Ontology highlight
ABSTRACT:
PROVIDER: PRJNA857755 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR20740732_1.fastq.gz | Fastqsanger.gz | |||
| SRR20740732_2.fastq.gz | Fastqsanger.gz | |||
| SRR20740733_1.fastq.gz | Fastqsanger.gz | |||
| SRR20740733_2.fastq.gz | Fastqsanger.gz | |||
| SRR20740734_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Anthropogenic perturbations to the nitrogen cycle, primarily through use of synthetic fertilizers, is driving an unprecedented increase in the emission of nitrous oxide (N2O), a potent greenhouse gas, and an ozone depleting substance, causing urgency in identifying the sources and sinks of N2O. Microbial denitrification is a primary contributor to the biotic production of N2O in anoxic regions of soil, marine systems, and wastewater treatment facilities. Here, through comprehensive genome analysis, we show that pathway partitioning is a ubiquitous mechanism of complete denitrification by microbial communities. We have further investigated the mechanisms and consequences of process partitioning through detailed physiological characterization and kinetic modeling of a synthetic community of Rhodanobacter R12 and Acidovorax 3H11. We have discovered that these two bacterial isolates from a heavily NO3- contaminated superfund site complete denitrification through the exchange of nitrite (NO2-) and nitric oxide (NO). Our findings further demonstrate that cooperativity within this denitrifying community emerges through process partitioning of denitrification and other processes, including amino acid metabolism. We demonstrate that certain contexts, such as high NO3-, cause unbalanced growth of community members, due to differences in their substrate utilization kinetics and inter-enzyme competition. The altered growth characteristics of community members drives accumulation of toxic NO2- , which disrupts denitrification causing N2O off gassing.
2025-06-18 | GSE272493 | GEO
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:Biological denitrification bacterial community YEM003
| PRJNA1051279 | ENA
Project description:Anthropogenic perturbations to the nitrogen cycle, primarily through use of synthetic fertilizers, have caused unprecedented increases in the emission of nitrous oxide (N2O) in recent decades. As a potent greenhouse gas, and an ozone depleting substance, understanding the sources and sinks of N2O is of vital importance. Nitrate (NO3-) reducing microbes are a primary contributor to the biotic production of N2O in anoxic regions of soil, marine systems, and wastewater treatment facilities through the process of denitrification. Thus, developing a better understanding of denitrifying microbial communities, and the environmental factors that influence N2O emissions may provide strategies to mitigate emissions in agriculture and wastewater treatment. Here, through comprehensive genome analysis, we show that pathway partitioning is a common strategy utilized by microbial communities to perform complete denitrification. Through detailed physiological characterization and kinetic modeling of a cooperative synthetic community (SynCom) assembled by pairing bacterial isolates from a field site heavily contaminated with NO3-, we also provide insight into the controls of N2O emissions. We demonstrate that members of this SynCom cooperate to perform complete denitrification through exchange of nitrite (NO2-) and nitric oxide (NO), and that community context drives global physiological changes in each member. We identify links between amino acid metabolism and denitrification activity as well as indicators of competition and amino acid exchange. We also show that NO2- toxicity with unbalanced growth of community members drives N2O production, suggesting that this SynCom provides a simplified, environmentally relevant, model of pathway partitioning in denitrifying communities. This SynCom should provide a framework with which to further explore how environmental context can impact cooperation and lead to the production of N2O
2025-06-24 | PXD051979 | Pride
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