Soil metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1056865 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Soil fungal diversity along elevation gradients
| PRJDB9516 | ENA
Project description:Plants in their natural and agricultural environments are continuously exposed to a plethora of diverse microorganisms resulting in microbial colonization of plants in the rhizosphere. This process is believed to be accompanied by an intricate network of ongoing simultaneous interactions. In this study, we compared transcriptional patterns of Arabidopsis thaliana roots and shoots in the presence and absence of whole microbial communities extracted from compost soil. The results show a clear growth promoting effect of Arabidopsis shoots in the presence of soil microbes compared to axenically grown plants under identical conditions. Element analyses showed that iron uptake was facilitated by these mixed microbial communities which also lead to transcriptional downregulation of genes required for iron transport. In addition, soil microbial communities suppressed the expression of marker genes involved in oxidative stress/redox signalling, cell wall modification and plant defense. While most previous studies have focussed on individual plant-microbe interactions, our data suggest that multi-species transcriptional profiling, using simultaneous plant and metatranscriptomics coupled to metagenomics may be required to further increase our understanding of the intricate networks underlying plant-microbe interactions in their diverse environments.
2013-03-09 | GSE44984 | GEO
Project description:Understanding the mechanisms underlying the establishment of invasive plants is critical in community ecology. According to a widely accepted theory, plant-soil-microbe interactions mediate the effects of invasive plants on native species, thereby affecting invasion success. However, the roles and molecular mechanisms associated with such microbes remain elusive. Using high throughput sequencing and a functional gene microarray, we found that soil taxonomic and functional microbial communities in plots dominated by Ageratina adenophora developed to benefit the invasive plant. There were increases in nitrogen-fixing bacteria and labile carbon degraders, as well as soil-borne pathogens in bulk soil, which potentially suppressed native plant growth. Meanwhile, there was an increase of microbial antagonism in the A. adenophora rhizosphere, which could inhibit pathogenicity against plant invader. These results suggest that the invasive plant A. adenophora establishes a self-reinforcing soil environment by changing the soil microbial community. It could be defined as a ‘bodyguard/mercenary army’ strategy for invasive plants, which has important insights for the mitigation of plant invasion.
2019-05-01 | GSE114498 | GEO
Project description:Plants in their natural and agricultural environments are continuously exposed to a plethora of diverse microorganisms resulting in microbial colonization of plants in the rhizosphere. This process is believed to be accompanied by an intricate network of ongoing simultaneous interactions. In this study, we compared transcriptional patterns of Arabidopsis thaliana roots and shoots in the presence and absence of whole microbial communities extracted from compost soil. The results show a clear growth promoting effect of Arabidopsis shoots in the presence of soil microbes compared to axenically grown plants under identical conditions. Element analyses showed that iron uptake was facilitated by these mixed microbial communities which also lead to transcriptional downregulation of genes required for iron transport. In addition, soil microbial communities suppressed the expression of marker genes involved in oxidative stress/redox signalling, cell wall modification and plant defense. While most previous studies have focussed on individual plant-microbe interactions, our data suggest that multi-species transcriptional profiling, using simultaneous plant and metatranscriptomics coupled to metagenomics may be required to further increase our understanding of the intricate networks underlying plant-microbe interactions in their diverse environments. Four samples were analysed in total. One corresponded to a pooled sample of RNA extracted from root tissues of 60 plants. The other three were biological replicates from shoot tissues, each of which contained 20 plants. Controls were used as reference and corresponded to tissues of plants grown in sterile conditions.
2013-03-09 | E-GEOD-44984 | biostudies-arrayexpress
Project description:The microbial community structure along an elevation gradient of the Shennongjia Mountain as characterized by 16s rRNA Illumina sequencing Genome sequencing
| PRJNA293738 | ENA
Project description:In general, the endosphere isolate EC18 showed more numbers of genes significantly altered in the presence of root exudates than the soil isolate SB8 . Some of the altered genes in the two strains showed overlap. Some of these genes were previously reported to be involved in microbe-plant interactions, such as organic substance metabolism, oxidation reduction, transmembrane transportation and a subset with putative or unknown function. It was also found some genes showed opposite trend among the two strains.
