Synthetic phyllosphere microbiota
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB32997 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR3372870_1.fastq.gz | Fastqsanger.gz | |||
| ERR3372870_2.fastq.gz | Fastqsanger.gz | |||
| ERR3372880_1.fastq.gz | Fastqsanger.gz | |||
| ERR3372880_2.fastq.gz | Fastqsanger.gz | |||
| ERR3372890_1.fastq.gz | Fastqsanger.gz |
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Project description:Plants are colonized by a variety of microorganisms, the plant microbiota. In the phyllosphere, the above-ground parts of plants, bacteria are the most abundant inhabitants. Most of these microorganisms are not pathogenic and the plant responses to commensals or to pathogen infection in the presence of commensals are not well understood. We report the Arabidopsis leaf transcriptome after 3 to 4 weeks of colonization by Methylobacterium extorquens PA1 and Sphingomonas melonis Fr1, representatives of two abundant genera in the phyllosphere, compared to axenic plants. In addition, we also sequenced the transcriptome of Arabidopsis 2 and 7 days after spray-infection with a low dose of P. syringae DC3000 and in combination with the commensals.
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Project description:The identification of processes activated by specific microbes during microbiota colonization of plant roots has been hampered by technical constraints in metatranscriptomics. These include lack of reference genomes, high representation of host or microbial rRNA sequences in datasets, or difficulty to experimentally validate gene functions. Here, we recolonized germ-free Arabidopsis thaliana with a synthetic, yet representative root microbiota comprising 106 genome-sequenced bacterial and fungal isolates. We used multi-kingdom rRNA depletion, deep RNA-sequencing and read mapping against reference microbial genomes to analyse the in-planta metatranscriptome of abundant colonizers. We identified over 3,000 microbial genes that were differentially regulated at the soil-root interface. Translation and energy production processes were consistently activated in planta, and their induction correlated with bacterial strains’ abundance in roots. Finally, we used targeted mutagenesis to show that several genes consistently induced by multiple bacteria are required for root colonization in one of the abundant bacterial strains (a genetically tractable Rhodanobacter). Our results indicate that microbiota members activate strain-specific processes but also common gene sets to colonize plant roots.
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Project description:Non-targeted metabolomics of synthetic community created from the Arabidopsis phyllosphere microbiota.
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