BigFbNIOO6952
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB37839 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR4028530_1.fastq.gz | Fastqsanger.gz | |||
| ERR4028530_2.fastq.gz | Fastqsanger.gz | |||
| ERR4028540_1.fastq.gz | Fastqsanger.gz | |||
| ERR4028540_2.fastq.gz | Fastqsanger.gz | |||
| ERR4028550_1.fastq.gz | Fastqsanger.gz |
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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 study long-term elevated CO2 and enriched N deposition interactive effects on microbial community and soil ecoprocess, here we investigated soil microbial community in a grassland ecosystem subjected to ambient CO2 (aCO2, 368 ppm), elevated CO2 (eCO2, 560 ppm), ambient nitrogen deposition (aN) or elevated nitrogen deposition (eN) treatments for a decade. There exist antagonistic CO2×N interactions on microbial functional genes associated with C, N, P S cycling processes. More strong antagonistic CO2×N interactions are observed on C degradation genes than other genes. Remarkably antagonistic CO2×N interactions on soil microbial communities could enhance soil C accumulation.
2018-05-01 | GSE98512 | GEO
Project description:<div>Species-rich plant communities can induce unique soil biotic legacy effects through changing the abundance and composition of soil biota. These soil legacy effects can cause feedbacks to influence plant performance. In addition, soil biota can induce (defensive) secondary metabolites in shoots and roots and thus affect plant-herbivore interactions. We hypothesize that plant diversity-driven soil biotic legacy effects elicit changes in the shoot and root metabolome. <br></div><div><br></div><div>We tested this hypothesis by establishing an experiment with four plant species. We grew plants in a sterile substrate inoculated with soil conditioned by different plant species communities: (1) monocultures of either of the four species, (2) the four species in a mixture, (3) an eight species mixture including all four species, or (4) a sterile inoculum. After at least eight weeks in the field, we estimated shoot herbivory. At the same time, we took root and shoot samples for metabolomics analyses by liquid chromatography quadrupole time-of-flight mass spectrometry. <br></div><div><br></div><div>We found that shoot and root metabolomes of all plants grown in sterile soil differed significantly from those grown in living soil. The plant metabolomes in living soils differed by species and tissue. Across all species, shoots displayed a greater richness of secondary metabolites than roots. The richness of secondary metabolites differed by species and among living soils. The conditioning species richness significantly affected the Shannon diversity of secondary metabolites in Centaurea jacea. Shoot herbivory positively correlated with the richness and Shannon diversity of secondary metabolites in Leucanthemum vulgare. We detected multiple metabolites that together explained up to 88% of the variation in herbivory in the shoots of Centaurea jacea and Plantago lanceolata. <br></div><div><br></div><div>Synthesis: Our findings suggest that plant diversity-driven shifts in soil biota elicit changes in the composition and diversity of shoot and root secondary metabolites. However, these plant responses and their effect on shoot herbivores are species-specific. Tracking changes in plant secondary chemistry in response to soil biotic legacy effects will help to understand the mechanisms that govern species-specific plant-plant and plant-herbivore interactions.</div>
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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.
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Project description:Plant growth-promoting rhizobacteria (PGPR) are soil beneficial microorganisms that colonize plant roots for nutritional purposes and accordingly benefit plants by increasing plant growth or reducing disease. But it still remains unclear which mechanisms or pathways are involved in the interactions between PGPR and plants. To understand the complex plant-PGPR interactions, the changes in the transcriptome of typical PGPR standard Bacillus subtilis in responding to rice seedlings were analyzed.
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Project description:Microbes play key roles in diverse biogeochemical processes including nutrient cycling. However, responses of soil microbial community at the functional gene level to long-term fertilization, especially integrated fertilization (chemical combined with organic fertilization) remain unclear. Here we used microarray-based GeoChip techniques to explore the shifts of soil microbial functional community in a nutrient-poor paddy soil with long-term (21 years).The long-term fertilization experiment site (set up in 1990) was located in Taoyuan agro-ecosystem research station (28°55’N, 111°27’E), Chinese Academy of Sciences, Hunan Province, China, with a double-cropped rice system. fertilization at various regimes.
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Project description:In order to get insights into the ability of ectomycorrhizal fungi to perceive their biotic environment as well as into the mechanisms of the interactions between ectomycorrhizal fungi and soil bacteria, we analysed the transcriptomic response of the ectomycorrhizal fungus L. bicolor and of two beneficial, and neutral soil bacteria during their interactions in vitro.
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Project description:Microbial biofilms are omnipresent and implicated in a wide spectrum of areas ranging from bioremediation, food production and biomedical applications. To date little is understood about how biofilm communities develop and function on a molecular level, due to the complexity of these biological systems. Here we ap-ply a meta-proteomics approach to investigate the mechanism driving biofilm formation in a microbial model consortium of four bacterial soil isolates of Steno-trophomonas rhizophila, Xanthomonas retroflexus, Microbacterium oxydans and Paeni-bacillus amylolyticus. The protein abundances between community and the single species biofilms were compared to describe how different metabolic pathways were influenced by inter-species interactions. Our results indicate that community development is dependent on interactions between community members facilitat-ing surface attachment and cross-feeding on specific amino acids. Opposite regu-lation patterns of fermentation and nitrogen pathways in Paenibacillus amylolyticus and Xanthomonas retroflexus may, however, also indicate that competition for lim-ited resources affects community development. Overall our results demonstrate the multitude of pathways characterizing biofilm formation in mixed communities. In order to obtain full taxonomic resolution between closely related species and empower correct protein quantification, we developed a novel pipeline for removing peptide sequences shared between community members from the ref-erence proteomes used for spectral database searches. This pipeline can readily be applied to other microbial communities.
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