- Open Access
Complete genome sequence of Streptosporangium roseum type strain (NI 9100T)
Standards in Genomic Sciences volume 2, pages 29–37 (2010)
Streptosporangium roseum Crauch 1955 is the type strain of the species which is the type species of the genus Streptosporangium. The ‘pinkish coiled Streptomyces-like organism with a spore case’ was isolated from vegetable garden soil in 1955. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of a member of the family Streptosporangiaceae, and the second largest microbial genome sequence ever deciphered. The 10,369,518 bp long genome with its 9421 protein-coding and 80 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
Strain NI 9100T (= DSM 43021 = ATCC 12428 = JCM 3005) is the type strain of the species Streptosporangium roseum, which is the type species of the genus Streptosporangium, the type genus of the actinobacterial suborder Streptosporanineae [1–4]. S. roseum NI 9100T was isolated from vegetable garden soil and first described by Crouch in 1955 [2,4]. The name derives from ‘strepto’ from Greek meaning ‘coiled’ combined with ‘sporangium’, Latin for ‘spore case’, to mean ‘streptomyces-like’ but with sporangia [2,4]. The species epithet ‘roseum’ derives from the pinkish color on potato dextrose agar . Here we present a summary classification and a set of features for S. roseum NI 9100T, together with the description of the complete genomic sequencing and annotation.
Classification and features
The 16S rRNA genes of the thirteen other validly named species currently ascribed to the genus Streptosporangium share 96–100% (S. vulgare ) sequence identity with NI 9100T, but S. claviforme (94%) [6,7] apparently does not belong to this genus (but to the genus Herbidospora) and thus has been excluded from phylogenetic analysis (see below). Two reference strains, DSM 43871 (X89949), and DSM 44111 (X89947), differ by just one nucleotide from strain NI 9100T, whereas the effectively published named species ‘S. koreanum’ DSM 44110 [99.9%, 5], ‘S. brasiliense’ DSM 44109 [99.4%, 5] and ‘S. rubrum’ DSM 44095 [99.4%, 5] appear to members of the genus. Members of the species and genus are rare in nature, at least based on the habitats screened thus far as 16S rRNA in environmental samples and metagenomic surveys do not exceed 88–91% sequence similarity to the 16S rRNA gene sequence of strain NI 9100T (U48996, X70425, X89947; status August 2009). Figure 1a and Figure 1b show the phylogenetic neighborhood of S. roseum NI 9100T in a 16S rRNA based tree. The sequence of the six 16S rRNA gene copies in the genome do not differ from each other, and are identical to the previously published sequence generated from DSM 43021 (X89947), whereas the sequence generated in the same year from the JCM 3005 version of strain 9100T (U48996) differs by 24 nucleotides (1.7%).
A summary of the classification and features for S. roseum is listed in Table 1. We draw attention to the reader that we find quite an amount of contradictive results between old and more recent literature (see below). A potential but not ultimate source for this observation could be the usage of different experimental methods. A variety of media were used in the original description pertaining to cellular and mycelium morphology on (Figure 2).
The color of the substrate mycelium is red-brown to yellow-brown [2,24]. Strain NI 9100T utilizes glucose, arabinose, sucrose, xylose, fructose, and raffinose, but not inositol, mannose, rhamnose, or cellulose [19,20]. The strain is positive for arginine dihydrolase and acetoin production (Voges Proskauer test), weakly positive for citrate utilization, lysine decarboxylase, and ornithine decarboxylase, and negative for Kohn’s gelatin gelatinase, urease, o-nitro-phenyl-galactoside β-galactosidase, tryptophan desaminase, tryptophan indole production, H2S production from sodium thiosulfate [19,20]. Starch hydrolysis and nitrate reduction are positive, but growth at 42°C and iodinin production are negative . Mertz and Yao  reported that strain NI 9100T can utilize glycerol, arabinose, rhamnose and inositol, which is in part contradictory to other results [20,21]. Gelatin is liquefied, milk is peptonized and red-brown to purple-brown soluble pigments are produced . Zhang et al.  describe strain NI 9100T as utilizing sorbitol and sorbose but to be negative for L-arabinose, erythrose, D-fructose, D-galactose, inositol, D-mannose, maltose, raffinose, and rhamnose, which again is in part in conflict with other studies [18–20]. Strain NI 9100T produces a secondary metabolite, the antibiotic angucycline WS 79089B, which is an inhibitor of the endothelin-converting enzyme . In contrast to S. carneum, strain NI 9100T does not produce an antibiotic against Staphylococcus aureus .
