Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Wastewater metagenome

ABSTRACT: nitrogen fixation microbes Metagenome

PROVIDER: PRJNA310392 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR3140980_1.fastq.gz	Fastqsanger.gz
	SRR3140980_2.fastq.gz	Fastqsanger.gz
	SRR3140963_1.fastq.gz	Fastqsanger.gz
	SRR3140963_2.fastq.gz	Fastqsanger.gz
	SRR3140974_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 12

Similar Datasets

Soil metagenome from avocado orchards in Channybearup, Western Australia in 2024

Project description:Metagenome data from soil samples were collected at 0 to 10cm deep from 2 avocado orchards in Channybearup, Western Australia, in 2024. Amplicon sequence variant (ASV) tables were constructed based on the DADA2 pipeline with default parameters.

2025-06-15 | GSE298403 | GEO

soil metagenome

Project description:black soil nitrogen-fixation bacteria Metagenome

| PRJNA385763 | ENA

Anode respiration-dependent biological nitrogen fixation by Geobacter sulfurreducens

Project description:Our study revealed a synergistic effect between biological nitrogen fixation and current generation by G. sulfurreducens, providing a green nitrogen fixation alternative through shifting the nitrogen fixation field from energy consumption to energy production and having implications for N-deficient wastewater treatment.

2021-10-09 | GSE185414 | GEO

Project description:Nitrogen fixation

| PRJNA869511 | ENA

Transcriptional dynamics of nitrogen fixation and senescence in soybean nodules: A dual perspective on host and Bradyrhizobium regulation

Project description:The soybean–Bradyrhizobium symbiosis enables symbiotic nitrogen fixation (SNF) within root nodules, reducing reliance on synthetic N fertilizers. However, nitrogen fixation is transient, peaking several weeks after Bradyrhizobium colonization and declining as nodules senesce in coordination with host development. To investigate the regulatory mechanisms governing SNF and senescence, we conducted a temporal transcriptomic analysis of soybean nodules colonized with Bradyrhizobium diazoefficiens USDA110. Weekly nodule samples (2 to 10 weeks postinoculation, wpi) were analyzed using RNA and small RNA sequencing, and acetylene reduction assays assessed nitrogenase activity from 4 to 7 wpi. We identified three major nodule developmental phases: early development (2 to 3 wpi), nitrogen fixation (3 to 8 wpi), and senescence (8 to 10 wpi). Soybean showed extensive transcriptional reprogramming during senescence, whereas Bradyrhizobium underwent major transcriptional shifts early in development before stabilizing during nitrogen fixation. We identified seven soybean genes and several microRNAs as candidate biomarkers of nitrogen fixation, including lipoxygenases (Lox), suggesting roles for oxylipin metabolism. Soy hemoglobin-2 (Hb2), previously classified as nonsymbiotic, was upregulated during senescence, implicating oxidative stress responses within aging nodules. Upregulation of the Bradyrhizobium paa operon and rpoH during senescence suggesting metabolic adaptation for survival beyond symbiosis. Additionally, Bradyrhizobium nif gene expression showed stage-specific regulation, with nifK peaking at 2 wpi, nifD and nifA at 2 and 10 wpi, and nifH, nifW, and nifS at 10 wpi. These findings provide insights into SNF regulation and nodule aging, revealing temporal gene expression patterns that could inform breeding or genetic engineering strategies to enhance nitrogen fixation in soybeans and other legume crops.

2025-12-29 | GSE289665 | GEO

The NAC transcription factors SNAP1/2/3/4 are central regulators mediating high nitrogen responses in mature nodules of soybean

Project description:Legumes can utilize atmospheric nitrogen via symbiotic nitrogen fixation, but this process is inhibited by high soil inorganic nitrogen. So far, how high nitrogen inhibits N2 fixation in mature nodules is still poorly understood. Here we construct a co-expression network in soybean nodule and find that a dynamic and reversible transcriptional network underlies the high N inhibition of N2 fixation. Intriguingly, several NAC transcription factors (TFs), designated as Soybean Nitrogen Associated NAPs (SNAPs), are amongst the most connected hub TFs. The nodules of snap1/2/3/4 quadruple mutants show less sensitivity to the high N inhibition of nitrogenase activity and acceleration of senescence. Integrative analysis shows that these SNAP TFs largely influence the high N transcriptional response through direct regulation of a subnetwork of senescence-associated genes and transcriptional regulators. We propose that the SNAP-mediated transcriptional network may trigger nodule senescence in response to high N.

2023-07-05 | GSE236557 | GEO

soil metagenome

Project description:soil free-living nitrogen fixation (PRJCA039690)

| PRJDB36659 | ENA

Transcriptional profile of Escherichia coli K12 strain DH10B harboring A1501 nitrogen fixation island (NFI) under nitrogen fixation conditions

Project description:A1501 NFI is a genomic island derived from Pseudomonas stutzeri A1501. To study the molecular interactions of the P. stutzeri nif genes with the E. coli genome during nitrogen fixation, the NIF of A1501 was transferred into E. coli and comparative transcriptomics analyses were performed between nitrogen fixation conditions and nitrogen excess conditions.

2015-08-05 | GSE37780 | GEO

Project description:Nitrogen fixation H

| PRJNA869518 | ENA

CPOP1 is the key heme synthesis enzyme required for nodule microenvironment control and successful symbiotic nitrogen fixation in Lotus japonicus

Project description:Heme is utilized as the cofactor of diverse proteins and plays critical roles in different redox reactions. The fixation active nodules of legumes are abundant with heme-containing leghemoglobin to buffer the oxygen concentration. Symbiotic rhizobia could also synthesize heme, and employ heme for efficient respiration and iron uptake regulation. However, the role and regulation of host-controlled heme production during symbiotic nitrogen fixation have not been directly investigated and experimentally proved. Here, we identified the coproporphyrinogen III oxidase plastid related 1 (CPOP1) as a key regulator of symbiotic heme synthesis enzyme in Lotus japonicus. CPOP1 is specifically highly expressed in nitrogen-fixing nodules, and knocking out CPOP1 alone causes leaf etiolation and dwarfism which could be fully recovered by the exogenous application of nitrogen source, indicating nitrogen fixation defect. The cpop1 mutant shows significantly increased nodule oxygen level and decreased nitrogen fixation activity compared to the wild type (WT). Moreover, cell division and related gene expression of bacteroids are also affected upon CPOP1 knockout. We conclude that CPOP1 is essential for the microaerophilic environment control of infected cells and the activation of rhizobial nitrogenase required for symbiotic nitrogen fixation, through host-regulated nodule heme synthesis.

2025-09-01 | GSE262662 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data