Nanosized microbiomes from pig manure alter soil microbial communities and increase antibiotic resistance gene abundance

Agricultural ecosystems are continuously exposed to exogenous phages, including those introduced via animal manure fertilization, yet their colonization dynamics and ecological impacts remain unclear. Using a microcosm experiment, we investigated how pig manure-derived nanosized microbiome (NSM; <0.22 μm) influences phage-bacterial interactions, antibiotic resistance gene (ARG) dissemination, and microbial evolution in paddy soil. NSM addition transiently elevated high-risk ARG abundance, particularly linked to Acinetobacter proliferation from manure. These dynamics were driven by manure-derived Acinetobacter and their associated phages/plasmids, which dominated soil phage communities despite their low initial abundance. Both Acinetobacter and their phages exhibited microdiversity shifts under environmental fluctuations, with strong native soil phage-bacterial correlations disrupted post-NSM introduction. Our findings highlight the environmental risks of pig manure-derived NSM, emphasizing Acinetobacter and their phages as key drivers of high-risk ARG spread and microbial community evolution. This underscores the need for manure pretreatment strategies to mitigate soil resistome hazards. Pig-manure-derived nanosized microbiomes transiently elevated high-risk antibiotic resistance gene abundance and microdiversity, which is driven by manure-derived Acinetobacter and their associated phages, based on an analysis of an agricultural soil microcosm experiment.