The characteristics of the ribosomal protein AT-L30 of strain S. roseum JCM2178T in comparison to other bacteria of the genus Streptosporangium is described elsewhere . These data should be taken cautiously, as according to the Japanese Collection of Microorganisms (JCM) catalogue the strain number “JCM2178” is affiliated with Aspergillus oryzae (accessed to JCM in August 09), hence the true nature of strain S. roseum JCM2178T in the study of Ochi  is unclear.
The major fatty acids (relative ratio %) are iso-C16:0 (40.0), C17:0 10-methyl (23.0), C16:0 (1.95), C16:0 10-methyl (6.0), iso-C14:0 (14.0) (Reiner Kroppenstedt, personal communication). Partly different fatty acid patterns are reported elsewhere [18–20,26,27]. The proportions of diaminopimelic acid (A2pm) in the cell wall of strain S. roseum NI 9100T are 71% meso-A2pm and 29% LL-A2pm . The phospholipids of strain S. roseum NI 9100T are phosphatidylethanolamine, hydroxyphosphatidylethanolamine, ninhydrin-positive and sugar-positive phospholipids, disphosphatidylglycerol, and posphatidylinositol . The menaquinone compositions are MK-9 (III, VIII-H4) (56.5%), MK-9 (H2) (37.8%), MK-9 (H0) (5.0%), and MK-9 (H6) (0.7%) . Galactose and madurose are present in whole cell sugars extracts, rhamnose is absent . In general, the genus Streptosporangium is characterized by the whole-cell sugar type B or C, the phospholipid type IV and of the fatty acid type 3c .
Genome sequencing and annotation
Genome project history
This organism was selected for sequencing on the basis of its phylogenetic position, and is part of the Genomic Encyclopedia of Bacteria and Archaea project. The genome project is deposited in the Genome OnLine Database  and the complete genome sequence is deposited in GenBank. Sequencing, finishing and annotation were performed by the DOE Joint Genome Institute (JGI). A summary of the project information is shown in Table 2.
Growth conditions and DNA isolation
S. roseum NI 9100T, DSM 43021, was grown in DSMZ medium 535, Trypticase Soy Broth , at 28°C. DNA was isolated from 0.5–1 g of cell paste using the JGI CTAP procedure with modification ALM as described in .
Genome sequencing and assembly
The genome was sequenced using a combination of Sanger and 454 sequencing platforms. All general aspects of library construction and sequencing performed at the JGI can be found at http://www.jgi.doe.gov/. 454 Pyrosequencing reads were assembled using the Newbler assembler version 1.1.02.15 (Roche). Large Newbler contigs were broken into 11,709 overlapping fragments of 1,000 bp and entered into assembly as pseudo-reads. The sequences were assigned quality scores based on Newbler consensus q-scores with modifications to account for overlap redundancy and to adjust inflated q-scores. A hybrid 454/Sanger assembly was made using the parallel phrap assembler (High Performance Software, LLC). Possible mis-assemblies were corrected with Dupfinisher  or transposon bombing of bridging clones (Epicentre Biotechnologies, Madison, WI). Gaps between contigs were closed by editing in Consed, custom primer walk or PCR amplification. A total of 2,837 Sanger finishing reads were produced to close gaps, to resolve repetitive regions, and to raise the quality of the finished sequence. The error rate of the completed genome sequence is less than 1 in 100,000. Together all sequence types provided 36.05× coverage of the genome. The final assembly contains 128,042 Sanger and 1,033,578 Pyrosequence reads.
