SGM Journals
Actinobacteria

Reclassification of Streptomyces flavidofuscus as a synonym of Nocardiopsis dassonvillei subsp. dassonvillei

Tomohiko Tamura, Yuumi Ishida, Misa Otoguro, Kazunori Hatano, Ken-ichiro Suzuki

  • NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation, 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
  • Correspondence
    Tomohiko Tamura
    tamura-tomohiko{at}nite.go.jp

    • International Journal of Systematic and Evolutionary Microbiology 2008; 58(10):2321–2323 · https://doi.org/10.1099/ijs.0.65559-0

    View at publisher PubMed

    Abstract

    During the course of quality control studies of the collection of the NITE Biological Resource Center (NBRC), phylogenetic analysis based on 16S rRNA gene sequences of actinomycetes revealed that Streptomyces flavidofuscus NBRC 15404T formed a cluster with Nocardiopsis dassonvillei and Nocardiopsis synnemataformans. Strain NBRC 15404T contained meso-diaminopimelic acid as a cell-wall diamino acid and DNA–DNA hybridization studies also showed that S. flavidofuscus NBRC 15404T was a close relative of N. dassonvillei subsp. dassonvillei NBRC 14626T. Based on chemotaxonomic, phenotypic and genetic analysis of the type strain, Streptomyces flavidofuscus should be reclassified as a later heterotypic synonym of Nocardiopsis dassonvillei subsp. dassonvillei.

    • The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of strain NBRC 15404T is AB184655.

    The genus Streptomyces is the largest genus of actinomycetes, containing more than 500 species with validly published names. They are characterized phenotypically by morphology and the presence of a type I cell wall. The genus Nocardiopsis was established by Meyer (1976) on the basis of morphological characteristics and the presence of cell-wall type III/C. The genus currently comprises more than 20 species. Members of this taxon are characterized chemotaxonomically by possessing phosphatidylcholine and phosphatidylmethylethanolamine as diagnostic phospholipids, menaquinone (MK)-10 with variable degrees of saturation (Collins et al., 1977), iso-, anteiso- and 10-methyl-branched fatty acids (fatty acid type 3d sensu Kroppenstedt, 1985) and meso-diaminopimelic acid (meso-A2pm). They lack diagnostic sugars (cell-wall chemotype III/C sensu Lechevalier & Lechevalier, 1970) and mycolic acids. They contain the acetyl type of muramic acid and have a G+C content of 64–69 mol% (Grund & Kroppenstedt, 1990).

    During the course of quality control of the collection of the NITE Biological Resource Center (NBRC), it was revealed that NBRC 15404T, the type strain of Streptomyces flavidofuscus (Gause et al., 1983), was classified phylogenetically within the genus Nocardiopsis. Therefore, the taxonomic position of S. flavidofuscus was studied further.

    PCR amplification and 16S rRNA gene sequencing and phylogenetic analysis were performed as described previously (Tamura & Hatano, 2001). 16S rRNA gene sequence analysis revealed that S. flavidofuscus NBRC 15404T was incorporated in a monophyletic cluster with members of the genus Nocardiopsis (Fig. 1⇓). The binary similarity value of the 16S rRNA gene sequence of S. flavidofuscus NBRC 15404T was 99.5 % with Nocardiopsis dassonvillei subsp. dassonvillei DSM 43111T, 99.7 % with N. dassonvillei subsp. albirubida NBRC 13392T and 99.8 % with Nocardiopsis synnemataformans IMMIB D-1215T. The sequence of S. flavidofuscus NBRC 15404T was 100 % similar to the sequence submitted to GenBank as AY999914, derived from S. flavidofuscus NRRL B-16366T. This means the phylogenetic position of the type strain of S. flavidofuscus has been confirmed by using multiple strains preserved in different culture collections.

    Figure image not available in archive
    Fig. 1.

