Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1138460 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR29931146.fastq.gz | Fastqsanger.gz | |||
| SRR29931147.fastq.gz | Fastqsanger.gz | |||
| SRR29931148.fastq.gz | Fastqsanger.gz | |||
| SRR29931149.fastq.gz | Fastqsanger.gz | |||
| SRR29931150.fastq.gz | Fastqsanger.gz |
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Project description:Microbial communities in the rhizosphere make significant contributions to crop health and nutrient cycling. However, their ability to perform important biogeochemical processes remains uncharacterized. Important functional genes, which characterize the rhizosphere microbial community, were identified to understand metabolic capabilities in the maize rhizosphere using GeoChip 3.0-based functional gene array method. Triplicate samples were taken for both rhizosphere and bulk soil, in which each individual sample was a pool of four plants or soil cores. To determine the abundance of functional genes in the rhizosphere and bulk soils, GeoChip 3.0 was used.
2014-09-12 | E-GEOD-61338 | biostudies-arrayexpress
Project description:Microbial communities in the rhizosphere make significant contributions to crop health and nutrient cycling. However, their ability to perform important biogeochemical processes remains uncharacterized. Important functional genes, which characterize the rhizosphere microbial community, were identified to understand metabolic capabilities in the maize rhizosphere using GeoChip 3.0-based functional gene array method. Triplicate samples were taken for both rhizosphere and bulk soil, in which each individual sample was a pool of four plants or soil cores. To determine the abundance of functional genes in the rhizosphere and bulk soils, GeoChip 3.0 was used.
2014-12-10 | E-MTAB-2920 | biostudies-arrayexpress
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.
2020-03-06 | GSE146427 | GEO
Project description:Understanding the environmental factors that shape microbial communities is crucial, especially in extreme environments, like Antarctica. Two main forces were reported to influence Antarctic soil microbes: birds and plants. Both birds and plants are currently undergoing unprecedented changes in their distribution and abundance due to global warming. However, we need to clearly understand the relationship between plants, birds and soil microorganisms. We therefore collected rhizosphere and bulk soils from six different sampling sites subjected to different levels of bird influence and colonized by Colobanthus quitensis and Deschampsia antarctica in the Admiralty Bay, King George Island, Maritime Antarctic. Microarray and qPCR assays targeting 16S rRNA genes of specific taxa were used to assess microbial community structure, composition and abundance and analyzed with a range of soil physico-chemical parameters. The results indicated significant rhizosphere effects in four out of the six sites, including areas with different levels of bird influence. Acidobacteria were significantly more abundant in soils with little bird influence (low nitrogen) and in bulk soil. In contrast, Actinobacteria were significantly more abundant in the rhizosphere of both plant species. At two of the sampling sites under strong bird influence (penguin colonies), Firmicutes were significantly more abundant in D. antarctica rhizosphere but not in C. quitensis rhizosphere. The Firmicutes were also positively and significantly correlated to the nitrogen concentrations in the soil. We conclude that the microbial communities in Antarctic soils are driven both by bird and plants, and that the effect is taxa-specific.
2012-06-01 | GSE33847 | GEO
Project description:We present metaproteome data from wheat rhizosphere from saline and non-saline soil. For collection and acquisition of metaproteome from wheat rhizosphere under saline and normal conditions, a survey was conducted in regions of Haryana, India. Samples from 65 days old plants (wheat var HD2967) were collected and pooled and based on EC,saline (NBAIM B; EC 6mS cm-1; pH 9.0; Bhaupur 2, Haryana, INDIA; 29°19'8"N;76°48'53"E) and normal soil samples (NBAIM C; EC 200 uS cm-1; pH 7.2; Near Nainform, Haryana, INDIA; 29°19'8"N;76°48'53"E) were selected for isolation of proteome with the standardized protocol at our laboratory followed by metaproteome analysis with the standardized pipepline. In total 1538 and 891 proteins were obtained from wheat rhizosphere from saline and non-saline respectively with the given parameters and software. Among 1410 proteins unique for saline soil, proteins responsible for glycine, serine and threonine metabolism and arginine and proline biosynthesis were found in saline and absent in non-saline. The present study extends knowledge about the physiology and adaptations of the wheat rhizosphere associated microbiota under saline soil.
