Revealing new bacterial functions in the plant rhizoplane

Abstract Background Microorganisms play important ecological roles during interactions with plants. Although some microorganisms promote plant performance and are applied as biofertilizers, the molecular cross-talk of bacteria and plants is not fully understood. We aim to reveal which bacterial genes are tightly associated with the adaptation to the plant host by merging the outcomes of RNA-Seq data of a bacterium colonizing roots and comparative genomics analyses. Results Here, we show the expression of genes in a plant growth-promoting Pseudomonas strain interacting with plant roots. Our findings highlight that many of the upregulated genes have not been previously associated with this interaction. The occurrence of 184 of the upregulated bacterial genes in the interaction was higher in Pseudomonas isolates from plants compared to bacteria from other habitats, such as soils, animals or water. We argue that these genes may play relevant biological roles in this host, but only a few have been previously shown to be associated with plant-bacteria interactions. One of these genes is the yafL gene, encoding a cysteine peptidase with an NlpC/P60 hydrolytic domain, for which we demonstrate its involvement in bacterial plant growth promotion through the comparison of a wild-type bacterium with a yafL knockout strain. Conclusions Microbial plant growth promotion is a complex process with potential involvement of numerous bacterial genes, many of which still await characterization. By integrating the outcomes from in vivo RNA-Seq experiments and comparative genomic analyses, we have revealed several plant-associated genes and functions. Moreover, we have experimentally demonstrated the role of one of these genes in plant growth promotion.