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

Sampling

Nitrate-reducing iron(II)-oxidizing (NDFO) 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. A second NDFO culture, culture BP, was obtained with a sample taken in 2015 at the same pond and cultured in a similar way. 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 BP.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 BP and of environmental samples from the pond where culture BP originates from. 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 near full-length 16S (primers 27F and 1492R) sequenced with PacBio Sequel SMRT at the Helmholtz research institute, Munich, Germany. (3) Raw sequencing data of shotgun metagenomics. Library was prepared with TruSeq DNA PCR-Free Kit (Illumina) and sequenced with PE 150 bp on a NovaSeq 6000 totalling 91 Gbp by CeGaT, Tuebingen, Germany. (4) Short reads were assembled with MEGAHIT v1.2.7 using https://github.com/nf-core/mag v1.0.0. (5) Raw sequencing data of shotgun metatranscriptomes (2 conditions, triplicates). Library preparation including bacterial ribodepletion (Illumina Stranded Total RNA Prep with Ribo-Zero Plus kit) and Illumina NextSeq v2.5 sequencing with PE 75 bp and 6 to 53 Mio clusters per sample were performed by Microsynth AG (Balgach, Switzerland).

Method steps

1. Pipeline used: https://www.ebi.ac.uk/metagenomics/pipelines/5.0