Denitrification experiments - bacteria
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB42532 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| ERR5285000.fastq.gz | Fastqsanger.gz | |||
| ERR5285010.fastq.gz | Fastqsanger.gz | |||
| ERR5285020.fastq.gz | Fastqsanger.gz | |||
| ERR5285030.fastq.gz | Fastqsanger.gz |
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Project description:Denitrification, a crucial biochemical pathway prevalent among haloarchaea in hypersaline ecosystems, has garnered considerable attention in recent years due to its ecological implications. Nevertheless, the underlying molecular mechanisms and genetic regulation governing this respiration/detoxification process in haloarchaea remain largely unexplored. In this study, RNA-sequencing was used to compare the transcriptomes of the haloarchaeon Haloferax mediterranei under oxic and denitrifying conditions, shedding light on the intricate metabolic alterations occurring within the cell such as the accurate control of the metal homeostasis. Furthermore, the investigation identifies several genes encoding transcriptional regulators and potential accessory proteins with putative roles in denitrification. Among these are bacterioopsin transcriptional activators, proteins harbouring a domain of unknown function (DUF2249), and a cyanoglobin. Additionally, the study delves into the genetic regulation of denitrification, finding a regulatory motif within promoter regions that activates numerous denitrification-related genes. This research serves as a starting point for future molecular biology studies in haloarchaea, offering a promising avenue to unravel the intricate mechanisms governing haloarchaeal denitrification, a pathway of paramount ecological importance.
2024-04-22 | GSE245042 | GEO
Project description:Coastal marine sediments, as locations of substantial fixed nitrogen loss, are very important to the nitrogen budget and to the primary productivity of the oceans. Coastal sediment systems are also highly dynamic and subject to periodic natural and anthropogenic organic substrate additions. The response to organic matter by the microbial community involved in nitrogen loss processes was evaluated using mesocosms of Chesapeake Bay sediments. Over the course of a 50-day incubation, rates of anammox and denitrification were measured weekly using 15N tracer incubations, and samples were collected for genetic analysis. Rates of both nitrogen loss processes and gene abundances associated with them corresponded loosely, probably because heterogeneities in sediments obscured a clear relationship. The rates of denitrification were stimulated more by the higher organic matter addition, and the fraction of nitrogen loss attributed to anammox slightly reduced. Furthermore, the large organic matter pulse drove a significant and rapid shift in the denitrifier community as determined using a nirS microarray, indicating the diversity of these organisms plays an essential role in responding to anthropogenic inputs. We also suggest that the proportion of nitrogen loss due to anammox in these coastal estuarine sediments may be underestimated due to temporal dynamics as well as from methodological artifacts related to conventional sediment slurry incubation approaches.
2015-01-30 | GSE65430 | GEO
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:Coastal marine sediments, as locations of substantial fixed nitrogen loss, are very important to the nitrogen budget and to the primary productivity of the oceans. Coastal sediment systems are also highly dynamic and subject to periodic natural and anthropogenic organic substrate additions. The response to organic matter by the microbial community involved in nitrogen loss processes was evaluated using mesocosms of Chesapeake Bay sediments. Over the course of a 50-day incubation, rates of anammox and denitrification were measured weekly using 15N tracer incubations, and samples were collected for genetic analysis. Rates of both nitrogen loss processes and gene abundances associated with them corresponded loosely, probably because heterogeneities in sediments obscured a clear relationship. The rates of denitrification were stimulated more by the higher organic matter addition, and the fraction of nitrogen loss attributed to anammox slightly reduced. Furthermore, the large organic matter pulse drove a significant and rapid shift in the denitrifier community as determined using a nirS microarray, indicating the diversity of these organisms plays an essential role in responding to anthropogenic inputs. We also suggest that the proportion of nitrogen loss due to anammox in these coastal estuarine sediments may be underestimated due to temporal dynamics as well as from methodological artifacts related to conventional sediment slurry incubation approaches. Two color array (Cy3 and Cy5): the universal standard 20-mer oligo is printed to the slide with a 70-mer oligo (an archetype). Environmental DNA sequences (fluoresced with Cy3) within 15% of the 70-mer conjugated to a 20-mer oligo (fluoresced with Cy5) complementary to the universal standard will bind to the oligo probes on the array. Signal is the ratio of Cy3 to Cy5. Three replicate probes were printed for each archetype. Two replicate arrays were run on duplicate targets.
