Root metagenome
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REPOSITORIES: ENA
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Project description:Soybean (Glycine max) is susceptible to root rot when subjected to continuous cropping, and this disease can seriously diminish the crop yield. Herein, isobaric tag for relative and absolute quantitation (iTRAQ) labeling and liquid chromatography-tandem mass spectrometry (LC-MS/MS) were employed for proteomic analysis of continuously cropped soybean inoculated with the arbuscular mycorrhizal (AM) fungus Funneliformis mosseae. Differential expression of proteins in soybean roots was determined following 1 year of continuous cropping. A total of 131 differentially expressed proteins (DEPs) were identified in F. mosseae-treated samples, of which 49 and 82 were up- and down-regulated, respectively. The DEPs were annotated with 117 Gene Ontology (GO) terms, with 48 involved in biological processes, 31 linked to molecular functions, and 39 associated with cell components. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis mapped the DEPs to 113 mainly metabolic pathways including oxidative phosphorylation, glycolysis and amino acid metabolism. Expression of glucan 1,3-beta-glucosidase, chalcone isomerase, calcium-dependent phospholipid binding and other defense-related proteins was up-regulated by F. mosseae, suggesting inoculation promotes the growth and development of soybean and increases disease resistance. The findings provide an experimental basis for further research on the molecular mechanisms of AM fungi in resolving problems associated with continuous soybean cropping.
2019-11-12 | PXD009911 | Pride
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:Many of the microorganisms that are normally present in the soil, actually inhabit the rhizosphere and interact with plants. Those plant–microorganisms interactions may be beneficial or harmful. Among the first are the arbuscular mycorrhizal fungi (AMF). These soil fungi have been reported to improve plant resistance/tolerance to pests and diseases. On the other hand, soilborne pathogens represent a threat to agriculture generating important yield losses, depending upon the pathogen and the crop. One example is the “Sudden Death Syndrome” (SDS), a severe disease in soybean (Glycine max (L.) Merr) caused by a complex of at least four species of Fusarium sp., among which Fusarium virguliforme and F. tuccumaniae are the most prevalent in Argentina. This study provides, under strict in vitro culture conditions, a global analysis of transcript modifications in mycorrhizal and non-mycorrhizal soybean root associated with F. virguliforme inoculation. Microarray results showed qualitative and quantitative changes in the expression of defense-related genes in mycorrhizal soybean, suggesting that AMF are good candidates for sustainable plant protection against F. virguliforme.
2018-11-12 | GSE108964 | GEO
Project description:Macrophomina phaseolina, a soil borne pathogen with a wide host range, causes the charcoal rot in soybean (Glycine max (L.) Merr). In Argentina, soybean is the most important crop as far as sowing surface cultivation concerns, and for this reason it is important to assess integrated disease management strategies in order to minimize the incidence of this disease and the consequent loss of performance culture. Previous studies have demonstrated the protective effect that arbuscular mycorrhizal can promote on their hosts against various pathogens invasion, especially against soil borne fungi. Therefore, the goal of this study was to analyze the phenomenon of mycorrhizae mediated protection by characterizing transcriptional changes using cDNA microarrays as a tool. The objective of the present study was to investigate, under strict in vitro culture conditions, the global transcriptional change in the roots of pre-mycorrhized soybean plantlets challenged by M. phaseolina as compared to non-mycorrhizal soybean plantlets. The MapMan software was used to distinguish transcriptional change under these conditions, with special emphasis on plant defence response.
2017-12-19 | GSE87740 | GEO
Project description:Arbuscular mycorrhizal symbiosis is a predominant relationship between plant and arbuscular mycorrhizal fungi. To idendify arbuscular mycorrhiza responsive miRNAs, small RNA libraries were constructed in tomato roots colonized with Rhizophagus irregularis and without Rhizophagus irregularis. We identify miRNAs in tomato roots and provide a new profile of tomato miRNAs. And we found that some miRNAs were responsive to arbuscular mycorrhiza by comparing miRNAs in treatment with that in control.
2016-07-20 | GSE76204 | GEO
Project description:Arbuscular mycorrhizal symbiosis is a predominant relationship between plant and arbuscular mycorrhizal fungi. To idendify arbuscular mycorrhiza responsive miRNAs, small RNA libraries were constructed in tomato roots colonized with Rhizophagus irregularis and without Rhizophagus irregularis. We identify miRNAs in tomato roots and provide a new profile of tomato miRNAs. And we found that some miRNAs were responsive to arbuscular mycorrhiza by comparing miRNAs in treatment with that in control. Examination of arbuscular mycorrhiza responsive miRNAs in tomato through high-throughput small RNA sequencing of roots with Rhizophagus irregularis and that without Rhizophagus irregularis
2016-07-20 | E-GEOD-76204 | biostudies-arrayexpress
Project description:Impacts of cover crop residue management on the arbuscular mycorrhizal fungal communities of maize
| PRJDB8585 | ENA
Project description:Arbuscular mycorrhiza (AM) interactions between plants and Glomeromycota fungi primarily support phosphate aquisition of most terrestrial plant species. To unravel gene expression in Medicago truncatula root colonization by AM fungi, we used genome-wide transcriptome profiling based on whole mycorrhizal roots. We used GeneChips to detail the global programme of gene expression in response to colonization by arbuscular mycorrhizal fungi and in response to a treatment with phosphate and identified genes differentially expressed during this process. Medicago truncatula roots were harvested at 28 days post inoculation with the two different arbuscular mycorrhizal fungi Glomus intraradices (Gi-Myc) and Glomus mosseae (Gm-Myc) under low phosphate conditions (20 µM phosphate) or after a 28 days treatment with 2 mM phosphate in the absence of arbuscular mycorrhizal fungi (2mM-P). As a control, uninfected roots grown under low phosphate conditions (20 µM phosphate) were used (20miM-P). Three biological replicates consisting of pools of five roots were used for RNA extraction and hybridization on Affymetrix GeneChips.
2011-10-28 | E-GEOD-32208 | biostudies-arrayexpress
Project description:To investigate the involvement of arbuscular mycorrhizal symbiosis in the moleular regulation in foxtail millet roots and the effects of genetic variation on AMS-mediated molecular regulation, we isolated total RNA from the roots of 3 different landraces for comprehensive transcriptomic analysis. We then performed gene expression profiling analysis using data obtained from RNA-seq of 3 different landraces (Hanevalval, TT8, ICE36) after 6-week mock or arbuscular mycorrhizal fungi treatments.
2022-10-20 | GSE213843 | GEO
Project description:Plant species posses a special set of genes functional only in arbuscular mycorrhizal symbiosis. So, the model plant Medicago truncatula (Jemalong 5) was used for transcriptome comparative analysis while infected with compatible rhizobia Sinorhizobium meliloti (strain 10) and with or without arbuscular mycorrhizal fungus Rhizophagus irregularis (SYM5). Whole shoot and whole root were used for RNA isolation and processed via one of the European certified Affymetrix core labs (http://core.img.cas.cz).
2019-04-21 | GSE126833 | GEO