Long-term organic fertilization regulates the abundance of major nitrogen-cycling-related genes in aggregates from an acidic Ultisol

The soil nitrogen (N) cycle is crucial to biogeochemical cycling, plant nutrient absorption, and greenhouse gas emissions and is primarily mediated by microorganisms. Although organic fertilization regulating aggregation has been well studied in various soils, how organic fertilization mediates microbial groups involved in soil N cycle in aggregates remained largely unclear. Therefore, the objective was to investigate the effect of 27 years of application of mineral and organic fertilizers (peanut straw, rice straw, radish, and pig manure) on the abundance of major microbial groups involved in the soil N cycle in four soil aggregate size classes. The results showed that organic fertilizers exerted significant impacts on the communities of microbes possessing N-cycling related genes, with pig manure having a more important effect than plant residues. However, aggregate size classes contributed more to the variation (20%) than organic fertilizers (12%). Organic fertilizer types did not impact the abundance of ammonia-oxidizing archaea (AOA) or ammonia-oxidizing bacteria (AOB). However, aggregate size strongly altered the abundance of AOA, but not AOB, with AOA being particularly abundant in <53 mu m aggregates. Organic fertilizers and aggregate size significantly influenced the abundance of the nirS gene rather than the nirK gene. There were greater amounts of nirS in the soils treated with rice straw and pig manure, primarily due to the higher soil organic matter content. As for fungal denitrification, there was a greater abundance of FnirK in microaggregates than in macroaggregates. Organic fertilizers and aggregate size significantly influenced the abundance of nosZ I and nosZ II genes, with aggregate size playing a more pronounced role. The abundance of nosZ I increased with increasing aggregate size while the abundance of nosZ II gene showed the opposite trends. This result revealed the clear niche differentiation of nosZ I and nosZ II genes in Ultisols, with nosZ I and nosZ II preferred to inhabit in macroaggregates and microaggregates, respectively. Overall, our results provide critical insights into the ecophysiology of major N-cycling-related genes in aggregates from an acidic Ultisol.