2015-01-30 | E-GEOD-65430 | biostudies-arrayexpress
Project description:High-temperature fermentation of the Bacillus subtilis isolated from the black part of maotai Daqu. Studying on the gene expression profile using microarray for analyzing the connection between metabolites and the maotai flavor substances. 84 differential expressed genes were obtained, including 40 up-regulated genes and 44 down-regulated genes.The differentially expressed genes involved in the metabolic pathways were just only KBL (glycine C - acetyltransferase) and ripA (bifunctional 3, 4 - dihydroxy - 4-2 - butanone phosphate synthase), up-regulated 2.9 and 2.9 times respectively, and their catalytic reaction prodction of aminobutyric acid and dihydroxy ethyl ketone phosphate, respectively. They may be further derived into alcohol and ketone flavoring substances. However, a large number of differential expressed genes was related to sporulation, such as ybaN (polysaccharide deacetylase) and rapA (aspartic acid phosphatase), they were up-regulated 17.5 times and down-regulated 112.5 times. YbaN is closely related to the formation of spore cortex and high temperature group spore cortex obvious thickening by TEM. RapA is signaling molecules to restrain spore formation, its lower expression can promote the sporulation in group A. Formation and release of peptidoglycan and the DPA (2, 6 - Pyridinedicarboxylic acid) of spore cortex during theseveral rounds of low temperature to high temperature circulation fermentation may be the main source of furan and pyranand nitrogen heterocyclic compounds in maotai flavor substances . In this paper, the formation of high-temperature fermentation Bacillus subtilis spores is closely related to the generation of maotai flavor substances.
2016-07-18 | GSE71067 | GEO
Project description:Oxygen deficient zones (ODZs) are major sites of net natural oceanic nitrous oxide (N2O) production and emissions. In order to understand changes in the magnitude of N2O production in response to global change, knowledge on the individual contributions of the major microbial pathways (nitrification and denitrification) to N2O production and their regulation is needed. In the ODZ of the coastal area off Peru, the sensitivity of N2O production to oxygen and organic matter was investigated using 15N-tracer experiments in combination with qPCR and microarray analysis of total and active functional genes targeting archaeal amoA and nirS as marker genes for nitrification and denitrification, respectively. Denitrification was responsible for the highest N2O production with mean 8.7 nmol L-1 d-1 but up to 118 ± 27.8 nmol L-1 d-1 just below the oxic-anoxic interface. Highest N2O production from AO of 0.16 ± 0.003 nmol L-1 d-1 occurred in the upper oxycline at O2 concentrations of 10 - 30 µmol L-1 which coincided with highest archaeal amoA transcripts/genes. Oxygen responses of N2O production varied with substrate, but production and yields were generally highest below 10 µmol L-1 O2. Particulate organic matter additions increased N2O production by denitrification up to 5-fold suggesting increased N2O production during times of high particulate organic matter export. High N2O yields from ammonium oxidation of 2.1% were measured, but the overall contribution to N2O production stays an order of magnitude behind denitrification as an N2O source. Hence, these findings show that denitrification is the most important N2O production process in low oxygen conditions fueled by organic carbon supply which implies a positive feedback of the total oceanic N2O sources in response to increasing oceanic deoxygenation. [SUBMITTER_CITATION]: Frey, C., Bange, H. W., Achterberg, E. P., Jayakumar, A., Löscher, C. R., Arévalo-Martínez, D. L., León-Palmero, E., Sun, M., Sun, X., Xie, R. C., Oleynik, S., and Ward, B. B.: Regulation of nitrous oxide production in low-oxygen waters off the coast of Peru, Biogeosciences, 17, 2263-2287
2020-01-07 | GSE142805 | GEO
