Objectives Inoculation rhizobial is an important technology for increasing soybean yields and reducing the use of chemical nitrogen (N) fertilizers. Diverse soil types can influence symbiotic N fixation, as well as N transformations within the rhizosphere, thereby affecting the efficacy of rhizobial inoculation in soybeans. However, the mechanistic roles of soil type in these processes remain to be elucidated.

Methods In this study, two major soil types, yellow cinnamon (Y) soil and lime concretion black (M) soil, were selected in the Huai River Basin, the main soybean production area in China, to investigate the impacts of rhizobial inoculation on soybean N accumulation, symbiotic N fixation, rhizospheric N transformation including free-living N-fixation, nitrification and denitrification capacity, and associated with the community composition of ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), nitrite reductase gene (narG) and nitrogenase gene (nifH)

Results Inoculation rhizobial affected symbiotic N-fixation, rhizospheric free-living N-fixation, nitrification and denitrification processes and associated microbial community composition of soybean differed significantly across soil types. In Y soil, rhizobial inoculation significantly improved plant nitrogen accumulation. Compared to the non-inoculated treatment, plant N accumulation was increased by 33.6% and 24.9% at the initial flowering stage (R1) and flowering and pod stage (R4), respectively. Structural equation modelling (PLS-PM) results indicated that the increase in plant N accumulation was associated with an increase in nodules number, an increase in the symbiotic N-fixation capacity of the rhizomes, and a decrease in the nitrification potential by decreasing the abundance of AOA and AOB. In M soil, rhizobial inoculation significantly reduced plant N accumulation. Compared to the non-inoculated treatment, plant nitrogen accumulation was reduced by 21.7% and 20.7% at R1 and R4 stages, respectively. PLS-PM showed that the reduction in plant N accumulation was associated with changes in the structure of endophytic N-fixing bacteria in the rhizomes and reduced nodules number inhibiting symbiotic N-fixing capacity and enhancing nitrification potential by increasing the abundance of AOB.

Conclusions The differences in the effects of inoculation rhizobium in different soil types are related to changes in the community structure of endophytic N-fixing bacteria in nodules, the number of nodules, and the intensity of nitrification processes in the rhizosphere. The regulation of these processes is key to overcoming the limitations imposed by different soil types on the effectiveness of inoculation rhizobium.