DNA metabarcoding diet analysis in reindeer is quantitative and integrates feeding over several weeks

Authors
Affiliations
Stefaniya Kamenova

Centre for Ecological and Evolutionary Synthesis, University of Oslo

Departments of Ecology and Natural Resource Management, Norwegian University of Life Sciences

National Museum of Natural History, Bulgarian Academy of Sciences

Pernille Meyer

Centre for Ecological and Evolutionary Synthesis, University of Oslo

Anne Krag Brysting

Centre for Ecological and Evolutionary Synthesis, University of Oslo

Leo Rescia

Department of Arctic and Marine Biology, The Arctic University of Norway

Lars P. Folkow

Department of Arctic and Marine Biology, The Arctic University of Norway

Galina Gusarova

Centre for Ecological and Evolutionary Synthesis, University of Oslo

Department of Arctic and Marine Biology, The Arctic University of Norway

The Arctic University Museum of Norway, The Arctic University of Norway

Department of Botany, St Petersburg State University

Eric Coissac

Laboratoire d’Ecologie Alpine, CNRS, Université Grenoble Alpes

Abstract

Dietary DNA metabarcoding is an established method, especially useful for resolving the diverse diets of large mammalian herbivores (LMH). However, despite longstanding research interest on the topic, we still lack unequivocal evidence on the potential of DNA metabarcoding to reflect proportions of ingested dietary plants in LMH. One major aspect to consider is the time window during which ingested diet remains detectable in faecal samples. This parameter is currently unknown for LMH, thus potentially hindering the scope of ecological conclusions. Another unknown factor is quantitative performance, i.e. the extent to which the amount of ingested biomass can be assessed based on sequence reads abundances. We assessed DNA metabarcoding, quantitative performance and DNA half-life detectability for plants with different digestibilities in a controlled feeding experiment with three female Eurasian tundra reindeer (Rangifer tarandus tarandus). Reindeer were fed birch twigs (Betula pubescens) and increasing biomass of lichen (mainly Cladonia stellaris). Relative reads abundance positively correlated with ingested lichen biomass, suggesting potential for deriving dietary proportions in free-ranging reindeer on natural pasture. Dietary DNA was consistently detected within a few hours upon ingestion, with a mean half-life detectability of 25 and 16 hours for birch and lichen, respectively. However, dietary DNA remained detectable in faeces for at least 26 days post-feeding, indicating that a single faecal sample can provide an unsuspectedly integrative estimate of diet in ruminants. Together, our findings provide novel empirical validation of DNA metabarcoding as a tool for diet analysis in LMH.

Github project

Every script and processed data are available from the RENIN-Project/Feeding-Experiment github project.

Preprocessing of the raw data

The OBITools commands used to preprocess the data from the raw FASTQ files are described in the following bash script.

Filtering of the data

  • For the Spermatophyta Sper01 marker ((PDF)[SPER01_Filtering.pdf])
  • For the Eukaryota Euka02 marker ((PDF)[EUKA02_Filtering.pdf])

Ecological analysis

Every code producing the presented results including the production of the figures is available here, and can be downladed as a PDF.

Processed data sets and results

Each processed dataset is composed of three coma separated values files (.csv files).