DNRA dominates denitrification in rhizosphere and non-rhizosphere soil
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA625432 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR11585717.fastq.gz | Fastqsanger.gz | |||
| SRR11585718.fastq.gz | Fastqsanger.gz | |||
| SRR11585719.fastq.gz | Fastqsanger.gz | |||
| SRR11585720.fastq.gz | Fastqsanger.gz | |||
| SRR11585721.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 48 |
Similar Datasets
Project description:DNRA Acididesulfobacillus acetoxydans
| PRJEB64595 | ENA
Project description:Elevated atmospheric CO2 can influence the structure and function of rhizosphere microorganisms by altering root growth and the quality and quantity of compounds released into the rhizosphere via root exudation. In these studies we investigated the transcriptional responses of Bradyrhizobium japonicum cells growing in the rhizosphere of soybean plants exposed to elevated atmospheric CO2. The results of microarray analyses indicated that atmospheric elevated CO2 concentration indirectly influences on expression of large number of Bradyrhizobium genes through soybean roots. In addition, genes involved in C1 metabolism, denitrification and FixK2-associated genes, including those involved in nitrogen fixation, microanaerobic respiration, respiratory nitrite reductase, and heme biosynthesis, were significantly up-regulated under conditions of elevated CO2 in the rhizosphere, relative to plants and bacteria grown under ambient CO2 growth conditions. The expression profile of genes involved in lipochitinoligosaccharide Nod factor biosynthesis and negative transcriptional regulators of nodulation genes, nolA and nodD2, were also influenced by plant growth under conditions of elevated CO2. Taken together, results of these studies indicate that growth of soybeans under conditions of elevated atmospheric CO2 influences gene expressions in B. japonicum in the soybean rhizosphere, resulting in changes to carbon/nitrogen metabolism, respiration, and nodulation efficiency.
2010-07-29 | GSE23296 | GEO
Project description:Gene expression patterns of the plant colonizing bacterium,Pseudomonas putida KT2440 were evaluated as a function of growth in the Arabidopsis thaliana rhizosphere. Gene expression in rhizosphere grown P. putida cells was compared to gene expression in non-rhizosphere grown cells. Keywords: Gene expression
2008-01-11 | GSE9005 | GEO
Project description:N retention in soils can be stimulated by microorganisms carrying out dissimilatory reduction of nitrate to ammonia (DNRA), a respiratory activity that converts nitrate and/or nitrite to ammonia. Geobacter lovleyi has recently being recognized as a key driver of DNRA, providing a model to investigate the environmental signals that promote nitrate ammonification. Here we show that low nitrate concentrations (5mM) induce DNRA in G. lovleyi independently of the concentration of the electron donor, thus challenging the prevailing view that high carbon-to-nitrogen (C/N) ratio triggers this process. The nitrate transcriptome revealed a complex metabolic network of periplasmic (Nap) and cytoplasmic (Nar) nitrate reductase systems for the reduction of nitrate to nitrite. The transcriptome also included a canonical (NrfA-1), two Geobacter-specific nitrite reductases (NrfA-2 and NrfA-3) and a membrane-bound NrfH cytochrome, which electronically connects NrfA to the menaquinone pool. Flagellar motility and chemotaxis proteins were also among the most upregulated genes in the nitrate cultures, consistent with an adaptive response that allows Geobacter cells to sense and access the limited supply of nitrate in anaerobic zones of the soils and sediments. This is the first demonstration of the ability of the bacteria to use DNRA pathway under nitrate limiting conditions independently of the C/N ratio. G. lovleyi provides a model for study DNRA process and it is a good candidate that could contribute in the retention of nitrogen in soils leading to efficient use of nitrogen containing fertilizers and preventing nitrate leaching.
