Vibrio fischeri serves as a valuable model of bacterial bioluminescence, its regulation, and its functional significance. Light output varies more than 10,000-fold in wild-type isolates from different environments, yet dim and bright strains have similar organization of the light-producing lux genes, with the activator-encoding luxR divergently transcribed from luxICDABEG. By comparing the genomes of bright strain MJ11 and the dimmer ES114, we found that the lux region has diverged more than most shared orthologs, including those flanking lux. Divergence was particularly high in the intergenic sequence between luxR and luxI. Analysis of the intergenic lux region from 18 V. fischeri strains revealed that, with one exception, sequence divergence essentially mirrored strain phylogeny but with relatively high substitution rates. The bases conserved among intergenic luxR-luxI sequences included binding sites for known regulators, such as LuxR and ArcA, and bases of unknown significance, including a striking palindromic repeat. By using this collection of diverse luxR-luxI regions, we found that expression of P luxI -lacZ but not P luxR -lacZ transcriptional reporters correlated with the luminescence output of the strains from which the promoters originated. We also found that exchange of a small stretch of the luxI-luxR intergenic region between two strains largely reversed their relative brightness. Our results show that the luxR-luxI intergenic region contributes significantly to the variable luminescence output among V. fischeri strains isolated from different environments, although other elements of strain backgrounds also contribute. Moreover, the lux system appears to have evolved relatively rapidly, suggesting unknown environment-specific selective pressures.Bioluminescence is widespread within the Vibrionaceae; however, the selective pressures driving its evolution are not always clear (62). Further adding to the mystery of bacterial bioluminescence, light output can vary over orders of magnitude between different environmental isolates. For example, obvious visible luminescence has been frequently associated with a number of species, such as Vibrio fischeri, Vibrio harveyi, Photobacterium leiognathi, and Photobacterium phosphoreum; however, dim and even "cryptic" luminescence has also been observed upon careful examination of certain isolates, such as Vibrio salmonicida (20). Even isolates of the same species can vary in luminescence output (23, 49). Such variation is dramatically evident in V. fischeri (5,32,45,62), which is a longstanding model for studying bioluminescence, its functional roles, and its regulation.Bioluminescence in V. fischeri is directed by the lux genes. The genes responsible for bioluminescence, luxABCDE and luxG are clustered with the regulatory genes luxR and luxI and are arranged in two divergent transcripts composed of luxR and luxICDABEG (17,18,22,41). The regulatory genes, luxI and luxR, constitute a pheromone-mediated regulatory mechanism referred to as quorum sensing. LuxI prod...