PRJNA686278
16S rRNA amplicon sequencing of in-situ aquifer incubations from an alluvial aquifer system of the Red River delta (Van Phuc, Hanoi) in Vietnam.
We used in-situ aquifer incubations i) to evaluate how different biogenic and abiogenic Fe(III) minerals are transformed in a strongly reducing, As-rich aquifer compared to a suboxic As-free aquifer and ii) to assess which microbial taxa were involved in these Fe transformations. Overall, this study shows that biogenic minerals are more prone to be colonized by microorganisms, including general Fe(III)-reducers, but also implies the role of fermenters and methanotrophs in Fe(III) reduction.Different kinds of mineral mixtures were produced (both, biogenic or abiogenic) and 4.5 g were placed in a wafer or in pouches made from a permeable mesh membrane tightened with nylon cable ties. Wafers and pouches were attached to thick fishing line, weighed down with stainless hex nuts and placed in the monitoring wells for the period of 3 weeks. One set was incubated in the strongly reducing As contaminated, Fe2+ and CH4 rich water, while the other one in As, Fe2+ and CH4 free suboxic water. After 3 weeks of incubations the minerals were pooled out of the wells. Minerals incubated in the mesh pouches were immediately transferred to the 15 mL sterile Falcone tubes and immersed in the LifeGuard Soil Preservation Solution (Qiagen) in order to stabilize the microbial DNA and RNA. Samples were stored on dry ice during transport, placed in a -80C freezer upon arrival at the laboratory and later used for microbial community and qPCR analysis.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 86,887 and 87,365 read pairs were obtained for each sample.