    Phylogenetic tree derived from the 16S rRNA gene sequences of S. flavidofuscus NBRC 15404T and members of the genus Nocardiopsis. N. dassonvillei subsp. dassonvillei DSM 43884 is the type strain of Nocardiopsis antarctica. The tree was constructed using the neighbour-joining method (Saitou & Nei, 1987). The sequence of Streptomyces ambofaciens ATCC 23877T was used as an outgroup. Bar, 0.01 Knuc in nucleotide sequences. Numbers on branches are confidence limits estimated by bootstrap analysis with 1000 replicates (only values above 500 are presented).

    Cell-wall amino acids, whole-cell sugars, cellular fatty acids, isoprenoid quinones and DNA base composition were analysed as described previously (Tamura et al., 1994). Freeze-dried cells for chemotaxonomic analyses were prepared from cultures grown in yeast extract-glucose broth [containing (l−1) 10 g yeast extract and 10 g d-glucose, pH 7.2] on a rotary shaker at 28 °C for 3 days. The predominant menaquinones were MK-10(H6) and MK-10(H8), with MK-10(H4), MK-9(H6) and MK-9(H8) as minor components. The strain contained meso-A2pm, alanine and glutamic acid in the cell wall and ribose and mannose as whole-cell sugars. The major cellular fatty acids were iso-C16 : 0 (50 %), 10-methyl C18 : 0 (12 %) and anteiso-C17 : 0 (10 %). The DNA G+C content was 71 mol%. The chemotaxonomic characteristics of S. flavidofuscus NBRC 15404T were consistent with those of the genus Nocardiopsis.

    The microplate hybridization method developed by Ezaki et al. (1988, 1989) was used for the determination of DNA–DNA relatedness. The relatedness values of S. flavidofuscus NBRC 15404T to N. dassonvillei subsp. dassonvillei NBRC 14626T, N. dassonvillei subsp. albirubida NBRC 13392T and N. synnemataformans NBRC 102581T were 81–87, 55–79 and 55–63 %, respectively. N. dassonvillei subsp. albirubida NBRC 13392T exhibited high relatedness (59–73 %) to N. dassonvillei subsp. dassonvillei NBRC 14626T, as reported by Evtushenko et al. (2000). Further, N. synnemataformans NBRC 102581T exhibited 43–61 % relatedness to N. dassonvillei subsp. dassonvillei NBRC 14626T and 53–79 % relatedness to N. dassonvillei subsp. albirubida NBRC 13392T. These species and subspecies are genetically closely related to each other.

    The cultural characteristics of S. flavidofuscus NBRC 15404T were similar to those of N. dassonvillei subsp. dassonvillei NBRC 14626T, i.e. they produced a pale-brown soluble pigment in NBRC medium 229 [containing (l−1) 5 g yeast extract, 50 g glycerol, 1 g CaCO3 and 20 g agar, pH 7.3; NBRC catalogue] and developed colourless to pale-brown colonies on NBRC medium 229, yeast extract-starch agar [(l−1) 2 g yeast extract, 10 g soluble starch and 18 g agar, pH 7.3], Bennett's maltose agar [(l−1) 1 g yeast extract, 1 g beef extract, 2 g NZ amine type A, 10 g maltose and 20 g agar, pH 7.3] and yeast extract-malt extract agar (ISP 2; Shirling & Gottlieb, 1966). However, S. flavidofuscus NBRC 15404T differed from N. dassonvillei subsp. dassonvillei NBRC 14626T with regard to the production of a pale-brown soluble pigment on yeast extract-starch, Bennett's maltose and yeast extract-malt extract agars.

    The results of the present study revealed that strain NBRC 15404T, the type strain of S. flavidofuscus, was identified as a strain of N. dassonvillei subsp. dassonvillei. The identity of the 16S rRNA gene sequence of strain NBRC 15404T to that of NRRL B-16366T strongly suggests that this is not merely true for this particular strain but is generalized to the concept of the species. Therefore, the name Streptomyces flavidofuscus Preobrazhenskaya 1986 should be treated as a later heterotypic synonym of Nocardiopsis dassonvillei subsp. dassonvillei (Brocq-Rousseau 1904) Meyer 1976.

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