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Quantification via eDNA metabarcoding

Researchers from the University of Notre Dame (Indiana, USA) and the Central Michigan University (Michigan, USA) published a study on the potential of the eDNA metabarcoding approach to accurately measure species diversity and abundance in aquatic assemblages.

In June 2015, Evans et al. published a paper entitled  “Quantification of mesocosm fish and amphibian species diversity via eDNA metabarcoding”. This study aimed to determine if eDNA sampling and metabarcoding analysis can be used to accurately measure species diversity in aquatic mesocosms differing in species abundance and density.

Summary: Freshwater fauna are particularly sensitive to environmental change and disturbance. Management agencies frequently use fish and amphibian biodiversity as indicators of ecosystem health and a way to prioritize and assess management strategies. Traditional aquatic bioassessment that relies on capture of organisms via nets, traps, and electrofishing gear typically has low detection probabilities for rare species and can injure individuals of protected species. In this paper, the Authors manipulated the density and relative abundance of eight fish and one amphibian species in replicated 206 liter mesocosms. Environmental DNA was filtered from water samples, and six mitochondrial gene fragments were sequenced using Next Generation Sequencing technologies to measure species diversity in each mesocosm. Metabarcoding detected all nine species in all treatment replicates. Additionally, a modest but positive relationship was found between species abundance and sequencing read abundance. Such results illustrate the potential for eDNA sampling and metabarcoding approaches to improve quantification of aquatic species diversity in natural environments. eDNA metabarcoding could then be used in the future as an index of macrofaunal species abundance.

Reference: Evans, N.T., Olds, B.P., Turner, C.R., Renshaw, M.A., Li, Y., Jerde, C.L., Mahon, A.R., Pfrender, M.E., Lamberti, G.A., Lodge, D.M. 2015. Quantification of mesocosm fish and amphibian species diversity via eDNA metabarcodingMolecular Ecology Resources. doi: 10.1111/1755-0998.12433.