Metagenomics reveals diversity and predation of DNA viruses in activated sludge and anaerobic digester

Abstract

Abstract Background Prevalent viral particles are found in activated sludge (AS) and anaerobic digester (AD) during wastewater treatment processes. In contrast to the conventional approaches, culture-independent metagenomic method opens up the possibility to characterize uncultured viruses, which were previously inaccessible. In this study, we aimed to investigate the involvement of viruses in AS, mesophilic AD, and thermophilic AD using metagenomic sequences. We constructed the viromes, predicted the potential host, and profiled the functional genes in the viral genome. Results From a total of 64 samples, 42,548 viruses were detected. Among them, 43.6% were classified to Uncultivated Viral Genomes (UViGs) by the IMG/VR database and 28.5% were clustered into viral clusters (VCs) using vConTACT2. In total, only 18.2% of the viruses were taxonomically assigned to known viral families, with Siphoviridae, Myoviridae, Inoviridae, and Podoviridae being the most commonly observed. Most of the detected viruses were associated with engineered ecosystem, and more viruses in AS were associated with environmental ecosystem than in mesophilic and thermophilic AD. Diversity analysis suggested that the local habitat has a greater impact on the AD viromes than the immigration effect. Host prediction revealed that viruses in AD were mostly linked to site-specific active populations involved in syntrophic fatty acid oxidation, methanogenesis, hydrolysis, and fermentation. Functional gene annotation revealed that the viral gene profile follows the microbial gene profile, suggesting that viruses in AD not only tend to infect site-specific active hosts but also acquire functional genes transferred from the hosts. Conclusions Overall, this study provided insights of the viral diversity in the wastewater treatment process and uncovered the potential viral involvement in AD.