PhytOakmeter root-associated microbiome
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB35688 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR3770420_1.fastq.gz | Fastqsanger.gz | |||
| ERR3770420_2.fastq.gz | Fastqsanger.gz | |||
| ERR3770430_1.fastq.gz | Fastqsanger.gz | |||
| ERR3770430_2.fastq.gz | Fastqsanger.gz | |||
| ERR3770440_1.fastq.gz | Fastqsanger.gz |
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Project description:Broad-host root endophytes establish long-term interactions with a large variety of plants, thereby playing a significant role in natural and managed ecosystems and in evolution of land plants. To exploit plants as living substrates and to establish a compatible interaction with morphologically and biochemically extremely different hosts, endophytes must respond and adapt to different plant signals and host metabolic states. Here we identified host-adapted colonization strategies and host-specific effector candidates of the mutualistic root endophyte Piriformospora indica by a global investigation of fungal transcriptional responses to barley and Arabidopsis at different symbiotic stages. Additionally we examined the role played by nitrogen in these two diverse associations. Cytological studies and colonization analyses of a barley mutant and fungal RNAi strains show that distinct physiological and metabolic signals regulate host-specific lifestyle in P. indica. This is the foundation for exploring how distinct fungal and host symbiosis determinants modulate biotrophy in one host and saprotrophy in another host and, ultimately, gives hints into the mechanisms underlying host adaptation in root symbioses.
2013-07-22 | GSE47775 | GEO
Project description:Low phosphate concentrations are frequently a constraint for maize growth and development, and therefore, enormous quantities of phosphate fertilizer are expended in maize cultivation, which increases the cost of planting. Low phosphate stress not only increases root biomass but can also cause significant changes in root morphology. Low phosphate availability has been found to favor lateral root growth over primary root growth by dramatically reducing primary root length and increasing lateral root elongation and lateral root density in Arabdopsis. While in our assay when inbred line Q319 subjected to phosphate starvation, The numbers of lateral roots and lateral root primordia were decreased after 6 days of culture in a low phosphate solution (LP) compared to plants grown under normal conditions (sufficient phosphate, SP), and these differences were increased associated with the stress caused by phosphate starvation. However, the growth of primary roots appeared not to be sensitive to low phosphate levels. This is very different to Arabidopsis. To elucidate how low phosphate levels regulate root modifications, especially lateral root development, a transcriptomic analysis of the 1.0-1.5 cm lateral root primordium zone (LRZ) of maize Q319 treated after 2 and 8 days by low phosphate was completed respectively. The present work utilized an Arizona Maize Oligonucleotide array 46K version slides, which contained 46,000 maize 70-mer oligonucleotides designated by TIGR ID, and the sequence information is available at the website of the Maize Oligonucleotide Array Project as the search item representing the >30,000 identifiable unique maize genes (details at http://www.maizearray.org). Keywords: low phosphate, Lateral Root Primordium Zone, maize Two-condition experiment, low phosphate treated lateral root primordium zone of maize root vs. normal cultrued lateral root primordium zone. Biological replicates: 9 control, 9 treated, independently grown and harvested. One replicate per array.
2012-03-09 | E-GEOD-36368 | biostudies-arrayexpress
Project description:Broad-host root endophytes establish long-term interactions with a large variety of plants, thereby playing a significant role in natural and managed ecosystems and in evolution of land plants. To exploit plants as living substrates and to establish a compatible interaction with morphologically and biochemically extremely different hosts, endophytes must respond and adapt to different plant signals and host metabolic states. Here we identified host-adapted colonization strategies and host-specific effector candidates of the mutualistic root endophyte Piriformospora indica by a global investigation of fungal transcriptional responses to barley and Arabidopsis at different symbiotic stages. Additionally we examined the role played by nitrogen in these two diverse associations. Cytological studies and colonization analyses of a barley mutant and fungal RNAi strains show that distinct physiological and metabolic signals regulate host-specific lifestyle in P. indica. This is the foundation for exploring how distinct fungal and host symbiosis determinants modulate biotrophy in one host and saprotrophy in another host and, ultimately, gives hints into the mechanisms underlying host adaptation in root symbioses. Arabidopsis and barley roots were inoculated with Piriformospora indica and grown for 14 days. Additionally P. indica was grown on 1/10 PNM medium alone. Samples were taken 3 and 14 dpi (Arabidopsis), 14 dpi (barley) and 3dpi (1/10 PNM). Each experiment was performed in three independent biological repetitions. Piriformospora indica gene expression examined only.
2013-07-22 | E-GEOD-47775 | biostudies-arrayexpress
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Project description:Zinc (Zn) excess negatively impacts primary root growth in Arabidopsis. The effects of Zn excess on root growth processes in the root tip are not well understood.
Transcriptomics, ionomics and metabolomics were used to examine the specific impact of Zn excess on the root tip (RT) compared to the remaining root (RR).
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Project description:Impact of tree mycorrhizal type, tree species identity and tree diversity in tree species pair root associated microbiomes
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Project description:Background: The soil environment is responsible for sustaining most terrestrial plant life on earth, yet we know surprisingly little about the important functions carried out by diverse microbial communities in soil. Soil microbes that inhabit the channels of decaying root systems, the detritusphere, are likely to be essential for plant growth and health, as these channels are the preferred locations of new root growth. Understanding the microbial metagenome of the detritusphere and how it responds to agricultural management such as crop rotations and soil tillage will be vital for improving global food production. Methods: The rhizosphere soils of wheat and chickpea growing under + and - decaying root were collected for metagenomics sequencing. A gene catalogue was established by de novo assembling metagenomic sequencing. Genes abundance was compared between bulk soil and rhizosphere soils under different treatments. Conclusions: The study describes the diversity and functional capacity of a high-quality soil microbial metagenome. The results demonstrate the contribution of the microbiome from decaying root in determining the metagenome of developing root systems, which is fundamental to plant growth, since roots preferentially inhabit previous root channels. Modifications in root microbial function through soil management, can ultimately govern plant health, productivity and food security.
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Project description:Low phosphate concentrations are frequently a constraint for maize growth and development, and therefore, enormous quantities of phosphate fertilizer are expended in maize cultivation, which increases the cost of planting. Low phosphate stress not only increases root biomass but can also cause significant changes in root morphology. Low phosphate availability has been found to favor lateral root growth over primary root growth by dramatically reducing primary root length and increasing lateral root elongation and lateral root density in Arabdopsis. While in our assay when inbred line Q319 subjected to phosphate starvation, The numbers of lateral roots and lateral root primordia were decreased after 6 days of culture in a low phosphate solution (LP) compared to plants grown under normal conditions (sufficient phosphate, SP), and these differences were increased associated with the stress caused by phosphate starvation. However, the growth of primary roots appeared not to be sensitive to low phosphate levels. This is very different to Arabidopsis. To elucidate how low phosphate levels regulate root modifications, especially lateral root development, a transcriptomic analysis of the 1.0-1.5 cm lateral root primordium zone (LRZ) of maize Q319 treated after 2 and 8 days by low phosphate was completed respectively. The present work utilized an Arizona Maize Oligonucleotide array 46K version slides, which contained 46,000 maize 70-mer oligonucleotides designated by TIGR ID, and the sequence information is available at the website of the Maize Oligonucleotide Array Project as the search item representing the >30,000 identifiable unique maize genes (details at http://www.maizearray.org). Keywords: low phosphate, Lateral Root Primordium Zone, maize
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