Authors: Alexander Van Nynatten, Nathan Lovejoy, Nicholas E. Mandrak
Monitoring the impact of industrial applications on aquatic species is a critical step in ensuring the conservation of resources, including Indigenous, commercial, and recreational fisheries. DNA metabarcoding can be used to sequence samples containing DNA from multiple individuals. Such samples may include ichthyoplankton (bulk samples of larval fishes and eggs) or water containing environmental DNA (eDNA). We used DNA metabarcoding to estimate the presence and abundance of species in bulk samples of early-life-stage fishes collected in Lake Huron. We measured and hemisected each larval fish and extracted DNA from the anterior half separately. Posterior halves were combined with all other individuals from the same sampling location, homogenized, and extracted as a bulk sample. We also filtered and extracted DNA from the ethanol that larval fishes were stored in as a non-destructive approach and a proxy for eDNA. We compared the accuracy, efficiency, and cost of processing these samples using each approach and to other conventional approaches used to identify larval fishes. We found that metabarcoding bulk samples is by far the most efficient and cost-effective approach for processing large amounts of ichthyoplankton but does result in decreased accuracy per sample. This is especially problematic when samples contain larval fishes from species that vary in size and extent of decomposition, as found in entrained individuals at Bruce Nuclear Power Plant (BPNP). To overcome these challenges and the limitations to sampling entrained individuals, we are examining the potential of eDNA to replace conventional and metabarcoding larval sampling in future entrainment monitoring programs of the BPNP condenser cooling water system.
