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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 72, Issue 10

sp. nov., isolated from soil in Malaysia No Access

Abstract

A urease-producing Gram-stain-positive actinobacterium, designated strain T5, was isolated from a soil sample collected at a highway hillslope in Selangor, Malaysia. The strain was found to produce pale yellowish-pink aerial mycelia with smooth long chain spores and extensively branched light yellowish-pink substrate mycelia on oatmeal agar. Strain T5 grew at 15–37 °C, pH 6–11, and tolerated up to 9 % (w/v) NaCl, with optimal growth occurring at 28 °C, pH 6–9 and without NaCl. The whole-cell sugar hydrolysate of strain T5 contained galactose, glucose and ribose. The -diaminopimelic acid isomer was detected in the cell wall. Diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylinositol were found to be the predominant polar lipids. The main fatty acids were anteiso-C, iso-C, anteiso-C and iso-C. Comparative analysis of the 16S rRNA gene sequences indicated that strain T5 belonged to of the family with the highest 16S rRNA gene sequence similarity to LCR6-01 (99.0 %). The overall genome relatedness indices revealed that the closest related species was LCR6-01 with 89.4 % average nucleotide identity and 33.7 % digital DNA–DNA hybridization. Phylogeny analyses showed that strain T5 was closely related to , , , and . Based on these polyphasic data, strain T5 represents a novel species, for which the name sp. nov. is proposed. The type strain is T5 (=TBRC 5137= DSM 42166).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): actinomycetota , draft genome sequence and polyphasic taxonomy
Funding
This study was supported by the:
  • UMRG (Award RP005C-13SUS)
    • Principle Award Recipient: GeokYuan Annie Tan
© 2022 The Authors
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2022-10-25
2024-05-05
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References

