Effects of various manure-derived organic fertilizers on microbial community characteristics and antibiotic resistance genes in irrigation-silted soils of Ningxia

Manure-derived organic fertilizers are widely promoted as substitutes for chemical fertilizers in soil improvement, but their source-specific effects on soil antibiotic resistance genes (ARGs) remain unclear. A long-term field experiment was conducted with conventional chemical fertilization as the control (CK) and three treatments in which 30% of chemical N was replaced by organic fertilizers derived from sheep manure (T1), dairy cattle manure (T2), or chicken manure (T3). Soil physicochemical properties, microbial diversity, mobile genetic elements (MGEs), and ARG profiles were characterized using soil analyses and metagenomic sequencing, while redundancy analysis (RDA) and partial least squares path modeling (PLS-PM) were used to explore potential drivers of ARG variation. Compared with CK, all manure-derived organic fertilizer treatments reduced soil bulk density and increased the >2 mm water-stable aggregate fraction. T1 increased soil organic matter by 9.20%, the bacterial Simpson index by 23.33%, and the fungal Shannon index by 22.11%. T2 reduced available phosphorus and potassium and the relative abundance of Chloroflexota, while tending to increase total salt content. Metagenomic analysis detected 15 ARG classes and 58 subtypes. T3 showed higher abundances of multidrug-, β-lactam-, and bacitracin-resistance ARGs and increased IS91 absolute abundance by 115.14%. RDA and PLS-PM identified fungal Simpson diversity and the >2 mm aggregate fraction as key biotic and abiotic variables associated with ARG variation, while MGEs showed high explained variance (R 2 = 0.93) and acted as a hub variable indirectly associated with ARGs. These findings provide a reference for safer organic fertilizer application in irrigation-silted soils.