Genome-resolved metatranscriptomics reveals conserved root colonization strategies in a synthetic microbiota
Over evolutionary time, microbes have developed complex mechanisms to colonize plant roots and to survive in the host environment. Identification of global processes activated by phylogenetically distant microbiota members during root colonization has been hampered by technical constraints in metatranscriptomic analysis. This includes lack of reference genomes in databases, high representation of host and microbial rRNA sequences in sequencing datasets, or difficulty to experimentally validate candidate genes of interest. To alleviate these constraints, we recolonized germ-free Arabidopsis thaliana with a synthetic root microbiota comprising phylogenetically diverse and genome-sequenced bacterial (84) and fungal (22) isolates that are representative of naturally-occurring root microbiomes. Extensive depletion of plant, bacterial and fungal rRNA reads, combined with deep-RNA sequencing and read mapping against the 106 reference microbial genomes allowed us to capture the transcriptome of abundant root colonizers and to identify 3,162 microbial genes differentially regulated in roots compared to soil samples. Biological processes such as translation and energy production were consistently activated upon host contact and their induction correlated with bacterial abundance at roots. We experimentally validated the relevance of several genes that were consistently induced by multiple bacterial strains during root colonization, including those encoding the phosphate uptake system PstABCS, the ribosome-binding GTPase TypA and a component of the Ton motor complex ExbD . Our results suggest that phylogenetically unrelated bacteria activate strain-specific processes but also a common set of conserved genes to colonize and persist in the root environment.