Different Impacts of Long-Term Tillage and Manure on Yield and N Use Efficiency, Soil Fertility, and Fungal Community in Rainfed Wheat in Loess Plateau

Conservation tillage and fertilization are widely adopted in agricultural systems to enhance soil fertility and influence fungal communities, thereby improving agroecosystems. However, the effects of no-tillage combined with manure on grain yield, nitrogen use efficiency (NUE), soil fertility, and rhizosphere fungal communities remain poorly understood, particularly in rainfed wheat fields on the Loess Plateau. A 15-year field experiment was conducted at the Niujiawa Experimental Farm of the Cotton Research Institute, Shanxi Agricultural University. Five treatments were assessed: conventional tillage without fertilizer (C), no-tillage with chemical fertilizer (NT), no-tillage with chemical fertilizer and manure (NTM), conventional tillage with chemical fertilizer (T), and conventional tillage with chemical fertilizer and manure (TM). The results demonstrated that the NTM treatment significantly increased grain yield by 124.95%, NT by 65.88%, TM by 68.97%, and T by 41.75%, compared to the C treatment (<i>p</i> < 0.05). NUE in the NTM treatment was improved by 58.73%-200.59%. Compared with the C treatment, NTM significantly enhanced soil nutrients, including organic matter (OM) by 70.68%, total nitrogen (TN) by 8.81%, total phosphorus (TP) by 211.53%, available nitrogen (AN) by 90.00%, available phosphorus (AP) by 769.12%, and available potassium (AK) by 89.01%. Additionally, the NTM treatment altered the rhizosphere fungal community of winter wheat, with <i>Ascomycota</i> (81.36%-90.24%) being the dominant phylum, followed by <i>Mucoromycota</i> (5.40%-12.83%) and <i>Basidiomycota</i> (1.50%-8.53%). At the genus level, NTM significantly increased the abundance of <i>Mortierella</i> and <i>Dendrostilbella</i>. An α-diversity analysis revealed that the richness and diversity of soil fungi were highest under NTM. The unweighted pair-group method with arithmetic mean (UPGMA) and principal coordinates analysis (PCoA) based on Bray-Curtis distances indicated that NTM formed a distinct fungal community with the highest phylogenetic diversity, which differed significantly from other treatments. Redundancy analysis (RDA) demonstrated that soil chemical properties variably influenced fungal community dynamics, with higher abundances of <i>Ascomycota</i> and <i>Zoopagomycota</i> positively correlated with OM, AN, AP, TP, and AK. Correlation analysis showed that wheat yield and NUE were positively correlated with <i>Mortierella</i> and <i>Dendrostilbella</i>, and negatively correlated with <i>Fusarium</i>, <i>Chaetomium</i>, and <i>Alternaria</i>. In conclusion, no-tillage with manure not only enhanced soil fertility but also enhanced soil fungal community structure, leading to greater wheat yield and NUE. These findings provide guidance for agricultural practices in rainfed wheat fields of the Loess Plateau.