16S rRNA gene amplicon sequencing of aquifer sediments in Van Phuc (Hanoi/Vietnam), incubated in microcosms experiment

16S rRNA gene amplicon sequencing of aquifer sediments in Van Phuc (Hanoi/Vietnam) and microcosms thereof to study the effect of natural organic matter on As mobilization.Sacrificial microcosms were set up by mixing 1 g of sediments from 30 m depth (oxidized, orange sandy sediments) with 5 mL sterile synthetic groundwater medium, modified from Rathi et al. (2017) in 20 mL headspace vials. Five different treatments (all contained sediment/medium) were prepared 1) biotic control (CON+), no amendments; 2) abiotic control (CON -), amended with 160 mM NaN3 and 1 mM acetate/lactate mix; 3) amended with 1 mM OM extracted from clay sediments (OMC); 4) amended with 1 mM OM extracted from sandy sediments (OMS); 5) amended with 1 mM acetate/lactate mix (A/L). All microcosms were prepared in the glovebox; anoxic conditions were maintained by closing the bottles with rubber stoppers and aluminum caps. Afterwards microcosms were kept at 28°C in the dark until analysis. Samples were collected at the beginning of the experiment, after 10 days (when maximum Fe(III) reduction and As release were observed) and at the end of the experiment (100 days). DNA extraction was performed following 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 (Nextera, Illumina) and 250 bp paired-end sequencing with MiSeq (Illumina, San Diego, CA, USA) using v2 chemistry were performed by Microsynth AG (Switzerland) and between 25000 and 75000 read pairs were obtained for each sample.