Genes were identified using Prodigal  as part of the Oak Ridge National Laboratory genome annotation pipeline, followed by a round of manual curation using the JGI GenePRIMP pipeline (http://geneprimp.jgi-psf.org) . The predicted CDSs were translated and used to search the National Center for Biotechnology Information (NCBI) nonredundant database, UniProt, TIGRFam, Pfam, PRIAM, KEGG, COG, and InterPro databases. Additional gene prediction analysis and functional annotation was performed within the Integrated Microbial Genomes - Expert Review (IMG-ER) platform .
The genome consists of a 10,341,314 bp long chromosome and a small 28,204 bp plasmid with a 70.9% GC content (Table 3 and Figure 3). Of the 9,501 genes predicted, 9,421 were protein coding genes, and 80 RNAs. In addition, 446 pseudogenes were identified. The majority of protein-coding genes (62.5%) were assigned a putative function while those remaining were annotated as hypothetical proteins. The distribution of genes into COGs functional categories is presented in Table 4.
Stackebrandt E, Kroppenstedt RM, Jahnke KD, Kemmerling C, Gürtler H. Transfer of Streptosporangium viridogriseum (Okuda et al. 1966), Streptosporangium viridogriseum subsp. kofuense (Nonomura and Ohara 1969), and Streptosporangium albidum (Furumai et al. 1968) to Kutzneria gen. nov. as Kutzneria viridogrisea comb. nov., Kutzneria kofuensis comb. nov., and Kutzneria albida comb. nov., respectively, and emendation of the Genus Streptosporangium. Int J Syst Bacteriol 1994; 44:265–269.
Couch JN. A new genus and family of the Actinomycetales, with a revision of the genus Actinoplanes. J Elisha Mitchell Sci Soc 1955; 71:148–155.
Skerman VBD, McGowan V, Sneath PHA. Approved Lists of Bacterial Names. Int J Syst Bacteriol 1980; 30:225–420.
Couch JN, Bland CE. Genus III. Streptosporangium Couch 1955, 148. In: Buchanan RE, Gibbons NE (eds), Bergey’s Manual of Determinative Bacteriology, Eighth Edition, The Williams and Wilkins Co., Baltimore, 1974, p. 711–715.
Nonomura H, Ohara Y. Distribution of the actinomycetes in soil. IV. The isolation and classification of the genus Streptosporangium. J Ferment Technol 1960; 38:405–409.
Petrolini B, Quaroni S, Sardi P, Saracchi M, Andriolollo N. A sporangiate actinomycete with unusual morphological features: Streptosporangium claviforme sp. nov. Actinomycetes 1992; 3:45–50.
Ward-Rainey N, Rainey FA, Stackebrandt E. The phylogenetic structure of the genus Streptosporangium. Syst Appl Microbiol 1996; 19:50–55.
Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 2000; 17:540–552. PubMed
Lee C, Grasso C, Sharlow MF. Multiple sequence alignment using partial order graphs. Bioinformatics 2002; 18:452–464. PubMed doi:10.1093/bioinformatics/18.3.452
Stamatakis A, Hoover P, Rougemont J. A Rapid Bootstrap Algorithm for the RAxML Web Servers. Syst Biol 2008; 57:758–771. PubMed doi:10.1080/10635150802429642
Liolios K, Mavromatis K, Tavernarakis N, Kyrpides NC. The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res 2008; 36:D475–D479. PubMed doi:10.1093/nar/gkm884
Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thompson N, Allen MJ, Anguiuoli SV, et al. The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol 2008; 26:541–547. PubMed doi:10.1038/nbt1360
Woese CR, Kandler O, Wheelis ML. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci USA 1990; 87:4576–4579. PubMed doi:10.1073/pnas.87.12.4576
Garrity GM, Holt JG. The Road Map to the Manual. In: Garrity GM, Boone DR, Castenholz RW (eds), Bergey’s Manual of Systematic Bacteriology, Second Edition, Volume 1, Springer, New York, 2001, p. 119–169.
Stackebrandt E, Rainey FA, Ward-Rainey NL. Proposal for a New Hierarchic Classification System, Actinobacteria classis nov. Int J Syst Bacteriol 1997; 47:479–491.
