16S and 18S rRNA genes metabarcoding of soil, runoff and marine coastal sediment from land-sea continuum microcosms
DNA was extracted from 250 mg of soil or sediment sample and from the filter of runoffs using the PowerSoil DNA Isolation Kit (MoBio Laboratories) according to the manufacturers recommendations. PCR amplification of the V4-V5 hypervariable region of the 16S rRNA genes were performed using the Archaea/Bacteria primers 515F and 928R. 18S rRNA genes were also amplified using the eukaryotic primers FF390 and FR1 targetingthe V7-V8 region. The reverse and forward primers included Illumina adapters. Amplifications were performed in triplicate using AmpliTaq Gold 360 Master Mix (Applied Biosystems) to prepare 25 l reactions containing 2 ng (archaea/bacteria) or 4 ng (eukaryotes) of DNA. The 2x250 paired-end Ssequencing by synthesis was carried out at the Genotoul platform (Toulouse, France) with Illumina-MiSeq.