Reduced dependence of rhizosphere microbiome on plant-derived carbon in 32-year long-term inorganic and organic fertilized soils

Root-derived carbon (C) is considered as critical fuel supporting the interaction between plant and rhizosphere microbiome, but knowledge of how plant–microbe association responds to soil fertility changes in the agroecosystem is lacking. We report an integrative methodology in which stable isotope probing (SIP) and high-throughput pyrosequencing are combined to completely characterize the root-feeding bacterial communities in the rhizosphere of wheat grown in historical soils under three long-term (32-year) fertilization regimes. Wheat root-derived 13C was dominantly assimilated by Actinobacteria and Proteobacteria (notably Burkholderiales), accounting for nearly 70% of root-feeding microbiome. In contrast, rhizosphere bacteria utilizing original soil organic matter (SOM) possessed a higher diversity at phylum level. Some microbes (e.g. Bacteroidetes and Chloroflexi) enhancing in the rhizosphere were not actively recruited through selection by rhizodeposits, indicating a limited range of action of root exudates. Inorganic fertilization decreased the dependence of Actinobacteria on root-derived C, but significantly increased its proportion in SOM-feeding microbiome. Furthermore, significantly lower diversity of the root-feeding microbiome, but not the SOM-feeding microbiome, was observed under both organic and inorganic fertilizations. These results revealed that long-term fertilizations with increasing nutrients availability would decrease the preference of rhizosphere microbiome for root-derived substrates, leading to a simpler crop–microbe association.