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PROVIDER: PRJNA1124006 | 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:Anthropogenic activities such as urbanization and agriculture can potentially pose a threat to neighboring freshwaters through nitrate and phosphorous contamination, which over time may lead to lake eutrophication. In such nitrogen-polluted environments, oxygen is depleted, and plants die and decompose. This enhances denitrifying microbes that respire under hypoxic/anoxic conditions by reducing nitrate instead of molecular oxygen and using plant remnants (lignocellulose) as carbon source. Microbial lignocellulose degradation has been well-studied for both aerobic- and anaerobic conditions; however, its degradation during denitrification remains largely unknown. Here we have applied a combination of gas kinetics and meta-omics techniques to enrich and analyze microbial communities from 10 eutrophic lakes to identify a set of core microbial metagenome-assembled genomes (MAGs) present in all the eutrophic lakes. We have further investigated their strategies and enzyme profiles for degrading lignocellulose under denitrifying conditions. We identified Pseudomonadota, Bacteroidota, Verrucomicrobiota, and Actinomycetota as the most abundant phyla and they were present in enrichments from all eutrophic lakes having a key role in denitrification and fermentation. Lignocellulose degradation was, however, dominated by species outside the core microbiome, i.e., there were differing key degraders between lakes, suggesting some level of lake-specialization. Among these we observed potential respiratory DNRA pathways, and they expressed a broad range of CAZymes targeting the various lignocellulose subfractions. Interestingly, many of the detected MAGs contained NO dismutases, enzymes postulated to convert NO to molecular oxygen and dinitrogen gas.
2026-04-30 | PXD069160 | Pride
Project description:Sulfur autotrophic denitrification reactor Raw sequence reads
| PRJNA1117246 | ENA
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
| PXD078319 |