Mr John Kronenberger1,2,3, Dr Taylor Wilcox3, Prof Mike Schwartz3
1James Cook University, Townsville, Australia, 2Centre for Tropical Water and Aquatic Ecosystem Research (TropWATER), Townsville, Australia, 3National Genomics Center for Wildlife and Fish Conservation, Missoula, United States
Biography:
John Kronenberger has specialized in eDNA research for over eight years and is passionate about helping the field maximize its potential. He has developed dozens of targeted assays and innovative methods for assay specificity prediction, high-throughput qPCR, and metabarcoding of novel environmental substrates. Formerly of the National Genomics Center for Wildlife and Fish Conservation—a premier eDNA institution in the United States—John has recently moved to Australia to pursue his PhD at James Cook University. His thesis focuses on sequencing multiple eDNA and eRNA barcodes in parallel to expand inference beyond species detection.
Abstract:
Environmental DNA has revolutionized invasive species surveillance, but the scale of potential invaders and invaded areas remains monumental. Tackling this problem requires technology that is both highly sensitive and cost-effective when many species are of interest—the best of both worlds between targeted assays (highly sensitive) and metabarcoding (cost-effective). Recently, high-throughput qPCR (HT-qPCR) has emerged to meet this demand via thousands of nanoliter-scale reactions that simultaneously screen for dozens of species with high sensitivity. In this talk, I will provide an overview of HT-qPCR for eDNA and discuss SmartScreen-AIS: a 46-assay chip that we developed to surveil for invasive species throughout the continental United States. Performance was rigorously validated in the laboratory and demonstrated using 200 eDNA samples from three military installations. Relative to conventional qPCR, we noted significantly higher sensitivity and at least 75% cost savings. Running all 46 assays required only 12 µL of eDNA extract. Subsets of the assay panel can be chosen to match project goals and run on smaller 34-, 22- and 10-assay chip formats. This work suggests that HT-qPCR is capable of meeting the demands of invasive species surveillance at national scales.