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The beneficial effects of plant growth-promoting rhizobacteria (PGPR) on crop growth and yield have been widely recognized. However, the application of PGPR in traditional planting systems is often restricted due to the concerns about the incompatibility between PGPR and chemical agricultural inputs. The aim of this study is to test whether the application of PGPR has a beneficial effect on the productivity and sustainability of the green planting system, where the use of low-toxic chemical pesticides and proper amount of chemical fertilizer is allowed. In the current study, field trials of four agriculture systems: green agriculture system, green agriculture system supplemented with beneficial microorganism consortium, organic agriculture system supplemented with the consortium and the control system, were carried out with white, yellow and purple flesh sweet potato varieties. The application of PGPR increased the plant growth and suppressed the stem nematode disease in green system. As a consequence, PGPR increased the yield by 26.44% and raised the farmers' projected returns in green system on an average of the two-year assessment. Moreover, PGPR promoted the product nutritive quality by 7.51% in soluble sugar and 14.30% in vitamin C content, and also increased the anthocyanin content of the purple sweet potato by 10.73%. Exogenous PGPR significantly retarded the depletion of soil fertility during the crop cultivation, promoted the soil bacterial diversity and altered the bacteria community structure. PGPR treatment increased the relative abundances of Pseudomonas and Lysobacter in the rhizosphere soil, while reduced the amounts of Erwinia and Ralstonia. The changes of soil nutrient and microbes were correlated with the application of exogenous beneficial bacteria regardless of in organic or green agriculture system. Here, we showed the ability of PGPR to efficiently improve the productivity in green agriculture system under the tested condition, and provided evidence for the feasibility of using exogenous PGPR to achieve agricultural sustainability by constructing a positive feedback in crop-soil-microbe interactions. [Display omitted] • PGPR increased soil micro ecological diversity and remodeled population structure. • PGPR in green agriculture system improved the sustainability of agricultural soil. • Proposed the virtuous cycle of plant-soil-microbe driven by PGPR. • PGPR help to develop a balance between productivity, environment and economics. [ABSTRACT FROM AUTHOR]