Rhizosphere metagenome
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ABSTRACT:
PROVIDER: PRJNA344016 | ENA |
REPOSITORIES: ENA
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Project description:Enhancing nutrient use efficiency and productivity in rice based system
| PRJNA393493 | ENA
Project description:To increase crop yield without polluting the environment, improving crop nutrient efficiency is of great importance. The RSA of plants is centrally involved in nutrient use efficiency. Therefore, to uncover the molecular mechanisms that regulate RSA of maize under nutrient-deficiency conditions and to improve maize nutrient use efficiency based on this knowledge, we investigated the morphological changes and ribonucleic acid sequencing (RNA-seq) profiles of maize roots during growth under normal and N-, P-, and K-deficiency conditions. We analyzed the data in different aspects and verified the reliability of the RNA-seq data by real-time quantitative polymerase chain reaction (RT-qPCR). These results will provide theoretical support for improving plant nutrient use efficiency. The maize (Z. mays) inbred line DengHai 605 was used in this study. Provided for four treatment conditions: normal N, P, and K level (CK); potassium deficiency (K-DEF); nitrogen deficiency (N-DEF); and phosphorus deficiency (P-DEF). The experiments were carried out by combining sand culture with water culture. The standard for evaluating differential gene expression is fold change (FC) > 2 or FC < -2 and p value < 0.05.The numbers of DEGs under N-, P-, and K-deficiency conditions were 3494 (1801 up-regulated and 1693 down-regulated), 3424 (1761 up-regulated and 1663 down-regulated), and 1830 (827 up-regulated and 1003 down-regulated), respectively. A total of 1483, 1470, and 519 genes were specifically expressed under the N-, P-, and K-deficiency conditions, respectively.
2022-01-01 | GSE125417 | GEO
Project description:Projected responses of ocean net primary productivity (NPP) to climate change are highly uncertain. The climate sensitivity of phytoplankton nutrient limitation in the low-latitude Pacific plays a crucial role, but field measurements are insufficient to provide suitable constraints. Here we quantify two decades of nutrient limitation in the Equatorial Pacific with satellite observations. Using field nutrient addition experiments, proteomics, and above-water hyperspectral radiometry, we demonstrate that physiological responses of phytoplankton to iron limitation led to ~3-fold increases in chlorophyll-normalized phytoplankton fluorescence. Extension to the >18-year satellite fluorescence record showed that Equatorial Pacific iron limitation was robust to changes in physical forcing through multiple El Niño–Southern Oscillation cycles, despite coherent fluctuations in limitation strength. In contrast, these iron limitation changes were overestimated 2-fold by a state-of-the-art climate model. Such synoptic constraints provide a powerful new approach for benchmarking the realism of model NPP projections to climate changes.
2023-06-26 | PXD030610 | Pride
Project description:Global climate change increasingly challenges agriculture with flooding and salinity. Among strategies to enhance crop resilience to these stresses, we showed two mangrove strains that can enhance flooding and salinity tolerance in rice plants. Two strains massively enhanced the growth and yield of Oryza sativa cv. Nipponbare under hydroponic growth conditions with and without salt treatment. The bacteria-induced transcriptome changes in O. sativa roots related to ABA-signaling with suberin deposition in root tissues explain the altered responses of colonized rice plants to hypoxic and saline stress conditions. While enhancing yield and grain quality, bacterially colonized rice plants also show much earlier flowering, thereby massively shortening the life cycle of rice plants and opening the possibility for an additional harvest per year. These results show that microbes can be a powerful tool for enhancing the yield and resilience of rice to hypoxic and saline stress conditions.
2025-01-05 | GSE269165 | GEO
Project description:Freshwater is a limited and dwindling global resource; therefore, efficient water use is required for food crops that have high water demands, such as rice, or for the production of sustainable energy biomass. We show here that expression of the Arabidopsis HARDY (HRD) gene in rice improves water use efficiency, the ratio of biomass produced to the water used, by enhancing photosynthetic assimilation and reducing transpiration. These drought tolerant low-water-consuming rice plants exhibit increased shoot biomass under well irrigated conditions and an adaptive increase in root biomass under drought stress. The HRD gene, an AP2/ERF-like transcription factor, identified by a gain-of-function Arabidopsis mutant hrd-D having roots with enhanced strength, branching, and cortical cells, exhibits drought resistance and salt tolerance, accompanied by an enhancement in the expression of abiotic stress associated genes. Although HRD overexpression in Arabidopsis produces thicker leaves with more chloroplast-bearing mesophyll cells, in rice there is an increase in leaf biomass and bundle sheath cells that probably contribute to the enhanced photosynthesis assimilation and efficiency. HRD overexpression was also studied for clues of molecular mechanisms involved using microarrays. The results exemplify application of a gene identified from the model plant Arabidopsis for the improvement of water use efficiency coincident with drought resistance in the crop plant rice. Keywords: Genetic modification transcription factor overexpression mutant
2007-09-05 | GSE8936 | GEO
Project description:Genome-wide transcriptional profiling of Arabidopsis thaliana to a combination of heatwave and drought under ambient and elevated CO2. Goal of this study was elucidate the transcriptional responses to a combination of heat wave and drought, and to see how these responses are modifed under future climate (high) CO2. Climate changes increasingly threaten plant growth and productivity. Such changes are complex and involve multiple environmental factors, including rising CO2 levels and climate extreme events. As the molecular and physiological mechanisms underlying plant responses to realistic future climate extreme conditions are still poorly understood, a multiple organizational level-analysis (i.e. eco-physiological, biochemical and transcriptional) was performed, using Arabidopsis exposed to incremental heat wave and water deficit under elevated CO2.The climate extreme resulted in biomass reduction, photosynthesis inhibition, and considerable increases in stress parameters. Photosynthesis was a major target as demonstrated at the physiological and transcriptional levels. In contrast, the climate extreme treatment induced a protective effect on oxidative membrane damage, most likely as a result of strongly increased lipophilic antioxidants and membrane-protecting enzymes. Elevated CO2 significantly mitigated the negative impact of a combined heat and drought, as apparent in biomass reduction, photosynthesis inhibition, chlorophyll fluorescence decline, H2O2 production and protein oxidation. Analysis of enzymatic and molecular antioxidants revealed that the stress-mitigating CO2 effect operates through up-regulation of antioxidant defense metabolism, as well as by reduced photorespiration resulting in lowered oxidative pressure. Therefore, exposure to future climate extreme episodes will negatively impact plant growth and production, but elevated CO2 is likely to mitigate this effect.
2014-04-24 | GSE57035 | 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:Gene expression analysis of rice seedling under potassium deprivation
2015-05-13 | E-GEOD-44250 | ExpressionAtlas
Project description:Transcriptomic Analysis of Responses to Imbalanced Carbon:Nitrogen Availabilities in Rice Seedlings
2020-04-06 | E-MTAB-5118 | ExpressionAtlas
Project description:Microarray analysis of transcriptional responses to alkali stress in two rice genotypes
2016-01-08 | E-GEOD-45724 | ExpressionAtlas