Objectives Red paddy soils are important cultivated land resources for the food safety of China, however, the large proportion of middle and low yield fields need improvement to take the responsibility. We compared the fertility variation characteristics across soil profiles in different yield levels, to propose the key points of low yield field improvement and serve the national strategic goal of “storing grain in the ground”.

Methods The research was carried out in Jinxian County, Jiangxi Province. The paddy soils were divided into high-, middle- and low-yield fields according to annual rice yield of >15000 kg/hm², 12000−15000 kg/hm² and <10000 kg/hm². At the three yield level fields, soil samples were collected on the arable layer, plough pan and waterlogged layer for measurement of layer depth, bulk density, penetration resistance, pH, cation exchange capacity (CEC), organic matter, total and available NPK, and microbial biomass carbon (MBC) and nitrogen (MBN). The relationship between soil profile properties and rice yield was analyzed using the linear correlation analysis and random forest analysis.

Results In high and low yield fields, the plough layer depth is around 16 cm and 13 cm, soil bulk density was 1.09 g/cm³ and 1.21 g/cm³, respectively. The plough pan thickness and density were in descent order of high-, middle- and low-yield fields. The chemical properties of plough layer in high-yield fields are organic matter 38.82 g/kg, total N 2.33 g/kg, available N 198.54 mg/kg, total P 0.81 g/kg, available P 33.04 mg/kg, while those in low yield fields were 29.75 g/kg, 1.89 g/kg, 158.71 mg/kg, 0.62 g/kg, 23.51 mg/kg, respectively. The MBC and MBN of plough layer were 929.2 mg/kg and 42.5 mg/kg in high-yield fields, while those were 533.6 mg/kg and 30.8 mg/kg in low yield fields, respectively. The soil pH and the organic C, N, P, and microbial biomass showed obvious “surface aggregation” characteristics along soil profile, and declined with the yield from high to low level. However, the K content in all the tested fields increased with the soil profile down to deep, especially in low yield fields. The total K content was 8.12 g/kg in the plough layer, and increased to 10.77 g/kg in the parent material horizon. The results of correlation analysis and random forest analysis showed that rice yield was positively (P<0.05) correlated with the tested soil properties in plough layer, and these properties explained 53.7% of rice yield differences. Among them, MBC, MBC/MBN and plough layer depth were the most important factors affecting rice yield, with the explanatory power of 9.2%, 8.7% and 7.9%, respectively.

Conclusions The thickness and the microbial biomass of the plough layer are the key environmental factors regulating rice yield. Compared with low-yield fields, high-yield fields have thicker plough layer with lighter bulk density and higher organic matter in it. So the key measurements for low-yield field improvement are the construction of thick and fertile plough layer.