A Phylogenetic Analysis of the Genus Saccharomonospora Conducted with 16S rRNA Gene Sequences

Abstract

Nearly complete sequences of 16s rRNA genes of representative strains of the genus Saccharomonospora were determined following the isolation and cloning of the amplified genes. The sequences were aligned with those of representatives of the family Pseudonocardiaceae, and a phylogenetic tree was inferred by the neighborjoining method. The genus Saccharomonospora formed a distinct clade within the evolutionary radiation encompassed by the family Pseudonocardiaceae. The average nucleotide similarity value found between the type strains of the four validly described Saccharomonospora species was 97.5% k 1.0%. The most distant relationship was found between Saccharomonospora azurea and Saccharomonospora viridis K73 (96.3% similarity). In contrast, Sacchuromonospora azurea K161 and "Saccharomonospora caesia" K163 had identical 16s rRNA gene sequences. The nucleotide sequence data suggest that the genus Saccharomonospora contains several new centers of variation.The genus Saccharomonospora was proposed by Nonomura and Ohara (30) for monosporic actinomycetes that contained meso-diaminopimelic acid, arabinose, and galactose in the peptidoglycan (wall chemotype IV sensu Lechevalier Lechevalier [25]). Subsequently, additional chemical markers were found to characterize the taxon, notably the presence of major amounts of iso-and anteiso-fatty acids, 2-hydroxy fatty acids, phosphatidylethanolamine, and menaquinones that were tetrahydrogenated with nine isoprene units (21,25).There are currently four validly described Saccharomonospora species, namely, Saccharomonospora azurea (32), Saccharomonospora cyanea (33), Saccharomonospora glauca (17), and Saccharomonospora viridis (30), the type species of the genus. A fifth species, "Saccharomonospora caesia," was proposed by for organisms previously classified as Micropolyspora caesia (20,22); this organism did not appear in the Approved Lists of Bacterial Names (35) and has not been added subsequently, and hence, it has not been validly published. It is important to distinguish between members of validly described and putatively new Saccharomonospora species, as some kinds of saccharomonosporae can cause hypersensitivity pneumonitis. S. viridis is strongly implicated as one the causal agents of farmer's lung disease (3,16).It is also important to determine the taxonomic structure of the genus Saccharomonospora in order to discover the relationships between the existing taxa and between them and prospective new species. It appears from preliminary 16s rRNA sequence studies that the genus Saccharomonospora forms a distinct phyletic line within the evolutionary radiation encompassed by the family Pseudonocardiaceae (5, 9, 10, 28, 36). To date, three Saccharomonospora strains have been the subject of 16s rRNA sequencing analyses, the type strain of S. viridis, the putative type strain of "S. caesia," and an isolate from stored grain, Saccharomonospora sp. strain A1206, that was tentatively considered, subject to additional sequencing studies, to be the nucleus of a new species (36). ...

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

“…Table 1 shows the strain designations and the GenBank accession numbers for the 16S-23s and 23S-5s ITS sequences. The sources of strains have been described previously (12,39).…”

“…(14). Recently, a 16s ribosomal DNA (rDNA) sequence analysis showed that the genus Saccharomonospora is a distinct phyletic group within the evolutionary radiation of the family Pseudonocardiaceae (12). However, the 16s rDNA sequences of the four validly described Saccharomonospora species exhibited relatively high levels of nucleotide similarity (97.5% * 1.0%), and the levels of homology between strains of the same species were high.…”

“…The results of recent numerical phenetic studies (11) and results obtained by nucleic acid techniques (12,(39)(40)(41) suggest that the strains of "S. caesia" are very closely related to S. azurea K161T. It has been determined that strains of S. viridis cause farmer's lung disease ( 1,6) and are significant agents of hypersensitivity pneumonitis (12,39). (14).…”

“…Although "Saccharomonospora caesia" was proposed by Greiner-Mai et al (8) as a fifth taxon for strains previously classified as Micropolyspora caesia (9, 13), this organism was not included on the Approved Lists of Bacterial Names (28) and has not been validly published on subsequent Approved Lists or Validation Lists. The results of recent numerical phenetic studies (11) and results obtained by nucleic acid techniques (12,(39)(40)(41) suggest that the strains of "S. caesia" are very closely related to S. azurea K161T. It has been determined that strains of S. viridis cause farmer's lung disease ( 1, 6) and are significant agents of hypersensitivity pneumonitis Recently, a 16s ribosomal DNA (rDNA) sequence analysis showed that the genus Saccharomonospora is a distinct phyletic group within the evolutionary radiation of the family Pseudonocardiaceae (12).…”

Paenibacillus campinasensis sp. nov., a cyclodextrin-producing bacterium isolated in Brazil

“…The ssDNA templates produced were directly used for the sequencing reaction. The sequencing was performed as described previously (Kim et al, 1995) using a-35S-labelled dATP and a DNA sequencing kit (US Biochemical). The sequencing primers were derived from conserved regions of previously described 16s rRNA gene sequences of eubacteria.…”