Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1015442 | ENA |
REPOSITORIES: ENA
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Project description:Biological nitrogen fixation (BNF) is an essential source of new nitrogen for terrestrial ecosystems. The abiotic factors regulating BNF have been extensively studied in various ecosystems and laboratory settings. Despite this, our understanding of the impact of neighbouring bacteria on N2 fixer activity remains limited. Here, we explored this question using a coculture of the free-living diazotroph Azotobacter vinelandii and the non-fixing plant growth-promoting rhizobacteria Bacillus subtilis. We assessed the interaction between the two bacteria under low N availability.
2024-10-15 | PXD056293 | Pride
Project description:Casuarina glauca belongs to a family of angiosperms called actinorhizal plants because they can develop nitrogen-fixing nodules in association with the soil bacteria Frankia. The aim of this transcriptomic study was to get a global view of the plant symbiotic genetic program and to identify new key plant genes that control nodulation during symbiosis in C. glauca. Symbiosis between C. glauca and Frankia was obtained after inoculation of young plant with a concentrated culture of the bacteria. Inoculation was performed in a medium depleted in nitrogen which favors the induction of nitrogen fixing symbiosis. For this study we considered two stages of symbiosis: - an early stage where inoculated roots were harvested 7 days after inoculation with the bacteria and compared to two controls (non-inoculated roots grown with or without nitrogen and harvested at the same time) - a late stage where nodules (nitrogen-fixing specific organs) were harvested 21 days after inoculation and compared to non-inoculated roots harvested on the day of inoculation (which is our reference time 0d). Three biological replicates were used for each condition.
2011-04-07 | GSE24158 | GEO
Project description:Alnus glutinosa belongs to a family of angiosperms called actinorhizal plants because they can develop nitrogen-fixing nodules in association with the soil bacteria Frankia. The aim of this transcriptomic study was to get a global view of the plant symbiotic genetic program and to identify new key plant genes that control nodulation during symbiosis in A. glutinosa. Symbiosis between A. glutinosa and Frankia was obtained after inoculation of young plant with a concentrated culture of the bacteria. Inoculation was performed in a medium depleted in nitrogen which favors the induction of nitrogen fixing symbiosis. For this study we considered two stages of symbiosis: - an early stage where inoculated roots were harvested 7 days after inoculation with the bacteria and compared to two controls (non-inoculated roots grown with or without nitrogen and harvested at the same time) - a late stage where nodules (nitrogen-fixing specific organs) were harvested 21 days after inoculation and compared to non-inoculated roots harvested on the day of inoculation (which is our reference time 0d). Three biological replicates were used for each condition.
2011-04-11 | GSE24153 | GEO
Project description:Casuarina glauca belongs to a family of angiosperms called actinorhizal plants because they can develop nitrogen-fixing nodules in association with the soil bacteria Frankia. The aim of this transcriptomic study was to study the role of the plant growth regulator auxin during actinorhizal symbiosis and to identify key plant genes that are involved in auxin signaling during symbiosis in C. glauca. Symbiosis between C. glauca and Frankia was obtained after inoculation of young plant with a concentrated culture of the bacteria. Inoculation was performed in a medium depleted in nitrogen (N2) which favors the induction of nitrogen fixing symbiosis. For auxin role study, plant were treated with 25µM 1-naphtoxy acetic acid (1-NOA) all along nodulation time. Nodule were harvested 3 weeks after inoculation. For this study we considered two stages: - 21 days old nodules obtained on plants not treated with 1-NOA (control condition) - 21 days old nodules obtained on plants supplemented with 25µM of 1-NOA. Three biological replicates were used for each condition, however due to non valid staistics, two of the replicates (one for control condition, one for treated condition were removed.
2014-12-31 | GSE55582 | GEO
Project description:The bacterium, Sinorhizobium meliloti, interacts symbiotically with leguminous plants such as Medicago truncatula to form nitrogen-fixing root nodules. During symbiosis, plant and bacterial cells differentiate in a coordinated manner, resulting in specialized plant cells that contain nitrogen-fixing bacteroids. Medicago nodules are organized in structurally distinct tissue zones, representing different stages of bacterial and plant differentiation. We used laser-capture microdissection (LCM) to analyze bacterial and plant gene expression in four root nodule regions. In parallel, we analyzed gene expression in nodules formed by wild type bacteria on six plant mutants with nitrogen fixation deficiencies (dnf). We found that bacteroid metabolism is drastically remodeled during bacteroid differentiation. Many processes required for bacterial growth are down-regulated in the nitrogen fixation zone. The overall transcriptional changes are similar to those occurring during nutrient limitation by the stringent response. We also observed differential expression of bacterial genes involved in nitrogen fixation, cell envelope homeostasis, cell division, stress response and polyamine biosynthesis at distinct stages of nodule development. In M. truncatula we observed the differential regulation of several host processes that may trigger bacteroid differentiation and control bacterial infection. We analyzed plant and bacterial gene expression simultaneously, which allowed us to correlate processes in both organisms.
