Viruses
influence biogeochemical cycles in oceans, freshwater,
soil, and human gut through infection and by modulating virocell metabolism
through virus-encoded auxiliary metabolic genes (vAMGs). However,
the geographical distribution, potential metabolic function, and engineering
significance of vAMGs in wastewater treatment plants (WWTPs) remain
to be explored. Here, 752 single-contig viral genomes with high confidence,
510 of which belonged to Caudovirales, were recovered
from the activated sludge metagenomes of 32 geographically distributed
WWTPs. A total of 101 vAMGs involved in various metabolic pathways
were identified, the most common of which were the queuosine biosynthesis
genes folE, queD, and queE and the sulfur metabolism gene cysH. Phylogenetic
analysis and virus–host relationship prediction revealed the
probable evolutionary histories of vAMGs involved in carbon (acpP and prsA), nitrogen (amoC), sulfur (cysH), and phosphate (phoH) metabolism, which potentially mediate microbial carbon and nutrient
cycling. Notably, 11 of the 38 (28.3%) vAMGs identified in the metagenomes
with corresponding metatranscriptomes were transcriptionally expressed,
implying an active functional state. This meta-analysis provides the
first broad catalog of vAMGs in municipal WWTPs and how they may assist
in the basic physiological reactions of their microbial hosts or nutrient
cycling in the WWTPs, and therefore, may have important effects on
the engineering of wastewater treatment processes.