Soil metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJDB11175 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| DRR272362_1.fastq.gz | Fastqsanger.gz | |||
| DRR272362_2.fastq.gz | Fastqsanger.gz | |||
| DRR272363_1.fastq.gz | Fastqsanger.gz | |||
| DRR272363_2.fastq.gz | Fastqsanger.gz | |||
| DRR272364_1.fastq.gz | Fastqsanger.gz |
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2022-03-01 | PXD009773 | 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:Microbial community analysis with DNA oligonucleotide microarrays targeting ribosomal RNA (rRNA) provides a highly parallel interrogation of nucleic acids isolated from environmental samples. High fidelity readout is essential for accurate interpretation of hybridisations. We describe the hybridisation of in vitro transcribed 16S rRNA from an uncontaminated and 2,4,6-trinitrotoluene contaminated soil to an oligonucleotide microarray containing group- and species-specific perfect match (PM) probes and their 2 corresponding mismatch (MM) probes. Thermal dissociation analysis was used to determine the specificity of each PM-MM probe set. Functional ANOVA often discriminated PM-MM probe sets when Td values (temperature at 50% probe-target dissociation) could not. Maximum discrimination for many PM and MM probes often occurred at temperatures greater than the Td. Comparison of signal intensities measured prior to dissociation analysis from hybridisations of the two soil samples revealed significant differences in domain-, group- and species-specific probes. Functional ANOVA showed significantly different dissociation curves for 11 PM probes when hybridisations from the two soil samples were compared, even though initial signal intensities for 3 of the 11 did not vary. This approach provides a highly parallel, multi-level analysis that incorporates MM probes and dissociation curves into high fidelity microarray analysis of complex environmental nucleic acid profiles. Keywords: Microbial diversity, thermal dissociation analysis
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Project description:The goal of this growth chamber experiment was to investigate the effects of diverse soil microbial communities on the transcriptional responses of plants to drought. Specifically, we sought to understand how soil microbiomes' past exposure to water-limited conditions (either long-term exposure to dry conditions in low-precipitation sites, or recent acute drought) impacted their interactions with plants. Six soils collected from remnant prairies crossing a steep precipitation gradient in Kansas, USA were used as the starting microbial communities. Thirty-two pots (or mesocosms) of each soil were divided among four treatments: droughted or well-watered, and with or without a host plant (Tripsacum dactyloides) in a factorial design. The soil mesocosms were "conditioned" in these treatments for five months. (Metagenome and metatranscriptome data from the baseline soils and the post-conditioning soils are available in a separate BioProject on NCBI SRA and GEO). Then, a microbial slurry extracted from each of the 192 conditioned soils was used to inoculate 4 plants in a subsequent experiment (the “Test Phase”): one pot per combination of watering treatment (droughted or control) and host species (Zea mays or Tripsacum dactyloides). After 4 weeks (for maize) or 5 weeks (for eastern gamagrass) we harvested one crown root per plant for 16S rRNA sequencing and another crown root for RNA-seq. The 16S and RNA-seq data for these plants (both species) are contained in this BioProject. Note that 16S rRNA sequencing data are available for all plants in this experiment, but we conducted RNA-seq only for a subset (all plants grown in microbiomes originating from the 2 driest and 2 wettest collection sites).
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