Bradyrhizobium sp.
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ABSTRACT:
PROVIDER: PRJNA362972 | ENA |
REPOSITORIES: ENA
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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
Project description:Nodule-forming bacteria play crucial roles in plant health and nutrition by fixing atmospheric nitrogen. Despite the importance of this relationship, how nodule-forming bacteria are affected by plant exudates and soil minerals is not fully characterized. Of particular interest are the effects of plant-derived methanol and lanthanide metals on the growth of nitrogen-fixing Rhizobiales. Prior work has demonstrated that select Bradyrhizobium are able to assimilate methanol only in the presence of lanthanide metals; however, the pathway enabling assimilation remains unknown. Here we characterize Bradyrhizobium sp. USDA 3456 to determine the pathways involved in methanol metabolism. Based on genomic analyses, we hypothesized that methanol assimilation in these organisms occurs via the lanthanide-dependent methanol dehydrogenase XoxF, followed by oxidation of formaldehyde via the glutathione-linked oxidation pathway, subsequent oxidation of formate via formate dehydrogenases, and finally assimilation of CO2 via the Calvin Benson Bassham (CBB) pathway. Transcriptomics revealed upregulation of the aforementioned pathways in Bradyrhizobium sp. USDA 3456 during growth on methanol. Assays demonstrated increased activity of the glutathione-linked oxidation pathway and formate dehydrogenases during growth on methanol compared to succinate. 13C-labeling studies demonstrate the presence of CBB intermediates and label incorporation during growth on methanol. Our findings provide multiple lines of evidence supporting the proposed XoxF-CBB pathway and, combined with genomic analyses, suggest that this metabolism is widespread among Bradyrhizobium and Sinorhizobium species.
2025-06-27 | GSE295604 | GEO
Project description:Analysis of a Bradyrhizobium japonicum pmtA mutant. PmtA catalyzes the first of three consecutive methylation reactions leading to phosphatidylcholine (PC) formation in B. japonicum. Disruption of the pmtA gene results in a significantly reduced PC content causing a defect in symbiosis with the soybean host. This study provides the first insight into global transcriptomic changes of a bacterial phosphatidylcholine biosynthesis mutant. Cells of the pmtA mutant and the wild type were grown to mid-exponential phase in full medium (PSY) under aerobic culture conditions. Keywords: genetic modification
2008-04-17 | GSE11187 | GEO
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:To dissect differences in gene expression profile of soybean roots inoculated with wild-type and type III secretion mutant rhizobia, we have employed microarray analysis. Seeds of soybean (Glycine max L. cv. BARC-2 (Rj4/Rj4)) were surface-sterilized and germinated at 25 °C for 2 days and were transferred to the seed pack (Seed Pack; Daiki rika Kogyo Co., Ltd., Shiga, Japan) watered with B&D nitrogen-free medium (Broughton and Dilworth 1971). One day after transplant, each seedling was inoculated with Bradyrhizobium elkanii USDA61 or its type III secretion mutant BErhcJ. Plants were cultivated in a growth chamber at 25°C and 70% humidity with a daytime of 16 h followed by a nighttime of 8 h. To determine the gene expression, RNA was extracted from the roots 2 and 4 days after inoculation. Gene expression in soybean roots inoculated with Bradyrhizobium elkanii USDA61, its type III secretion mutant BErhcJ was measured 2 and 4 days after inoculation. Three independent experiments were performed at each inoculation.
2016-03-09 | E-GEOD-79015 | biostudies-arrayexpress
Project description:Global bottom-up proteomics analysis of proteins purified from soybean root nodules infected with either WT or nifH- mutant Bradyrhizobium japonicum. Nine glycoproteins containing Lewis-a N-glycans, with 3 distinct Lewis-a epitopes (Hex:5 HexNAc:4 dHex:3 Pent:1, Hex:4 HexNAc:4 dHex:2 Pent:1, and Hex:4 HexNAc:3 dHex:2 Pent:1) were observed. Proteins purified from WT and nifH- infected soybean root nodules (five biological replicates each) were reduced using dithiothreitol, alkylated with iodoacetamide and trypsin digested followed by C18 SPE clean-up and LC-MS/MS analysis. Raw data files were processed using FragPipe v17.1, then output files 'combined_modified_peptide.tsv' and 'combined_protein.tsv' were used to identify glycopeptides and for global protein quantitation. These files, along with Excel files containing global quantitation analysis files for soybean nodule (Glycine max) and bacterial (Bradyrhizobium), are available in directory 'Quantification/MSFragger_results'. Glycopeptide data were also processed with PMI Byonic, and Excel file results are available in directory 'Quantification/PMI_Byonic_results'.
