Viral Genomes and Viruses-encoded Auxiliary Metabolic Genes of Global Wastewater Treatment Plants

Viruses can impact biogeochemical cycles in ocean, freshwater, soil, and human gut by lytic infection and modulating virocell metabolism through viruses-encoded auxiliary metabolic genes (vAMGs). However, the geographical distribution, metabolic function and engineering significance of vAMGs in wastewater treatment plants (WWTPs) remain under-explored. Here, 752 single-contig viral genomes of high confidence were carefully recovered from activated sludge metagenomes of 32 global WWTPs, and mostly (510) classified as Caudovirales. From the viral genomes, 101 vAMGs were identified and found to involve in various metabolic pathways, with sulfur metabolism gene (cysH) and queuosine biosynthesis genes (folE, queD, and queE) the most prevalent gene types. Further phylogenetic analysis, coupled with host relationship prediction, showed probable evolutionary histories of vAMGs involved in carbon (acpP and prsA), nitrogen (amoC), sulfur (cysH), and phosphate (phoH) metabolism, which may take responsibility for microbial nutrients cycling. Notably, 11 out of 38 (28.3%) vAMGs identified in the samples with corresponding metatranscriptomes, were found to be expressed, implied an active state to exercise their function. Overall, this meta-analysis of viromes sketches the first broad catalog of vAMGs of global WWTPs and reveals that viruses can act as ecological drivers and play important biochemical roles with engineering significance in WWTPs.