Impacts of organic materials amendment on the soil antibiotic resistome in subtropical paddy fields

Zongming Li; Jupei Shen; Fangfang Wang; Meihui Wang; Jianlin Shen; Yong Li; Qihong Zhu; Jinshui Wu

doi:10.3389/fmicb.2022.1075234

Impacts of organic materials amendment on the soil antibiotic resistome in subtropical paddy fields

Front Microbiol. 2023 Jan 24:13:1075234. doi: 10.3389/fmicb.2022.1075234. eCollection 2022.

Authors

Zongming Li^{1

2}, Jupei Shen³, Fangfang Wang⁴, Meihui Wang^{1

2}, Jianlin Shen^{1

2}, Yong Li^{1

2}, Qihong Zhu^{1

2}, Jinshui Wu^{1

2}

Affiliations

¹ Key Laboratory of Agro-Ecological Processes in Subtropical Region and Changsha Research Station for Agricultural and Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China.
² College of Resources and Environment, University of the Chinese Academy of Sciences, Beijing, China.
³ School of Geographical Sciences, Fujian Normal University, Fuzhou, China.
⁴ State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China.

Abstract

The organic material amendment has been proven to change the soil antibiotic resistance genes (ARGs) profile, which may threaten human health through the food chain, but the effects and mechanisms of different organic materials on ARGs in paddy soils are less explored. In this study, a field experiment was set up with the treatments of conventional chemical fertilization (NPK) and common organic material amendment [rice straw (RS), swine manure (SM), and biochar (BC)] to explore the effects and mechanisms. In total, 84 unique ARGs were found across the soil samples with different organic material amendments, and they conferred resistance to the major antibiotic classes. Compared with NPK, SM significantly increased the detected number and relative abundance of ARGs. A higher detected number of ARGs than NPK was observed in BC, whereas BC had a lower relative abundance of ARGs than NPK. Compared with NPK, a detected number decrease was observed in RS, although abundance showed no significant differences. Compared with other treatments, a higher detected number and relative abundance of mobile genetic elements (MGEs) were observed in BC, indicating a higher potential for horizontal gene transfer. There were significantly positive relationships between the relative abundances of total ARGs and MGEs and the bacterial abundance. The network analysis suggested the important role of MGEs and bacterial communities in shaping the ARGs profile. Mantel test and redundancy analysis (RDA) suggested that soil carbon, nitrogen, and C/N were the major chemical drivers of the ARGs profile. The risk of ARGs spreading to the food chain should be considered when applying SM and biochar, which shifted the ARGs and MGEs profiles, respectively. Pre-treatment measures need to be studied to reduce the dissemination of ARGs in paddy fields.

Keywords: antibiotic resistance genes; bacterial community; biochar; organic materials; paddy soil.

Grants and funding

This research was funded by National Key Research and Development Project of China (2022YFD1700700), National Natural Science Foundation of China (42077104), Key Research and Development Program of Hunan Province (2020NK2011), Chinese Academy of Science and Technology Service Network Initiative Project (KFJ-STS-QYZD-2021-22-002), and Youth Innovation Promotion Association of the Chinese Academy of Sciences (Y2021102).