Large-scale genome-centric metagenomics reveals the prevalence of lysogenic virus-host interactions in activated sludge

Abstract

Bacteriophages are the most common organisms in the activated sludge (AS) of wastewater treatment plants (WWTPs), playing an important role in maintaining or regulating the microbial community. However, lysogenic virus-host interactions in artificial AS systems remain poorly understood. To comprehensively characterize integrated prophages in AS, we reconstructed metagenome-assembled genomes (MAGs) from 44 full-scale WWTPs across five countries. Results showed that lysogenic virus-host interactions were prevalent in AS systems, with > 55% lysogenic MAGs (lysogens), and Proteobacteria (13.8%) and Bacteroidota (12.7%) were the most common lysogenic bacterial phyla. Gene-sharing network analysis revealed that most prophages (~ 99%) could not be categorized into the recognized viral genera, indicating that AS is an untapped source of novel and diverse viruses. The community structure and diversity of lysogens and parasitic prophages in AS systems showed evidently spatial variations, but AS systems from different locations possessed common functional lysogenic microorganisms. In addition, the parasitic prophages detected within lysogens were active and inducible. The active prophages were found to be able to lyse the microorganisms involved in the removal of organic matter, nitrogen, and phosphorous. To our best knowledge, this is the first study to reveal the predominance of lysogenic virus-host interactions in AS systems by large-scale genome-centric metagenomics, which enhanced our understanding of the pivotal role of the prophages in the AS microbiome.