Multi-omics of the nitrate-reducing iron(II)-oxidizing culture KS

Nitrate-reducing iron(II)-oxidizing bacteria are widespread in the environment contribute to nitrate removal and influence the fate of the greenhouse gases nitrous oxide and carbon dioxide. The autotrophic growth of nitrate-reducing iron(II)-oxidizing bacteria is rarely investigated and poorly understood. The most prominent model system for this type of studies is enrichment culture KS, which originates from a freshwater sediment in Bremen, Germany. To gain insights in the metabolism of nitrate reduction coupled to iron(II) oxidation under in the absence of organic carbon and oxygen limited conditions, we performed metagenomic, metatranscriptomic and metaproteomic analyses of culture KS.This dataset contains: (1) Raw sequencing data of 16S (V4 region, primers 515f and 806r) rRNA amplicon sequencing of the microbial community composition of the autotrophic NRFeOx enrichment culture KS. Illumina MiSeq sequencing (Illumina, San Diego, CA, USA) using PE 250 bp MiSeq Reagent Kit v2 (500 cycles kit) were performed at Microsynth AG (Balgach, Switzerland). (2) Raw sequencing data of shotgun metagenomics. For short reads, library was prepared with TruSeq DNA PCR-Free Kit (Illumina) and sequenced with PE 150 bp on a NovaSeq 6000 totalling 55 and 48 Gbp by CeGaT, Tuebingen, Germany. For long read sequencing, library preparation with ONT Native Ligation Kit was followed by sequencing with PromethION (Oxford Nanopore Technologies) flow cell (version 9.4.1) for 72h with standard settings (basecalling with HAC mode, bias voltage -180 mV) yielding 53 Gbp in 5 million reads by the NGS Competence Center Tuebingen (NCCT) of the University of Tuebingen, Germany. (3) Short and long reads were assembled with metaSPAdes v3.13.1 using https://github.com/nf-core/mag v1.0.0. (4) Raw sequencing data of shotgun metatranscriptomes (2 conditions, triplicates). Library preparation including bacterial ribodepletion (NuGen Universal Prokaryotic RNA-Seq kit incl. bacterial ribodepletion) and Illumina NextSeq v2.5 sequencing with PE 75 bp and 21 to 62 Mio clusters per sample were performed by Microsynth AG (Balgach, Switzerland).

硝酸盐还原铁（II）氧化细菌在环境中分布广泛，对硝酸盐的去除及温室气体一氧化二氮和二氧化碳的命运产生显著影响。这类细菌的自主生长过程鲜有研究，且理解不足。此类研究中最显著的模型系统为源自德国不来梅淡水沉积物的富集培养 KS。为了在无有机碳和氧气限制条件下，深入探究硝酸盐还原与铁（II）氧化偶联的代谢机制，我们对培养 KS 进行了宏基因组、宏转录组及宏蛋白质组分析。本数据集包含以下内容：（1）自养型 NRFeOx 富集培养 KS 微生物群落组成的 16S（V4 区域，引物 515f 和 806r）rRNA 扩增子测序的原始测序数据。采用 Illumina MiSeq 测序平台（Illumina，圣地亚哥，美国加利福尼亚州）及 PE 250 bp MiSeq Reagent Kit v2（500 循环试剂盒）进行测序，测序工作由瑞士巴尔加赫的 Microsynth AG 完成。（2）宏基因组鸟枪法测序的原始测序数据。对于短读段，使用 TruSeq DNA PCR-Free Kit（Illumina）制备文库，并在 NovaSeq 6000 测序仪上以 PE 150 bp 进行测序，总测序量为 55 Gb 和 48 Gb，由德国图宾根的 CeGaT 完成。对于长读段测序，采用 ONT Native Ligation Kit 制备文库，随后使用 PromethION（Oxford Nanopore Technologies）流式细胞（版本 9.4.1）进行测序，持续 72 小时，标准设置下（使用 HAC 模式进行碱基调用，偏置电压 -180 mV），由图宾根大学的 NGS 竞争力中心（NCCT）产生 5 百万读段，总测序量为 53 Gb。（3）短读段和长读段均使用 metaSPAdes v3.13.1 进行组装，使用 https://github.com/nf-core/mag v1.0.0 工具。（4）宏转录组鸟枪法测序的原始测序数据（2 种条件，每个样本三重复）。文库制备包括细菌核糖体去除（使用 NuGen Universal Prokaryotic RNA-Seq kit 包含细菌核糖体去除）和 Illumina NextSeq v2.5 测序，每个样本使用 PE 75 bp 测序，每个样本产生 21 至 62 Mio 个簇，由瑞士巴尔加赫的 Microsynth AG 完成。