2017-04-26 | GSE98148 | GEO
Project description:The endophytic fungus Piriformospora indica is a member of Sebacinales. It colonizes the roots of many plant species including the model plant Arabidospis thaliana (Peskan-Berghofer et al. 2004). P. indica promotes plant growth (Peskan-Berghofer et al. 2004), seed production (Shahollari et al. 2007) and confers resistance to biotic (Camehl et al. 2011) and abiotic stresses (Sherameti et al., 2008, Matsuo et al., 2015). Vadassery et al. (2009) have shown that a cell wall extract from P. indica induces cytoplasmic calcium elevation in Arabidopsis Col-0 roots. Johnson et al. (2017) isolated an ethylmethane-induced mutant cycam (cytoplasmic calcium elevation mutant) which fails to induce cytoplasmic calcium elevation in response to the cell wall preparation. The active compound was identified as cellotriose (CT) (Johnson et al., 2017). The cycam mutant shows a wild-type response to treatment with chitin. The expression profiles compare the response of WT and cycam roots to treatments with CT and chitin. References: Camehl I, Drzewiecki C, Vadassery J, Shahollari B, Sherameti I, Forzani C, Munnik T, Hirt H, Oelmüller R. (2011) The OXI1 kinase pathway mediates Piriformospora indica-induced growth promotion in Arabidopsis. PLoS Pathog. 7(5):e1002051. Johnson JM, Thürich J, Petutschnig EK, Altschmied L, Meichsner D, Sherameti I, Dindas J, Mrozinska A, Paetz C, Scholz S, Furch A, Lipka V, Hedrich R, Schneider B, Svatoš S, Oelmüller R. (2017) Cellotriose-induced cytoplasmic calcium elevation is controlled by a poly(A) ribonuclease in Arabidopsis root. (submitted to elife). Matsuo M, Johnson JM, Hieno A, Tokizawa M, Nomoto M, Tada Y, Godfrey R, Obokata J, Sherameti I, Yamamoto YY, Böhmer FD, Oelmüller R. (2015) High REDOX RESPONSIVE TRANSCRIPTION FACTOR1 Levels Result in Accumulation of Reactive Oxygen Species in Arabidopsis thaliana Shoots and Roots. Mol Plant. 8(8):1253-73. Peškan-Berghöfer T, Shahollari B, Giang PH, Hehl S, Markert C, Blanke V, Varma AK, Oelmüller R. (2004) Association of Piriformospora indica with Arabidopsis thaliana roots represents a novel system to study beneficial plant–microbe interactions and involves early plant protein modifications in the endoplasmatic reticulum and at the plasma membrane. Physiol. Plant. 122: 465–477. Shahollari B, Vadassery J, Varma A, Oelmüller R. (2007) A leucine-rich repeat protein is required for growth promotion and enhanced seed production mediated by the endophytic fungus Piriformospora indica in Arabidopsis thaliana. Plant J. 50(1):1-13. Sherameti, I., Tripathi, S., Varma, A., and Oelmüller, R. (2008). The root-colonizing endophyte Pirifomospora indica confers drought tolerance in Arabidopsis by stimulating the expression of drought stress-related genes in leaves. Mol. Plant Microbe Interact. 21: 799-807. Vadassery, J., Ranf, S., Drzewiecki, C., Mithöfer, A., Mazars, C., Scheel, D., Lee, J., and Oelmüller, R. (2009) A cell wall extract from the endophytic fungus Piriformospora indica promotes growth of Arabidopsis seedlings and induces intracellular calcium elevation in roots. Plant J. 59: 193-206.
2018-02-09 | GSE98880 | GEO
Project description:bacterial diversity along elevation gradient Metagenome
| PRJNA906103 | ENA
Project description:Bromeliad microbiome along an elevation gradient
| PRJEB52870 | ENA