Marine nitrite-oxidizing bacteria
Ontology highlight
ABSTRACT:
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR324309.fastq.gz | Fastqsanger.gz | |||
| ERR324310.fastq.gz | Fastqsanger.gz | |||
| ERR324311.fastq.gz | Fastqsanger.gz | |||
| ERR324312.fastq.gz | Fastqsanger.gz | |||
| ERR324313.fastq.gz | Fastqsanger.gz |
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Project description:Ecology of ammonia oxidizing and nitrite oxidizing microorganisms in the Namibian coastal upwelling oxygen minimum zone
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Project description:Nitrite-oxidizing bacteria are vital players in the global nitrogen cycle that convert nitrite to nitrate during the 2nd step of nitrification. Within this functional guild, the genus Nitrospira is among the most widespread and phylogenetically and physiologically diverse nitrite oxidizers and its members drive nitrite oxidation in many natural and biotechnological ecosystems. Despite their ecological and biotechnological importance, our understanding of Nitrospira’s energy metabolism is still limited. The main bottleneck for a detailed biochemical characterization of Nitrospira is biomass production, since they are slow-growing organisms and fastidious to culture. In this study, we cultured Nitrospira moscoviensis in a continuous stirred tank reactor system (CSTR) allowing constant biomass harvesting. Additionally, this cultivation setup enabled accurate control of physicochemical parameters and thus avoided fluctuating levels of nitrite and accumulation of nitrate. We performed transcriptome analysis and confirmed constant gene expression profiles in the chemostat culture over a period of two weeks. The transcriptomic data supports the predicted core metabolism of N. moscoviensis, including the reductive TCA cycle as a CO2 fixation pathway, the novel bd-like oxidase as terminal oxidase and the octaheme nitrite reductase involved in nitrogen assimilation. Additionally, the expression of multiple copies of respiratory complexes suggests functional differentiation of these copies within the respiratory chain. Transcriptome analysis also suggests a soluble and a membrane-bound gamma subunit as part of the nitrite oxidoreductase (NXR), the enzyme catalyzing nitrite oxidation. Overall, the transcriptome data provided novel insights into the metabolism of Nitrospira supporting the genome-based prediction of key pathways. Moreover, the application of a CSTR to cultivate Nitrospira is an important foundation for future proteomic and biochemical characterizations, which are crucial for a better understanding of canonical and complete nitrifying microorganisms.
2019-07-03 | GSE123406 | GEO
Project description:Macrobrachium nipponense is one of the commonest species threatened by ambient superfluous nitrite. The mechanism of nitrite stress at the molecular level was studied using de novo RNA-Seq to explore the molecular pathways in M. nipponense exposed to the acute nitrite stress (26.05 mg/L nitrite-N) for 24h and the chronic nitrite stress (6.58 mg/L nitrite-N) for 21d. A total of 175.13 million reads were obtained and assembled into 58,871 unigenes with an average length of 1,028.7 bp and N50 of 1,294bp. 2,824 and 2,610 unigenes in the acute and chronic nitrite stress were significantly differentially expressed respectively. Based on the change in GO analysis and KEGG pathway analysis, pathways both in the acute and chronic nitrite stress were glycosphingolipid biosynthesis - ganglio series, alanine aspartate and glutamate metabolism, biotin metabolism and amino sugar and nucleotide sugar metabolism which revealed the commonly functional pathways in acute and chronic nitrite stress. The markedly altered pathways were divided into four sections of immunity, metabolism, cell and others. Immunity section contained the most pathways among the classifications as phagosome, folate biosynthesis, glycerolipid metabolism, glycine, serine and threonine metabolism, selenoamino acid metabolism, cysteine and methionine metabolism, amino sugar and nucleotide sugar metabolism and taurine and hypotaurine metabolism in the acute nitrite stress and lysosome, alanine, aspartate and glutamate metabolism, arginine and proline metabolism, glycosaminoglycan degradation and amino sugar and nucleotide sugar metabolism in the chronic nitrite stress. This is the first report of whole molecular responses of M. nipponense under acute and chronic nitrite stress through de novo transcriptome sequencing. The findings of this study will further promote the understanding of the underlying molecular mechanisms of the nitrite stress for crustacean species.
