Ontology highlight
ABSTRACT:
PROVIDER: PRJNA593383 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10585600_1.fastq.gz | Fastqsanger.gz | |||
| SRR10585600_2.fastq.gz | Fastqsanger.gz | |||
| SRR10585700_1.fastq.gz | Fastqsanger.gz | |||
| SRR10585700_2.fastq.gz | Fastqsanger.gz | |||
| SRR10585800_1.fastq.gz | Fastqsanger.gz |
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Project description:Plants are naturally associated with diverse microbial communities, which play significant roles in plant performance, such as growth promotion or fending off pathogens. The roots of Alkanna tinctoria L. are rich in naphthoquinones, particularly the medicinally used chiral compounds alkannin, shikonin and their derivatives. Former studies already have shown that microorganisms may modulate plant metabolism. To further investigate the potential interaction between A. tinctoria and associated microorganisms we performed a greenhouse experiment, in which A. tinctoria plants were grown in the presence of three distinct soil microbiomes. At four defined plant developmental stages we made an in-depth assessment of bacterial and fungal root-associated microbiomes as well as all primary and secondary metabolites. Our results showed that the plant developmental stage was the most important driver influencing the plant metabolite content, revealing peak contents of alkannin/shikonin at the fruiting stage. In contrast, the soil microbiome had the biggest impact on the plant root microbiome. Correlation analyses performed on the measured metabolite content and the abundance of individual bacterial and fungal taxa suggested a dynamic, at times positive or negative relationship between root-associated microorganisms and root metabolism. In particular, the bacterial Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium group and the fungal species Penicillium jensenii were found to be positively correlated with higher content of alkannins.
2021-11-28 | ST002021 | MetabolomicsWorkbench
Project description:Legumes interact with soil fungi, leading to the development of arbuscular mycorrhizal (AM) roots. Diffusible AM fungal signals were identified as sulphated and non-sulphated LCOs (sMyc-LCOs and nsMyc-LCOs). Applying Myc-LCOs on roots of symbiotic mutants, we used GeneChips to detail the global programme of gene expression in these mutants in response to the external application of Myc-LCOs.
2012-05-31 | GSE33637 | GEO
Project description:Legumes interact with soil fungi, leading to the development of arbuscular mycorrhizal (AM) roots. Diffusible AM fungal signals were identified as sulphated and non-sulphated LCOs (sMyc-LCOs and nsMyc-LCOs). Applying Myc-LCOs on roots of symbiotic mutants, we used GeneChips to detail the global programme of gene expression in these mutants in response to the external application of Myc-LCOs. Keywords: Expression profiling by array
2015-11-12 | GSE67166 | 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.
2013-03-09 | GSE44984 | GEO
Project description:Plants deploy pattern recognition receptors to detect microbe- and damage-associated molecular patterns. Arabidopsis thaliana receptor-like protein RLP30 contributes to innate immunity to the necrotrophic fungus Sclerotinia sclerotiorum by recognizing SCLEROTINIA CULTURE FILTRATE ELICITOR 1 (SCFE1). Here we show that the S. sclerotiorum small cysteine-rich protein SCP1 accounts for elicitor activity of SCFE1. RLP30 recognizes SCP1 and its homologs from divergent fungi and oomycetes, as well as an SCP1-unrelated and conserved pattern from bacterial Pseudomonads. Stable expression of RLP30 in Nicotiana tabacum confers enhanced immunity to bacterial, fungal, and oomycete pathogens. Unlike Arabidopsis, which requires intact SCP1 for RLP30-mediated immunity, other Brassicaceae and Solanaceae respond to smaller immunogenic SCP1 epitopes. We conclude that Arabidopsis RLP30 recognizes immunogenic patterns from three microbial kingdoms and that mechanistically different SCP1 perception has evolved in other plant species, likely as a result of convergent evolution.
2023-06-14 | PXD036013 | Pride
Project description:Because of severe abiotic limitations, Antarctic soils represent simplified ecosystems, where microorganisms are the principle drivers of nutrient cycling. This relative simplicity makes these ecosystems particularly vulnerable to perturbations, like global warming, and the Antarctic Peninsula is among the most rapidly warming regions on the planet. However, the consequences of the ongoing warming of Antarctica on microorganisms and the processes they mediate are unknown. Here, using 16S rRNA gene pyrosequencing and qPCR, we report a number of highly consistent changes in microbial community structure and abundance across very disparate sub-Antarctic and Antarctic environments following three years of experimental field warming (+ 0.5-2°C). Specifically, we found significant increases in the abundance of fungi and bacteria and in the Alphaproteobacteria-to-Acidobacteria ratio. These alterations were linked to a significant increase in soil respiration. Furthermore, the shifts toward generalist or opportunistic bacterial communities following warming weakened the linkage between bacterial diversity and functional diversity. Warming also increased the abundance of some organisms related to the N-cycle, detected as an increase in the relative abundance of nitrogenase genes via GeoChip microarray analyses. Our results demonstrate that soil microorganisms across a range of sub-Antarctic and Antarctic environments can respond consistently and rapidly to increasing temperatures, thereby potentially disrupting soil functioning. We conducted in situ warming experiments for three years using open-top chambers (OTCs) at one sub-Antarctic (Falkland Islands, 52ºS) and two Antarctic locations (Signy and Anchorage Islands, 60ºS and 67ºS respectively) (see Supplementary Fig. 1 for a map). OTCs increased annual soil temperature by an average of 0.8°C (at a depth of 5 cm), resulting in 8-43% increase in positive-degree days annually and a decrease in freeze-thaw cycle frequency by an average of 15 cycles per year (8). At each location, we included densely vegetated and bare fell-field soils in the experimental design for a total of six environments. Densely vegetated and bare environments represent two contrasting environments for Antarctic soil microorganisms, with large differences in terms of C and N inputs to soils. Massively parallel pyrosequencing (Roche 454 GS FLX Titanium) of 16S rRNA gene amplicons was used to follow bacterial diversity and community composition [GenBank Accession Numbers: HM641909-HM744649], and functional gene microarrays (GeoChip 2.0)(11) were used to assess changes in functional gene distribution. Bacterial and fungal communities were also quantified using real-time PCR.
2010-12-30 | E-GEOD-22825 | biostudies-arrayexpress
Project description:Fungal communities associated with Douglas-fir roots
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Project description:This SuperSeries is composed of the following subset Series: GSE27548: cRNA hybridizations of 10 Spring annual accessions of Arabidopsis thaliana under well-watered and mild soil drying GSE27549: Genomic dna hybridizations of 10 Spring annual accessions of Arabidopsis thaliana GSE27550: cRNA hybridizations of 18 accessions of Arabidopsis thaliana under well-watered and mild soil drying GSE27551: Genomic dna hybridizations of 8 winter annual accessions of Arabidopsis thaliana Refer to individual Series
2012-03-09 | E-GEOD-27552 | biostudies-arrayexpress