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.

本研究在越南河内范福（Van Phuc）附近开展了高分辨率地质微生物学调查，同步开展沉积物化学与矿物学分析。微生物群落分析结果显示，发酵微生物、产甲烷古菌与甲烷氧化菌为优势类群；对46米深沉积物岩芯的矿物学分析则表明，其不仅含有多种铁矿物，还存在因微生物驱动的碳降解作用形成的碳酸盐矿物。2018年，本研究实施钻探工作，采用旋转钻探技术采集地下深度达46米的沉积物岩芯，岩芯直径10厘米，单段长度约3米。沉积物采集使用经乙醇灭菌的刮铲，转移至无菌15mL Falcon管中。采集后的沉积物即刻浸没于LifeGuard土壤保存液（Qiagen）中，以稳定微生物的DNA与RNA。样品运输过程中置于干冰保存，抵达实验室后立即转移至-80℃冰箱储存。参照Lueders等人（Lueders et al., 2004）的实验方案，采用酚-氯仿法提取沉积物总DNA。使用融合有Illumina接头的通用引物515f（序列：GTGYCAGCMGCCGCGGTAA，Parada et al., 2016）与806r（序列：GGACTACNVGGGTWTCTAAT，Apprill et al., 2015），对细菌与古菌的16S rRNA基因进行扩增。后续文库构建步骤及采用2×250 bp MiSeq试剂试剂盒v2（500循环试剂盒）的Illumina MiSeq测序（Illumina，美国加利福尼亚州圣地亚哥）均在瑞士巴尔加奇的Microsynth AG公司完成。每个样品获得的读段对（read pairs）数量介于38425至172443之间。