In order to deal with various environmental conditions, most living organisms adapt and respond to environmental cues through nucleotide-based second-messenger signaling. Such signals regulate various endogenous factors required for environmental adaptation. In bacteria, there are five kinds of nucleotide-based second messengers, one of which is cyclic di-guanosine monophosphate (c-di-GMP). The molecule is known to regulate many cellular functions including growth, motility, biofilm formation, and virulence. Various environmental cues cause changes in the intracellular concentration of c-di-GMP, depending on the activity of specific c-di-GMP synthases and hydrolases in cells. In this review, we provide insights into nucleotide signaling in bacteria, emphasizing its impact on basic metabolism, its association with other signaling mechanisms, and its role in regulating the virulence of a wide range of bacteria. Moreover, we discuss recent studies suggesting a role for the implicated signaling molecules in bacterial persistence and antibiotic resistance.