Assessment of Preservation and Extraction Methods for Environmental <scp>DNA</scp> in Sediments

ABSTRACT Sediments host diverse benthic organisms, but natural and anthropogenic disturbances threaten their biodiversity and the ecosystem services they provide. Accurate sediment biodiversity assessments are pivotal for biomonitoring and conservation. Environmental DNA (eDNA) allows studies of multiple taxonomic groups to be performed at broad spatial scales. However, standardized operational protocols are needed from DNA collection to data analysis to ensure data reliability and replicability. Here, we assessed the effects of eDNA preservation methods on the ecological results obtained for bacterial, fungal, microeukaryotic, and metazoan communities in marine and freshwater ecosystems. We used preservation methods such as freezing, room temperature (RT), silicagel, and Longmire buffer for 1 and 3 weeks and compared eDNA metabarcoding results to those obtained when eDNA was extracted on the day of sampling (control). For each strategy, we extracted DNA using two protocols targeting extracellular (Phosphate) or both extracellular and intracellular DNA (PowerMax). Both protocols led to similar ecological conclusions, with controls showing shared eukaryote taxa across extraction methods, while Phosphate extracted most bacterial taxa. Preservation methods slightly affected community composition, with patterns differing across groups and habitats. Community composition was shaped by preservation strategies, with heterogeneous responses across bacterial, fungal, and eukaryotic assemblages. Preservation methods significantly influenced alpha diversity, with effects varying across taxonomic groups, habitats, and extraction protocols. These results highlight the importance of choosing appropriate preservation methods for eDNA in sediments, depending on the study goal, and offer insights into cost‐effective available extraction techniques for sediment biomonitoring.