Species-level biodiversity assessment using marine environmental DNA metabarcoding requires protocol optimization and standardization
MetadataShow full item record
Funding and Sponsorship
DNA extraction from environmental samples (environmental DNA; eDNA) for metabarcoding-based biodiversity studies is gaining popularity as a noninvasive, time-efficient, and cost-effective monitoring tool. The potential benefits are promising for marine conservation, as the marine biome is frequently under-surveyed due to its inaccessibility and the consequent high costs involved. With increasing numbers of eDNA-related publications have come a wide array of capture and extraction methods. Without visual species confirmation, inconsistent use of laboratory protocols hinders comparability between studies because the efficiency of target DNA isolation may vary. We determined an optimal protocol (capture and extraction) for marine eDNA research based on total DNA yield measurements by comparing commonly employed methods of seawater filtering and DNA isolation. We compared metabarcoding results of both targeted (small taxonomic group with species-level assignment) and universal (broad taxonomic group with genus/family-level assignment) approaches obtained from replicates treated with the optimal and a low-performance capture and extraction protocol to determine the impact of protocol choice and DNA yield on biodiversity detection. Filtration through cellulose-nitrate membranes and extraction with Qiagen's DNeasy Blood & Tissue Kit outperformed other combinations of capture and extraction methods, showing a ninefold improvement in DNA yield over the poorest performing methods. Use of optimized protocols resulted in a significant increase in OTU and species richness for targeted metabarcoding assays. However, changing protocols made little difference to the OTU and taxon richness obtained using universal metabarcoding assays. Our results demonstrate an increased risk of false-negative species detection for targeted eDNA approaches when protocols with poor DNA isolation efficacy are employed. Appropriate optimization is therefore essential for eDNA monitoring to remain a powerful, efficient, and relatively cheap method for biodiversity assessments. For seawater, we advocate filtration through cellulose-nitrate membranes and extraction with Qiagen's DNeasy Blood & Tissue Kit or phenol-chloroform-isoamyl for successful implementation of eDNA multi-marker metabarcoding surveys.
Showing items related by title, author, creator and subject.
Environmental DNA (eDNA) metabarcoding reveals strong discrimination among diverse marine habitats connected by water movementJeunen, G.; Knapp, M.; Spencer, H.; Lamare, M.; Taylor, H.; Stat, M.; Bunce, Michael; Gemmell, N. (2018)While in recent years environmental DNA (eDNA) metabarcoding surveys have shown great promise as an alternative monitoring method, the integration into existing marine monitoring programs may be confounded by the dispersal ...
eDNA metabarcoding survey reveals fine-scale coral reef community variation across a remote, tropical island ecosystemWest, K.M.; Stat, Michael ; Harvey, Euan ; Skepper, C.L.; Di Battista, Joey ; Richards, Zoe ; Travers, M.J.; Newman, Stephen ; Bunce, Michael (2020)Environmental DNA (eDNA) metabarcoding, a technique for retrieving multispecies DNA from environmental samples, can detect a diverse array of marine species from filtered seawater samples. There is a growing potential to ...
Challenges for assessing vertebrate diversity in turbid Saharan water-bodies using environmental DNAEgeter, B.; Peixoto, S.; Brito, J.; Jarman, Simon; Puppo, P.; Velo-Antón, G. (2018)The Sahara desert is the largest warm desert in the world and a poorly explored area. Small water-bodies occur across the desert and are crucial habitats for vertebrate biodiversity. Environmental DNA (eDNA) is a powerful ...