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ABSTRACT:
PROVIDER: PRJNA950209 | ENA |
REPOSITORIES: ENA
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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: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: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:Reforestation is effective in restoring ecosystem functions and enhancing ecosystem services of degraded land. The three most commonly employed reforestation methods of natural reforestation, artificial reforestation with native Masson pine (Pinus massoniana Lamb.), and introduced slash pine (Pinus elliottii Engelm.) plantations were equally successful in biomass yield in southern China. However, it is not known if soil ecosystem functions, such as nitrogen (N) cycling, are also successfully restored. Here, we employed a functional microarray to illustrate soil N cycling. The composition and interactions of N-cycling genes in soils varied significantly with reforestation method. Natural reforestation had more superior organization of N-cycling genes, and higher functional potential (abundance of ammonification, denitrification, assimilatory, and dissimilatory nitrate reduction to ammonium genes) in soils, providing molecular insight into the effects of reforestation.
2019-11-04 | GSE100379 | 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:PAH degradation under dissimilatory nitrate reducing conditions
| PRJNA374525 | ENA
Project description:The role of sulfur cycle and enzyme activity in dissimilatory nitrate reduction processes in heterotrophic sediments
| PRJNA784359 | ENA
Project description:The role of sulfur cycle and enzyme activity in dissimilatory nitrate reduction processes in heterotrophic sediments
| PRJNA784358 | ENA