Microbial community and antibiotic resistance gene distribution in food waste, anaerobic digestate, and paddy soil

Xin-Rong Pan; Seyit Yuzuak; Jia-Min Lou; Lei Chen; Yin Lu; Jian-E Zuo

doi:10.1016/j.scitotenv.2023.164192

Microbial community and antibiotic resistance gene distribution in food waste, anaerobic digestate, and paddy soil

Sci Total Environ. 2023 Sep 1:889:164192. doi: 10.1016/j.scitotenv.2023.164192. Epub 2023 May 15.

Authors

Xin-Rong Pan¹, Seyit Yuzuak², Jia-Min Lou³, Lei Chen⁴, Yin Lu⁵, Jian-E Zuo⁶

Affiliations

¹ College of Biology and Environmental Engineering, Zhejiang Shuren University, Hangzhou 310015, PR China; State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, PR China.
² Department of Molecular Biology and Genetics, Burdur Mehmet Akif Ersoy University, Burdur 15030, Turkey.
³ College of Biology and Environmental Engineering, Zhejiang Shuren University, Hangzhou 310015, PR China.
⁴ State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, PR China.
⁵ College of Biology and Environmental Engineering, Zhejiang Shuren University, Hangzhou 310015, PR China. Electronic address: luyin@zjsru.edu.cn.
⁶ State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, PR China; Institute of Environment and Ecology, Tsinghua Shenzhen International Graduate School, Shenzhen 518055, PR China. Electronic address: jiane.zuo@tsinghua.edu.cn.

PMID: 37196953
DOI: 10.1016/j.scitotenv.2023.164192

Abstract

The study assessed the occurrence and distribution of microbial community and antibiotic resistance genes (ARGs) in food waste, anaerobic digestate, and paddy soil samples, and revealed the potential hosts of ARGs and factors influencing their distribution. A total of 24 bacterial phyla were identified, of which 16 were shared by all samples, with Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria accounting for 65.9-92.3 % of the total bacterial community. Firmicutes was the most abundant bacteria in food waste and digestate samples, accounting for 33-83 % of the total microbial community. However, in paddy soil samples with digestate, Proteobacteria had the highest relative abundance of 38-60 %. Further, 22 ARGs were detected in food waste and digestate samples, with multidrug, macrolide-lincosamide-streptogramin (MLS), bacitracin, aminoglycoside, tetracycline, vancomycin, sulfonamide, and rifamycin resistance genes being the most abundant and shared by all samples. The highest total relative abundance of ARGs in food waste, digestate, and soil without and with digestate was detected in samples from January 2020, May 2020, October 2019, and May 2020, respectively. The MLS, vancomycin, tetracycline, aminoglycoside, and sulfonamide resistance genes had higher relative abundance in food waste and anaerobic digestate samples, whereas multidrug, bacteriocin, quinolone, and rifampin resistance genes were more abundant in paddy soil samples. Redundancy analysis demonstrated that aminoglycoside, tetracycline, sulfonamide, and rifamycin resistance genes were positively correlated with total ammonia nitrogen and pH of food waste and digestate samples. Vancomycin, multidrug, bacitracin, and fosmidomycin resistance genes had positive correlations with potassium, moisture, and organic matter in soil samples. The co-occurrence of ARG subtypes with bacterial genera was investigated using network analysis. Actinobacteria, Proteobacteria, Bacteroidetes, and Acidobacteria were identified as potential hosts of multidrug resistance genes.

Keywords: Anaerobic digestate; Antibiotic resistance; Food waste; Paddy soil; Potential host.

MeSH terms

Aminoglycosides
Anaerobiosis
Anti-Bacterial Agents / pharmacology
Bacitracin
Bacteria
Drug Resistance, Microbial / genetics
Food
Genes, Bacterial
Microbiota*
Refuse Disposal*
Rifamycins*
Soil
Tetracyclines
Vancomycin

Substances

Anti-Bacterial Agents
Vancomycin
Bacitracin
Soil
Rifamycins
Aminoglycosides
Tetracyclines