Ontology highlight
ABSTRACT:
PROVIDER: PRJNA915635 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Development of cereal crops with high nitrogen-use efficiency (NUE) is a priority for worldwide agriculture. In addition to conventional plant breeding and genetic engineering, the use of the plant microbiome offers another approach to improve crop NUE. To gain insight into the bacterial communities associated with sorghum lines that differ in NUE, a field experiment was designed comparing 24 diverse sorghum lines under sufficient and deficient nitrogen (N). Amplicon sequencing and untargeted gas chromatography-mass spectrometry (GC-MS) were used to characterize the bacterial communities and the root metabolome associated with sorghum genotypes varying in sensitivity to low N. We demonstrated that N stress and sorghum type (energy, sweet, and grain sorghum) significantly impacted the root-associated bacterial communities and root metabolite composition of sorghum. We found a positive correlation between sorghum NUE and bacterial richness and diversity in the rhizosphere. The greater alpha diversity in high NUE lines was associated with the decreased abundance of a dominant bacterial taxa, Pseudomonas. Multiple strong correlations were detected between root metabolites and rhizosphere bacterial communities in response to low-N stress. This indicates that the shift in the sorghum microbiome due to low-N is associated with the root metabolites of the host plant. Taken together, our findings suggest that host genetic regulation of root metabolites plays a role in defining the root-associated microbiome of sorghum genotypes differing in NUE and tolerance to low-N stress.
2023-08-29 | MSV000092783 | MassIVE
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:Bacterial diversity in strawberry fruits
| PRJNA1039505 | ENA
Project description:Strawberry cultivation is associated with high mineral fertilizer doses and excessive use of chemical plant protection products. Based on previous research, we expected that chitin application to the growing medium will increase the nutrient availability and activate the plant’s systemic defense response, resulting in higher strawberry yields and less disease symptoms. We set up two experiments in which the temporal variability and differences in initial nutrient concentrations of the growing media were taken into account. Chitin induced the plant’s shoot biomass, explained by elevated N concentration in the growing medium and/or the attraction of plant-growth promoting fungal genera towards the plant root, such as Mortierella and Umbelopsis. The over-excessive N concentration and P and K deficiencies in the chitin treatment led to nutrient disbalances. This may explain the decreased fruit yield and disease resistance of the fruits towards Botrytis cinerea. In contrast, chitin caused a clear defense priming effect of the strawberry leaves, with a strong induction of the jasmonic acid response, resulting in less disease symptoms. Chitin caused positive effects on shoot growth and disease resistance of the leaves, but caution needs to be taken for nutrient disbalances leading to negative influences on fruit production and disease susceptibly.
2021-01-01 | GSE144526 | GEO
Project description:To investigate the root system, three indoor cultivation systems, including water agar, deep water, and vermiculite-based hydroponics, are commonly used. However, their effects on the root development of rice (Oryza sativa L.) remain unknown. In this study, we assessed the effect of these indoor cultivation systems on the maximum root length (MRL) and examined the changes in phosphorylated protein profiles by LC-MS/MS.
2024-09-28 | PXD050876 | JPOST Repository
Project description:Breeding day-neutral strawberry (Fragaria x ananassa Duchesne) is pivotal to extend fruit-bearing season and increase the efficiency of production. However, genetic improvement of day-neutrality by the means of molecular marker technologies remains slow due to genome complexity of octoploid strawberry. This study employs an innovative approach by integrating the Subtracted Diversity Array (SDA) technology and Bulked Segregant Analysis (BSA) to facilitate the identification of molecular markers associated with day-neutrality in octoploid strawberry. A Fragaria Discovery Panel (FDP) containing 287 features specific to strawberry genome was constructed as a platform for rapid screening of DNA polymorphism between one short day (SD) strawberry DNA bulk and three day-neutral (DN) bulks varrying in flowering strength. Differential array hybridisation patterns between the DN and SD bulks revealed a novel molecular marker, FaP2E11, closely linked to CYTOKININ OXIDASE 1 (CKX1) gene possibly involved in promoting flowering under non-inductive condition. Interestingly, a 12 bp deletion was observed within the FaP2E11 sequence cloned from SD genotypes but not DN genotypes. As cytokinin is required to induce flowering, this result indicates that full sequence of FaP2E11 and the sequence with deletion are allelic variants linked to the low enzyme activity CKX1 and the wild type alleles, respectively.
2017-02-09 | GSE70145 | GEO
Project description:Chitin and Biochar in strawberry cultivation
| PRJNA603963 | ENA
Project description:Considering the crucial role of root exudates, we hypothesized that continuous wheat cultivation would lead to lower glucose release, resulting in lower microbial growth, activity, and biomass. For the first time in situ glucose imaging was optimized for studying the interactions in the first (W1) and third (W3) wheat after break crop plots in the field. Glucose imaging method combined with soil microbial respiration, enzyme kinetics and the quantification SWEET genes expression levels in wheat plants. W3 had the lowest proportion of hotspots for glucose release with 1.35 % of the total soil surface area, indicating a 17.7 % decline compared to W1. Also, the expressions of functional orthologous genes of SWEET1a in wheat roots were significantly upregulated in W3 compared to W1. The growing microbial biomass in the rhizosphere soil of W1 was about five times higher than W3. Differences in SWEET gene expression and shift in glucose release is linked to altered root physiology and exudation processes, potentially reflecting the plant's strategy to create a less favourable environment for opportunistic pathogens. Hence, this study provides novel insights into the complex interactions between continuous wheat cultivation, root exudation, microbial dynamics, gene expression, and enzymatic activities.
2025-06-18 | GSE299883 | GEO