Genome annotation and comparative genomics allowed the identification of an extended set of genes specific to the plant niche adaptation of this bacterium. This includes genes that code for putative proteins involved in rhizosphere survival, root adhesion (pili, adhesion, hemagglutinin, cellulose biosynthesis), colonization/establishment inside the plant (chemiotaxis, flagella, cellobiose phosphorylase), plant protection against fungal and bacterial infections (siderophore production and synthesis of the antimicrobial compounds 4-hydroxybenzoate and 2-phenylethanol), and improved poplar growth and development through the production of the phytohormones indole acetic acid, acetoin and 2,3-butanediol.
Metabolite analysis and quantitative PCR pointed to a remarkable interaction between Enterobacter sp. 638 and its poplar host with the endophyte responsible of the production of acetoin and 2,3-butanediol, whose synthesis turned out to be dependent on the presence of plant synthesized compounds, such as sucrose. The genetic determinants required for sucrose metabolism and phytohormone synthesis are clustered on a genomic island, further confirming their tight interplay.
Our results provide a basis to better understanding the synergistic interactions between poplar and Enterobacter sp. 638. This information can be further exploited to improve establishment and sustainable production of poplar on marginal, non-agricultural soils using endophytic bacteria such as Enterobacter sp. 638 as growth promoting agents.