We commonly acknowledge that bacterial viruses (phages) shape the composition and evolution of bacterial communities in nature and therefore have important roles in ecosystem functioning. This view stems from studies in the 1990s to the first decade of the twenty-first century that revealed high viral abundance, high viral diversity and virus-induced microbial death in aquatic ecosystems as well as an association between collapses in bacterial density and peaks in phage abundance. The recent surge in metagenomic analyses has provided deeper insight into the abundance, genomic diversity and spatio-temporal dynamics of phages in a wide variety of ecosystems, ranging from deep oceans to soil and the mammalian digestive tract. However, the causes and consequences of variations in phage community compositions remain poorly understood. In this Review, we explore current knowledge of the composition and evolution of phage communities, as well as their roles in controlling the population and evolutionary dynamics of bacterial communities. We discuss the need for greater ecological realism in laboratory studies to capture the complexity of microbial communities that thrive in natural environments.

我们普遍承认，细菌病毒（噬菌体）塑造了自然界中细菌群落的组成和进化，因此在生态系统功能中发挥着重要作用。这一观点源于 1990 年代至 21 世纪头十年的研究，这些研究揭示了水生生态系统中的高病毒丰度、高病毒多样性和病毒诱导的微生物死亡，以及细菌密度崩溃与噬菌体峰值之间的关联丰富。最近宏基因组分析的激增为从深海到土壤和哺乳动物消化道等各种生态系统中噬菌体的丰度、基因组多样性和时空动态提供了更深入的了解。然而，噬菌体群落组成变化的原因和后果仍然知之甚少。在这篇评论中，我们探索了目前关于噬菌体群落的组成和进化的知识，以及它们在控制细菌群落的种群和进化动态方面的作用。我们讨论了在实验室研究中需要更大的生态现实主义，以捕捉在自然环境中繁衍生息的微生物群落的复杂性。