Fungal communities in rhizosphere and non-rhizosphere soils
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1183635 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR31296900_1.fastq.gz | Fastqsanger.gz | |||
| SRR31296900_2.fastq.gz | Fastqsanger.gz | |||
| SRR31297000_1.fastq.gz | Fastqsanger.gz | |||
| SRR31297000_2.fastq.gz | Fastqsanger.gz | |||
| SRR31296901_1.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: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: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. The study was carried out at the Brazilian Antarctic Station Comandante Ferraz (EACF, 62M-BM-004M-bM-^@M-^YS, 58M-BM-021M-bM-^@M-^YW), located in Martel Inlet, Admiralty Bay, King George Island, Antarctic Peninsula, which is part of the South Shetlands Archipelago in Maritime Antarctica. It is a medium sized research station with a population of 10 to 15 people during the winter months (March to November) and about 60 people during the austral summer months (November to March). During the austral summers of 2006 M-bM-^@M-^S 2007 and 2008 M-bM-^@M-^S 2009, the vascular plants D. antarctica or C. quitensis were sampled, where both plants were found, in triplicate at six different sites: A M-bM-^@M-^S Arctowski (2006 M-bM-^@M-^S 2007), Q M-bM-^@M-^S Quimica (2006 M-bM-^@M-^S 2007), I M-bM-^@M-^S Ipanema (2006 M-bM-^@M-^S 2007), M M-bM-^@M-^S North Mountain (2008 M-bM-^@M-^S 2009), D M-bM-^@M-^S Demay Point (2008 M-bM-^@M-^S 2009), C M-bM-^@M-^S Copacabana (2008 M-bM-^@M-^S 2009) (Figure 1). Points A, C and D were located inside an environmental protected area. Point A is close to the Arctowski Polish Station and next to a colony of Adelie penguins (Pygoscelis adeliae), point C is next to the USA summer station Copacabana in a Gentoo penguin (P. papua) colony, and point D is near to a Polish refuge next to a colony of Chinstrap penguins (P. antarcticus). At point I, there were no penguin colonies present, but this section was used as a nesting site by local species of flying birds. Point Q was located in the vicinity of the EACF; thus there has been (and continues to be) an intense anthropogenic influence on this spot, which is not the case at the other sampling sites. Point M was located at the top of North Mountain, around 200 m altitude. This site has no influence from penguin colonies and only a few nests of skua (Catharacta sp.) were observed. At each sampling site, triplicate soil samples were taken for chemical and biological analyses, with the exception of the Arctowski site (A) where we only took two replicates. Each vascular plant sample was frozen (-20M-BM-0C) at the EACF.
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Project description:characterization of rhizosphere communities of arabidopsis with metagenomics, metaproteomics and proteomic SIP
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Project description:characterization of rhizosphere communities of maize with metagenomics, metaproteomics and proteomic SIP
2018-11-30 | PXD011891 | Pride
Project description:characterization of rhizosphere communities of wheat with metagenomics, metaproteomics and proteomic SIP
2018-11-30 | PXD011892 | Pride
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.
2024-01-08 | PXD015387 | Pride
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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