Effectiveness of eDNA for monitoring riverine macroinvertebrates

Environmental DNA (eDNA) is a technique increasingly used for monitoring organisms in the natural environment including riverine macroinvertebrates. However, the effectiveness of eDNA for monitoring riverine macroinvertebrates compared with the more traditional method of sampling the organisms directly and identifying them via morphological analysis, has not been well established. Furthermore, the ability of the various gene markers and PCR primer sets to detect the full range of riverine invertebrate taxa has not been quantified. Here we conducted a meta -analysis of the available literature, to assess the effectiveness of eDNA sampling for detecting riverine macroinvertebrates compared with sampling for the organisms directly and applying morphological analysis. We found, on average, eDNA sampling, irrespective of the gene marker used, detected fewer riverine invertebrates than morphological sampling. The most effective PCR primer set for identifying taxa was mlCOIintF/jgHCO2198, (mlCOIintF - forward primer, jgHCO2198, - reverse primer). Regardless of the gene marker or primer sets used, however, many taxa were not detected by eDNA metabarcoding that were detected by sampling directly for these invertebrates, including over 100 members of Arthropoda. eDNA sampling failed to detect any species belonging to Nematoda, Platyhelminthes, Cnidaria or Nematomorpha and these markers applied for eDNA sampling in terrestrial systems also do not detect members of Nematoda. In addition to these issues, uncertainties relating to false positives from upstream DNA sources, the stability of DNA from different species, differences in the propensity for DNA release into the environment for different organisms, and lack of available sequence information for numerous taxa illustrates the use of eDNA is not yet applicable as a robust stand-alone method for the monitoring of riverine invertebrates. As a primary consideration, further methodological developments are needed to ensure eDNA captures some of the key freshwater taxa, notably taxa belonging to the phyla Arthropoda, Nematoda, Platyhelminthes, Cnidaria and Nematomorpha.