Humic Acids and EDTA Added to Marine Sediments Improve eDNA Detectability

ABSTRACT

Sediments are complex and challenging matrices for DNA detections. Humic acids, a major component of dissolved organic matter in freshwater and marine sedimentary environments, can inhibit environmental DNA (eDNA) amplification. Past studies have assessed the effect of these compounds on the PCR step, however this does not reflect a typical eDNA sample workflow which typically includes an extraction step. In this study, we investigated the effect of increasing concentrations of humic acid sodium salts on DNA detectability by adding exogenous DNA to a chemically treated sediment matrix prior to DNA extraction. We showed that DNA detectability increases by 16.8% with the maximal humic acid sodium salts concentration added, that is, 10.00 mg·g ⁻¹ of sediment. Additional tests suggested that humic acids chelate inhibitors still present in the chemically treated sediments. Adding the chelating compound ethylenediaminetetraacetic acid (EDTA) prior to the DNA lysis also improved detectability. At an EDTA concentration of 20.0 mg·g ⁻¹ of sediment, DNA detectability improved by 11.1%. Together, our findings reveal that the role of humic acids in environmental matrices is opposite to previous expectations and provide avenues for optimization of eDNA detection protocols applicable to multiple environmental matrices.