Bacteria and their viruses (bacteriophages or phages) have a complex relationship that is in constant flux. Studies in natural environments, and by manipulations of phages and bacteria in a laboratory setting, have demonstrated that phages can profoundly influence bacterial populations. Phages can alter the density of different bacteria by lytic infection, and the genetic makeup of bacteria can be altered by lysogeny or transduction. Phages are promiscuous mediators of genetic exchange and often carry genes capable of altering the phenotypes of their bacterial hosts. The genetic traits acquired from phages can influence adaptation of bacteria to an environment by providing enhanced or novel metabolic properties, resistance to other phages or protozoan predators, and acquisition of antibiotic resistance or new virulence traits. The improvement in sequencing technology that sparked the microbial metagenomic revolution has provided another tool for understanding the impact of phages on bacterial populations. Metagenomic analysis of virus populations (“viromics”) has provided insight into the surprising extent that phages modulate the bacterial genome. While the benefit to the phages for transferring novel properties to its host is often poorly understood, this relationship clearly provides a selective advantage because these properties are maintained in many environments and including otherwise adverse conditions for the bacterial host. In this chapter, we will discuss how phages influence the fitness of bacteria in particular environmental niches.