Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1010562 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR25820400_1.fastq.gz | Fastqsanger.gz | |||
| SRR25820400_2.fastq.gz | Fastqsanger.gz | |||
| SRR25820401_1.fastq.gz | Fastqsanger.gz | |||
| SRR25820401_2.fastq.gz | Fastqsanger.gz | |||
| SRR25820402_1.fastq.gz | Fastqsanger.gz |
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Project description:Fire is a crucial event regulating the structure and functioning of many ecosystems. Yet few studies focused on how fire affects both the taxonomic and functional diversity of soil microbial communities, along with plant diversity and soil carbon (C) and nitrogen (N) dynamics. Here, we analyze these effects for a grassland ecosystem 9-months after an experimental fire at the Jasper Ridge Global Change Experiment (JRGCE) site in California, USA. Fire altered soil microbial communities considerably, with community assembly process analysis indicating that environmental selection pressure was higher in burned sites. However, a small subset of highly connected taxa were able to withstand the disturbance. In addition, fire decreased the relative abundances of most genes associated with C degradation and N cycling, implicating a slow-down of microbial processes linked to soil C and N dynamics. In contrast, fire stimulated plant growth, likely enhancing plant-microbe competition for soil inorganic N. To synthesize our findings, we performed structural equation modeling, which showed that plants but not microbial communities were responsible for the significantly higher soil respiration rates in burned sites. In conclusion, fire is well-documented to considerable alter the taxonomic and functional composition of soil microorganisms, along with the ecosystem functioning, thus arousing feedback of ecosystem responses to affect global climate.
2022-02-19 | GSE126737 | 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:Plant growth and development depends on the availability of nutrients and water resources in the soil. The increased frequencies of drought events over recent years have affected nutrient availability soil systems. Crops reutilising winter cover crop root channels allows access to resources from distal regions in the soil horizon. However, the availability of information regarding root channel reutilisation under drought, specifically bacterial community structures and functions is unknown. In this study, we observed the changes inflicted by drought on bacterial communities in maize (Zea mays L.) rhizospheres after reusing the winter cover crop root channels. The techniques of 16S rRNA (ribosomal ribonucleic acid) gene-based microbial profiling and metaproteomics were used to study the alterations in biochemical pathways of those communities under drought at three different locations (Hohenschulen, Karkendamm and Reinshof) comprising three different soli types (Luvisol, Podzol and Phaeozem) respectively. Besides the influence of soil properties, we noticed that under drought the relative abundances of Acidobacteriota, Actinomycetota, Planctomycetota, and Pseudomonadota increased, while Chloroflexota, Methylomirabilota, Patescibacterota, and Verrucomicrobiota decreased. At drought-prone soil types Luvisol and Podzol, aerobic communities Pseudomonadota and Verrucomicrobiota increased abundance of the glyoxylate cycle as a means of conserving carbon and energy for plausible survival measures. Higher abundance of catalase-glutathione peroxidase (CAT-PER) through the methionine cycle-transsulfuration pathway possibly alleviate reactive oxygen species (ROS) levels. Overall, bacterial communities in the reused cover crop root channels respond to drought by taking mitigative measures for survival.
2025-09-22 | PXD062138 | Pride
Project description:The association between soil microbes and plant roots is present in all natural and agricultural environments. Microbes can be beneficial, pathogenic, or neutral to the host plant development and adaptation to abiotic or biotic stresses. Progress in investigating the functions and changes in microbial communities in diverse environments have been rapidly developing in recent years, but the changes in root function is still largely understudied. The aim of this study was to determine how soil bacteria influence maize root transcription and microRNAs (miRNAs) populations in a controlled inoculation of known microbes over a defined time course. At each time point after inoculation of the maize inbred line B73 with ten bacterial isolates, DNA and RNA were isolated from roots. The V4 region of the 16S rRNA gene was amplified from the DNA and sequenced with the Illumina MiSeq platform. Amplicon sequencing of the 16S rRNA gene indicated that most of the microbes successfully colonized maize roots. The colonization was dynamic over time and varied with the specific bacterial isolate. Small RNA sequencing and mRNA-Seq was done to capture changes in the root transcriptome from 0.5 to 480 hours after inoculation. The transcriptome and small RNA analyses revealed epigenetic and transcriptional changes in roots due to the microbial inoculation. This research provides the foundational data needed to understand how plant roots interact with bacterial partners and will be used to develop predictive models for root response to bacteria.
