Nitrospira_nxrB_pH_experiment
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB47406 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Amplicon study of comammox Nitrospira responding to pH changes
| PRJEB47390 | ENA
Project description:Amplicon study of Nitrososphareales responding to pH changes
| PRJEB47407 | ENA
Project description:Seasonal amplicon study of comammox Nitrospira
| PRJEB47424 | ENA
Project description:Seasonal amplicon study of Nitrospira sp.
| PRJEB47446 | ENA
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:A large-scale discovery proteomics experiment was performed on biomass of Nitrospira moscoviensis (Lab head, Dr. Sebastian Lücker, RU, NL). The soluble protein fraction was analysed following high pH reverse-phase peptide fractionation. The insoluble membrane fraction was solubilised by an optimised protocol and analysed following cleavage using different proteolytic enzymes to maximise proteome coverage.
2021-07-22 | PXD019583 | Pride
Project description:We examined the methylation state of upstream intergenic regions associated with two aromatase genes (cyp19a1A and cyp19a1B) in P. pulcher, a cichlid fish with pH-based sex and male morph determination. Methylation levels in fry head and trunk and adult brain and gonad samples were assessed with a bisulfite amplicon sequencing assay and sequence data was processed through two pipelines to determine % methylation of individual CpG sites and abundance of specific patterns of methylated and unmethylated CpGs (i.e., epialleles).
2020-07-20 | GSE135681 | GEO
Project description:Nitrification, the oxidation of ammonia via nitrite to nitrate, has always been considered to be a two-step process catalysed by chemolithoautotrophic microorganisms oxidizing either ammonia or nitrite. No known nitrifier carries out both steps, although complete nitrification should be energetically advantageous. This functional separation has puzzled microbiologists for a century. Here we report on the discovery and cultivation of a completely nitrifying bacterium from the genus Nitrospira, a globally distributed group of nitrite oxidizers. The genome of this chemolithoautotrophic organism encodes the pathways both for ammonia and nitrite oxidation, which are concomitantly activated during growth by ammonia oxidation to nitrate. Genes affiliated with the phylogenetically distinct ammonia monooxygenase and hydroxylamine dehydrogenase genes of Nitrospira are present in many environments and were retrieved on Nitrospira contigs in new metagenomes from engineered systems. These findings fundamentally change our picture of nitrification and point to completely nitrifying Nitrospira as key components of nitrogen-cycling microbial communities.
2019-03-15 | PXD013103 | Pride
Project description:Amplicon sequencing of genus Nitrospira from nine Austrian saline-alkaline lakes
| PRJEB34917 | ENA