Data and code from: Assessment of preservation and extraction methods for environmental DNA in sediments

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), silica gel, and Longmire
buffer for one and three 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.