Ontology highlight
ABSTRACT:
PROVIDER: PRJNA752264 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:We used wheat as rotational crop to assess the influence of continuous cropping on microbiome in Pinellia ternata rhizosphere and the remediation of rotational cropping to the impacted microbiota. Illumina high-throughput sequencing technology was utilized for this method to explore the rhizosphere microbial structure and diversity based on continuous and rotational cropping.
2016-12-10 | GSE91083 | GEO
Project description:Phosphate (P) fertilization impacts many rhizosphere processes, driving plant P use efficiency. However, less is known about the induced molecular and physiological root-rhizosphere traits in responses to polyphosphates (PolyP), particularly root transcriptome and belowground functional traits responsible for P acquisition. The present study aims to investigate physiological and transcriptomic belowground mechanisms explaining the enhanced durum wheat P acquisition under PolyP (PolyB and PolyC) supply. Root molecular traits were differentially expressed in response to PolyP, where PolyB induced upregulation of OGDH, MDH, and ENO, PAP21 and downregulation of PFK, and LDH genes. The modulation of gene expression can presumably explain the PolyP-induced changes in rhizosphere (root, rhizosphere soil, soil solution) acidification (pH decreased from 8 to 6.3) and acid phosphatase activities, which were concomitant with enhanced rhizosphere soil P availability and shoot Pi content (145% and 36% compared to OrthoP, respectively) along with changes in morphological and transcriptomic root (particularly, the upregulation of AUX1 and ABA transporter genes) traits. These findings provide novel insights that P acquisition from polyphosphates involves the coordinated regulation of genes governing root-rhizosphere processes and root development, ultimately enhancing wheat P acquisition.
2025-05-31 | GSE277488 | GEO
Project description:<p>Wheat is a major staple crop grown across the globe. Fusarium crown rot (FCR) of wheat, caused by Fusarium pseudograminearum, is a destructive soil-borne disease that lacks effective sustainable control measures. Here, we assembled a cross-kingdom synthetic microbial community (SMC) comprising Trichoderma harzianum T19, Bacillus subtilis BS-Z15, and four other Bacillus strains, and evaluated its biocontrol efficacy against FCR under non-sterile soil conditions. The SMC treatment significantly suppressed FCR, reducing the disease severity index by approximately 70%. Wheat growth and yield were simultaneously enhanced: SMC inoculation nearly doubled plant biomass (with fresh and dry weights ~100% higher) and increased thousand-kernel weight by ~14% compared to the controls. In the rhizosphere, SMC improved soil health by elevating soil organic matter and nitrogen levels by over 50%, while mitigating pathogen-induced nutrient imbalances (excess available P and K) and boosting nutrient-cycling enzyme activities. Amplicon sequencing revealed that SMC suppressed pathogenic Fusarium in the rhizosphere and enriched beneficial microbes, including antagonistic fungi (Trichoderma, Chaetomium) and plant growth-promoting bacteria (Pseudomonas, Paenibacillus). Co-occurrence network analysis showed that SMC treatment restructured the rhizosphere microbial network with higher connectivity, stability, and a prevalence of positive cooperative interactions under F. pseudograminearum stress. Defense-related metabolites, such as epi-jasmonic acid, allantoin, Nβ-acetyltryptamine, and dihydrodaidzein, accumulated to higher levels with SMC, consistent with KEGG enrichment in pathways related to amino acid biosynthesis, carbon metabolism, signal transduction, and plant defense. These findings demonstrate that the cross-kingdom SMC modulates soil nutrients, microbial community structure, and rhizosphere metabolites to synergistically promote wheat growth and enhance resistance to FCR.</p>
2025-09-06 | MTBLS12946 | MetaboLights
Project description:<p>Background</p><p>Wheat crown rot (WCR) caused by Fusarium spp. lacks durable, sustainable control. Engineering the rhizosphere with defined synthetic microbial communities (SynComs) offers a route to combined disease suppression and growth promotion. We aimed to build a cross-kingdom SynCom and evaluate its impacts on plant performance and the soil–microbiome system.</p><p>Results</p><p>We assembled a two-member SynCom comprising an antagonistic fungus (Trichoderma harzianum) and a growth-promoting bacterium (Bacillus rugosus). In greenhouse trials, SynCom inoculation reduced WCR severity by ~71% and improved vigor, more than doubling shoot and root biomass and increasing grain weight by ~13% versus non-inoculated controls. SynCom-treated plants maintained higher chlorophyll and antioxidant enzyme activities under pathogen challenge, with reduced oxidative stress markers relative to pathogen-only plants. Amplicon sequencing showed increased rhizosphere microbial diversity, enrichment of beneficial taxa (e.g., Mortierella), and suppression of Fusarium. SynCom also enhanced soil enzyme activities and nutrient availability and promoted accumulation of defense-related metabolites in the rhizosphere.</p><p>Conclusions</p><p>A tailored cross-kingdom SynCom establishes a disease-suppressive, growth-promoting soil environment that mitigates wheat crown rot while improving yield components. These findings support microbiome engineering as a practical, sustainable strategy for wheat production and warrant field-scale validation and formulation development.</p>
2025-09-06 | MTBLS12945 | MetaboLights
Project description:<p>Soil-borne diseases, with their high incidence and frequency in monoculture systems, pose a major challenge in contemporary agricultural production. Intercropping can promote beneficial soil legacy effects, thereby effectively mitigating the occurrence and damage of soil-borne diseases. In this study, we employed an integrated approach combining 16S rRNA sequencing, ITS amplicon sequencing, and untargeted metabolomics to systematically compare the differences in soil microbial community structure and metabolite profiles between soybean-tobacco intercropping and tobacco monoculture systems. Furthermore, we elucidated the mechanisms through which these differences influence the incidence of tobacco root rot. The results showed that intercropping significantly enhanced the survival rate of tobacco plants under Fusarium.spp infection (P < 0.01). Furthermore, intercropping markedly increased soil microbial community diversity and significantly reduced the relative abundance of Fusarium (by 53.17%). Additionally, intercropping disrupted the cooperative relationships between Fusarium and other microbial taxa, leading to reduced connectivity within the interaction network and a notable decline in its ecological competitive advantage. Metabolomic analysis revealed that intercropping promoted the accumulation of antimicrobial metabolites such as indole, and indole content was significantly negatively correlated with Fusarium abundance (P < 0.05). Further integrated microbiome-metabolome analysis demonstrated that intercropping fostered a more complex microbial-metabolite interaction network, which helped suppress the recolonization of pathogenic Fusarium. In conclusion, this study provides a theoretical basis for leveraging intercropping systems to modulate the rhizosphere micro-environment and control soil-borne diseases, offering new insights for developing sustainable green control strategies.</p>
2025-09-05 | MTBLS12940 | MetaboLights
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
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