Poultry Litter Application Enriches Soil Microbiome and Antimicrobial Resistance Genes

Strategic Insights -

Investigators at the U.S. Department of Agriculture (USDA) have published a new study on the effects of poultry litter (PL) on soil microbiome and antimicrobial resistance genes. The research, published in Science of The Total Environment, found that PL application significantly enriches soil microbiome and resistome profiles, leading to the differential enrichment of microbial species, functional pathway genes, virulence factor genes, and antimicrobial resistance genes. The study suggests that PL application may shift microbial composition, diversity, and abundance through nutrient enrichment rather than direct transfer.

Key Takeaways:

  • Poultry litter (PL) is often used as an alternative to chemical fertilizers, but it may also enrich microbial and antimicrobial resistance genes in applied soil.
  • The study found that PL application significantly enriched soil microbiome and resistome profiles, with Actinomycetota and Pseudomonadota being the most prevalent phyla among the soil samples.
  • PL amended soils showed increased abundance of Gammaproteobacteria and fungal Saccharomycetes, as well as a greater diversity and abundance of microbial species.
  • The PL microbiome was primarily composed of the phylum Bacillota, with Virgibacillus alimentarius being the most abundant species.
  • The PL resistome was dominated by Macrolides-lincosamides-streptogramin (MLS) resistance genes.
  • The study suggests that PL application may shift microbial composition, diversity, and abundance through nutrient enrichment rather than direct transfer.
  • Researchers used a completely randomized block design to apply PL, chemical fertilizer, and untreated control to corn plots, and analyzed soil samples using shotgun sequencing.

Statistics:

  • 72 soil samples were obtained for metagenomic DNA sequencing on d0, d7, and d28.
  • 8 PL samples were pooled and sequenced for comparison.
  • The abundance of Actinomycetota and Pseudomonadota was significantly higher in PL amended soils (p < 0.05).
  • The PL resistome was dominated by MLS resistance genes, which were the most abundant genes enriched in PL amended soils.
  • 999:180306 is the reference number for the published research in Science of The Total Environment.

Sources:

  • Enrichment of soil microbiome and antimicrobial resistance genes following poultry litter application. Science of The Total Environment, 2025;999:180306. Elsevier, Radarweg 29, 1043 Nx Amsterdam, Netherlands.
  • U.S. Department of Agriculture (USDA) Release. Researchers at U.S. Department of Agriculture (USDA) Release New Data on Science (Enrichment of soil microbiome and antimicrobial resistance genes following poultry litter application). Science Letter. September 19, 2025; p 3605.