Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1023498 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR26320624_1.fastq.gz | Fastqsanger.gz | |||
| SRR26320624_2.fastq.gz | Fastqsanger.gz | |||
| SRR26320625_1.fastq.gz | Fastqsanger.gz | |||
| SRR26320625_2.fastq.gz | Fastqsanger.gz | |||
| SRR26320626_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 12 |
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Project description:The microbiota plays a crucial role in protecting plants from pests and pathogens. The protection provided by the microbiota constitutes not just the plant’s first line of defense, but possibly its most potent one, as experimental disruptions to the microbiota cause plants to succumb to otherwise asymptomatic infections. To understand how microbial plant defense is deployed, we applied a complex and tractable plant-soil-microbiome microcosm. This system, consisting of Arabidopsis plants and a 150-member bacterial synthetic community, provides a platform for the discovery of novel bacterial plant-beneficial traits, under a realistically complex microbial community context. To identify which components of the plant microbiota are critical for plant defense, we deconstructed this microcosm top-down, removing different microbial groups from the community to examine their protective effect on the plant when challenged with the leaf pathogen Pseudomonas syringae. This process of community deconstruction revealed a critical role for the genus Bacillus in protecting the plant from infection. Using plant RNA-seq and bacterial co-culturing experiments, we demonstrated that Bacillus-provided plant protection is independent of plant immune system activation. We also show that the level of plant protection is strongly dependent on the diversity of the protective inoculum. We show that deconstructing the microbiome top-down is a powerful tool for identifying and prioritizing microbial taxa with specific functions within it.
2025-01-01 | GSE285599 | 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 | PXD033803 | 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 | PXD033692 | 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 | PXD033802 | Pride
Project description:Human saliva microbiota is phylogenetically divergent among host individuals yet their roles in health and disease are poorly appreciated. We employed a microbial functional gene microarray, HuMiChip 1.0, to reconstruct the global functional profiles of human saliva microbiota from ten healthy and ten caries-active adults. Saliva microbiota in the pilot population featured a vast diversity of functional genes. No significant distinction in gene number or diversity indices was observed between healthy and caries-active microbiota. However, co-presence network analysis of functional genes revealed that caries-active microbiota was more divergent in non-core genes than healthy microbiota, despite both groups exhibited a similar degree of conservation at their respective core genes. Furthermore, functional gene structure of saliva microbiota could potentially distinguish caries-active patients from healthy hosts. Microbial functions such as Diaminopimelate epimerase, Prephenate dehydrogenase, Pyruvate-formate lyase and N-acetylmuramoyl-L-alanine amidase were significantly linked to caries. Therefore, saliva microbiota carried disease-associated functional signatures, which could be potentially exploited for caries diagnosis. The DMFT INDEX (Decayed, Missing, Filled [DMF] teeth index used in dental epidemiology) values are provided for each sample
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Project description:Human saliva microbiota is phylogenetically divergent among host individuals yet their roles in health and disease are poorly appreciated. We employed a microbial functional gene microarray, HuMiChip 1.0, to reconstruct the global functional profiles of human saliva microbiota from ten healthy and ten caries-active adults. Saliva microbiota in the pilot population featured a vast diversity of functional genes. No significant distinction in gene number or diversity indices was observed between healthy and caries-active microbiota. However, co-presence network analysis of functional genes revealed that caries-active microbiota was more divergent in non-core genes than healthy microbiota, despite both groups exhibited a similar degree of conservation at their respective core genes. Furthermore, functional gene structure of saliva microbiota could potentially distinguish caries-active patients from healthy hosts. Microbial functions such as Diaminopimelate epimerase, Prephenate dehydrogenase, Pyruvate-formate lyase and N-acetylmuramoyl-L-alanine amidase were significantly linked to caries. Therefore, saliva microbiota carried disease-associated functional signatures, which could be potentially exploited for caries diagnosis. The DMFT INDEX (Decayed, Missing, Filled [DMF] teeth index used in dental epidemiology) values are provided for each sample We employed a microbial functional gene microarray, HuMiChip 1.0, to reconstruct the global functional profiles of human saliva microbiota from ten healthy and ten caries-active adults.
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Project description:We identified target genes for NHR-25 by ChIP-seq at L1 stage of C. elegans. Transcription factor genes were tagged with GFP and their expression examined at L1 stage. Since there are no direct target genes known for NHR-25 that can be used for assessment of enrichment efficiency by quantitative PCR (qPCR), we chose to repeat ChIP-seq experiment of another GFP tagged transcription factor, PHA-4 for which the ChIP-seq was performed during a pilot experiment of modENCODE project using the same transgenic strain and antibody (a gift from Tony Hyman lab). pha-4 and nhr-25 transgenic worm were studied in Fed L1 stage.
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Project description:Leaves are colonised by a complex mix of microbes, termed the leaf microbiota. Even though the leaf microbiota is increasingly recognised as an integral part of plant life and health, our understanding of its interactions with the plant host is still limited. Here, mature, axenically grown Arabidopsis thaliana plants were spray-inoculated with different densities of the non-pathogenic bacterium Williamsia sp. Leaf354. High bacterial titers caused disease phenotypes and led to severe transcriptional reprogramming with a strong focus on plant defence.
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