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PROVIDER: PRJNA1073387 | ENA |
REPOSITORIES: ENA
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Project description:Roothans et al., analyzed heterotrophic denitrification processes that can be an important source of nitrous oxide. We employed planktonic nitrification-inhibited denitrifying enrichment cultures under alternating oxic-anoxic conditions. The dynamic conditions resulted in a general presence of the denitrifying enzymes. Overall, we show that aerobic denitrification should not be neglected as an ecologically relevant process. Contact author: m.laureni@tudelft.nl
2024-07-17 | PXD042057 | Pride
Project description:Beller, H. R., T. E. Letain, A. Chakicherla, S. R. Kane, T. C. Legler, and M. A. Coleman. 2006. Whole-genome transcriptional analysis of chemolithoautotrophic thiosulfate oxidation by Thiobacillus denitrificans under aerobic vs. denitrifying conditions. Journal of Bacteriology 188:7005-7015. Thiobacillus denitrificans is one of the few known obligate chemolithoautotrophic bacteria capable of energetically coupling thiosulfate oxidation to denitrification as well as aerobic respiration. As very little is known about the differential expression of genes associated with key chemolithoautotrophic functions (such as sulfur-compound oxidation and CO2 fixation) under aerobic versus denitrifying conditions, we conducted whole-genome, cDNA microarray studies to explore this topic systematically. The microarrays identified 277 genes (approximately ten percent of the genome) as differentially expressed using Robust Multi-array Average statistical analysis and a 2-fold cutoff. Genes upregulated (ca. 6- to 150-fold) under aerobic conditions included a cluster of genes associated with iron acquisition (e.g., siderophore-related genes), a cluster of cytochrome cbb3 oxidase genes, cbbL and cbbS (encoding the large and small subunits of form I ribulose 1,5-bisphosphate carboxylase/oxygenase, or RubisCO), and multiple molecular chaperone genes. Genes upregulated (ca. 4- to 95-fold) under denitrifying conditions included nar, nir, and nor genes (associated respectively with nitrate reductase, nitrite reductase, and nitric oxide reductase, which catalyze successive steps of denitrification), cbbM (encoding form II RubisCO), and genes involved with sulfur-compound oxidation (including two physically separated but highly similar copies of sulfide:quinone oxidoreductase and of dsrC, associated with dissimilatory sulfite reductase). Among genes associated with denitrification, relative expression levels (i.e., degree of upregulation with nitrate) tended to decrease in the order nar > nir > nor > nos. Reverse transcription, quantitative PCR analysis was used to validate these trends. Keywords: bacterial metabolism
2006-10-06 | GSE5256 | GEO
Project description:This study aimed to evaluate the transcriptomic response of Paracoccus denitrificans PD1222 exposed to an applied electric potential of +200 mV under aerobic denitrification conditions. RNA-seq analysis was conducted on five biological samples: three independent replicates under 200 mV and two control samples at 0 mV. Differential gene expression changes revealed genes associated with amino acid metabolism, carbohydrate metabolism, membrane transport, and energy metabolism.
2025-11-06 | GSE299670 | GEO
Project description:An aerobic photosynthetic bacterium Roseobacter denitrificans OCh114 has two DNR- and one FNR-type transcriptional regulators, which are predicted to sense nitric oxide and oxygen, respectively. To investigate the role of these regulators in regulation of the denitrification genes, transcriptome profiles of mutant strains of R. denitrificans OCh114 deficient in the genes for the DNR- or FNR-type regulators were determined by NimbleGen Prokaryotic Expression array (12x135K).
2021-06-30 | GSE153074 | GEO
Project description:This study systematically evaluated the denitrification performance and tolerance mechanisms of the highly efficient heterotrophic nitrifying–aerobic denitrifying strain Klebsiella sp. WH-E under Zn²⁺ stress. Under 100 mg/L Zn²⁺ stress, the heterotrophic nitrification and aerobic denitrification capabilities of Klebsiella sp. WH-E resulted in an ammonia nitrogen removal rate of 95.53% and a nitrate nitrogen removal rate of 74.00%. and the nitrite nitrogen removal rate was 72.75%. The activities of the key denitrification enzymes NAR and NIR remained largely stable, and the accumulation of NO₃⁻-N and NO₂⁻-N during nitrogen transformation was limited. Multi-omics analysis revealed that Zn²⁺ stress significantly upregulated nitrogen metabolism-related genes (narG, nirB) and metal homeostasis regulatory genes (zntA, arsR, czcC), while simultaneously regulating ABC transporters and two-component systems to maintain intracellular Zn²⁺ homeostasis. The abundance of sulfur metabolism and antioxidant-related metabolit
2026-05-13 | PXD078319 |