Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1032109 | ENA |
REPOSITORIES: ENA
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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:Root exudates are composed of primary and secondary metabolites known to modulate the rhizosphere microbiota. Glucosinolates are defense compounds present in the Brassicaceae family capable of deterring pathogens, herbivores and biotic stressors in the phyllosphere. In addition, traces of glucosinolates and their hydrolyzed byproducts have been found in the soil, suggesting that these secondary metabolites could play a role in the modulation and establishment of the rhizosphere microbial community associated with this family. We used Arabidopsis thaliana mutant lines with disruptions in the indole glucosinolate pathway, liquid chromatography-tandem mass spectrometry (LC-MS/MS) and 16S rRNA amplicon sequencing to evaluate how disrupting this pathway affects the root exudate profile of Arabidopsis thaliana, and in turn, impacts the rhizosphere microbial community. Chemical analysis of the root exudates from the wild type Columbia (Col-0), a mutant plant line overexpressing the MYB transcription factor ATR1 (atr1D) which increases glucosinolate production, and the loss-of-function cyp79B2cyp79B3 double mutant line with low levels of glucosinolates confirmed that alterations to the indole glucosinolate biosynthetic pathway shifts the root exudate profile of the plant. We observed changes in the relative abundance of exuded metabolites. Moreover, 16S rRNA amplicon sequencing results provided evidence that the rhizobacterial communities associated with the plant lines used were directly impacted in diversity and community composition. This work provides further information on the involvement of secondary metabolites and their role in modulating the rhizobacterial community. Root metabolites dictate the presence of different bacterial species, including plant growth-promoting rhizobacteria. Our results suggest that alterations in the indole glucosinolate pathway cause disruptions beyond the endogenous levels of the plant, significantly changing the abundance and presence of different metabolites in the root exudates of the plants as well as the microbial rhizosphere community.
2023-05-31 | MSV000092068 | MassIVE
Project description:Understanding the mechanisms underlying the establishment of invasive plants is critical in community ecology. According to a widely accepted theory, plant-soil-microbe interactions mediate the effects of invasive plants on native species, thereby affecting invasion success. However, the roles and molecular mechanisms associated with such microbes remain elusive. Using high throughput sequencing and a functional gene microarray, we found that soil taxonomic and functional microbial communities in plots dominated by Ageratina adenophora developed to benefit the invasive plant. There were increases in nitrogen-fixing bacteria and labile carbon degraders, as well as soil-borne pathogens in bulk soil, which potentially suppressed native plant growth. Meanwhile, there was an increase of microbial antagonism in the A. adenophora rhizosphere, which could inhibit pathogenicity against plant invader. These results suggest that the invasive plant A. adenophora establishes a self-reinforcing soil environment by changing the soil microbial community. It could be defined as a ‘bodyguard/mercenary army’ strategy for invasive plants, which has important insights for the mitigation of plant invasion.
2019-05-01 | GSE114498 | 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:Advances in DNA sequencing technologies has drastically changed our perception of the structure and complexity of the plant microbiome. By comparison, our ability to accurately identify the metabolically active fraction of soil microbiota and its specific functional role in augmenting plant health is relatively limited. Here, we combined our recently developed protein extraction method and an iterative bioinformatics pipeline to enable the capture and identification of extracellular proteins (metaexoproteomics) synthesised in the rhizosphere of Brassica spp. We first validated our method in the laboratory by successfully identifying proteins related to a host plant (Brassica rapa) and its bacterial inoculant, Pseudomonas putida BIRD-1. This identified numerous rhizosphere specific proteins linked to the acquisition of plant-derived nutrients in P. putida. Next, we analysed natural field-soil microbial communities associated with Brassica napus L. (oilseed rape). By combining metagenomics with metaexoproteomics, 1882 proteins were identified across bulk and rhizosphere samples. Meta-exoproteomics identified a clear shift (p<0.001) in the metabolically active fraction of the soil microbiota responding to the presence of B. napus roots that was not apparent in the composition of the total microbial community (metagenome). This metabolic shift was associated with the stimulation of rhizosphere-specialised bacteria, such as Gammaproteobacteria, Betaproteobacteria and Flavobacteriia and the upregulation of plant beneficial functions related to phosphorus and nitrogen mineralisation. Together, our metaproteomic assessment of the ‘active’ plant microbiome at the field-scale demonstrates the importance of moving past a genomic assessment of the plant microbiome in order to determine ecologically important plant-microbe interactions underpinning plant health.
2022-07-01 | PXD033802 | Pride
Project description:Advances in DNA sequencing technologies has drastically changed our perception of the structure and complexity of the plant microbiome. By comparison, our ability to accurately identify the metabolically active fraction of soil microbiota and its specific functional role in augmenting plant health is relatively limited. Here, we combined our recently developed protein extraction method and an iterative bioinformatics pipeline to enable the capture and identification of extracellular proteins (metaexoproteomics) synthesised in the rhizosphere of Brassica spp. We first validated our method in the laboratory by successfully identifying proteins related to a host plant (Brassica rapa) and its bacterial inoculant, Pseudomonas putida BIRD-1. This identified numerous rhizosphere specific proteins linked to the acquisition of plant-derived nutrients in P. putida. Next, we analysed natural field-soil microbial communities associated with Brassica napus L. (oilseed rape). By combining metagenomics with metaexoproteomics, 1882 proteins were identified across bulk and rhizosphere samples. Meta-exoproteomics identified a clear shift (p<0.001) in the metabolically active fraction of the soil microbiota responding to the presence of B. napus roots that was not apparent in the composition of the total microbial community (metagenome). This metabolic shift was associated with the stimulation of rhizosphere-specialised bacteria, such as Gammaproteobacteria, Betaproteobacteria and Flavobacteriia and the upregulation of plant beneficial functions related to phosphorus and nitrogen mineralisation. Together, our metaproteomic assessment of the ‘active’ plant microbiome at the field-scale demonstrates the importance of moving past a genomic assessment of the plant microbiome in order to determine ecologically important plant-microbe interactions underpinning plant health.
2022-07-01 | PXD033803 | Pride