Ontology highlight
ABSTRACT:
PROVIDER: PRJNA933345 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR23425900.fastq.gz | Fastqsanger.gz | |||
| SRR23426000.fastq.gz | Fastqsanger.gz | |||
| SRR23426100.fastq.gz | Fastqsanger.gz | |||
| SRR23425901.fastq.gz | Fastqsanger.gz | |||
| SRR23426001.fastq.gz | Fastqsanger.gz |
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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:The experiment was designed to test the interactions of Spartina alterniflora, its microbiome, and the interaction of the plant-microbe relationship with oil from the Deepwater Horizon oil spill (DWH). Total RNA was extracted from leaf and root microbiome of S. alterniflora in soils that were oiled in DWH oil spill with or without added oil, as well as those grown in unoiled soil with or without added oil. The work in its entirety characterizes the transport, fate and catabolic activities of bacterial communities in petroleum-polluted soils and within plant tissues.
2020-04-10 | GSE148431 | GEO
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:Opioids such as morphine have many beneficial properties as analgesics, however, opioids may induce multiple adverse gastrointestinal symptoms. We have recently demonstrated that morphine treatment results in significant disruption in gut barrier function leading to increased translocation of gut commensal bacteria. However, it is unclear how opioids modulate the gut homeostasis. By using a mouse model of morphine treatment, we studied effects of morphine treatment on gut microbiome. We characterized phylogenetic profiles of gut microbes, and found a significant shift in the gut microbiome and increase of pathogenic bacteria following morphine treatment when compared to placebo. In the present study, wild type mice (C57BL/6J) were implanted with placebo, morphine pellets subcutaneously. Fecal matter were taken for bacterial 16s rDNA sequencing analysis at day 3 post treatment. A scatter plot based on an unweighted UniFrac distance matrics obtained from the sequences at OTU level with 97% similarity showed a distinct clustering of the community composition between the morphine and placebo treated groups. By using the chao1 index to evaluate alpha diversity (that is diversity within a group) and using unweighted UniFrac distance to evaluate beta diversity (that is diversity between groups, comparing microbial community based on compositional structures), we found that morphine treatment results in a significant decrease in alpha diversity and shift in fecal microbiome at day 3 post treatment compared to placebo treatment. Taxonomical analysis showed that morphine treatment results in a significant increase of potential pathogenic bacteria. Our study shed light on effects of morphine on the gut microbiome, and its role in the gut homeostasis.
2018-04-16 | E-MTAB-5546 | biostudies-arrayexpress
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 | 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 | PXD033802 | Pride
Project description:<p>Drought stress negatively impacts microbial activity, but the magnitude of stress responses are likely dependent on a diversity of below ground interactions. Populus trichocarpa individuals and no plant bulk soils were exposed to extended drought (~0.03% gravimetric water content (GWC) after 12d), re-wet, and a 12-d 'recovery' period to determine the effects of plant presence in mediating soil microbiome stability to water stress. Plant metabolomic analyses indicated that drought exposure increased host investment in C and N metabolic pathways (amino acids, fatty-acids, phenolic glycosides) regardless of recovery. Several metabolites positively correlated with root-associated microbial alpha diversity, but not those of soil communities. Soil bacterial community composition shifted with P. trichocarpa presence and with drought relative to irrigated controls, whereas soil fungal composition only shifted with plant presence. However, root fungal communities strongly shifted with drought, whereas root bacterial communities changed to a lesser degree. The proportion of bacterial water-stress opportunistic OTUs (enriched counts in drought) were high (~11%) at the end of drying phases, and maintained after re-wet, and recovery phases in bulk soils, but declined over time in soils with plants present. For root fungi opportunistic OTUs were high at the end of recovery in drought treatments (~17% abundance), although relatively not responsive in soils, particularly planted soils (< 0.5% abundance for sensitive or opportunistic). These data indicate that plants modulate soil and root associated microbial drought responses via tight plant-microbe linkages during extreme drought scenarios, but trajectories after extreme drought vary with plant habitat and microbial functional groups.</p>
2020-06-19 | MTBLS1463 | MetaboLights