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Antibiotic resistome mostly relates to bacterial taxonomy along a suburban transmission chain

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Abstract

Antibiotic resistance genes comprising antibiotic resistome are of great concern due to their increase in the environment. Recent evidence of shared resistomes between soils and animal husbandry has imposed potential risks to human health. However, the correlation between a given community’s resistome and bacterial taxonomic composition is controversial. Here, a transmission chain of resistomes from swine manure to compost and compost-amended soil were analyzed in five suburban areas of Beijing, China, with unamended agricultural soils as control soils. Antibiotic resistomes and bacterial taxonomic compositions were distinct between (I) manure and compost; and (II) compost-amended and control soils. In manure, compost, and compost-amended soils, the β-diversity of the resistome and bacterial taxonomic composition was significantly correlated, while no correlation was detected in control soils. Bacterial taxonomic composition explained 36.0% of total variations of the resistome composition, much higher than environmental factors. Together, those results demonstrated that antibiotic resistome was closely related to bacterial taxonomic composition along the suburban transmission chain.

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Acknowledgements

This work was sponsored by the National Key R&D Program of China (No. 2019YFC1806204) and the National Natural Science Foundation of China (Grant Nos. 41825016 and 41430856).

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Authors and Affiliations

  1. State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China

    Ziyan Qin, Qun Gao, Qi Qi, Yifan Su, Suo Liu, Tianjiao Dai, Jingmin Cheng & Yunfeng Yang

  2. Institute of Chemical Defense, Beijing, 102205, China

    Qiang Dong

  3. Institute for Environmental Genomics, and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA

    Joy D. Van Nostrand & Jizhong Zhou

  4. School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, 73019, USA

    Jizhong Zhou

  5. Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA

    Jizhong Zhou

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  1. Ziyan Qin
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  2. Qun Gao
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  3. Qiang Dong
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  4. Joy D. Van Nostrand
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  5. Qi Qi
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Correspondence to Qun Gao or Yunfeng Yang.

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Highlights

• The α-diversities of resistome were lower in manure and compost than in soils.

• There were significant correlations between the resistome and bacterial taxonomy.

• Bacterial taxonomy was the highest in explaining resistome variances.

Authorship Contribution Statement

Ziyan Qin: Conceptualization, Methodology, Investigation, Visualization, Writing- original draft, Writing-review and editing. Qun Gao: Conceptualization, Investigation, Methodology, Writing- original draft, Writing- review and editing. Qiang Dong: Investigation, Formal analysis. Joy D. Van Nostrand: Writing- review and editing. Qi Qi: Writing- review and editing. Tianjiao Dai: Writing- review and editing. Jingmin Cheng: Writing- review and editing. Jizhong Zhou: Resources, Supervision, Funding acquisition. Yunfeng Yang: Validation, Writing- review and editing, Supervision, Funding acquisition.

Declaration of Competing Interest

The authors declare no conflicts of interest.

Data Availability

GeoChip data are available in the NCBI GEO database under project no. GSE132839. DNA sequences of the 16S rRNA gene are available in the NCBI Sequence Read Archive under project no. PRJNA516026.

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Qin, Z., Gao, Q., Dong, Q. et al. Antibiotic resistome mostly relates to bacterial taxonomy along a suburban transmission chain. Front. Environ. Sci. Eng. 16, 32 (2022). https://doi.org/10.1007/s11783-021-1466-7

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  • DOI: https://doi.org/10.1007/s11783-021-1466-7

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