Objectives Green manure root morphology and traits act as gatekeepers for soil quality and productivity in Ultisol by influencing the soil microbial community characteristics. Understanding the effects of green manure root traits on soil microbial community characteristics is vital to lay a theoretical significance for the scientific application of green manure in the red soil region of southern China.

Methods A winter green manure-sweet potato rotation system was initiated in 2022 after the sweet potato harvest in the countryside of Jinxian County, Jiangxi Province. The experiment includes five green manure amendments: winter fallow (CK), hairy vetch (HV), ryegrass (RS), radish (RD), and rapeseed (RP). Topsoil samples were collected at the blooming period of winter green manures in 2023. Soil properties were analyzed using conventional methods, and bacterial communities characteristics were comprehensively analyzed using high-throughput sequencing technology, ecological network, and FAPROTAX functional prediction methods. Green manure root samples were then extracted for determination of carbon and nitrogen contents using chemical methods, and for the scanning and measurement of root traits using software WINRHIZO. At maturity, sweet potato pods were collected and weighed to obtain yield data.

Results Hairy vetch and ryegrass (high root length and root N content) were characterized as the acquisitive strategy, while radish and rapeseed (high diameter and root C:N ratio) were characterized as the conservative strategy. We found that conservative green manures supported higher soil organic carbon (SOC), total phosphorus (TP), soil quality index (SQI) and sweet potato yield, with an increase of 14.02%−19.13%, 18.84%−20.29%, 28.76%−30.06% and 1.51%−14.26%, respectively, compared with CK treatment. Conservative green manures were associated with increases in soil bacteria richness and the relative abundances of Gemmatimonadaceae, while taxa belonging to GP4 and GP6 were plentiful in the acquisitive green manure amendments. Using a network analytic approach, we showed that conservative green manures significantly increased bacterial community network complexity, but decreased network stability. In contrast, acquisitive green manures significantly elevated bacterial community network stability. Functional prediction based on FAPROTAX found that conservative green manures increased the potential of stable C decomposition of soil bacteria, while acquisitive green manures enhanced the potential of nitrogen conversion of soil bacteria. Structure equation modeling revealed that root length and root C/N ratio could primarily modulate soil bacterial community characteristics mainly through changes in SOC and TP availability of soil.

Conclusions Resource-conservative green manure enhances the species richness and network complexity of soil bacterial communities, thereby improving their decomposition potential for recalcitrant carbon sources. In contrast, resource-acquisitive green manure boosts the network stability of soil bacterial communities and enhances their conversion potential for nitrogen components. Combining green manure crops with complementary traits through integrated planting is expected to achieve synergistic improvements in both complexity and stability of soil bacterial communities.