Goodfellow M, Stanton LJ, Simpson KE, Minnikin DE. Numerical and chemical classification of Actinoplanes and some related actinomycetes. J Gen Microbiol 1990; 136:19–36.
List Editor. Validation List no. 34. Validation of the publication of new names and new combinations previously effectively published outside the IJSB. Int J Syst Bacteriol 1990; 40:320–321.
Mertz FP, Yao RC. Streptosporangium carneum sp. nov. Isolated from soil. Int J Syst Bacteriol 1990; 40:247–253.
Wink JM. http://www.gbif-prokarya.de/-microorganisms/files/Methods.pdf. 2009.
Wink JM. Compendium of Actinobacteria. http://www.dsmz.de/microorganisms/wink_pdf/DSM43021.pdf. 2009
Zhang LP, Zhang LM, Zhang XM. Streptosporangium canum sp. nov., isolated from soil. Int J Syst Evol Microbiol 2009; 59:1715–1719. PubMed doi:10.1099/ijs.0.007401-0
Biological Agents. Technical rules for biological agents www.baua.de TRBA 466
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al. Gene Ontology: tool for the unification of biology. Nat Genet 2000; 25:25–29. PubMed doi:10.1038/75556
Shearer MC, Colman PM, Nash CH, III. Streptosporangium fragile sp. nov. Int J Syst Bacteriol 1983; 33:364–368.
Ochi K, Miyadoh S. Polyacrylamide Gel Electrophoresis Analysis of Ribosomal Protein AT-L30 from an Actinomycete Genus, Streptosporangium. Int J Syst Bacteriol 1992; 42:151–155. PubMed
Gyobu Y, Miyadoh S. Proposal to transfer Actinomadura carminata to a new subspecies of the genus Nonomuraea as Nonomuraea roseoviolacea subsp. carminata comb. nov. Int J Syst Evol Microbiol 2001; 51:881–889. PubMed
Kudo T, Seino A. Transfer of Streptosporangium indianense Gupta 1965 to the Genus Streptomyces as Streptomyces indiaensis (Gupta 1965) comb. nov. Int J Syst Bacteriol 1987; 37:241–244.
List of growth media used at DSMZ: http://www.dsmz.de/microorganisms/media_list.php.
Wu D, Hugenholtz P, Mavromatis K, Pukall R, Dalin E, Ivanova NN, Kunin V, Goodwin L, Wu M, Tindall BJ, et al. A phylogeny-driven genomic encyclopedia of Bacteria and Archaea. Nature 2009; 462:1056–1060. PubMed doi:10.1038/nature08656
Sims D, Brettin T, Detter JC, Han C, Lapidus A, Copeland A, Glavina Del Rio T, Nolan M, Chen F, Lucas S, et al. Complete genome sequence of Kytococcus sedentarius type strain (541T). Stand Genomic Sci 2009; 1:12–20. doi:10.4056/sigs.761
Pati A, Ivanova N, Mikhailova N, Ovchinikova G, Hooper SD, Lykidis A, Kyrpides NC. GenePRIMP: A gene prediction improvement pipeline for microbial genomes. (Submitted).
Markowitz VM, Mavromatis K, Ivanova NN, Chen IMA, Chu K, Kyrpides NC. Expert review of functional annotations for microbial genomes. Bioinformatics 2009; 25:2271–2278. PubMed doi:10.1093/bioinformatics/btp393
We would like to gratefully acknowledge the help of Susanne Schneider (DSMZ) for DNA extraction and quality analysis. This work was performed under the auspices of the US Department of Energy’s Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, and Los Alamos National Laboratory under contract No. DE-AC02-06NA25396, as well as German Research Foundation (DFG) INST 599/1-1.
About this article
Cite this article
Nolan, M., Sikorski, J., Jando, M. et al. Complete genome sequence of Streptosporangium roseum type strain (NI 9100T). Stand in Genomic Sci 2, 29–37 (2010). https://doi.org/10.4056/sigs.631049
- vegetative and aerial mycelia
- non-motile spores
- S. cloviforme