Mild organic substitution is advantageous for sustainable agricultural development. In order to determine the proper fertilization strategy, it is essential to investigate the impact of substituting chemical fertilizers with varying levels of organic manure on soil nutrients, microbial communities, and crop productivity. Four treatments were implemented: no fertilizer, sole chemical fertilizer, 20% organic manure substitution, and 40% organic manure substitution. Bacterial and fungal communities were characterized through high-throughput sequencing of the 16S rRNA gene V3–V4 region and the V4 region, respectively. The 20% and 40% organic manure substitutions increased soil organic matter (SOM) content, total nitrogen (TN) content, and reduced soil pH compared to the control (CK). The 20% organic manure substitution showed the most significant improvements in soil alkaline phosphatase, urease, and invertase activities. Soil nutrient enhancement increased bacterial alpha diversity, with a milder impact on fungal alpha diversity compared to bacteria. Different fertilization treatments elevated the relative abundance of bacterial Bacteroidetes (8.11%, 21.25%, and 1.88%), Actinomycetes (12.65%, 26.36%, and 15.33%), and fungal Ascomycota (16.19%, 10.44%, and 12.69%), known for degrading recalcitrant organic matter. The sole chemical fertilizer treatment increased the pathogenic Cheatotryiales. Shared species, primarily from bacterial Actinomycetes, Firmicutes, Proteobacteria, and fungal Ascomycota phyla, were found at 20% and 40% organic manure substitution levels. Specifically, the 20% organic manure substitution level promoted the relative abundance of beneficial plant growth-promoting taxa, Oxalobacteraceae and Massilia, and suppressed pathogens, with an increase in the relative abundance of the Purpureocillium genus and Mortierellomycota. These findings suggest that a 20% OF substitution can maintain crop yield, enhance soil nutrients and enzyme activities by fostering beneficial soil bacteria, inhibiting soil-borne pathogens, and refining microbial community structure.

To better understand the source–sink flow and its relationships with zinc (Zn) and other nutrients in wheat (Triticum aestivum L.) plants for biofortification and improving grain nutritional quality, the effects of reducing the photoassimilate source (through the flag leaf removal and spike shading) or sink (through the removal of all spikelets from one side of the spike, i.e., 50% spikelets removal) in the field of the accumulation of Zn and other nutrients in grains of two wheat cultivars (Jimai 22 and Jimai 44) were investigated at two soil Zn application levels. The kernel number per spike (KNPS), single panicle weight (SPW), thousand kernel weight (TKW), total grain weight (TGW) sampled, concentrations and yields of various nutrient elements including Zn, iron (Fe), manganese (Mn), copper (Cu), nitrogen (N), phosphorus (P), potassium (K), calcium (Ca) and magnesium (Mg), phytate phosphorus (phytate-P), phytic acid (PA) and phytohormones (ABA: abscisic acid, and the ethylene precursor ACC: 1-aminocylopropane-1-carboxylic acid), and carbon/N ratios were determined. Soil Zn application significantly increased the concentrations of grain Zn, N and K. Cultivars showing higher grain yields had lower grain protein and micronutrient nutritional quality. SPW, KNPS, TKW (with the exception of TKW in the removal of half of the spikelets), TGW, and nutrient yields in wheat grains were most severely reduced by half spikelet removal, secondly by spike shading, and slightly by flag leaf removal. Grain concentrations of Zn, N and Mg consistently showed negative correlations with SPW, KNPS and TGW, but positive correlations with TKW. There were general positive correlations among grain concentrations of Zn, Fe, Mn, Cu, N and Mg, and the bioavailability of Zn and Fe (estimated by molar ratios of PA/Zn, PA/Fe, PA × Ca/Zn, or PA × Ca/Fe). Although Zn and Fe concentrations were increased and Ca was decreased in treatments of half spikelet removal and spike shading, the treatments simultaneously increased PA and limited the increase in bioavailability of Zn and Fe. In general, different nutrient elements interact with each other and are affected to different degrees by source–sink manipulation. Elevated endogenous ABA levels and ABA/ACC ratios were associated with increased TKW and grain-filling of Zn, Mn, Ca and Mg, and inhibited K in wheat grains. However, the effects of ACC were diametrically opposite. These results provide a basis for wheat grain biofortification to alleviate human malnutrition.