2022-01-31 | MSV000088754 | MassIVE
Project description:Metabolomics and transcriptomics of Bradyrhizobium diazoefficiens-induced root nodules Bradyrhizobium diazoefficiens is a nitrogen-fixing endosymbiont, which can grow inside root-nodule cells of the agriculturally important soybean and other host plants. Our previous studies described B. diazoefficiens host-specific global expression changes occurring during legume infection at the transcript and protein level. In order to further characterize nodule metabolism, we here determine by flow injection -time of flight mass spectrometry analysis the metabolome of i) nodules and roots from four different B. diazoefficiens host plants, ii) soybean nodules harvested at different time points during nodule development, and iii) soybean nodules infected by two strains mutated in key genes for nitrogen fixation, respectively. Ribose (soybean), tartaric acid (mungbean), hydroxybutanoyloxybutanoate (siratro) and catechol (cowpea) were among the metabolites found to be specifically elevated in one of the respective host plants. While the level of C4-dicarboxylic acids decreased during soybean nodule development, we observed an accumulation of trehalose-phosphate at 21 days post infection (dpi). Moreover, nodules from non-nitrogen-fixing bacteroids (nifA and nifH mutants) showed specific metabolic alterations; these were also supported by transcriptomics data that was generated for the two mutant strains and were helpful to separate for some examples the respective bacterial and plant contributions to the metabolic profile. The alterations included signs of nitrogen limitation in both mutants, and an increased level of a phytoalexin in nodules induced by the nifA mutant, suggesting that the tissue of these nodules exhibits defense and stress reactions.
2016-11-28 | GSE79811 | GEO
Project description:Lipo-chitooligosaccharides (LCOs) produced by N2-fixing rhizobacteria initiate host nodule formation. Foliar application of LCOs has been shown to induce stress-related genes under optimal growth conditions. To study the effects of LCO foliar spray under stressed conditions, soybean seedlings grown at optimal temperature were exposed to sub-optimal temperature. After a 5-day acclimation period, the first trifoliolate leaves were sprayed with 10-7 M LCO (NodBj-V (C18:1, MeFuc)) produced by Bradyrhizobium japonicum, and harvested at 0 and 48 h following treatment. Microarray analysis was performed using Affymetrix GeneChip® Soybean Genome Arrays. A total of 147 genes were differentially expressed 48 h after LCO treatment, including a number of stress-related genes and transcription factors. In addition, during the 48 h following treatment, hundreds of genes were differentially expressed in LCO-treated plants, indicating that the dynamic soybean foliar transcriptome was highly responsive to LCO treatment. The microarray data was supported by quantitative real-time PCR data. Soybean seedlings grown at optimal temperature (25 °C) were exposed to sub-optimal temperature (15 °C). After a 5-day acclimation period, the first trifoliolate leaves were sprayed with 10-7 M LCO (NodBj-V (C18:1, MeFuc)) produced by Bradyrhizobium japonicum, and harvested at 0 and 48 h following treatment. Total RNA was extracted and microarray analysis was performed using Affymetrix GeneChip® Soybean Genome Arrays.
2010-03-20 | E-GEOD-20972 | biostudies-arrayexpress
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. Transciptomic expression profiles indicated that genes involved in carbon/nitrogen metabolism, 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, 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. Bradyrhizobium japonicum strains were grown in the soybean rhizosphere under two different CO2 concentrations. Transcriptional profiling of B. japonicum was compared between cells grown under elevated CO2 and ambient conditions. Four biological replicates of each treatment were prepared, and four microarray slides were used for each strain.
2010-07-28 | E-GEOD-23296 | biostudies-arrayexpress