Viruses, the most diverse of all biological entities, are ubiquitous and can influence nearly all life forms on Earth. The preliminary pathway through which viruses affect microbial metabolism and evolution is viral infection. There are two distinct infection modes for viruses interacting with prokaryotes, namely temperate and virulent lifestyles. Virulent viruses trigger their hosts’ death by lysis once they invade the host cells, whereas temperate viruses can replicate alongside their host in the lysogenic cycle until a lytic cycle is induced. It has been reported that viral lifestyles are key determinants of virus-encoded auxiliary metabolic genes (AMGs) that are crucial toolboxes for viruses to reprogram host metabolisms. An in-depth investigation of virus-microbe infection modes over a broad geographical scale is thus vital for understanding the potential effects of viruses on the microbial community and biogeochemical cycles. However, the determinants of community-level virus-microbe interaction modes and how their interactions affect the microbial community and ecosystem function are currently unclear.