1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 73, Issue 4

sp. nov., an actinomycete isolated from solar saltern soil No Access

Abstract

An actinobacterium, designated strain SS06011, was isolated from solar saltern soil collected from Samut Sakhon province, Thailand. The taxonomic position of this strain was established using the polyphasic taxonomic approach. The strain produced grey aerial spore mass on International Project 2 seawater agar that differentiated into spiral spore chains with rugose-surfaced spores. Strain SS06011 was found to have -diaminopimelic acid in the cell peptidoglycan. Whole-cell hydrolysates contained galactose, glucose and ribose. MK-9(H) and MK-9(H) were major menaquinones. The major cellular fatty acids comprised -C, -C and -C. Diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylinositol were detected in cells. These characteristics were coincident with the typical morphological and chemotaxonomic properties of the genus . The taxonomic affiliation at the genus level of this strain could also be confirmed by its 16S rRNA gene sequence data. Strain SS06011 showed the highest 16S rRNA gene sequence similarity to NRRL B-1773 (99.1 %), NBRC 15399 (99.1 %) and OU-40 (99.1 %). Digital DNA–DNA hybridization (dDDH), average nucleotide identity- (ANIb) and average amino acid identity (AAI) values between strain SS06011 and its closely related type strains, NBRC 15402, NBRC 15399 and JCM 17657, were in the range of 45.4–48.4 % (for dDDH), 90.8–91.9 % (for ANIb) and 90.8–91.7 % (for AAI), respectively, which are lower than the cut-off criteria for species delineation. The DNA G+C content of genomic DNA was 71.9 mol%. With the differences in physiological, biochemical and genotypic data, strain SS06011 could be discriminated from its closest neighbours. Thus, strain SS06011 should be recognized as representing a novel species of the genus , for which the name sp. nov. is proposed. The type strain is SS06011 (=TBRC 9951=NBRC 113998).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): 16S rRNA gene , solar saltern soil , Streptomyces and whole-genome analysis
Funding
This study was supported by the:
  • The School of Science, King Mongkut’s Institute of Technology Ladkrabang (Award Grant number: 2561-01-05-68)
    • Principle Award Recipient: KlanbutKhanungkan
© 2023 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005863
2023-04-25
2024-05-14
Loading full text...

Full text loading...

