Microbial density-dependent viral dynamics and low activity of temperate phages in the activated sludge process

Ruyin Liu; Zong Li; Ganghua Han; Shujuan Cun; Deyin Hou; Zhisheng Yu; Kai Xue; Xinchun Liu

doi:10.1016/j.watres.2023.119709

Microbial density-dependent viral dynamics and low activity of temperate phages in the activated sludge process

Water Res. 2023 Apr 1:232:119709. doi: 10.1016/j.watres.2023.119709. Epub 2023 Feb 5.

Authors

Ruyin Liu¹, Zong Li², Ganghua Han², Shujuan Cun², Deyin Hou³, Zhisheng Yu², Kai Xue⁴, Xinchun Liu⁵

Affiliations

¹ College of Resources and Environment, University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, Beijing 100049, China; RCEES-IMCAS-UCAS Joint-Lab of Microbial Technology for Environmental Science, University of Chinese Academy of Sciences, Beijing, China; Yanshan Earth Critical Zone National Research Station, University of Chinese Academy of Sciences, Beijing, China; Binzhou Institute of Technology, Weiqiao-UCAS Science and Technology Park, Binzhou City, Shandong Province, China. Electronic address: Lry1981@ucas.ac.cn.
² College of Resources and Environment, University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, Beijing 100049, China; RCEES-IMCAS-UCAS Joint-Lab of Microbial Technology for Environmental Science, University of Chinese Academy of Sciences, Beijing, China; Yanshan Earth Critical Zone National Research Station, University of Chinese Academy of Sciences, Beijing, China.
³ Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.
⁴ College of Resources and Environment, University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, Beijing 100049, China; Yanshan Earth Critical Zone National Research Station, University of Chinese Academy of Sciences, Beijing, China.
⁵ College of Resources and Environment, University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, Beijing 100049, China; Yanshan Earth Critical Zone National Research Station, University of Chinese Academy of Sciences, Beijing, China. Electronic address: xcliu@ucas.ac.cn.

PMID: 36764107
DOI: 10.1016/j.watres.2023.119709

Abstract

The ecological behavior of bacteriophages (phages), the most abundant biological entity in wastewater treatment systems, is poorly understood, especially that of temperate phages. Here, the temporal dynamics of lytic and temperate phages in a laboratory-scale activated sludge reactor with a sludge bulking issue was investigated using coupled sludge metagenomic and viromic analyses. The lysogenic fragments (prophages) identified were widely distributed in the reconstructed metagenome-assembled genomes (61.7%, n = 227). However, only 12.3% of the identified prophages experienced lysogenic-lytic switching, and the abundance contribution of prophages to free virus communities was only 0.02-0.3%, indicating low activity of temperate phages. Although the sludge community changed dramatically during reactor operation, no massive prophage induction events were detected. Statistical analyses showed strong correlations between sludge concentration and free virus and temperate phage communities, suggesting microbial density-dependent virus dynamics in the sludge microbiota.

Keywords: Activated sludge; Metagenomics; Temperate phages; Viruses; Wastewater treatment.

MeSH terms

Bacteriophages*
Lysogeny
Microbiota*
Prophages
Sewage

Substances

Sewage