Ontology highlight
ABSTRACT:
PROVIDER: PRJNA623646 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description: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.
2024-12-31 | GSE164776 | GEO
Project description:Acididesulfobacillus acetoxydans is an acidophilic sulfate reducer that can dissimilatory reduce nitrate to ammonia (DNRA). However, no known nitrite reductase is encoded. This study was performed to investigate how A. acetoxydans reduces nitrate to nitrite and elucidated a novel DNRA mechanism and potential nitrosative stress resistance mechanisms in acidophiles.
2024-01-26 | PXD045135 | Pride
Project description:The conversion of nitrate to ammonium, known as nitrate reduction, consumes large amounts of reductants in plants. Previous studies have observed that mitochondrial alternative oxidase (AOX) is upregulated under conditions of limited nitrate reduction, such as low or no nitrate availability, or when ammonium serves as the sole nitrogen (N) source. Electron transfer from ubiquinone to AOX bypasses the proton-pumping complexes III and IV, thereby consuming reductants efficiently. Therefore, the upregulation of AOX under conditions of limited nitrate reduction may help dissipate excessive reductants and mitigate oxidative stress. However, firm evidence supporting this hypothesis is lacking due to the absence of experimental systems capable of directly analyzing the relationship between nitrate reduction and AOX. To address this gap, we developed a novel culturing system that allows for the manipulation of nitrate reduction and AOX activities separately, without inducing N starvation, ammonium toxicity, or disrupting the nitrate signal. Using this system, we investigated genome-wide gene expression with RNA-seq to gain insight into the relationship between AOX and nitrate reduction.
2024-04-23 | E-MTAB-14027 | biostudies-arrayexpress
Project description:Dissimilatory nitrate reduction to ammonia (DNRA) is an important part of the microbial N-cycle both in natural and man-made habitats, although its significance in wastewater treatment plants is not well understood. Nitrate-limited enrichments from activated sludge with acetate as e-donor consistently resulted in a domination of two closely related genotypes of ammonifying members of Deltaproteobacteria belonging to the genus Geobacter. One of the two was isolated in pure culture which appears to be an extremely specialized ammonifier, actively growing only with acetate as e-donor and C source and nitrate as e-acceptor. The shotgun proteomic raw data obtained from whole cell lysates are provided. First and corresponding author: Dimitry Y. Sorokin soroc@inmi.ru; d.sorokin@tudelft.nl
2023-07-11 | PXD031212 | Pride
Project description:Low levels of nitrate rather than high carbon-nitrogen ratios induce Dissimilatory Nitrate Reduction to Ammonia (DNRA) in Geobacter lovleyi SZ.
| PRJNA691925 | ENA
Project description:Dissimilatory iron reduction by hyperthermophilic archaea occurs in many geothermal environments and generally relies on microbe-mineral interactions that transform various iron oxide minerals. In this study, the physiology of dissimilatory iron and nitrate reduction was examined in the hyperthermophilic crenarchaeon Pyrodictium delaneyi Su06T. Protein electrophoresis showed that the c-type cytochrome and general protein compositions of P. delaneyi changed when grown on ferrihydrite relative to nitrate. Differential proteomic analyses using tandem mass tagged protein fragments and mass spectrometry detected 660 proteins and differential production of 127 proteins. Among these, two putative membrane-bound molybdopterin-dependent oxidoreductase complexes increased in relative abundance 60- to 3,000-fold and 50-100-fold in cells grown on iron oxide. A putative 8-heme c-type cytochrome was 60-fold more abundant in iron grown cells and was unique to the Pyrodictiaceae. There was also a >14,700-fold increase in a membrane transport protein in iron grown cells. There were no changes in the abundances of flagellin proteins nor a putative nitrate reductase, but a membrane nitric oxide reductase was more abundant on nitrate. These data help to elucidate the mechanisms by which hyperthermophilic crenarchaea generate energy and transfer electrons across the membrane to iron oxide minerals.
2020-12-23 | PXD020757 | Pride
Project description:Shewanella algae C6G3 can conduct dissimilative nitrate reduction into ammonium and MnIV reduction. This bacteria have the unusual ability to produce anaerobically nitrite from ammonium in the presence of MnIV. This property may explain NO2/3- accumulation observed in some anaerobic zones of marine sediments. To gain insight into their metabolic capabilities, global mRNA expression patterns were investigated by RNA-seq and qRT-PCR in cells growing with lactate and ammonium as carbon and nitrogen sources and with MnIV or nitrate as electron acceptors. Genes exhibiting higher expression levels in the presence of MnIV belonged to functional categories of carbohydrate, coenzyme, lipid metabolisms and inorganic ion transport. Furthermore, comparative transcriptomic pattern between MnIV and NO3 revealed that the strain presented an ammonium limitation status with MnIV, despite the presence of identical and non-limiting concentration of ammonium in both culture conditions. Regulators ntrB/nrtC, ammonium channel, nitrogen regulatory protein P-II, glutamine synthetase and asparagine synthetase glutamine dependent genes were over-expressed. In nitrate condition, genes involved in synthesis of several amino acids were over expressed. Among the genes associated with the stress response, Kat E was highly expressed particularly under manganese condition
2018-12-31 | GSE109146 | GEO