Unveiling diel river microbial dynamics: eDNA traces structural and functional microbial fingerprints

This dataset accompanies the article “Unveiling diel river microbial dynamics: eDNA traces structural and functional microbial fingerprints” and contains the data generated and analyzed to investigate diel (day–night) microbial dynamics in a riverine ecosystem using environmental DNA (eDNA). This dataset contains curated 16S rRNA gene metabarcoding data from riverine microbial communities sampled across a 24-hour diel cycle in the Saja catchment (northern Spain). The dataset includes a merged OTU and taxonomy table, along with associated metadata describing sampling location, replicate, and time interval. Raw Oxford Nanopore sequencing reads were basecalled using Dorado with a super-accuracy model, followed by duplex processing to improve read quality. Reads were quality-filtered (Q > 10) and size-selected to retain sequences corresponding to the expected 16S rRNA amplicon length (200–500 bp). Subsequent processing included demultiplexing, primer removal, and chimera filtering using standard bioinformatic tools. Sequences were clustered into OTUs at 97% sequence identity, with consensus polishing applied to improve accuracy. Taxonomic assignments were performed using curated reference databases (MiDAS, SILVA, and RefSeq), retaining high-confidence matches based on sequence identity and alignment criteria. Taxonomic assignments were based on BLAST results, and only matches with a sequence identity of ≥97% were retained to ensure high-confidence identification at the species level. The dataset was further curated by removing contaminants through blank correction and decontamination procedures. Additionally, the dataset includes a final OTU table with inferred functional profiles generated using PICRUSt2, representing the predicted abundance of KEGG Orthology (KO) groups for each sample. The final dataset represents a high-quality, filtered OTU table capturing microbial community composition and its fine-scale temporal variation across riverine systems, as well as inferred functional profiles based on PICRUSt2, represented as KEGG Orthology (KO) abundances.