Detection and Transformation of Genome Segments Variable within a Coastal Population of Vibrio cholerae

Division of Infectious Diseases and Geographic Medicine; Department of Medicine; Stanford University School of Medicine; Stanford University; Stanford, California 94305; Department of Civil & Environmental Engineering; Stanford University; Stanford, California 94305

^* To whom correspondence should be addressed. Email: mcmiller{at}stanford.edu.

	Abstract

Vibrio cholerae is an autochthonous member of diverse aquatic ecosystems around the globe. Collectively, the genomes of environmental V. cholerae compose a large repository of encoded functions which can be acquired by individual V. cholerae lineages through uptake and recombination. To characterize the genomic diversity of environmental V. cholerae, we used comparative genome hybridization to study 41 environmental strains isolated from diverse habitats along the central California coast, a region free of endemic cholera. These data were used to classify genes of the epidemic V. cholerae O1 sequenced strain, N16961, as conserved, variably present or absent from the isolates. For the most part, absent genes were restricted to large mobile elements and have known functions in pathogenesis. Conversely, genes present in some, but not all, California isolates were in smaller contiguous clusters and were less likely to be near genes with functions in DNA mobility. Two such clusters of variable genes encoding different selectable metabolic phenotypes (mannose or diglucosamine utilization) were transformed into the genomes of environmental isolates by chitin-dependent competence, indicating that this mechanism of general genetic exchange is conserved among V. cholerae. Transformed DNA had an average size of 22.7 kbp, demonstrating that natural competence can mediate the movement of large chromosome fragments. Thus, whether variable genes arise through acquisition of new sequence by horizontal gene transfer or by loss of pre-existing DNA though deletion, natural transformation provides a mechanism by which V. cholerae clones can gain access to the V. cholerae pan-genome.