Decoupling the Dynamics of Bacterial Taxonomy and Antibiotic Resistance Function in a Subtropical Urban Reservoir as Revealed by High-Frequency Sampling.

Peiju Fang,Jun Yang,Peng Xiao,Xiaofei Gao,Feng Peng

doi:10.3389/fmicb.2019.01448

Abstract

Aquatic environments serve as important reservoirs of antibiotic resistance genes (ARGs), but the information on the high-resolution temporal pattern of ARGs in waterbodies is extremely limited. In this study, the weekly dynamics of ARGs and their relationships with microbial taxonomic communities and environmental variables were analyzed in a subtropical urban reservoir over the period of 1 year using high-throughput approaches. In total, 197 ARGs and 10 mobile genetic elements (MGEs) were detected. The results showed that the bacterial community had a seasonal pattern, while ARGs composition did not exhibit seasonality, thereby indicating the asynchrony or decoupling of temporal patterns of microbial taxonomy and function. More importantly, bacterial abundance and community diversity were more strongly correlated with 17 measured environmental variables than ARGs (36 significant correlations for OTUs, 11 for ARGs). However, stochastic processes appeared to have a minor role in the structuring of the ARG profiles, but a more important role in the structuring of bacterial taxonomic communities. Furthermore, we found that precipitation and turbidity were significantly correlated with the richness and diversity of ARGs, suggesting that multiple environmental factors influence the composition and dynamics of ARGs in complex ways. MGEs were abundant and showed significant positive correlations with ARGs, indicating a plausible influence of MGEs on the variation of ARGs. This is the first study which provides an overview of high-resolution dynamics of ARGs in a subtropical waterbody. Our results improve the understanding of microbial processes and mechanisms of ARGs at fine temporal scale, and offer empirical data of use in the monitoring, assessment and management of the urban water environments.

Highlights

In aquatic ecosystems many studies have been carried out on nitrogen, phosphorus, and microbial community (Yang et al, 2012; Zhang et al, 2019), various “emerging” pollutants including antibiotics and antibiotic resistance genes (ARGs) have been rapidly drawing increased attention from the public and government (Pruden et al, 2006; Zhu et al, 2017; Yang et al, 2018).Decoupling Bacterial Taxonomy and ARGsAntibiotics, first discovered by Sir Alexander Fleming in 1928, were regarded as panacea for any microbial infections (World Health Organization [WHO], 2014)
We simultaneously investigated the dynamics of bacterial operational taxonomy units (OTUs) and ARGs in the urban reservoir using high-throughput Quantitative PCR (qPCR) and 16S rRNA gene sequencing on a weekly basis over a 1-year period
The absolute abundance of ARGs ranged from 4.03 × 106 copies/L to 3.72 × 109 copies/L, while the absolute abundance of mobile genetic elements (MGEs) varied from 6.62 × 105 copies/L to 1.84 × 109 copies/L (1.92 × 108 ± 5.28 × 107)

Summary

Introduction

In aquatic ecosystems many studies have been carried out on nitrogen, phosphorus, and microbial community (Yang et al, 2012; Zhang et al, 2019), various “emerging” pollutants including antibiotics and antibiotic resistance genes (ARGs) have been rapidly drawing increased attention from the public and government (Pruden et al, 2006; Zhu et al, 2017; Yang et al, 2018).Decoupling Bacterial Taxonomy and ARGsAntibiotics, first discovered by Sir Alexander Fleming in 1928, were regarded as panacea for any microbial infections (World Health Organization [WHO], 2014). In aquatic ecosystems many studies have been carried out on nitrogen, phosphorus, and microbial community (Yang et al, 2012; Zhang et al, 2019), various “emerging” pollutants including antibiotics and antibiotic resistance genes (ARGs) have been rapidly drawing increased attention from the public and government (Pruden et al, 2006; Zhu et al, 2017; Yang et al, 2018). With the emerging problem of antibiotic resistance, antibiotic resistant bacteria (ARB) and ARGs have been identified as a significant issue, posing a serious threat to the health of humans and the environment (Pruden et al, 2006; Berendonk et al, 2015). ARGs occurrence and their temporal dynamics in the aquatic environment have become an important issue in environmental science (Yang et al, 2018)

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