Growing plant roots are a primary source of soil organic carbon, exuding changing combinations of compounds, including sugars, organic acids, amino acids, fatty acids and secondary metabolites. The rhizosphere is thus a hotspot of nutrient cycling and biological interactions in soil. Microbial succession in the rhizosphere of growing plant roots has been reported in multiple studies. However, how bacterial traits interact with the changing chemistry of root exudates to yield changing bacterial abundances in rhizosphere remains unclear. Our study site, the Hopland UC research field station in Northern California, is a semi-arid annual grassland that has supported Avena sp. plants as dominant grasses for over one hundred years. Here we examine the succession of rhizosphere bacteria at strain-level during the plant developmental stages using both isolation and metagenomic approaches. Metagenome reads from bulk and rhizosphere soils during plant developmental stages were mapped to the genomes of thirty nine bacterial isolates numerically abundant and phylogenetically representative of these soils, and also to ninety seven metagenome-derived genome bins. We classified these bacteria into three groups, representing positive, negative and neutral responders to root growth. Comparative analyses of these genomes were used to identify bacterial traits that may be important in higher abundance in rhizosphere.
Multiple functional genes involved in sugar, amino acid, aromatic compound, secondary metabolite and nitrogen metabolism, chemotaxis, motility and antibiotics resistance were more abundant in bacteria with positive response to root growth. Fragment recruitment of metagenome reads to bacterial genomes was used to further reveal the extent of strain variation not fully represented by isolate and genome bins, showing that closely related strains have divergent responses to root development. We compared the genomes of three closely related Bradyrhizobium isolates and one Bradyrhizobium genome bin and identified regions unique to the positive responders. These regions encoded genes for amino acid transporters, chemotaxis/flagellar assembly and function, and xylanase/chitin degradation amongst others. This study suggests that the acquisition of these genes could result in niche optimization and improved fitness, thus influencing rhizosphere bacterial succession. Further investigation on linkages to changing root chemistry will help us better understand the interactions between plant development and soil microbial communities.