Ontology highlight
ABSTRACT:
PROVIDER: PRJNA953854 | ENA |
REPOSITORIES: ENA
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Project description:Global food production is reliant on the application of finite phosphorus (P) fertilisers. Numerous negative consequences associated with intensive P fertilisation have resulted in a high demand to find alternative sustainable methods that will enhance crop P uptake. Bacteroidetes, primarily from the genus Flavobacterium, have recently been shown to be abundant members of the plant microbiome, but their general ecological role and potential to mobilise P in the rhizosphere remains very poorly characterised. Here, we sought to determine the P mobilisation potential of Flavobacterium strains isolated from the rhizosphere of oilseed rape (Brassica napus L.). In contrast to other abundant rhizosphere bacteria, such as Pseudomonas, all Flavobacterium strains exhibited constitutive phosphatase activity independent of external phosphate (Pi) concentrations. Interestingly, a combination of exoproteomic analysis and molecular microbiology techniques revealed that Flavobacterium have a complex and largely unique repertoire of proteins to mobilise and acquire Pi. This includes the expression of novel, as yet unidentified, phosphatases, and numerous proteins of unknown function. We also discovered that Flavobacterium expresses certain SusCD-like transporters, whose role is typically associated with specialised carbon acquisition, in response to Pi-starvation. Furthermore, the genes encoding these unusual Pi-responsive proteins were enriched in plant-associated Flavobacterium strains suggesting that this machinery represents niche-adaptive strategies for overcoming P scarcity in this genus. We propose that abundant rhizosphere-dwelling Flavobacterium spp. have evolved unique mechanisms for coping with Pi-stress which may provide novel solutions for future sustainable agricultural practices.
2021-09-08 | PXD014380 | Pride
Project description:Genome sequences of seven Parmales (Bolidophyceae) strains
| PRJDB13844 | ENA
Project description:Purpose:Salinity is an important environmental factor that affects the physiological activities of fish. Flavobacterium cloumnare is a major aquaculture pathogen infecting various saltwater and freshwater fish. The goals of this study are investigating the mechanism of the immune responses to Flavobacterium cloumnare in grass carp under saline-alkali stress. Methods: Grass carp individuals, averaging 12 cm in body length, were obtained from Duofu fish farm (Wuhan, China) and cultured at recirculating aquaculture system for 2 weeks before the experiment began. For the challenge, all grass carp were randomly divided into three groups, and then cultured at saline-alkali water with the concentration of 0, 3‰ and 6‰. After 30 days, Groups of grass carp were were infected with 2 × 105 CFU/mL Flavobacterium cloumnare G4 strains for 3 h .Gills from each group at 24 hpi, 3dpi and 6dpi were collected. Total RNA of all samples was isolated using TRIzol® Reagent (Invitrogen) according to the manufacturer's introduction. gill per group at 24 hpi and 48 hpi were rinsedRNA integrity was assessed using an Agilent 2100 bioanalyzer (Agilent, USA). Samples with RNA integrity numbers (RINs) ≥ 7.5 were subjected to cDNA library construction using TruseqTM RNA sample prep Kit (Illumina). Results:A total of 27 were processed for transcriptome sequencing, generating 177.79Gb Clean Data. At least 5.73Gb clean data were generated for each sample with minimum 93.70% of clean data achieved quality score of Q30. Clean reads of each sample were mapped to specified reference genome. Mapping ratio ranged from 88.11% to 92.33%. The expression of genes was quantified and differentially expressed genes were identified based on their expression.Criteria for differentially expressed genes was set as Fold Change(FC)≥1.5 and Pvalue<0.05. Fold change(FC) refers to the ratio of gene expression in two samples. These DEGs were further processed for functional annotation and enrichment analysis. Conclusions: Our study represents the immune response of zebrafish against Flavobacterium cloumnare infection in saline-alkali stress conditions, and reveal the discrepant expression pattern of NOD-like pattern recognition receptors in the gills.
2021-10-13 | GSE185641 | GEO
Project description:We constructed seven small RNA libraries of Rhizoctonia solani AG1 IA and sequenced using Illumina GA II. The seven samples include mycelium cultured on PDA without rice incubated, 6 different stages at 10 hours (10h), 18h, 24h, 32h, 48h and 72h spanning the Rhizoctonia solani AG1 strains infection rice. We identified miRNA-like small RNAs (milRNAs) using MIREAP and mirdeep2. The milRNAs were used for further analysis of interactions between milRNA and mRNA that may involve in plant-infection.
2016-04-23 | GSE68236 | GEO
Project description:This model is part of a collection comprising eight strain-specific genome-scale metabolic models of five different Acinetobacter baumannii strains. Seven of these models have been previously published and were now collected and carefully curated. All models were checked with the SBML validator, MEMOTE, and FROG. The covered strains include Acinetobacter baumannii AYE, AB0057, ATCC 19606, ATCC 17978, and AB5075.
2024-06-25 | MODEL2406250010 | BioModels
Project description:This model is part of a collection comprising eight strain-specific genome-scale metabolic models of five different Acinetobacter baumannii strains. Seven of these models have been previously published and were now collected and carefully curated. All models were checked with the SBML validator, MEMOTE, and FROG. The covered strains include Acinetobacter baumannii AYE, AB0057, ATCC 19606, ATCC 17978, and AB5075.
2024-06-25 | MODEL2406250011 | BioModels
Project description:This model is part of a collection comprising eight strain-specific genome-scale metabolic models of five different Acinetobacter baumannii strains. Seven of these models have been previously published and were now collected and carefully curated. All models were checked with the SBML validator, MEMOTE, and FROG. The covered strains include Acinetobacter baumannii AYE, AB0057, ATCC 19606, ATCC 17978, and AB5075.
2024-06-25 | MODEL2406250006 | BioModels
Project description:This model is part of a collection comprising eight strain-specific genome-scale metabolic models of five different Acinetobacter baumannii strains. Seven of these models have been previously published and were now collected and carefully curated. All models were checked with the SBML validator, MEMOTE, and FROG. The covered strains include Acinetobacter baumannii AYE, AB0057, ATCC 19606, ATCC 17978, and AB5075.
2024-06-25 | MODEL2406250008 | BioModels
Project description:This model is part of a collection comprising eight strain-specific genome-scale metabolic models of five different Acinetobacter baumannii strains. Seven of these models have been previously published and were now collected and carefully curated. All models were checked with the SBML validator, MEMOTE, and FROG. The covered strains include Acinetobacter baumannii AYE, AB0057, ATCC 19606, ATCC 17978, and AB5075.
2024-06-25 | MODEL2406250009 | BioModels