DNA barcoding vs morphology: Assessing different methods for invertebrate identification and determination of industrial effluent impacts

In Canada, all active metal and diamond mines and pulp and paper mills discharging effluent are required to monitor potential effluent related impacts on benthic invertebrate communities through regulated Environmental Effects Monitoring (EEM) programs. Currently, EEMs include sampling benthic invertebrates and identifying them morphologically to the family level. We sought to directly compare traditional taxonomic identification methods with DNA barcoding of each specimen as they apply to EEM studies. Five industry sites were sampled, each with a sample area receiving effluent and a reference area not receiving effluent for a total of 67 benthic invertebrate sample stations across all five sites. Specimens were identified morphologically and with DNA barcoding and statistical differences of four endpoints between paired freshwater areas were assessed. Additionally, OTU (operational taxonomic unit) level analyses were compared to the family-level results to determine if the OTU level could be more informative of differences in community composition between effluent receiving environments and their reference areas. Family-level morphology vs. family-level barcode-based identifications delivered the same conclusions for paired-area comparisons over 70% of the time. DNA barcoding results at the OTU level differed when determining impacts between paired areas 19–30% of the time across all four endpoints compared to family-level barcoding and family-level morphology, respectively. Overall, DNA barcoding could be used in EEM studies as it demonstrated similar results as morphological identifications at the family level and provides greater taxonomic resolution and sensitivity for detecting paired area differences.