Comparison of an extracellular v. total DNA extraction approach for environmental DNA-based monitoring of sediment biota

Monitoring sediment biota is an essential step for the quality assessment of aquatic ecosystems. Environmental DNA-based approaches for biomonitoring are increasing in popularity; yet, commercial kits and protocols for extracting total DNA from sediments remain expensive and time-consuming. Furthermore, they can accommodate only small amounts of sediments, potentially preventing an adequate representation of local biodiversity, especially for macro-organisms. Here, we assessed the reliability of a cost- and time-effective extracellular DNA extraction approach able to account for large volumes of starting material, for characterising bacterial, eukaryote and metazoan communities in three sedimentary environments. DNA concentrations extracted with the extracellular approach were at least similar to those obtained with the commercial kit. Local diversity estimates were not biased towards any particular extraction method, although specific responses were observed depending of the sediment type. Community composition and beta-diversity patterns were moderately affected by the extraction approach and the initial amount of starting material; differences being more important for macro- than microorganisms. Thus, the extracellular DNA approach appears as robust and efficient as those based on the commercially available kit for biomonitoring sedimentary communities. Its low cost and fast processing time make it a promising alternative for large-scale ecological assessments of aquatic environments.