DNA extraction protocols applied to waterbody in the Paris-Saclay region

Water samples were collected from a 330 m² artificial lake in Paris-Saclay (Gif-sur-Yvette, France; 48.715506° N, 2.157887° E) during two field campaigns in 2023. After sequential prefiltration (100 µm and 30 µm), 200 mL of homogenized water were filtered onto 0.2-µm membranes. A total of 57 samples were analyzed, corresponding to 19 DNA extraction protocols tested in triplicate. Some protocols followed manufacturer instructions, while others included modified lysis and elution steps. Microbial community composition was determined by 16S rRNA gene amplicon sequencing (V4–V5 region) using primers U515F and Pk926R. Sequencing was performed on an Illumina MiSeq (2 × 250 bp),