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SRX9844014: GSM5018572: N3_S6_L006_R1_001; Geobacter lovleyi; RNA-Seq
1 ILLUMINA (Illumina HiSeq 2000) run: 35.2M spots, 1.8G bases, 717.9Mb downloads

Submitted by: NCBI (GEO)
Study: Low levels of nitrate rather than high carbon-nitrogen ratios induce Dissimilatory Nitrate Reduction to Ammonia (DNRA) in Geobacter lovleyi SZ.
show Abstracthide Abstract
N retention in soils can be stimulated by microorganisms carrying out dissimilatory reduction of nitrate to ammonia (DNRA), a respiratory activity that converts nitrate and/or nitrite to ammonia. Geobacter lovleyi has recently being recognized as a key driver of DNRA, providing a model to investigate the environmental signals that promote nitrate ammonification. Here we show that low nitrate concentrations (5mM) induce DNRA in G. lovleyi independently of the concentration of the electron donor, thus challenging the prevailing view that high carbon-to-nitrogen (C/N) ratio triggers this process. The nitrate transcriptome revealed a complex metabolic network of periplasmic (Nap) and cytoplasmic (Nar) nitrate reductase systems for the reduction of nitrate to nitrite. The transcriptome also included a canonical (NrfA-1), two Geobacter-specific nitrite reductases (NrfA-2 and NrfA-3) and a membrane-bound NrfH cytochrome, which electronically connects NrfA to the menaquinone pool. Flagellar motility and chemotaxis proteins were also among the most upregulated genes in the nitrate cultures, consistent with an adaptive response that allows Geobacter cells to sense and access the limited supply of nitrate in anaerobic zones of the soils and sediments. This is the first demonstration of the ability of the bacteria to use DNRA pathway under nitrate limiting conditions independently of the C/N ratio. G. lovleyi provides a model for study DNRA process and it is a good candidate that could contribute in the retention of nitrogen in soils leading to efficient use of nitrogen containing fertilizers and preventing nitrate leaching. Overall design: We extracted total RNA from exponential phase of growth in Geobacter lovleyi SZ when growth with or without 5 mM sodium nitrate.
Sample: N3_S6_L006_R1_001
SAMN17308654 • SRS8025721 • All experiments • All runs
Library:
Instrument: Illumina HiSeq 2000
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: cDNA
Layout: SINGLE
Construction protocol: Total RNA extraction following manufacturer's recommendation for QIAGEN RNeasy kit (QIAGEN) rRNA depletion used an Illumina TruSeq Total RNA Library Preparation kit with RiboZero Bacteria rRNA depletion beads. Libraries were quantified using Qubit and Advanced Analytical Fragment Analyzer High Sensitivity DNA NGS assays. The libraries were then pooled in equimolar amounts for multiplexed sequencing and the pool was quantified using the Kapa Biosystems Illumina Library Quantification qPCR kit.
Experiment attributes:
GEO Accession: GSM5018572
Links:
Runs: 1 run, 35.2M spots, 1.8G bases, 717.9Mb
Run# of Spots# of BasesSizePublished
SRR1342908235,237,1211.8G717.9Mb2025-01-02

ID:
12891190

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