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 extr..., Two libraries per marker were prepared by Fasteris (Geneva, Switzerland; https://www.fasteris.com/en-us/NGS) following the MetaFast protocol (Taberlet et al., 2018) and sequenced with the Illumina MiSeq platform using a paired-end approach (2x150 bp for Euka03 and 2x250 bp for Bact01). Raw sequence reads were analyzed using the OBITools software suite (Boyer et al., 2016) specially dedicated to the handling of metabarcoding data. All ecological analyses were performed using the R statistical software (version 4.3.0; R Core Team 2022)., , # Dataset for the assessment of preservation and extraction methods for environmental DNA in sediments [https://doi.org/10.5061/dryad.9zw3r22nf](https://doi.org/10.5061/dryad.9zw3r22nf) This dataset contains raw sequence data, filtered data, metadata and scripts to reproduce the bioinformatic and statistical analyses of the study. ## Description of the data and file structure For both Bact01 and Euka03 primer pairs, two libraries were sequenced with a paired-end approach (2x150 bp) and they are provided in a .fastq format. Each library is associated to a .ngs file containing information about sample identity. Raw sequence reads were analyzed using the OBITools software suite (Boyer et al., 2016)(see Code to reproduce bioinformatic analyses). raw_data.tar.xz \|- Bact01/ \| |- 211224_SN1126_A_L001_AOYG-97_R1.fastq/ \| |- 211224_SN1126_A_L001_AOYG-97_R2.fastq/ \| |- 211224_SN1126_A_L001_AOYG-98_R1.fastq/ \| |- 211224_SN1126_A_L001_AOYG-98_R2.fastq/ \| |- AOYG-97_Bact01.ngs/ \| |..., ,