Liming (L) is a common practice to mitigate soil acidification and enhance soil quality and crop productivity. However, in acidic soil, it is not clear how long-term application of lime and nitrogen (N)-based fertilizer affects soil chemical properties, the wheat and maize grain yields (GY), and N-use efficiency (NUE). Thus, to investigate the effects of N-based fertilizations without L (−L) and with L (+L) on wheat and maize GY and NUE through their effects on soil chemical properties, we analyzed a 28-year field experiment in acidic soil under a wheat-maize system in South China. The analysis was carried out between 1991 and 2010 (before L) and between 2011 and 2018 (after L). We categorized the treatments into (1) no fertilizer (C); nitrogen (N); N and phosphorus (NP); N and potassium (NK); N, P and K (NPK); and NPKC_R, NPK and crops residue (C_R) applications (NPKC_R), before L; and (2) C; N−L; N+L; NP−L; NP+L; NK−L; NK+L; NPK−L; NPK+L; NPKC_R−L and NPKC_R+L, after L. The effects of long-term fertilization resulted in lower soil pH by 15%, soil available K (AK) by 19%, P_Olsen by 6%, NO₃⁻-N by 15%, soil organic matter (SOM) by 16%, total N by 16%, and C:N ratio by 13% in −L soil than in +L soil. However, the accumulation of NH₄⁺-N was higher by 40% in −L soil than in +L soil. Wheat and maize GY, N recovery efficiency (RE_N), and N partial factor productivity (PEP_N) were more adversely affected by 8-year fertilizations in −L compared with fertilizations before L and in +L primarily because of the significantly decreased soil pH. Conversely, improvements in wheat and maize yields, RE_N, and PFP_N by 8-year fertilizations in +L were related to increasing soil pH, exchangeable base cations such as Ca²⁺, Mg²⁺, and the alleviated toxicity of Al³⁺. Overall, improvement of GY and NUE from the acidified soil in South China requires the long-term integrated use of fertilizer (NPK), retention of C_R, and the +L (i.e., NPKC_R+L).

The excessive use of chemical phosphorus (P) fertilizer can lower grain yield and P use efficiency (PUE) by aggravating soil acidity. Substituting organic manure for chemical fertilizer can alleviate the problem, although the long-term effect of organic manure incorporation is unknown. We conceptualized that substituting organic manure for chemical fertilizer may result in higher crop yields and PUE. Therefore, the impact of long-term fertilizer treatments: (i) CK (control), (ii) PK (phosphorus and potassium fertilizer), (iii) NP (nitrogen and P fertilizer), (iv) NK fertilizer, (v) NPK fertilizer, and (vi) NPKM (30% NPK fertilizer plus 70% manure) on rice yield, PUE, P uptake, and apparent balance (APB) was investigated. The results showed that rice yield under different fertilizer treatments ranged from 6.2 to 11.8 t ha⁻¹ (1984–1995), 7.9 to 12.7 t ha⁻¹ (1996–2007), and 6.6 to 12.8 t ha⁻¹ (2008–2018). The rice yield under NPKM was greatly improved compared to other treatments, except with that of NPK (1984–1995). Soil organic carbon (SOC), available P and phosphorus activation coefficient (PAC) under NPKM were significantly higher than other treatments during 1984–2018. Soil pH (1984–2018) was greatly higher under CK and NPKM than under other treatments. Soil total P under PK, NP, NPK, and NPKM was significantly higher than under CK and NK (1984–2018). Compared to other treatments, P uptake was significantly higher under NPKM, except with that of NPK (1984–1995 and 2008–2018). The average PUE (1984–2018) was 10.7, 20.2, 36.1, and 44.2 kg kg⁻¹ under PK, NP, NPK, and NPKM, respectively. The APB under NPKM was significantly lower as compared to PK, NP, and NPK treatments. Therefore, we conclude that in addition to improving soil organic carbon, cations inputs from organic manure can be a factor for the increase in soil pH, making organic manure substitution for chemical fertilizer a more efficient strategy for increasing PUE and crop yield.

Soil microbial activities are consistently restricted not only by phosphorus availability but also by microbial carbon requirements. Therefore, an incubation experiment was conducted with three soils (QY1, QY2 and QY3) selected on the basis of phosphorus limitation. Results revealed that high N₂O emissions, 17.44 µg kg⁻¹, were measured in phosphorus-deficient soil with addition of glucose. In phosphorus-adequate soils, the peaks of N₂O emission values in the glucose addition treatment were 20.8 µg kg⁻¹ and 24.7 µg kg⁻¹, which were higher than without glucose-added treatments. CH₄ emissions were higher with glucose addition, at 1.9 µg kg⁻¹ in phosphorus-deficient soil and 1.52 µg kg⁻¹ and 2.6 µg kg⁻¹ in two phosphorus-adequate soils. Phosphorus added to deficient and adequate soil significantly increased the cumulative CH₄ and N₂O emissions compared to the solely glucose added soil and the combination of glucose with phosphorus. Glucose addition significantly increased microbial biomass carbon (MBC) but decreased microbial biomass phosphorus (MBP), especially in the phosphorus-adequate soil. For MBC, the highest value obtained was 175.8 mg kg⁻¹, which was determined under glucose addition in phosphorus-adequate soil. The soil pH increased with glucose addition but decreased with phosphorus addition in phosphorus-deficient soil. The soil organic carbon (SOC) content was significantly affected by glucose addition in the phosphorus-deficient soil. Available phosphorus (AP) was highly influenced by phosphorus addition but did not appear to be affected by glucose addition. From the current study, we concluded that sole phosphorus and glucose addition increase CH₄ andN₂O emissions in phosphorus-deficient and also in phosphorus-adequate paddy soils. Further study will be conducted on sole and interactive effects of glucose and phosphorous on soil with plants and without plants.