Metagenome or environmental sample from alternating micro-aerobic/anaerobic ammonium oxidizing microbiome
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ABSTRACT:
PROVIDER: PRJNA559529 | ENA |
REPOSITORIES: ENA
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Project description:Simulteneous activity of anaerobic and aerobic ammonium- and methane oxidizing microorganisms under oxygen limitation.
| PRJEB39466 | ENA
Project description:This study evaluated the ammonium oxidizing communities (COA) associated with a potato crop (Solanum phureja) rhizosphere soil in the savannah of Bogotá (Colombia) by examining the presence and abundance of amoA enzyme genes and transcripts by qPCR and next-generation sequence analysis. amoA gene abundance could not be quantified by qPCR due to problems inherent in the primers; however, the melting curve analysis detected increased fluorescence for Bacterial communities but not for Archaeal communities. Transcriptome analysis by next-generation sequencing revealed that the majority of reads mapped to ammonium-oxidizing Archaea, suggesting that this activity is primarily governed by the microbial group of the Crenarchaeota phylum. In contrast,a lower number of reads mapped to ammonia-oxidizing bacteria.
2018-08-06 | GSE71824 | GEO
Project description:uncultured anaerobic ammonium-oxidizing bacterium overview
| PRJNA359227 | ENA
Project description:uncultured anaerobic ammonium-oxidizing bacterium Raw sequence reads
| PRJNA321081 | ENA
Project description:The study identified a total of 3169 gene transcripts (98.4% coverage). By comparing the anaerobic versus aerobic H2-oxidizing At. ferrooxidans cultures, a total of 371 DEGs were found. Of these, 168 DEGs were increased significantly during the aerobic growth on H2 (with O2 as the sole electron acceptor), while 203 DEGs increased significantly during anaerobic growth on H2 (with Fe3+ as the sole electron acceptor).
2020-11-23 | GSE154815 | GEO
Project description:Escherichia coli is a metabolically versatile bacterium that is able to grow in the presence and absence of oxygen. Here, the process of adaptation was investigated by determining changes in transcript profiles when aerobic steady-state cultures were depleted of air. Escherichia coli strain MG1655 was grown in a New Brunswick Scientific Bioflow 1000 fermentation vessels (1.8 l capacity) with culture agitation speed constant at 300 rpm and the temperature maintained at 37 °C. Oxygen levels were monitored using galvanic oxygen electrodes while the pH was maintained at 7.2 ±0.2 by automatic titration with sterile KOH. Evans defined medium was used as the growth medium with glucose (15 mM) as the carbon source with the dilution rate being 0.2 h-1. Aerobic cultures were maintained by sparging the chemostat with air (0.4 l min-1). The switch to micro-aerobic conditions was achieved by switching off the air sparging the culture. After a period of 5, 10, 15 and 60 min exposure to air, cells were harvested directly into RNA Protect (Qiagen) to stabilize RNA before total RNA purification using Qiagen’s Rneasy Midi kit as recommended by manufacturer’s instructions. Keywords: time-course, oxygen-depletion
2007-05-10 | GSE6644 | GEO
Project description:A heterotrophic ammonia-oxidizing bacterium Alcaligenes sp. HO-1 was isolated from the activated sludge of a bioreactor treating ammonia-rich piggery wastewater. The goal and objectives of this experiment are to analyze the transcriptome profiles of nitrogen-metabolism-related genes of Alcaligenes sp. HO-1 in response to ammonium stimulation over time and to find out potential genes involved in ammonia oxidation process. So the RNA-seq anaylsis was performed by setting up each time points (0, 3.5, 10, 22 hours) when strain HO-1 were exposed to ammonia. HO-1 was cultured with 83 mM succinate and 14 mM ammonium sulfate until ammonia was completely consumed and then another 14 mM of ammonium sulfate was added to the culture. Cells were harvested at 0 h, 3.5 h, 10 h and 22 h after the addition of ammonium sulfate. The sequencing data of RNAs obtained from strain HO-1 cells at each time was analyzed.
2022-05-20 | GSE174685 | GEO
Project description:Aerobic methanotrophic bacteria use methane as their sole source of carbon and energy and serve as a major sink for the potent greenhouse gas methane in freshwater ecosystems. Despite this important environmental role, little is known about the molecular details of how these organisms interact in the environment. Many bacterial species use quorum sensing systems to regulate gene expression in a density-dependent manner. We have identified a quorum sensing system in the genome of Methylobacter tundripaludum, a dominant methane-oxidizer in methane enrichments of sediment from Lake Washington (Seattle, WA, USA). We determined that M. tundripaludum primarily produces N-3-hydroxydecanoyl-L-homoserine lactone (3-OH-C10-HSL) and that production is governed by a positive feedback loop. We then further characterized this system by determining which genes are regulated by quorum sensing in this methane-oxidizer using RNA-seq, and discovered this system regulates the expression of a novel nonribosomal peptide synthetase biosynthetic gene cluster. These results identify and characterize a mode of cellular communication in an aerobic methane-oxidizing bacterium.
2016-08-16 | GSE85617 | GEO
Project description:Comparative gene expression on a co-culture of anaerobic ammonium and sulfur-oxidizing bacteria under ammonium and nitrate limitation
| PRJEB31138 | ENA
Project description:Nitric oxide (NO) has several important functions in biology and atmospheric chemistry as a toxin, signaling molecule, ozone depleting agent and the precursor of the greenhouse gas nitrous oxide (N2O). Even though NO is a potent oxidant, and was available on earth earlier than oxygen, its direct use by microorganisms for growth was not demonstrated before. Using physiological experiments, metatranscriptomics and metaproteomics, here we show that anaerobic ammonium-oxidizing (anammox) bacterium Kuenenia stuttgartiensis grow by coupling ammonium oxidation to NO reduction, and produce only N2. Such a metabolism could have existed on early earth, and has implications in controlling N2O and NO emissions both from natural and manmade ecosystems, where anammox bacteria contribute significantly to N2 release to the atmosphere.
2019-02-26 | PXD011763 | Pride