The MBON eDNA teams developed a set of steps and procedures to collect and process samples. USF, Stanford and MBARI researchers made significant process towards optimizing a standard operating procedure (SOP) for eDNA sample collection and processing. This required several controlled experiments testing different filter types and DNA extraction techniques.
The teams have now identified standard protocols that are acceptable for processing eDNA samples for full trophic level analysis and a subset of samples will now be processed from “microbes-to-whales”. Each team will perform amplificiation and sequencing for specific primers, and then data will be processed through a common pipeline and statistically analyzed.
Other notable methodological progress includes:
- Establishment and effective utilization of a common bioinformatics pipeline for analyzing all genetic markers.
- MB groups are developing quantitative PCR (QPCR) assays to detect select organisms including humpback whales, common murre, and rockfish.
- Development of sample selection priorities for all trophic levels to be compared in FK and MB.
- “Genetic and Manual Survey Methods Yield Different and Complementary Views of an Ecosystem” Ryan P. Kelly, Collin J. Closek, James L. O’Donnell, James E. Kralj, Andrew O. Shelton, and Jameal F. Samhouri (first two authors are part of the Sanctuaries MBON grant), an MBON manuscript submitted to Frontiers in Marine Science has been accepted with minor revisions.