DNA and RNA zooplankton metabarcoding to assess the efficacy of different oil spill clean-up techniques in a boreal lake

Emerging tools, namely metabarcoding, has promise for high-throughput and benchmarkable biomonitoring of freshwater zooplankton communities. Additionally, regulators require further information to select best practices for remediating freshwater ecosystems after oil spills. DNA and RNA metabarcoding, or present and active zooplankton, respectively, was applied to compare with traditional morphological identification of freshwater zooplankton in experimental boreal shoreline enclosures. DNA and RNA metabarcoding was also applied in the context of assessing response of the zooplankton community exposed to simulated spills of diluted bitumen (dilbit), with experimental remediation practices of enhanced monitored natural recovery and shoreline cleaner application. Zooplankton samples were collected via pump on day -3 and 11 and 38 days after the simulated dilbit spill. The zooplankton samples were co-extracted for DNA and RNA and were PCR amplified targeting the mitochondrial Cytochrome c Oxidase subunit I gene (CO1) region, with amplicon sequencing following. This dataset includes the demultiplexed sequencing output, the feature table with genus-level taxonomic annotation, and the sample metadata used for hypothesis testing. This dataset contains data from wetland habitat enclosures. Note that a similar study was conducted for rock habitat enclosures, with different analyses and interpretation being conducted on the data (dataset available at https://doi.org/10.20383/102.0332).