Viruses manipulate bacterial community function through lytic and lysogenic infections and the horizontal transfer of metabolic genes affecting biochemical cycling in their environment. Viral effects on microbial communities has been mostly characterized in the marine biome. However, as research on virus functions continues to expand, less studied biomes, like sediment and snow, become invaluable sources for studying alternate virus-microbe dynamics. Microbes in the sediment and snow biomes, in general, are subjected to resource limitations and environmental stress that are not present in the marine biome. In the sediment biome viral auxiliary metabolic genes influence the microbial functions differently at specific depths. Abundance of lysogenic phages increases with sediment depth, implying increased survivability of lysogens in the deep sediment biome. In the snow biome, the microbial community structure and functional capacity during an algal bloom were analyzed to determine how viruses manipulate snow microbes. The algal bloom brings about a shift in the microbial community structure due to additional energy provided by the algal photosynthate. The microbial functional capacity, however, is more influenced by the location and the auxiliary metabolic genes present in the neighboring viral community. Viruses in snow encode auxiliary metabolic genes involved in cellular respiration, protein synthesis, and de novo purine synthesis, suggesting that viruses provide microbial functions to exploit energy sources specific to the local environment. Together, these studies show a higher importance of lysogenic lifestyles and horizontal gene transfer of metabolic genes by viruses in extreme environments than previously recognized.