2015-06-01 | GSE53705 | GEO
Project description:Arabidopsis thaliana 4-day-old seedlings were treated with the plant growth promoting rhizobacteria Caulobacter RHG1 or the neutral bacteria Bacillus sp. At 12 and 48 hours after treatment, roots were harvested, RNA was extracted and RNA-Seq data were generated. The goal of this experiment was to detect changes at the transcript level that were specific for the plant growth promoting rhizobacteria RHG1.
2023-03-11 | E-MTAB-12690 | biostudies-arrayexpress
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:Casuarina glauca belongs to a family of angiosperms called actinorhizal plants because they can develop nitrogen-fixing nodules in association with the soil bacteria Frankia. They can also develop arbuscular mycorrhizae (AM) while associated with Glomeromycota fungi. The aim of this transcriptomic study was to get a global view of the plant symbiotic genetic program in AM and to identify new key plant genes involved in endosymbioses.
2012-10-22 | GSE36676 | GEO
Project description:Casuarina glauca belongs to a family of angiosperms called actinorhizal plants because they can develop nitrogen-fixing nodules in association with the soil bacteria Frankia. The aim of this transcriptomic study was to get a global view of the plant symbiotic genetic program and to identify new key plant genes that control nodulation during symbiosis in C. glauca. Symbiosis between C. glauca and Frankia was obtained after inoculation of young plant with a concentrated culture of the bacteria. Inoculation was performed in a medium depleted in nitrogen which favors the induction of nitrogen fixing symbiosis. For this study we considered two stages of symbiosis: - an early stage where inoculated roots were harvested 7 days after inoculation with the bacteria and compared to two controls (non-inoculated roots grown with or without nitrogen and harvested at the same time) - a late stage where nodules (nitrogen-fixing specific organs) were harvested 21 days after inoculation and compared to non-inoculated roots harvested on the day of inoculation (which is our reference time 0d). Three biological replicates were used for each condition. Microarrays were designed by Imaxio (Clermont Ferrand, France ; http://www.imaxio.com/index.php) which has been accredited by Agilent Technologies (Palo Alto, CA, USA; http://www.home.agilent.com/agilent/home.jspx) as a certified service provider for microarray technologies. Based on 14327 annotated unigenes for C. glauca, 60mers probes were designed using eArray software (1 probe per unigene) and custom 8 x 15K Oligo Microarrays were manufactured by Agilent.
2011-04-07 | E-GEOD-24158 | biostudies-arrayexpress
Project description:Alnus glutinosa belongs to a family of angiosperms called actinorhizal plants because they can develop nitrogen-fixing nodules in association with the soil bacteria Frankia. The aim of this transcriptomic study was to get a global view of the plant symbiotic genetic program and to identify new key plant genes that control nodulation during symbiosis in A. glutinosa. Symbiosis between A. glutinosa and Frankia was obtained after inoculation of young plant with a concentrated culture of the bacteria. Inoculation was performed in a medium depleted in nitrogen which favors the induction of nitrogen fixing symbiosis. For this study we considered two stages of symbiosis: - an early stage where inoculated roots were harvested 7 days after inoculation with the bacteria and compared to two controls (non-inoculated roots grown with or without nitrogen and harvested at the same time) - a late stage where nodules (nitrogen-fixing specific organs) were harvested 21 days after inoculation and compared to non-inoculated roots harvested on the day of inoculation (which is our reference time 0d). Three biological replicates were used for each condition. Microarrays were designed by Imaxio (Clermont Ferrand, France ; http://www.imaxio.com/index.php) which has been accredited by Agilent Technologies (Palo Alto, CA, USA; http://www.home.agilent.com/agilent/home.jspx) as a certified service provider for microarray technologies. Based on 14327 annotated unigenes for A. glutinosa, 60mers probes were designed using eArray software (1 probe per unigene) and custom 8 x 15K Oligo Microarrays were manufactured by Agilent
2011-04-11 | E-GEOD-24153 | biostudies-arrayexpress