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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:<p><strong>BACKGROUND:</strong> The coevolution and interaction between plants and microorganisms have long been a subject of significant research interest. Dark septate endophytes (DSE) have garnered great attention in contemporary research due to their functional diversity, in vitro cultivation ability, and ability to establish symbiotic associations with host plants. In the present study, three DSE strains, namely <em>Acrocalymma vagum</em>, <em>Zopfiella marina</em>, and <em>Phoma herbarum</em>, which were obtained from the roots of <em>Astragalus membranaceus</em>, were introduced into maize plants through inoculation. We evaluated the effects of DSE inoculation on maize growth and root secretion activity through a multi omics methods, and proposed mechanisms for 'internal pathways' and 'external pathways'.</p><p><strong>RESULTS:</strong> The findings indicated that A. vagum exhibited superior growth-promoting ability on maize compared to <em>Z. marina</em> and <em>P. herbarum</em>.GO and KEGG enrichment analysis found that <em>A. vagum</em> inoculation resulted in significant enrichment of differentially expressed genes in annotation functions related to hormone regulation and lipid metabolism. A. vagum inoculation revealed that the gene pathways involved in plant hormone signaling and plant pathogen interactions play a crucial role in promoting host growth, and <em>A. vagum</em> inoculation group exhibited the highest number of differentially expressed genes, the most intricate protein-protein interaction (PPI) model, and the most pronounced relationship between differentially expressed genes. After the inoculation of <em>A.vagum</em>, the levels of salicylic acid, zeatin, and IAA in maize plants significantly increased. Additionally, the diversity and abundance of endophytic fungi, as well as the proportion of harmful bacteria and beneficial fungi, had significantly increased. Compared with <em>Z. marina</em> and <em>P. herbarum</em>, the net photosynthetic rate (Pn) and stomatal conductance (Gs) of <em>A.vagum</em> inoculated plants significantly increased. Inoculation with <em>A.vagum</em> could enhance the ability of corn roots to secrete lipids, sugars, and amino acids, resulted in a notable augmentation of beneficial bacteria and fungi, accompanied by a significant reduction in the proportion of harmful bacteria in the rhizosphere soil, such as <em>Fusarium solani</em> and <em>Fusarium lacertarum</em>, exhibited significant inhibition, whereas <em>Bacillus niabensis</em> and <em>Bacillus nealsonii</em> demonstrated enrichment trends. Soil pH, organic matter, available potassium content, acid phosphatase, alkaline phosphatase and urease activity exhibited significant increases following the inoculation of <em>A. vagum</em>. Variance decomposition and structural equation modeling (SEM) analysis indicated that the 'internal pathway', maize growth is mainly influenced by the interaction of endogenous hormones, endophytic microorganisms, and photosynthetic parameters, whereas within the 'external pathway', the interaction between soil microorganisms and soil physicochemical properties exerted a dominant influence. Compared with the <em>Z. marina</em> and <em>P. herbarum</em> inoculation, <em>A. vagum</em> inoculation showed a more significant impact on maize growth, both in terms of 'internal pathway' and 'external pathway', in terms of pathway level and quantity.</p><p><strong>CONCLUSIONS:</strong> These findings provide a new perspective for understanding the potential mechanisms of 'microbe-plant' interactions and also contribute to the exploration of targeted functional microorganisms that promote growth and stress resistance.</p>
2023-12-15 | MTBLS8903 | MetaboLights
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2019-06-03 | GSE97107 | GEO
Project description:Cover cropping is an effective method to protect agricultural soils from erosion, promote nutrient and moisture retention, encourage beneficial microbial activity, and maintain soil structure. Reusing winter cover crop root channels with the maize roots during the summer allows the cash crop to extract resources from farther niches in the soil horizon. In this study, we investigate how reusing winter cover crop root channels to grow maize (Zea mays L.) affects the composition and function of the bacterial communities in the rhizosphere using 16S rRNA gene amplicon sequencing and metaproteomics. We discovered that the bacterial community significantly differed among cover crop variations, soil profile depths, and maize growth stages. Re-usage of the root channels increased bacterial abundance, and it further increases as we elevate the complexity from monocultures to mixtures. Upon mixing legumes with brassicas and grasses, the overall expression of several steps of the carbon cycle (C) and the nitrogen cycle (N) improved. The deeper root channels of legumes and brassicas compared to grasses correlated with higher bacterial 16S rRNA gene copy numbers and community roles in the respective variations in the subsoil regimes due to the increased availability of root exudates secreted by maize roots. In conclusion, root channel re-use (monocultures and mixtures) improved the expression of metabolic pathways of the important C and N cycles, and the bacterial communities, which is beneficial to the soil rhizosphere as well as to the growing crops.
2025-05-02 | PXD046832 | Pride
Project description:Casuarina glauca belongs to a family of angiosperms called actinorhizal plants because they can develop nitrogen-fixing nodules in association with the soil bacteria Frankia. They can also develop arbuscular mycorrhizae (AM) while associated with Glomeromycota fungi. The aim of this transcriptomic study was to get a global view of the plant symbiotic genetic program in AM and to identify new key plant genes involved in endosymbioses.
2012-10-22 | GSE36676 | GEO