Viral impacts on microbial activity and biogeochemical cycling in a seasonally anoxic freshwater lake

Microbial biogeochemical cycling relies on alternative electron acceptors when oxygen is unavailable, yet the role of viruses (bacteriophages) in these processes is understudied. We investigated how seasonal anoxia impacts viral and microbial biogeochemical cycling, by using paired total metagenomes, viromes, and metatranscriptomes, that were collected weekly. Stratification and anoxia drove microbial community composition, but dataset origin impacted the interpretation of viral community structure, activity, and function. Importantly, taxa abundance did not correlate with activity for both microbes and viruses. We identified virus-host linkages for 116 phages across 55 distinct hosts, many of which expressed genes for aerobic methane oxidation, nitrogen fixation, denitrification, and sulfate reduction. Overall, this work demonstrates the breadth and dynamics of virus-host interactions in mediating biogeochemistry. Additionally, we propose that viral community detection, functional potential, and activity are sensitive to pre-sequencing decisions, which must be kept in mind when interpreting genomic data in a biologically meaningful way.