Project description:Oxygen deficient zones (ODZs) are major sites of net natural oceanic nitrous oxide (N2O) production and emissions. In order to understand changes in the magnitude of N2O production in response to global change, knowledge on the individual contributions of the major microbial pathways (nitrification and denitrification) to N2O production and their regulation is needed. In the ODZ of the coastal area off Peru, the sensitivity of N2O production to oxygen and organic matter was investigated using 15N-tracer experiments in combination with qPCR and microarray analysis of total and active functional genes targeting archaeal amoA and nirS as marker genes for nitrification and denitrification, respectively. Denitrification was responsible for the highest N2O production with mean 8.7 nmol L-1 d-1 but up to 118 ± 27.8 nmol L-1 d-1 just below the oxic-anoxic interface. Highest N2O production from AO of 0.16 ± 0.003 nmol L-1 d-1 occurred in the upper oxycline at O2 concentrations of 10 - 30 µmol L-1 which coincided with highest archaeal amoA transcripts/genes. Oxygen responses of N2O production varied with substrate, but production and yields were generally highest below 10 µmol L-1 O2. Particulate organic matter additions increased N2O production by denitrification up to 5-fold suggesting increased N2O production during times of high particulate organic matter export. High N2O yields from ammonium oxidation of 2.1% were measured, but the overall contribution to N2O production stays an order of magnitude behind denitrification as an N2O source. Hence, these findings show that denitrification is the most important N2O production process in low oxygen conditions fueled by organic carbon supply which implies a positive feedback of the total oceanic N2O sources in response to increasing oceanic deoxygenation. [SUBMITTER_CITATION]: Frey, C., Bange, H. W., Achterberg, E. P., Jayakumar, A., Löscher, C. R., Arévalo-Martínez, D. L., León-Palmero, E., Sun, M., Sun, X., Xie, R. C., Oleynik, S., and Ward, B. B.: Regulation of nitrous oxide production in low-oxygen waters off the coast of Peru, Biogeosciences, 17, 2263-2287
2020-01-07 | GSE142804 | GEO
Project description:High-temperature fermentation of the Bacillus subtilis isolated from the black part of maotai Daqu. Studying on the gene expression profile using microarray for analyzing the connection between metabolites and the maotai flavor substances. 84 differential expressed genes were obtained, including 40 up-regulated genes and 44 down-regulated genes.The differentially expressed genes involved in the metabolic pathways were just only KBL (glycine C - acetyltransferase) and ripA (bifunctional 3, 4 - dihydroxy - 4-2 - butanone phosphate synthase), up-regulated 2.9 and 2.9 times respectively, and their catalytic reaction prodction of aminobutyric acid and dihydroxy ethyl ketone phosphate, respectively. They may be further derived into alcohol and ketone flavoring substances. However, a large number of differential expressed genes was related to sporulation, such as ybaN (polysaccharide deacetylase) and rapA (aspartic acid phosphatase), they were up-regulated 17.5 times and down-regulated 112.5 times. YbaN is closely related to the formation of spore cortex and high temperature group spore cortex obvious thickening by TEM. RapA is signaling molecules to restrain spore formation, its lower expression can promote the sporulation in group A. Formation and release of peptidoglycan and the DPA (2, 6 - Pyridinedicarboxylic acid) of spore cortex during theseveral rounds of low temperature to high temperature circulation fermentation may be the main source of furan and pyranand nitrogen heterocyclic compounds in maotai flavor substances . In this paper, the formation of high-temperature fermentation Bacillus subtilis spores is closely related to the generation of maotai flavor substances. There are total of eight samples. It divided two groups, set as group A (High temperature fermentation) and B (normal temperature fermentation, continuous 37C). There are four replicates for each group.
2016-07-18 | E-GEOD-71067 | biostudies-arrayexpress
Project description:Denitrification 16S rRNA Sequencing Raw sequence reads
| PRJNA599274 | ENA
Project description:Autotrophic and heterotrophic denitrification Raw sequence reads
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