16S rRNA amplicon sequencing of an alluvial aquifer system of the Red River delta (Van Phuc, Hanoi) in Vietnam.

A high resolution geomicrobiological investigation in combination with sediment chemistry and mineralogy was conducted close to Van Phuc, Hanoi, Vietnam. Microbial community analysis revealed a dominance of fermenters, methanogens and methanotrophs whereas sediment mineralogy along a 46m deep core showed diversity of iron minerals but also presence of carbonates formed as an effect of microbially driven C degradation. In 2018 a drilling campaign took place during which we collected sediment cores (10 cm diameter; each individual piece ca. 3 m long) up to 46 m below ground level using rotary drilling technique. Sediments were collected with ethanol sterilized spatula into sterile 15 mL Falcon tubes. Collected sediments were immediately immersed in LifeGuard Soil Preservation Solution (Qiagen) in order to stabilize the microbial DNA and RNA. Samples were stored on dry ice during transportation and placed in a -80 C freezer upon arrival at the laboratory. DNA was extracted using a phenol-chloroform method following a protocol from Lueders et al. (Lueders et al., 2004). Bacterial and archaeal 16S rRNA genes were amplified using universal primers 515f: GTGYCAGCMGCCGCGGTAA (Parada et al., 2016) and 806r: GGACTACNVGGGTWTCTAAT (Apprill et al., 2015) fused to Illumina adapters. Subsequent library preparation steps and Illumina MiSeq sequencing (Illumina, San Diego, CA, USA) using the 2 x 250 bp MiSeq Reagent Kit v2 (500 cycles kit) were performed at Microsynth AG (Balgach, Switzerland). Between 38,425 and 172,443 read pairs were obtained for each sample.