Enrichment of soil microbiome and antimicrobial resistance genes following poultry litter application

Poultry litter (PL) is often used for soil amendment as an alternative to chemical fertilizers. However, it may enrich microbial and antimicrobial resistance genes in applied soil. The objective of this study was to investigate changes in the soil microbiome and resistome profiles following PL application. Three treatments untreated control (UC), chemical fertilizer (CF), and PL were applied to corn plots in a completely randomized block design. Total soil (metagenomic) DNA (n = 72) obtained on d0, d7, and d28 were shotgun sequenced. A composite DNA sample pooled from PL samples (n = 8) was sequenced for comparison. While Actinomycetota and Pseudomonadota were the most prevalent phyla among the soil samples, their abundance was significantly higher in the PL amended soils. PL soil amendment shifted microbial composition (Gammaproteobacteria and fungal Saccharomycetes were enriched in PL amended soils), diversity, and abundance by differentially enriching several microbial species, functional pathway genes, virulence factor genes, and antimicrobial resistance genes. Macrolides-lincosamides-streptogramin (MLS) resistance genes were the most abundant genes enriched in PL amended soils. The PL microbiome was primarily composed of the phylum Bacillota with Virgibacillus alimentarius being the most abundant species, followed by Staphylococcus nepalensis and S. simulans. The PL resistome was dominated by MLS resistance genes. Virulence factor genes associated with the genera Bacteriodes, Enterococcus and Staphylococcus were the most prevalent. The study clearly showed that PL application enriches soil microbiome and resistome, the mechanism of which is more likely through nutrient enrichment rather than their direct transfer since PL and PL-amended soils had different microbiome profiles.