Manure fertilizer-derived soil emerging pollutants compromises its fertility benefits for vegetable quality: At the scale of soil aggregates

Substituting chemical fertilizers with organic manure in farmland management is a standard practice to alleviate soil degradation while improving soil quality and crop performance. However, the effects of organic manure fertilization on soil fertility quality and environmental quality across different aggregates remain unclear. Moreover, few studies have focused on assessing soil environment quality based on antibiotics and its resistance genes. In this study, we conducted a field trial to reveal the response of soil fertility quality index (SFI), environmental quality index (SEI) within aggregate fractions and pepper comprehensive quality index (PCQ) to fertilization treatments. We analyzed 16 soil biochemical indicators, 10 soil antibiotics and its resistance gene indicators, and 5 fruit indicators under four fertilization treatments (CK (no fertilizer), CF (chemical fertilizer), OF15 (85% CF + organic manure), OF30 (70% CF + organic manure)) as potential SQI, SEI and PCQ indicators, respectively. Results showed that, organic manure treatment significantly increased the indicator scores of total phosphorous, organic matter and nematode shannon in the microaggregate compared to CF, while decreased multidrug, rifamycin and tetracycline. In the large macroaggregates, organic manure significantly enhanced nematode shannon and body size compared to CF, while also leading to a notable decline in multidrug, rifamycin and tetracycline. Application of organic manure notably enhanced pepper yield and fruit quality in comparison to CK treatment, especially for OF15 treatment. Comparison to CF, organic manure application significantly improved SFI in the microaggregates fraction. While the SEI in the microaggregates and small macroaggregates fraction was significantly decreased by organic manure application compared to CK. The structural equation models revealed that organic manure application negatively affected PCQ indirectly by declining the SEI in microaggregates and small macroaggregate fractions. Overall, our study revealed that manure fertilization was conducive to soil fertility in microaggregates; however, these advantages were coupled with obvious limitations regarding antibiotics and its resistance genes contamination in aggregates. These findings provide a new microscale perspective for understanding the response of vegetable comprehensive quality to soil quality after organic manure application.