Objectives This study aimed to clarify the effects and underlying mechanisms of organic fertilizer substitution for chemical fertilizer (organic substitution) on the content of trace element in Lou soil and grains and crop yield, so as to provide a scientific basis for enhancing micronutrient availability in Lou soil and achieving high crop yields with improved quality.

Methods A long-term organic substitution field experiment (initiated in 2014) was conducted in a winter wheat-summer maize rotation at the National Agricultural Experimental Station for Soil Quality in Yangling. Soil and crop samples were collected in 2024 following crop harvest from plots under following treatments: no fertilizer control (CK), chemical fertilizer only (NPK), and substitution of 25%, 50%, 75%, and 100% of chemical nitrogen fertilizers with organic fertilizer (25%M, 50%M, 75%M, 100%M). Soil bulk density, organic matter and nutrient contents, as well as enzyme activities were analyzed. The contents of Fe, Mn, Cu, and Zn in grains, as well as crop yield were analyzed.

Results Fertilization significantly increased soil CEC, organic matter, total N, total P, available P, available K, and cellobiohydrolase (CBH) activity, and the enhancement effect raised with the increasing of the substitution ratios, relative to CK, however. Did not affect soil bulk densities. NPK treatment basically maintained the levels of total and available Fe, Mn, Cu, and Zn in soil, while organic substitution treatments significantly increased the total contents by an average of 14%、5%、17%、32%, and the available contents by 23%、32%、25%、244%, respectively. Compared with CK, both NPK and organic substitution treatments increased the contents of Fe, Mn, Cu, and Zn in humic acid-bound, iron-manganese oxide-bound, and orgainc strongly bound forms in soil, but the increment did not show obvious organic substitution ratio-dependent effect. Compared with CK, NPK significantly increased wheat and maize yields by 2.68 times and 1.26 times, respectively, 25%M treatment achieved comparable yields with NPK treatment, while the other organic substitution achieved significantly lower wheat yield, and similar maize yield. NPK treatment maintained comparable grain Fe, Mn, Cu, and Zn contents to CK, while organic substitution treatments significantly improved the by an average of 34%, 39%, 70%, and 38%, respectively, showing increased trace element enrichment effect with the increase of substitution ratios. Maize grains were analyzed overall higher trace element contents than in wheat grains, and the contents were also improved by increased organic substitution tatios. Both soil available trace elements and grain trace elements were positively (P<0.05) correlated with soil organic matter, CEC, CBH activity, and NPK nutrient contents.

Conclusions Organic fertilizer partially replacing chemical fertilizers increases soil CEC, organic matter and NPK contents, and enzyme activities, significantly improves the availability of soil trace elements, and further raises the yields of wheat and maize as well as the trace element contents in their grains. As the replacement ratio of organic fertilizer increases, the availability of soil trace elements and the trace element contents in crop grains show an upward trend, but the wheat yield decreases significantly while the maize yield has no notable change. When the replacement ratio is 25%, the wheat yield can maintain a high level and the trace element content is improved to a certain extent. Therefore, it is an effective measure to collaboratively achieve high crop yield, grain trace element biofortification and soil fertility improvement in the wheat-maize rotation system on Lou soil in the Guanzhong Plain.