2024-12-31 | GSE164776 | GEO
Project description:We present metaproteome data from wheat rhizosphere from saline and non-saline soil. For collection and acquisition of metaproteome from wheat rhizosphere under saline and normal conditions, a survey was conducted in regions of Haryana, India. Samples from 65 days old plants (wheat var HD2967) were collected and pooled and based on EC,saline (NBAIM B; EC 6mS cm-1; pH 9.0; Bhaupur 2, Haryana, INDIA; 29°19'8"N;76°48'53"E) and normal soil samples (NBAIM C; EC 200 uS cm-1; pH 7.2; Near Nainform, Haryana, INDIA; 29°19'8"N;76°48'53"E) were selected for isolation of proteome with the standardized protocol at our laboratory followed by metaproteome analysis with the standardized pipepline. In total 1538 and 891 proteins were obtained from wheat rhizosphere from saline and non-saline respectively with the given parameters and software. Among 1410 proteins unique for saline soil, proteins responsible for glycine, serine and threonine metabolism and arginine and proline biosynthesis were found in saline and absent in non-saline. The present study extends knowledge about the physiology and adaptations of the wheat rhizosphere associated microbiota under saline soil.
2024-01-08 | PXD015387 | Pride
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: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:Baiyangdian DNRA riparian zone Raw sequence reads
| PRJNA605093 | ENA
Project description:Denitrification and dissimilatory nitrate reduction to ammonium (DNRA) both require low oxygen and high organic carbon conditions common in wetland ecosystems. Denitrification permanently removes nitrogen from the ecosystem as a gas while DNRA recycles nitrogen within the ecosystem via production of ammonium. The relative prevalence of denitrification versus DNRA has implications for the fate of nitrate in ecosystems. Unplanned and unmanaged urban accidental wetlands in the Salt River channel near downtown Phoenix, Arizona, USA receive high nitrate relative to non-urban wetlands and have a high capacity for denitrification, but unknown capacity for DNRA. We conducted in-situ push-pull tests with isotopically labelled nitrate to measure denitrification and DNRA rates in three of the dominant vegetative patch types in these urban accidental wetlands. DNRA accounted for between 2 and 40% of nitrate reduction (DNRA plus denitrification) with the highest rates measured in patches of Ludwigia peploides compared to Typha spp. and non-vegetated patches. The wetland patches were similar with respect to dissolved organic carbon concentration but may have differed in carbon lability or strength of reducing conditions due to a combination of litter decomposition and oxygen supply via diffusion and aerenchyma. The ratio of DNRA to denitrification was negatively correlated with nitrate concentration, indicating that DNRA may become a more important pathway for nitrate attenuation at low nitrate concentration. Although DNRA was generally lower than denitrification, this pathway was an important component of nitrate attenuation within certain patches in these unmanaged urban accidental wetlands.
| S-EPMC8896236 | biostudies-literature
Project description:Arsenic (As) bioavailability in the rice rhizosphere is influenced by many microbial interactions, particularly by metal-transforming functional groups at the root-soil interface. This study was conducted to examine As-transforming microbes and As-speciation in the rice rhizosphere compartments, in response to two different water management practices (continuous and intermittently flooded), established on fields with high to low soil-As concentration. Microbial functional gene composition in the rhizosphere and root-plaque compartments were characterized using the GeoChip 4.0 microarray. Arsenic speciation and concentrations were analyzed in the rhizosphere soil, root-plaque, porewater and grain samples. Results indicated that intermittent flooding significantly altered As-speciation in the rhizosphere, and reduced methyl-As and AsIII concentrations in the pore water, root-plaque and rice grain. Ordination and taxonomic analysis of detected gene-probes indicated that root-plaque and rhizosphere assembled significantly different metal-transforming functional groups. Taxonomic non-redundancy was evident, suggesting that As-reduction, -oxidation and -methylation processes were performed by different microbial groups. As-transformation was coupled to different biogeochemical cycling processes establishing functional non-redundancy of rice-rhizosphere microbiome in response to both rhizosphere compartmentalization and experimental treatments. This study confirmed diverse As-biotransformation at root-soil interface and provided novel insights on their responses to water management, which can be applied for mitigating As-bioavailability and accumulation in rice grains.
2021-07-12 | GSE179671 | GEO