Abstract The microbial communities in anaerobic ammonium oxidation (anammox) bioreactors have been extensively studied to unveil their diversity and roles in nitrogen removal. Yet, the viruses infecting the key functional microorganisms in these systems remain unexplored. Here, we utilize genome-resolved metagenomics to systematically assess viral diversity, functions and interaction with microbial hosts in granular sludges of different sizes from three laboratory- and full-scale anammox reactors. Analysis of the 190 microbial genomes recovered through bulk metagenomics revealed the predominance (full-scale 29–54% and laboratory-scale 31–45%) of anammox species exclusively from the Brocadiae in all sludges examined. Viral metagenomics identified 5210 candidate viral species, 61.1∼97.3% of which were novel. Members of six genera from the Caudovirales order constitute the majority of the taxonomically assigned viral species. Between-group variance analysis revealed that both environment (reactor type) and granule size had a significant influence on the metabolic potential of viruses. In silico predictions showed that many of the important functional microbes were frequent targets of previously unrecognized viruses, including six viral populations infecting the anammox bacteria. Our results suggest that viruses actively infect microbial hosts and thus may have a major impact on the microbial metabolic processes and biogeochemical cycling in the anammox reactors.
Yang et al. (Fri,) studied this question.