Rearranging the sugarcane holobiont via plant-growth promoting bacteria and nitrogen input. Rearranging the sugarcane holobiont

Plant development, growth, health and productivity are not only based in genetical background or nutrient input but rather influenced by the complex microbial communities they host, the holobiont. In this sense, engineering beneficial root microbiomes emerges as a novel and sustainable approach to secure production with less nutrient input. Here, we tested six bacteria genomes, isolated from sugarcane stalks, on sugarcane growth and physiology and their effect on the dynamics of prokaryote community assembly in rizhosphererhizosphere and root endosphere under two N fertilization regimes. All six genomes Paraburkholderia caribensis strain IAC/BECa 88, Kosakonia oryzae strain IAC/BECa 90, Kosakonia radicincitans strain IAC/BECa 95, Paraburkholderia tropica strain IAC/BECa 135, Pseudomonas fluorescens strain IAC/BECa 141 and Herbaspirillum frisingense strain IAC/BECa 152 promoted a significant increase on shoot and root dry mass, when compared to controls that did not receive any inoculation. Inoculated plants showed a significant increase in concentration and accumulation of important macro- and micronutrients and selected aminoacids. However, the N input reduced the impact of the inoculation by shifting modulating the sugarcane microbiome (rizhosphere and root endosphere) and weakened the co-dependence between the sugarcane biomass and nutrients with the soil microbes. Intensifying crop productivity while reducing fertilization is feasible with the contribution of the six beneficial microbes that improved plant nutrient use efficiency. Our study demonstrated that reduced fertilization is not only desirable but essential for a higher impact of the beneficial bacteria on the sugarcane microbiome.