Copper (Cu) and iron (Fe) are essential micronutrients for plants and animals. How phosphorus (P) application affects Cu and Fe concentrations in maize grain still remains unclear. Two-year field studies were conducted in a long-term experiment with six P levels (0, 12.5, 25, 50, 100, and 200 kg∙ha⁻¹ P) on calcareous soil. Phosphorus application significantly decreased the average grain Cu concentration by 12.6% compared to no P treatment, but had no effect on grain Fe concentration. The copper content increased as the P application rate increased from 0 to 25 or 50 kg·ha⁻¹, but then decreased, while Fe content kept increasing. As the P application rate increased, the specific Cu uptake by the roots decreased, but not for Fe. The root length density in response to P application had a positive relationship with shoot Cu and Fe content. The shoot Cu content and grain Cu concentration decreased with the reduction in the arbuscular mycorrhizal fungi (AMF) colonization of roots due to increasing P application. The reduction in grain Cu concentration with increasing P rates could be partly explained by the decreasing uptake efficiency.

The partial substitution of chemical fertilizers with organic manure is an important strategy for improving agricultural sustainability. However, its effect on heavy metal (HM) pollution and its potential risk to human health remain unclear. Therefore, a field study was conducted to evaluate the effects of partial organic fertilizer substitution (0, 10%, 20%, 30%, and 40%) on health risks posed by HMs, including Zn, Cu, Ni, Cd, Pb, As, and Cr. The results showed that organic fertilizer substitution significantly increased Cu, Cd, Pb, and As accumulations in the soil. The Zn, Cu, Pb, and As contents were significantly higher in grains grown under organic fertilizer substitution (40%) conditions. The HM contents in the soil and grains were below the safety threshold limits in all treatments. Furthermore, the health risk caused by the exposure to As, Cu, and Zn accounted for 86% of the hazard index (HI) value. The HI value was significantly greater at a substitution ratio of 40% than in the no-nitrogen fertilizer treatment. Ingestion of the wheat grains grown at substitution ratios ≥ 30%) increased the carcinogenic risk of As and the total carcinogenic risk. In conclusion, organic fertilizer substitution at high ratios significantly increased the non-carcinogenic and carcinogenic risks associated with ingesting wheat grain. The optimal organic fertilizer substitution ratio (20%) maintained crop yields and improved soil fertility without increasing the non-carcinogenic or carcinogenic risks to human health. These findings highlight the importance of understanding the impacts of optimal organic fertilizer management in wheat growing systems.

The effect of organic fertilizer substitution (OFS) on crop micronutrients often varies due to differences in environmental conditions, soil types, and nutrient status. This study aims to evaluate the effects of OFS on wheat grain micronutrients and bioavailability across five sites in Shandong Province from 2021 to 2022. All experimental sites included five common treatments: control, traditional farming, optimized practices, and 15 and 30% OFS for chemical nitrogen. The results revealed regional variation in wheat yield; the average wheat yield was 9.06 Mg ha⁻¹, and the highest yield was 9.58 Mg ha⁻¹ in the 15%OF treatment. No significant differences in soil micronutrient availability were observed. Compared to the control, the OFS treatments exhibited significant increases in grain Fe (24.69%) and Zn (19.19%) contents. The OFS treatments significantly increased Fe and Zn bioavailability by reducing the PA/Fe and PA/Zn molar ratios. Organic fertilizer substitution also increased micronutrient nutritional yields and reduced the current health burden of Fe and Zn. Under the pessimistic scenario, the OFS treatment reduced health burdens of Zn and Fe deficiencies by 2.38 and 1.31%, respectively, whereas these mitigation efficiencies substantially increased to 7.15 and 3.94% under the optimistic scenario. In conclusion, OFS improved the content and bioavailability of Fe and Zn without affecting yield, which enhanced the nutritional quality of these nutrients, and alleviate the health burden of Fe and Zn deficiency. The findings demonstrate that a 15% organic fertilizer substitution (OFS) optimally enhances wheat grain Fe and Zn bioavailability and nutritional quality while maintaining crop yield, offering region-specific evidence for sustainable agricultural practices to mitigate micronutrient deficiencies and improve human health outcomes.