Can high-throughput sequencing detect macroinvertebrate diversity for routine monitoring of an urban river?

Macroinvertebrate families identified through morphological examination have traditionally been used in routine assessment of freshwater ecosystems. However, high throughput DNA sequencing (HTS) promises to improve routine assessment by providing rapid and cost-effective identification of macroinvertebrate species. In freshwater ecosystems in urbanised areas where family diversity is often low, new insights into ecosystem condition and impacting factors are likely through species-level assessments. Here we compare morphological identification to HTS based identification of macroinvertebrate families by considering 12 sites in an urban river system. Some taxa detected morphologically were not detected by HTS and vice versa. However, this had only a small impact on computed family-level metrics of ecological condition. We detected multiple species using HTS in the Chironomidae, Coenagrionidae, Hydrobiidae, Leptoceridae, Ceratopogonidae, Corixidae, Veliidae, Oligochaeta and Acarina. The highest species diversity was found in the Chironomidae, and for many of these species we had prior knowledge of their likely pollution sensitivity. In the Chironomidae, we showed that species level data was congruent with expectations based on measured levels of pollutants at sites and other family level metrics. Importantly, we also identified many species in the same family that differed in their distribution and likely pollution sensitivity in this urban river system. Therefore, HTS provided similar levels of information to traditional methods at the family level, but also generated new information for more accurate condition monitoring at the species level.