  1. Kämpfer P et al. Streptomyces. In Trujillo ME, Dedysh S, DeVos P, Hedlund B, Kämpfer P. eds Bergey’s Manual of Systematics of Archaea and Bacteria association with Bergey’s Manual Trust: John Wiley & Sons, Inc; 2015 pp 1–414
     [Google Scholar]
  2. Kämpfer P, Glaeser SP, Parkes L, Keulen G, Dyson P. The family Streptomycetaceae. In Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F. eds The Prokaryotes: Actinobacteria Berlin, Heidelberg: Springer; 2014 pp 889–1010
     [Google Scholar]
  3. Parte AC, Sardà Carbasse J, Meier-Kolthoff JP, Reimer LC, Göker M. List of prokaryotic names with standing in nomenclature (LPSN) moves to the DSMZ. Int J Syst Evol Microbiol 2020; 70:5607–5612 [View Article]
     [Google Scholar]
  4. Firn RD, Jones CG. The evolution of secondary metabolism - a unifying model. Mol Microbiol 2000; 37:989–994 [View Article] [PubMed]
     [Google Scholar]
  5. Goodfellow M, Fiedler HP. A guide to successful bioprospecting: informed by actinobacterial systematics. Antonie van Leeuwenhoek 2010; 98:119–142 [View Article] [PubMed]
     [Google Scholar]
  6. Labeda DP, Goodfellow M, Brown R, Ward AC, Lanoot B et al. Phylogenetic study of the species within the family Streptomycetaceae. Antonie van Leeuwenhoek 2012; 101:73–104 [View Article]
     [Google Scholar]
  7. Yu H-X, Wang C-Y, Tang M. Fungal and bacterial communities in the rhizosphere of Pinus tabulaeformis related to the restoration of plantations and natural secondary forests in the loess plateau, Northwest China. Sci World J 2013; 2013:606480
     [Google Scholar]
  8. Lin XG, Yin R, Zhang HY, Huang JF, Chen RR et al. Changes of soil microbiological properties caused by land use changing from rice-wheat rotation to vegetable cultivation. Environ Geochem Health 2004; 26:119–128 [View Article] [PubMed]
     [Google Scholar]
  9. Saini A, Aggarwal NK, Sharma A, Yadav A. Actinomycetes: a source of lignocellulolytic enzymes. Enzyme Res 2015; 2015:279381 [View Article]
     [Google Scholar]
  10. Chater KF, Biró S, Lee KJ, Palmer T, Schrempf H. The complex extracellular biology of Streptomyces. FEMS Microbiol Rev 2010; 34:171–198 [View Article]
     [Google Scholar]
  11. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966; 16:313–340 [View Article]
     [Google Scholar]
  12. Weisburg WG, Barns SM, Pelletier DA, Lane DJ. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 1991; 173:697–703 [View Article]
     [Google Scholar]
  13. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP et al. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 2016; 44:6614–6624 [View Article]
     [Google Scholar]
  14. Simão FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 2015; 31:3210–3212 [View Article]
     [Google Scholar]
  15. 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]
     [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]
     [Google Scholar]
  17. Rodriguez-R LM, Gunturu S, Harvey WT, Rosselló-Mora R, Tiedje JM et al. The microbial genomes atlas (MiGA) webserver: taxonomic and gene diversity analysis of archaea and bacteria at the whole genome level. Nucleic Acids Res 2018; 46:W282–W288 [View Article]
     [Google Scholar]
  18. 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]
     [Google Scholar]
  19. Labeda DP, Dunlap CA, Rong X, Huang Y, Doroghazi JR et al. Phylogenetic relationships in the family Streptomycetaceae using multi-locus sequence analysis. Antonie van Leeuwenhoek 2017; 110:563–583 [View Article]
     [Google Scholar]
  20. Tarlachkov SV, Starodumova IP. TaxonDC: Calculating the similarity value of the 16S rRNA gene sequences of prokaryotes or ITS regions of fungi. J Bioinf Genom 2017; 3:1–4
     [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]
     [Google Scholar]
  22. Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, Aluru S. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun 2018; 9:5114 [View Article]
     [Google Scholar]
  23. Avram O, Rapoport D, Portugez S, Pupko T. M1CR0B1AL1Z3R-a user-friendly web server for the analysis of large-scale microbial genomics data. Nucleic Acids Res 2019; 47:W88–W92 [View Article]
     [Google Scholar]
  24. 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]
     [Google Scholar]
  25. Hu S, Li K, Zhang Y, Wang Y, Fu L et al. New insights into the threshold values of multi-locus sequence analysis, average nucleotide identity and digital DNA-DNA hybridization in delineating Streptomyces pecies. Front Microbiol 2022; 13:910277 [View Article]
     [Google Scholar]
  26. Komaki H. Resolution of housekeeping gene sequences used in MLSA for the genus Streptomyces and reclassification of Streptomyces anthocyanicus and Streptomyces tricolor as heterotypic synonyms of Streptomyces violaceoruber. Int J Syst Evol Microbiol 2022; 72:005370 [View Article]
     [Google Scholar]
  27. Waksman SA. The Actinomycetes: a Summary of Current Knowledge New York: The Ronald Press Co; 1967
     [Google Scholar]
  28. Jones KL. Fresh isolates of actinomycetes in which the presence of sporogenous aerial mycelia is a fluctuating characteristic. J Bacteriol 1949; 57:141–145 [View Article]
     [Google Scholar]
  29. Kelly KL, Judd DB. Colour-name Charts Illustrated with Centroid Colours (Supplement to National Bureau of Standards USA Circular 553) USA: United States National Bureau of Standards; 1964
     [Google Scholar]
  30. Gordon RE, Barnett DA, Handerhan JE, Pang CH-N. Nocardia coeliaca, Nocardia autotrophica, and the nocardin strain. Int J Syst Bacteriol 1974; 24:54–63 [View Article]
     [Google Scholar]
  31. Gordon RE, MIHM JM. A comparative study of some strains received as nocardiae. J Bacteriol 1957; 73:15–27 [View Article] [PubMed]
     [Google Scholar]
  32. Yokota A, Tamura T, Hasegawa T, Huang LH. Catenuloplanes japonicus gen nov., sp. nov., nom. rev., a new genus of the order Actinomycetales. Int J Syst Bacteriol 1993; 43:805–812 [View Article]
     [Google Scholar]
  33. Mccarthy AJ, Cross T. A taxonomic study of Thermomonospora and other monosporic actinomycetes. Microbiology 1984; 130:5–25 [View Article]
     [Google Scholar]
  34. Staneck JL, Roberts GD. Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol 1974; 28:226–231 [View Article]
     [Google Scholar]
  35. Lechevalier MP, De Bievre C, Lechevalier H. Chemotaxonomy of aerobic actinomycetes: phospholipid composition. Biochem Syst Ecol 1977; 5:249–260 [View Article]
     [Google Scholar]
  36. Minnikin DE, Patel PV, Alshamaony L, Goodfellow M. Polar lipid composition in the classification of Nocardia and related bacteria. Int J Syst Bacteriol 1977; 27:104–117 [View Article]
     [Google Scholar]
  37. Tresner HD, Davies MC, Backus EJ. Electron microscopy of Streptomyces spore morphology and its role in species differentiation. J Bacteriol 1961; 81:70–80 [View Article]
     [Google Scholar]
  38. Han L, Zhang G, Miao G, Zhang X, Feng J. Streptomyces kanasensis sp. nov., an antiviral glycoprotein producing actinomycete isolated from forest soil around Kanas Lake of China. Curr Microbiol 2015; 71:627–631 [View Article]
     [Google Scholar]
  39. Reimer LC, Vetcininova A, Carbasse JS, Söhngen C, Gleim D et al. BacDive in 2019: bacterial phenotypic data for high-throughput biodiversity analysis. Nucleic Acids Res 2019; 47:D631–D636 [View Article]
     [Google Scholar]
  40. Saeng-In P, Phongsopitanun W, Savarajara A, Tanasupawat S. Streptomyces lichenis sp. nov., isolated from lichen. Int J Syst Evol Microbiol 2018; 68:3641–3646 [View Article]
     [Google Scholar]
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Streptomyces solincola sp. nov., isolated from soil in Malaysia
Int J Syst Evol Microbiol 72, 005594 (2022); https://doi.org/10.1099/ijsem.0.005594
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