Rhizosphere microbiome assembly involves seed-borne bacteria in compensatory phosphate solubilization

The rhizosphere microbiome plays a key role in plant nutrient provision. However, the impacts of the vertically transmitted seed microbiome on the assembly of the rhizosphere microbiome and consequently on the functional traits remain unclear. Here, to assess the role of seed-borne beneficial microbes on the assembly of rhizosphere microbiome, we conducted a guest-soil cultivation study using two maize cultivars and their corresponding native soils with different available nutrient contents. The assembly of the rhizosphere bacterial and fungal communities was assessed by amplicon DNA sequencing. Our results demonstrated that the soil microbiome dominates the assembly of the rhizosphere microbiome. A seed-borne beneficial bacterium, Burkholderia gladioli, was able to colonize the rhizosphere in great relative abundance, which significantly altered the assembly of the rhizosphere microbiome. Genome analysis demonstrated that this seed-borne beneficial bacterial species may contain extracellular phosphatase-encoding genes, and gene quantification confirmed their existence, suggesting the possible compensation of phosphate solubilizing function. This functional compensation, which is probably a response to the low concentration of soil available phosphorus, may consequently promote phosphorus acquisition of the host plant. Overall, this study provides new insights into our understanding of the assembly of the rhizosphere microbiome, suggesting that the seed microbiome serves as a functional compensation reservoir to enhance the fitness of progeny plants and highlighting the necessity to consider the seed microbiome during plant breeding.