16S amplicon sequencing of the microbial communities in the water column of the Northern Benguela Upwelling System

During expedition M157 in the Benguela Upwelling System (BUS) off the coast of Namibia we used a multidisciplinary approach to examine relationships between physical forcing, process rates, and microbial activities. For this, sampling was conducted between 18 August and 16 September 2019, using 10 L free-flow bottles (Hydrobios, Germany) attached to a rosette water sampler at 17°S, 23°S and 25°S. 16S rRNA gene and 16S rRNA sequences were generated from 1 L water samples collected on 0.22 µm pore-size polycarbonate filters. DNA and RNA was extracted using the AllPrep DNA/ RNA Mini Kit (Qiagen, Hilden, Germany). For the PCR amplifications the primers 341F (CCTAYGGGRBGCASCAG) and 806R (GGACTACNNGGGTATCTAAT), covering the V3/V4 region, were used (Sundberg et al. 2013). Sequences were generated on a MiSeq Illumina platform in a 2x300 bp paired-end run using V3 Chemistry (Illumina).