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Project description:characterization of rhizosphere communities of wheat with metagenomics, metaproteomics and proteomic SIP
2018-11-30 | PXD011892 | Pride
Project description:Phosphate (P) fertilization induces a myriad of plant rhizosphere processes, required for a better P plant use. However, extended knowledge about plant responses to polyphosphates (PolyP) is still scarce, particularly transcriptomic and functional traits of root-induced rhizosphere processes. The present study aims to investigate belowground traits related to root transcriptomic changes, rhizosphere acidification, root growth, and P acquisition of durum wheat under PolyPs (PolyB and PolyC) supply. Root molecular traits were differentially expressed in response to PolyPs types, with 2481 and 184 genes were differentially expressed (compared to OrthoP) under PolyB (445 up- and 2036 down-regulated) and PolyC (71 up- and 113 down-regulated), respectively. Specifically, PolyB significantly influenced the expression of genes encoding the key enzymes in glycolysis, citrate cycle and acid phosphatases, OGDH, MDH, and ENO, PAP21 genes were upregulated, while TPI, PFK and LDH genes were downregulated. The modulated expression of TCA cycle and PAP genes can presumably explain the induced rhizosphere acidification (pH decreased from 8 to 6.3) and acid phosphatases activity (in root, rhizosphere soil and rhizosphere soil solution) under PolyPs, which consequently increased rhizosphere soil P availability (145% compared to OrthoP). This increase in P availability was concomitant with the modulation of root morphological traits and the upregulation of the AUX1 and ABA transporters genes, indicating PolyPs regulatory role in root growth for efficient P uptake. Moreover, PolyB significantly upregulated the expression of SPX3, which is indispensable for the absorption and transport of inorganic P to both roots and shoots. This was physiologically reflected by the increased shoot (36%) and root (61%) Pi contents in response to PolyB compared to OrthoP. Taken together, our findings provide novel and consistent evidence that enhanced P acquisition from PolyPs entails coordinated regulation of the expression of genes related to root-rhizosphere processes (rhizosphere acidification and phosphatases exudation) and root morphology, which consequently induces physiological adaptive traits enabling enhanced availability, acquisition of P, and wheat growth performance.
2025-05-31 | GSE277488 | GEO
Project description:Plants and rhizosphere microbes rely closely on each other, with plants supplying carbon to bacteria in root exudates, and bacteria mobilizing soil-bound phosphate for plant nutrition. When the phosphate supply becomes limiting for plant growth, the composition of root exudation changes, affecting rhizosphere microbial communities and microbially-mediated nutrient fluxes. To evaluate how plant phosphate deprivation affects rhizosphere bacteria, Lolium perenne seedlings were root-inoculated with Pseudomonas aeruginosa 7NR, and grown in axenic microcosms under different phosphate regimes (330 uM vs 3-6 uM phosphate). The effect of biological nutrient limitation was examined by DNA microarray studies of rhizobacterial gene expression.
2011-07-01 | E-MEXP-2812 | biostudies-arrayexpress
Project description:Considering the crucial role of root exudates, we hypothesized that continuous wheat cultivation would lead to lower glucose release, resulting in lower microbial growth, activity, and biomass. For the first time in situ glucose imaging was optimized for studying the interactions in the first (W1) and third (W3) wheat after break crop plots in the field. Glucose imaging method combined with soil microbial respiration, enzyme kinetics and the quantification SWEET genes expression levels in wheat plants. W3 had the lowest proportion of hotspots for glucose release with 1.35 % of the total soil surface area, indicating a 17.7 % decline compared to W1. Also, the expressions of functional orthologous genes of SWEET1a in wheat roots were significantly upregulated in W3 compared to W1. The growing microbial biomass in the rhizosphere soil of W1 was about five times higher than W3. Differences in SWEET gene expression and shift in glucose release is linked to altered root physiology and exudation processes, potentially reflecting the plant's strategy to create a less favourable environment for opportunistic pathogens. Hence, this study provides novel insights into the complex interactions between continuous wheat cultivation, root exudation, microbial dynamics, gene expression, and enzymatic activities.
2025-06-18 | GSE299883 | GEO
Project description:Microbial communities in the rhizosphere make significant contributions to crop health and nutrient cycling. However, their ability to perform important biogeochemical processes remains uncharacterized. Important functional genes, which characterize the rhizosphere microbial community, were identified to understand metabolic capabilities in the maize rhizosphere using GeoChip 3.0-based functional gene array method.
2014-09-12 | GSE61338 | GEO