Low precipitation and poor soil quality are the main factors that limit wheat production in the Loess Plateau region of China. Straw incorporation and/or adding organic fertilizer can enhance wheat productivity by improving the soil water content (SWC) and soil fertility, but systematic long-term research has not yet been conducted. Thus, we conducted a 12-year continuous in-situ experiment in the Loess Plateau by testing four treatments: (1) CK: no fertilization and wheat straw removal; (2) FM: straw removal and application of inorganic fertilizer; (3) SI: straw incorporation and application of inorganic fertilizer; (4) SIOM: straw incorporation and application of inorganic fertilizer, with organic fertilizer added to replace 10% of the inorganic fertilizer. Under CK, the soil chemical properties and enzyme activities tended to decrease over the years. The soil fertility was significantly higher under FM than CK, and higher under SI and SIOM than FM (P < 0.05). SIOM significantly improved the soil nutrients and wheat productivity than other treatments (P < 0.05). Compared with FM, the soil bulk density in the 0–20 cm soil layer under SIOM decreased by 4.5%, while SOC, TN, TP, AN, and Olsen-P increased by 4.5%, 6.1%, 4.9%, and 12.3%, respectively. The DOC, DON, MBC, and MBN contents increased by 18.5%, 26.4%, 15.8%, and 16.2%, respectively. The activities of urease, sucrase, and catalase increased by 12.8%, 13.6%, and 22.8%, and the N uptake, nitrogen use efficiency (NUE), water use efficiency (WUE), water productivity, and wheat yield increased by 17.8%, 43.7%, 38.6%, 33.5%, and 22.4%. SIOM obtained the highest NUE, WUE, yield, and economic benefits of 37.83%, 14.34 kg ha–1 mm–1, 4579.16 kg ha–1, and 7990.39 Yuan ha–1, respectively. Linear mixed effects modeling showed that the year and treatment significantly affected the soil fertility and wheat productivity (P < 0.05). Random forest and structural equation modeling showed that the soil and fertilizer management strategies increased wheat productivity (R2 = 0.50) by improving the soil fertility. Therefore, straw incorporation and applying inorganic/organic fertilizers are effective management strategies for improving soil fertility and wheat productivity in semi-arid areas of Loess Plateau regions.
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