References

  1. Waksman SA, Henrici AT. The nomenclature and classification of the actinomycetes. J Bacteriol 1943; 46:337–341 [View Article] [PubMed]
     [Google Scholar]
  2. Pridham TG, Hesseltine CW, Benedict RG. A guide for the classification of streptomycetes according to selected groups; placement of strains in morphological sections. Appl Microbiol 1958; 6:52–79 [View Article] [PubMed]
     [Google Scholar]
  3. Bérdy J. Bioactive microbial metabolites. J Antibiot 2005; 58:1–26 [View Article] [PubMed]
     [Google Scholar]
  4. Li C, He H, Wang J, Liu H, Wang H et al. Characterization of a LAL-type regulator NemR in nemadectin biosynthesis and its application for increasing nemadectin production in Streptomyces cyaneogriseus. Sci China Life Sci 2019; 62:394–405 [View Article] [PubMed]
     [Google Scholar]
  5. Djaballah CE, Kitouni M, Raoult D, Khelaifia S. Streptomyces massilialgeriensis sp. nov., a new bacterial species isolated from an extremely saline soil collected from the dry lake of Ank el Djamel in Algeria. New Microbes New Infect 2018; 21:18–19 [View Article] [PubMed]
     [Google Scholar]
  6. Luo X-X, Gao G-B, Xia Z-F, Chen Z-J, Wan C-X et al. Streptomyces salilacus sp. nov., an actinomycete isolated from a salt lake. Int J Syst Evol Microbiol 2018; 68:1514–1518 [View Article] [PubMed]
     [Google Scholar]
  7. Yu Y, Fu Y, Guo X, Yan R, Wang H et al. Streptomyces durbertensis sp. nov., isolated from saline-alkali soil. Int J Syst Evol Microbiol 2018; 68:3635–3640 [View Article] [PubMed]
     [Google Scholar]
  8. Tatar D, Veyisoglu A, Saygin H, Sahin N. Streptomyces boncukensis sp. nov., isolated from saltern soil. Arch Microbiol 2021; 203:279–285 [View Article]
     [Google Scholar]
  9. Liu H, Xiao L, Wei J, Schmitz JC, Liu M et al. Identification of Streptomyces sp. nov. WH26 producing cytotoxic compounds isolated from marine solar saltern in China. World J Microbiol Biotechnol 2013; 29:1271–1278 [View Article] [PubMed]
     [Google Scholar]
  10. Kim S-H, Shin Y, Lee S-H, Oh K-B, Lee SK et al. Salternamides A-D from a halophilic Streptomyces sp. actinobacterium. J Nat Prod 2015; 78:836–843 [View Article] [PubMed]
     [Google Scholar]
  11. Bach D-H, Kim S-H, Hong J-Y, Park HJ, Oh D-C et al. Salternamide A suppresses hypoxia-induced accumulation of HIF-1α and induces apoptosis in human colorectal cancer cells. Mar Drugs 2015; 13:6962–6976 [View Article] [PubMed]
     [Google Scholar]
  12. Kim SH, Ha TKQ, Oh WK, Shin J, Oh DC. Antiviral indolosesquiterpenoid xiamycins C-E from a halophilic actinomycete. J Nat Prod 2016; 79:51–58 [View Article] [PubMed]
     [Google Scholar]
  13. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966; 16:313–340 [View Article]
     [Google Scholar]
  14. Tamaoka J. Determination of DNA base composition. In Goodfellow M, O’Donnell AG. eds Chemical Methods in Prokaryotic Systematics Chichester: John Wiley & Sons; 1994 pp 463–470
     [Google Scholar]
  15. Nakajima Y, Kitpreechavanich V, Suzuki K, Kudo T. Microbispora corallina sp. nov., a new species of the genus Microbispora isolated from Thai soil. Int J Syst Bacteriol 1999; 49:1761–1767 [View Article] [PubMed]
     [Google Scholar]
  16. Yoon S-H, Ha S-M, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017; 67:1613–1617 [View Article] [PubMed]
     [Google Scholar]
  17. Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analysis program for windows 95/98/NT. Nucleic Acids Symp Ser 1999; 41:95–98
     [Google Scholar]
  18. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article] [PubMed]
     [Google Scholar]
  19. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
     [Google Scholar]
  20. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406–417 [View Article]
     [Google Scholar]
  21. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms. Mol Biol Evol 2018; 35:1547–1549 [View Article] [PubMed]
     [Google Scholar]
  22. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980; 16:111–120 [View Article] [PubMed]
     [Google Scholar]
  23. Tamura K, Nei M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 1993; 10:512–526 [View Article] [PubMed]
     [Google Scholar]
  24. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
     [Google Scholar]
  25. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012; 19:455–477 [View Article] [PubMed]
     [Google Scholar]
  26. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [View Article] [PubMed]
     [Google Scholar]
  27. Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J. JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 2016; 32:929–931 [View Article] [PubMed]
     [Google Scholar]
  28. Rodriguez-R LM, Konstantinidis KT. Bypassing cultivation to identify bacterial species. Microbe Magazine 2014; 9:111–118 [View Article]
     [Google Scholar]
  29. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60–73 [View Article] [PubMed]
     [Google Scholar]
  30. Meier-Kolthoff JP, Göker M. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun 2019; 10:2182 [View Article] [PubMed]
     [Google Scholar]
  31. Lefort V, Desper R, Gascuel O. FastME 2.0: a comprehensive, accurate, and fast distance-based phylogeny inference program. Mol Biol Evol 2015; 32:2798–2800 [View Article] [PubMed]
     [Google Scholar]
