PRJNA678222
Sequencing of NRFeOx cultures originating from a karstified aquifer bacteria culture from Altingen, Germany
Removal of nitrate by microbial denitrification in freshwater aquifers is often limited by low concentrations of organic carbon. In these nutrient-poor ecosystems nitrate-reducing bacteria that can use inorganic compounds such as Fe(II) (NRFeOx) as electron donors could play a major role in nitrate degradation. Microbial communities for enrichment cultures were passively sampled (MTDs) and transferred to low phosphate medium (LPM) (Hegler et al. 2008) amended with 2 mM of NaNO3 and 2 mM of FeCl2. Enrichments were incubated at room temperature in the dark and transferred to fresh medium every 2-3 weeks (for about a year in total) after complete oxidation of iron(II). Conditions were always kept anoxic. This dataset contains the following data: (1) Raw sequencing data of 16S (V4 region) rRNA amplicon sequencing of the microbial community composition of a truly autotrophic NRFeOx enrichment culture. 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 23 Gbp by CeGaT, Tuebingen, Germany. For long read sequencing, library was prepared with Ligation Sequencing Kit (Oxford Nanopore Technologies) and sequenced with a GridION (Oxford Nanopore Technologies) totalling 13 Gbp in 2.5 M reads by GenXone Inc, Suchy Las, Poland. (3) Assembly of short and long reads with metaSPAdes v3.13.1 using https://github.com/nf-core/mag v1.0.0.