Metagenome of rhizosphere soils of garlic
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ABSTRACT:
PROVIDER: PRJNA1068935 | ENA |
REPOSITORIES: ENA
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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.
2020-03-06 | GSE146427 | 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. 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:Garlic rhizosphere microorganisms Raw sequence reads
| PRJNA1174389 | ENA
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
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:Garlic is a popular flavor enhancer in modern cuisines. Although anti-atherosclerotic, anti-proliferative, hypolipidemic and chemopreventative effects of garlic are known for a long time, the mechanisms of garlic as a dietary supplement ramain largely unknown. We used microarrays to analyze the global programme of gene expression in control (cellulose) and garlic-fed mice and identified erythropoietic and heme biosynthetic genes that could, in part, be responsible for the pleiotropic effects of garlic on health Keywords: diet, garlic
2008-12-31 | GSE10344 | GEO
Project description:Rhizosphere soils and soils treated with substancces Genome sequencing and assembly
| PRJNA702249 | ENA
Project description:Rhizosphere soils of wild rice (Oryza rufipogon) Metagenome
| PRJNA940606 | ENA
Project description:Garlic is a popular flavor enhancer in modern cuisines. Although anti-atherosclerotic, anti-proliferative, hypolipidemic and chemopreventative effects of garlic are known for a long time, the mechanisms of garlic as a dietary supplement ramain largely unknown. We used microarrays to analyze the global programme of gene expression in control (cellulose) and garlic-fed mice and identified erythropoietic and heme biosynthetic genes that could, in part, be responsible for the pleiotropic effects of garlic on health Experiment Overall Design: 8-week old male C57BL/6J mice were divided into two diet groups and maintained at an SPF facility. Mice were fed (ad libitum) a special diet (Yeh and Yeh, 1994) with 4% cellulose (Control group, 3 mice) or 4% lyophilized raw garlic powder (Treatment group, 3 mice). At the end of the 15-week treatment, spleen organs were used for RNA isolation and arraying.
2009-01-15 | E-GEOD-10344 | biostudies-arrayexpress