Fates of Antibiotic Resistance Genes in the Gut Microbiome from Different Soil Fauna under Long-Term Fertilization

Fei Zheng, Qing-Fang Bi, Madeline Giles, Roy Neilson, Qing-Lin Chen, Xian-Yong Lin, Yong-Guan Zhu, Xiao-Ru Yang (Lead / Corresponding author)

    Research output: Contribution to journalArticlepeer-review

    28 Citations (Scopus)


    Applying organic fertilizers has been well documented to facilitate the dissemination of antibiotic resistance genes (ARGs) in soil ecosystems. However, the role of soil fauna in this process has been seldom addressed, which hampers our ability to predict the fate of and to manage the spread of ARGs. Here, using high-throughput quantitative polymerase chain reaction (HT-qPCR), we examined the effect of long-term (5-, 8-, and 10-year) fertilization treatments (control, inorganic fertilizers, and mixed fertilizers) on the transfer of ARGs between soil, nematodes, and earthworms. We found distinct fates for ARGs in the nematodes and earthworms, with the former having higher enriched levels of ARGs than the latter. Fertilization impacted the number and abundance of ARGs in soil, and fertilization duration altered the composition of ARGs. Shared ARGs among soil, nematodes, and earthworm guts supported by a fast expectation-maximization microbial source tracking analysis demonstrated the trophic transfer potential of ARGs through this short soil food chain. The transfer of ARGs was reduced by fertilization duration, which was mainly ascribed to the reduction of ARGs in the earthworm gut microbiota. This study identified the transfer of ARGs in the soil-nematode-earthworm food chain as a potential mechanism for a wider dissemination of ARGs in the soil ecosystem.

    Original languageEnglish
    Pages (from-to)423-432
    Number of pages10
    JournalEnvironmental Science and Technology
    Issue number1
    Early online date17 Dec 2020
    Publication statusPublished - 5 Jan 2021


    • Food
    • Soils
    • Antibiotic resistance
    • Bacteria
    • Genetics

    ASJC Scopus subject areas

    • General Chemistry
    • Environmental Chemistry


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