a the g/h plant primer set amplifying the P6 loop on the trnL intron and a set of general Eukaryote 18S primers. This is the first time that the effect of DNA extraction method on reindeer diet composition has been investigated, and we expect that our results will fulfill important methodological gap in DNA metabarcoding diet studies, allowing for the further recommendation of optimized DNA extraction methods from reindeer rumen samples.
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