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Series GSE231841 Query DataSets for GSE231841
Status Public on Nov 03, 2023
Title Genome-resolved metatranscriptomics reveals conserved root colonization determinants in a synthetic microbiota
Organisms Arabidopsis thaliana; unidentified soil bacteria
Experiment type Expression profiling by high throughput sequencing
Summary 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.
 
Overall design Comparative gene expression profiling analysis of RNA-seq data from soil and root samples inoculated with Synthetic microbial consortia
 
Contributor(s) Vannier N, Mesny F, Getzke F, Chesneau G, Dethier L, Ordon J, Thiergart T, Hacquard S
Citation(s) 38092730
Submission date May 06, 2023
Last update date Jan 02, 2024
Contact name Fantin Mesny
E-mail(s) mesny@mpipz.mpg.de
Organization name Max Planck Institute for Plant Breeding Research
Department Plant-Microbes interaction
Lab Hacquard group
Street address Carl-von-Linné-Weg 10
City Cologne
ZIP/Postal code 50829
Country Germany
 
Platforms (2)
GPL21179 Illumina HiSeq 3000 (Arabidopsis thaliana)
GPL33384 Illumina HiSeq 3000 (unidentified soil bacteria)
Samples (6)
GSM7304760 Soil sample 1
GSM7304761 Soil sample 2
GSM7304762 Soil sample 3
Relations
BioProject PRJNA968016

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE231841_RAW.tar 35.4 Mb (http)(custom) TAR (of TAR)
GSE231841_reference.fasta.gz 282.4 Mb (ftp)(http) FASTA
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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