  32. Farris JS. Estimating phylogenetic trees from distance matrices. The American Naturalist 1972; 106:645–668 [View Article]
     [Google Scholar]
  33. Alanjary M, Steinke K, Ziemert N. AutoMLST: an automated web server for generating multi-locus species trees highlighting natural product potential. Nucleic Acids Res 2019; 47:W276–W282 [View Article] [PubMed]
     [Google Scholar]
  34. Blin K, Shaw S, Kloosterman AM, Charlop-Powers Z, van Wezel GP et al. antiSMASH 6.0: improving cluster detection and comparison capabilities. Nucleic Acids Res 2021; 49:W29–W35 [View Article] [PubMed]
     [Google Scholar]
  35. Wellington EMH, Stackebrandt E, Sanders D, Wolstrup J, Jorgensen NOG. Taxonomic status of Kitasatosporia, and proposed unification with Streptomyces on the basis of phenotypic and 16S rRNA analysis and emendation of Streptomyces Waksman and Henrici 1943, 339AL. Int J Syst Bacteriol 1992; 42:156–160 [View Article] [PubMed]
     [Google Scholar]
  36. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci 2009; 106:19126–19131 [View Article] [PubMed]
     [Google Scholar]
  37. Thompson CC, Chimetto L, Edwards RA, Swings J, Stackebrandt E et al. Microbial genomic taxonomy. BMC Genomics 2013; 14:913 [View Article] [PubMed]
     [Google Scholar]
  38. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018; 68:461–466 [View Article] [PubMed]
     [Google Scholar]
  39. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007; 57:81–91 [View Article] [PubMed]
     [Google Scholar]
  40. Zheng Y, Saitou A, Wang C-M, Toyoda A, Minakuchi Y et al. Genome features and secondary metabolites biosynthetic potential of the class Ktedonobacteria. Front Microbiol 2019; 10:893 [View Article] [PubMed]
     [Google Scholar]
  41. Itoh T, Kudo T, Parenti F, Seino A. Amended description of the genus Kineosporia, based on chemotaxonomic and morphological studies. Int J Syst Bacteriol 1989; 39:168–173 [View Article]
     [Google Scholar]
  42. Waksman SA. The Actinomycetes. In Classification, Identification and Description of Genera and Species Baltimore: Williams & Wilkins; 1961
     [Google Scholar]
  43. Kelly KL. Inter-Society Color Council – National Bureau of Standard Color Name Charts Illustrated with Centroid Colors Washington, DC: US Government Printing Office; 1964
     [Google Scholar]
  44. Arai T. Culture Media for Actinomycetes Tokyo: The Society for Actinomycetes Japan; 1975
     [Google Scholar]
  45. Williams ST, Cross T. Actinomycetes. In Booth C. eds Methods in Microbiology vol 4 London: Academic Press; 1971 pp 295–334
     [Google Scholar]
  46. Gordon RE, Barnett DA, Handerhan JE, Pang CHN. Nocardia coeliaca, Nocardia autotrophica, and the nocardin strain. Int J Syst Bacteriol 1974; 24:54–63 [View Article]
     [Google Scholar]
  47. Hasegawa T, Takizawa M, Tanida S. A rapid analysis for chemical grouping of aerobic actinomycetes. J Gen Appl Microbiol 1983; 29:319–322 [View Article]
     [Google Scholar]
  48. Komagata K, Suzuki KI. Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 1987; 19:161–207
     [Google Scholar]
  49. Minnikin DE, O’Donnell AG, Goodfellow M, Alderson G, Athalye M et al. An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 1984; 2:233–241 [View Article]
     [Google Scholar]
  50. Collins MD, Jones D. Lipids in the classification and identification of coryneform bacteria containing peptidoglycans based on 2, 4-diaminobutyric acid. J Appl Bacteriol 1980; 48:459–470 [View Article]
     [Google Scholar]
  51. Collins MD, Pirouz T, Goodfellow M, Minnikin DE. Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 1977; 100:221–230 [View Article] [PubMed]
     [Google Scholar]
  52. Tamaoka J, Katayama-Fujimura Y, Kuraishi H. Analysis of bacterial menaquinone mixtures by high performance liquid chromatography. J Appl Bacteriol 1983; 54:31–36 [View Article]
     [Google Scholar]
  53. Sasser M. Technical Note 101: Identification of bacteria by gas chromatography of cellular fatty acids Newark, DE: MIDI Inc; 1990
     [Google Scholar]
  54. Kämpfer P, Kroppenstedt RM. Numerical analysis of fatty acid patterns of coryneform bacteria and related taxa. Can J Microbiol 1996; 42:989–1005 [View Article]
     [Google Scholar]
  55. Komaki H, Tamura T. Reclassification of Streptomyces diastaticus subsp. ardesiacus, Streptomyces gougerotii and Streptomyces rutgersensis. Int J Syst Evol Microbiol 2020; 70:4291–4297 [View Article] [PubMed]
     [Google Scholar]
  56. Gauze GF, Preobrazhenskaya TP, Sveshnikova MA, Terekhova LP, Maximova TS. A guide for the determination of actinomycetes. In Genera Streptomyces, Streptoverticillium, and Chainia Nauka, Moscow, URSS: 1983
     [Google Scholar]
  57. Reddy TVK, Mahmood S, Paris L, Reddy YHK, Wellington EMH et al. Streptomyces hyderabadensis sp. nov., an actinomycete isolated from soil. Int J Syst Evol Microbiol 2011; 61:76–80 [View Article] [PubMed]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.005863
Loading
Streptomyces salinarius sp. nov., an actinomycete isolated from solar saltern soil
Int J Syst Evol Microbiol 73, 005863 (2023); https://doi.org/10.1099/ijsem.0.005863
/content/journal/ijsem/10.1099/ijsem.0.005863
/content/journal/ijsem/10.1099/ijsem.0.005863
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error