Quorum sensing (QS), or cell-cell communication in bacteria, is achieved through the production and subsequent response to the accumulation of extracellular signal molecules called autoinducers (AIs). To identify AI-regulated target genes in Vibrio cholerae El Tor (V. cholerae El ), the strain responsible for the current cholera pandemic, luciferase expression was assayed in an AI ؊ strain carrying a random lux transcriptional reporter library in the presence and absence of exogenously added AIs. Twenty-three genes were identified and shown to require the QS transcription factor, HapR, for their regulation. Several of the QS-dependent target genes, annotated as encoding hypothetical proteins, in fact encode HD-GYP proteins, phosphodiesterases that degrade the intracellular second messenger cyclic dimeric GMP (c-di-GMP), which is important for controlling biofilm formation. Indeed, overexpression of a representative QS-activated HD-GYP protein in V. cholerae El reduced the intracellular concentration of c-di-GMP, which in turn decreased exopolysaccharide production and biofilm formation. The V. cholerae classical biotype (V. cholerae Cl ), which caused previous cholera pandemics and is HapR ؊ , controls c-di-GMP levels and biofilm formation by the VieA signaling pathway. We show that the VieA pathway is dispensable for biofilm formation in V. cholerae El but that restoring HapR in V. cholerae Cl reestablishes QS-dependent repression of exopolysaccharide production. Thus, different pandemic strains of V. cholerae modulate c-di-GMP levels and control biofilm formation in response to distinct sensory pathways.Over the past century, pandemic outbreaks of the diarrheal disease cholera have been caused by only two Vibrio cholerae biotypes (11). The classical biotype (V. cholerae Cl ) was responsible for the sixth pandemic, which lasted from 1899 to 1923. The etiological agent of the current seventh pandemic that began in 1961 is V. cholerae El Tor (V. cholerae El ). V. cholerae is an aquatic organism and its life cycle includes only transient colonization of the human small intestine. In humans, virulence factors elicit diarrhea, which is often fatal to the host but is also critical for efficiently transmitting the bacterium back into the environment (12). In marine habitats, V. cholerae is often found attached to other organisms in microbial communities called biofilms (19,20). Ingestion of contaminated water or food is the mode of transmission into the human gastrointestinal tract. Understanding the mechanisms used by these two V. cholerae biotypes to control virulence factor production and biofilm formation, as well as understanding the factors responsible for the emergence of V. cholerae El as the dominant biotype, have been the focus of active research for decades.A bacterial cell-cell communication process called quorum sensing (QS) is used to control virulence and biofilm formation in V. cholerae El (14,34,56). QS is accomplished through the synthesis, release, and subsequent detection of signaling molecules cal...