Vibrio cholerae has multiple survival strategies which are reflected both in its broad distribution in many aquatic environments and its high genotypic diversity. To obtain additional information regarding the content of the V. cholerae genome, suppression subtractive hybridization (SSH) was used to prepare libraries of DNA sequences from two southern California coastal isolates which are divergent or absent in the clinical strain V. cholerae O1 El Tor N16961. More than 1,400 subtracted clones were sequenced. This revealed the presence of novel sequences encoding functions related to cell surface structures, transport, metabolism, signal transduction, luminescence, mobile elements, stress resistance, and virulence. Flanking sequence information was determined for loci of interest, and the distribution of these sequences was assessed for a collection of V. cholerae strains obtained from southern California and Mexican environments. This led to the surprising observation that sequences related to the toxin genes toxA, cnf1, and exoY are widespread and more common in these strains than those of the cholera toxin genes which are a hallmark of the pandemic strains of V. cholerae. Gene transfer among these strains could be facilitated by a 4.9-kbp plasmid discovered in one isolate, which possesses similarity to plasmids from other environmental vibrios. By investigating some of the nucleotide sequence basis for V. cholerae genotypic diversity, DNA fragments have been uncovered which could promote survival in coastal environments. Furthermore, a set of genes has been described which could be involved in as yet undiscovered interactions between V. cholerae and eukaryotic organisms.Although it is best known as the causative agent of the human disease cholera, Vibrio cholerae is also an autochthonous inhabitant of many aquatic environments, including estuarine and coastal waters (13). Indeed, the great majority of its more than 200 serogroups, excluding O1 and O139, are not associated with epidemic disease. V. cholerae has been isolated routinely from many aquatic environments throughout the world, often in association with plankton, plants, invertebrates, and fish, and there are some reports of its presence in water birds, seals, and diseased farm animals (2,26,27,33,43,56,66). The prevalence of V. cholerae in the environment is influenced by temperature and salinity (reviewed in reference 42) as well concentrations of dissolved organic carbon (44). A number of genes have been previously implicated in environmental survival, and this has already led to a better understanding of the genetic basis for V. cholerae adaptations. Genes have been uncovered which are important for biofilm formation (for examples, see references 68 and 73), zooplankton association (9), survival with filamentous blue cyanobacteria (28), and the degradation of nonbiting midge (Chironomos sp.) egg masses (24). These genes clearly provide V. cholerae with mechanisms to avoid environmental stresses and obtain nutrients in aquatic environments.The evol...