Affiliation:
1. Institut Des Sciences de la Mer Université du Québec à Rimouski Rimouski Québec Canada
2. Laboratory of Genomics Maurice Lamontagne Institute, Fisheries and Oceans Canada Mont‐Joli Québec Canada
3. Département de Biologie, Chimie et Géographie Université du Québec à Rimouski Rimouski Québec Canada
Abstract
AbstractNatural matrices affect environmental DNA (eDNA) detections. Effects of matrix‐eluted compounds on the polymerase chain reaction (PCR) step have been the focus of most inhibition studies. Factors affecting eDNA detections in a typical laboratory workflow, i.e., DNA extraction and PCR steps, are mostly unknown. Here, we assessed the effect of four metal ions (Ca2+, Fe3+, Mn2+, Cu2+) present in marine sediments on DNA detectability for both the extraction and the PCR detection steps. A single metal ion and exogenous DNA were added to marine sediments treated chemically to remove inhibitors. Our results showed that natural concentrations of calcium, iron, and manganese ions in surface marine sediments can impede completely DNA detections. Alternatively, copper ions added to the matrix increased DNA detectability by 7.7%. We also observed bimodal inhibitory effects of calcium and iron ions on DNA detectability, suggesting that the extraction and the PCR steps are both affected. Our findings highlight new limitations of eDNA detections. Avenues to optimize eDNA detection protocols applicable to multiple matrices are discussed.
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