Soil metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJDB12265 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Effect of plant species and soil depth on bacteria and fungi in a coastal wetland
| PRJDB12376 | ENA
Project description:This dataset contains raw files for metabolites collected from the soil and roots of four wetland plant species under non-sterile conditions, both in soil and hydroponically, during the day and night time periods.
2024-05-01 | MSV000094652 | MassIVE
Project description:The nitrogen rich compound guanidine occurs widely in nature and is used by microbes as a nitrogen source, but microorganisms that grow on guanidine have not yet been discovered. Here we show that complete ammonia-oxidizing microbes (comammox), but no other known nitrifiers, encode homologues of a guanidinase and that the comammox isolate Nitrospira inopinata grows on guanidine as sole source of energy and reductant. Proteomics, kinetic enzyme characterization, and the crystal structure of the N. inopinata guanidinase homologue demonstrated that it is a bona fide guanidinase. Transcription of comammox guanidinases was induced in wastewater treatment plant microbiomes upon incubation with guanidine, and guanidine degradation was detected in these systems. The discovery of guanidine as a selective growth substrate for comammox shows a unique niche of these globally important nitrifiers and offers new options for their isolation as well as for targeted manipulation of nitrifier communities.
2024-08-03 | PXD038826 | Pride
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:To unravel complex dynamics of environmental disturbance and microbial metabolic activities, we set up laboratory microcosms to investigate the effects of SO42- and O2 alone or in combination on microbial activities and interactions, as well as the resulting fate of carbon within wetland soil. We used proteogenomics to characterize the biochemical and physiological responses of microbial communities to individual perturbations and their combined effects. Stoichiometric models were employed to deconvolute carbon exchanges among the main functional guilds. These findings can contribute to the development of mechanistic models for predicting greenhouse gas emissions from wetland ecosystems under various climate change scenarios.
2024-05-19 | PXD047453 | Pride
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:Permafrost soil in high latitude tundra is one of the largest terrestrial carbon (C) stocks and is highly sensitive to climate warming. Understanding microbial responses to warming induced environmental changes is critical to evaluating their influence on soil biogeochemical cycles. In this study, a functional gene array (i.e. GeoChip 4.2) was used to analyze the functional capacities of soil microbial communities collected from a naturally degrading permafrost region in Central Alaska. Varied thaw history was reported to be the main driver of soil and plant differences across a gradient of minimally, moderately and extensively thawed sites. Compared with the minimally thawed site, the number of detected functional gene probes across the 15-65 cm depth profile at the moderately and extensively thawed sites decreased by 25 % and 5 %, while the community functional gene beta-diversity increased by 34% and 45%, respectively, revealing decreased functional gene richness but increased community heterogeneity along the thaw progression. Particularly, the moderately thawed site contained microbial communities with the highest abundances of many genes involved in prokaryotic C degradation, ammonification, and nitrification processes, but lower abundances of fungal C decomposition and anaerobic-related genes. Significant correlations were observed between functional gene abundance and vascular plant primary productivity, suggesting that plant growth and species composition could be co-evolving traits together with microbial community composition. Altogether, this study reveals the complex responses of microbial functional potentials to thaw related soil and plant changes, and provides information on potential microbially mediated biogeochemical cycles in tundra ecosystems.
2019-06-03 | GSE97107 | 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