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

doi:10.1007/s11783-021-1466-7

Front. Environ. Sci. Eng.

2022, Vol. 16

Issue (3) : 32 https://doi.org/10.1007/s11783-021-1466-7

RESEARCH ARTICLE

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

Ziyan Qin¹, Qun Gao¹(

), Qiang Dong², Joy D. Van Nostrand³, Qi Qi¹, Yifan Su¹, Suo Liu¹, Tianjiao Dai¹, Jingmin Cheng¹, Jizhong Zhou^3,^4,⁵, Yunfeng Yang¹(

)

¹. State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
². Institute of Chemical Defense, Beijing 102205, China
³. Institute for Environmental Genomics, and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA
⁴. School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK 73019, USA
⁵. Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA

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Abstract

• 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.

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.

Keywords Antibiotic resistance genes Resistome Bacterial taxonomy Transmission chain

Corresponding Author(s): Qun Gao,Yunfeng Yang

Issue Date: 13 July 2021

Cite this article:

Ziyan Qin,Qun Gao,Qiang Dong, et al. Antibiotic resistome mostly relates to bacterial taxonomy along a suburban transmission chain[J]. Front. Environ. Sci. Eng., 2022, 16(3): 32.

URL:

https://academic.hep.com.cn/fese/EN/10.1007/s11783-021-1466-7
https://academic.hep.com.cn/fese/EN/Y2022/V16/I3/32

Fig.1 Heatmaps of the (a) resistome and (b) bacterial phyla in manure, compost, compost-amended soil, and control soil, with 80 samples in total. The scale represents the relative abundance of each ARG or each bacterial phylum, which was normalized as a Z score detailed in the method.

Tab.1 Non-parametric multivariate dissimilarity analyses of resistome and bacterial taxonomic composition

Fig.2 Pearson correlations between richness (a), Shannon index (b), Simpson index (c), and β-diversity (based on Bray-Curtis dissimilarity) (d) of ARGs and bacterial OTUs. The significance of the correlation was determined by P<0.050. There are 80 samples in total.

Tab.2 Pearson correlations between richness, Shannon index, Simpson index, and β-diversity (based on Bray-Curtis dissimilarity) of ARGs and bacterial OTUs in manure, compost, compost-amended soil, and control soil

Fig.3 Significant positive Pearson correlation pairs between bacterial genera and resistome in the group of (a) manure, (b) compost, (c) compost-amended soil, and (d) control soil samples. The thickness of the edge represents correlation values. Green circles represent bacterial genus. Pink circles represent resistome. The size of the circle represents the degree of connectedness. The significance of the correlation was determined by P<0.050.

Tab.3 Contribution of bacterial taxonomic composition and environmental factors in shaping the resistome by multiple regression on distance matrices (MRM) in all samples, manure, compost, compost-amended soil, and control soil

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