Inter- and intraspecific genetic analysis of the genus Saccharomonospora with 16S to 23S ribosomal DNA (rDNA) and 23S to 5S rDNA internally transcribed spacer sequences.

In order to clarify interspecific relationships and to investigate the intraspecific phylogenetic structure of the genus Saccharomonospora, 16S to 23S ribosomal DNA (16S-23S) and 23S to 5S ribosomal DNA (23S-5S) internally transcribed spacers (ITSs) were used for sequence analyses. The 16S-23S and 23S-5S ITSs from 22 Saccharomonospora strains were amplified by PCR and directly sequenced. The average levels of nucleotide similarity of the 16S-23S and 23S-5S ITSs for the four valid species were 87.6% +/- 3.9% and 83% +/- 2.2%, respectively. For the most part, intraspecific sequence differences were not found in the two ITSs; the only exception was Saccharomonospora glauca K194, which differed from other S. glauca strains by 1 bp in the 23S-5S ITS. The Saccharomonospora viridis strains had a smaller 16S-23S ITS region than the other strains, which may be useful for differentiating these organisms from other Saccharomonospora species. The characteristics of the two ITS regions make them more useful than 16S rRNA sequences as a tool for defining and identifying Saccharomonospora strains. However, Saccharomonospora azurea K161T had two types of 23S-5S ITSs; rrnB, separated by XhoI digestion, had two additional nucleotides inserted between positions 52 and 55. Most of the 16S-23S and 23S-5S ITS sequences of S. azurea K161T and strains of "Saccharomonospora caesia" were identical; the only exception was rrnB in S. azurea K161T. The lengths and levels of sequence divergence of the two ITSs of Saccharomonospora sp. strain K180 were different from the lengths and levels of sequence divergence of the ITSs of other species. These findings suggest that a taxonomic revision of the genus Saccharomonospora is necessary. Two trees based on 16S-23S and 23S-5S ITS sequences revealed distinct interspecific relationships in the genus Saccharomonospora.