The nonrandom microheterogeneity of 16S rRNA genes in Vibrio splendidus may reflect adaptation to versatile lifestyles.

16S rRNA molecules in a microbial strain can differ due to nucleotide variation between their genes. This is a typical trait of fast-growing bacteria to cope with different niches. We investigated characteristics of 16S rRNA genes in Vibrio splendidus strain PB1-10, from the normal flora of Atlantic halibut. Sequencing of 16S rRNA gene clones detected 35 variable positions in a total of 13 different gene copies. More than two-thirds of the substitutions occurred in regions corresponding to helix H6 and helix H17 of the 16S rRNA molecule. Possible recombination between these helixes in related bacteria (Vibrio, Photobacterium, Colwellia) from similar environments impacts 16S rRNA-based phylogeny of V. splendidus. We argue that these nonrandom modifications are maintained to provide a fine-tuning of the ribosome function to optimize translation machinery performance and ultimately bacterial niche fitness.