Polymorphism in repeated 16S rRNA genes is a common property of type strains and environmental isolates of the genus Vibrio

Analysis of the 16S rDNAs obtained from cultures of single colonies of either type collection strains or environmental strains of the genus Vibrio revealed the presence of polymorphism in every one of the strains examined. Polymorphism was detected by visualization of heteroduplexes produced after 16S rDNA PCR amplification, a procedure that allows for the screening of a large number of isolates. Amplified 16S rDNAs obtained from both Vibrio parahaemoyticus and an environmental strain were cloned. Their nucleotide sequences revealed differences of up to 2% among 16S rDNAs from the same strain. Polymorphic sites were concentrated in a recognized variable stem-loop of bacterial 16S rRNA that contained in some cases up to 83% of the total mismatches observed. Most of the substitutions present in the stem-loop region showed compensating base covariation. The accumulation of so many compensating changes in the stem-loop region implies that the divergence of the different versions of this stem-loop is relatively ancient. This divergence could be the result of either a selection process or a lateral transfer of independently evolved genes.