2016-11-04 | GSE74684 | GEO
Project description:nitrite-oxidizing bacteria in activated sludge bioreactors at low temperatures Raw sequence reads
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Project description:nitrite-oxidizing bacteria in activated sludge bioreactors at low temperatures Raw sequence reads
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Project description:Global gene expression was compared between Nitrosomonas europaea wild-type and a nitrite reductase-deficient mutant using a genomic microarray. Keywords: wild-type to mutant global transcriptome comparison
2006-03-23 | GSE4517 | GEO
Project description:In this study, we investigated the metabolic potential of N. marina based on its complete genome sequence and performed physiological experiments to test genome-derived hypotheses. Our data confirm that N. marina benefits from additions of undefined organic carbon substrates, has adaptations to resist oxidative, osmotic and UV light-induced stress and low dissolved pCO2. Additionally, N. marina is able to grow chemoorganotrophically on formate, and is thus not an obligate chemolithoautotroph. We further investigated the metabolic response of N. marina to low (5.6 µM) O2 concentrations. In response to O2-limited conditions, the abundance of a potentially more efficient CO2-fixing pyruvate:ferredoxin oxidoreductase (POR) complex and a high-affinity cbb3-type terminal oxidase increased, suggesting a role in sustaining nitrite oxidation-driven autotrophy under O2 limitation.
2021-04-20 | PXD021606 | Pride
Project description:The microbiology of the biomass from a nitrite-oxidizing sequencing batch reactor (NOSBR) fed with an inorganic salts solution and nitrite as the sole energy source that had been operating for 6 months was investigated by microscopy, by culture-dependent methods, and by molecular biological methods, and the seed sludge that was used to inoculate the NOSBR was investigated by molecular biological methods. The NOSBR sludge comprised a complex and diverse microbial community containing gram-negative and gram-positive rods, cocci, and filaments. By culture-dependent methods (i.e., micromanipulation and sample dilution and spread plate inoculation), 16 heterotrophs (6 gram positive and 10 gram negative) were identified in the NOSBR sludge (RC), but no autotrophs were isolated. 16S ribosomal DNA clone libraries of the two microbial communities revealed that the seed sludge (GC) comprised a complex microbial community dominated by Proteobacteria (29% beta subclass; 18% gamma subclass) and high G + C gram-positive bacteria (10%). Three clones (4%) were closely related to the autotrophic nitrite-oxidizer Nitrospira moscoviensis. The NOSBR sludge was overwhelmingly dominated by bacteria closely related to N. moscoviensis (89%). Two clone sequences were similar to those of the genus Nitrobacter. Near-complete insert sequences of eight RC and one GC N. moscoviensis clone were determined and phylogenetically analyzed. This is the first report of the presence of bacteria from the Nitrospira phylum in wastewater treatment systems, and it is hypothesized that these bacteria are the unknown nitrite oxidizers in these processes.
| S-EPMC106245 | biostudies-literature
Project description:An efficient and simple source of nitroso reagents and their oxidation reactions are described. The combination of a Lewis acid and a metal nitrite was applied to the oxidation of silyl enol ethers. Amino acid and peptide derivatives were easily accessed through in situ C-C bond cleavage of fully substituted silyl enol ethers upon oxidation.
| S-EPMC3166854 | biostudies-literature
Project description:Background: Cardiac surgery-associated acute kidney injury (CS-AKI) is reported in 20-30% of patients undergoing cardiac surgery and, leading to poor outcomes and increased healthcare costs. Because the pathophysiology of CS-AKI is complex and has not been fully elucidated, no effective preventive and interventional strategy has been reported. Nitrite, a nitric oxide (NO) donor under hypoxic conditions, has shown to exert organ-protective effects in various kind of preclinical models, however, its efficacy in CS-AKI remains unclear. Objectives: This study aimed to generate a rat cardiopulmonary bypass (CPB) model to induce AKI, identify key molecular pathways involved in its pathophysiology, and evaluate the renoprotective effects of nitrite. Methods: A CPB model was established using rats and AKI was confirmed through molecular and histological analysis. RNA-seq was performed to identify differentially expressed genes and enriched pathway. Nitrite (2 mg/kg) was intravenously administered prior to CPB, and its effects on kidney injury markers and inflammation-related pathways were evaluated. Results: AKI was successfully produced in our rat CPB model, as evidenced by increased KIM-1 and NGAL expression and renal histological damage. RNA-seq revealed significant activation of multiple inflammation-related pathways, including TNF and NFκB signaling pathway. Nitrite administration significantly reduced KIM-1 and NGAL expression and suppressed these pathways associated with development of AKI. Conclusion: This study underscores the role of inflammation in CS-AKI pathophysiology and demonstrates the renoprotective potential of nitrite. These findings provide a foundation for further investigations into nitrite's mechanisms and its potential clinical application in cardiac surgery.
2025-03-01 | GSE290044 | GEO