1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 71, Issue 10

sp. nov., isolated from the top soil layer on basaltic material in Turkey No Access

Abstract

An actinobacterium, designated 14C53, was isolated from a soil sample on basaltic material from Samsun, Turkey. The growth ranges for NaCl concentration and pH of strain 14C53 were quite limited and the growth temperature range of the strain was 20–37 °C, with an optimum at 28 °C. Phylogenetic analysis of 16S rRNA gene sequences revealed that strain 14C53 was most closely related to A8036 (98.5 % similarity value), but in the phylogenetic tree, it formed a clade with D310A. The genome tree revealed a close relationship between the strain and DSM 43383. However, the digital DNA–DNA hybridization and average nucleotide identity values between strain 14C53 with A8036 and DSM 43383 were 28.6–30.2 % and 84.3–85.5 %, respectively, and comparative analyses based on the genome sequences demonstrated that it represents a novel species of the genus . The genome size of strain 14C53 was approximately 9.0 Mb and the genomic DNA G+C content of the strain was 71.3 mol%. The major cellular fatty acids of strain 14C53 were C and -C. Strain 14C53 contained -diaminopimelic acid as the diamino acid in the cell-wall peptidoglycan. The predominant menaquinones were MK-9(H) and MK-9(H). Based on evidence collected from the phenotypic, genotypic and phylogenetic analyses, a novel species sp. nov. is proposed, with 14C53 (=DSM 104447=KCTC 39878) as the type strain.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): 16S rRNA gene , Actinomadura soli , biosynthetic gene clusters and Whole-genome analyses
Funding
This study was supported by the:
  • Türkiye Bilimsel ve Teknolojik Araştirma Kurumu (Award TOVAG 213O073)
    • Principle Award Recipient: KamilIsik
© 2021 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005062
2021-10-27
2024-04-19
Loading full text...

Full text loading...

References

  1. Lechevalier HA, Lechevalier MP. A critical evaluation of the genera of aerobic actinomycetes. Prauser H. eds In The Actinomycetales Jena: VEB Gustav Fischer Verlag; 1970 pp 393–405
     [Google Scholar]
  2. Kroppenstedt RM, Stackebrandt E, Goodfellow M. Taxonomic revision of the actinomycete genera Actinomadura and Microtetraspora. Syst Appl Microbiol 1990; 13:148–160 [View Article]
     [Google Scholar]
  3. Zhang Z, Kudo T, Nakajima Y, Wang Y. Clarification of the relationship between the members of the family Thermomonosporaceae on the basis of 16S rDNA, 16S-23S rRNA internal transcribed spacer and 23S rDNA sequences and chemotaxonomic analyses. Int J Syst Evol Microbiol 2001; 51:373–383 [View Article] [PubMed]
     [Google Scholar]
  4. Zhang Z, Wang Y, Ruan J. Reclassification of Thermomonospora and Microtetraspora. Int J Syst Evol Microbiol 1998; 48:411–422 [View Article]
     [Google Scholar]
  5. Miyadoh S, Miyara T. The Society for Actinomycetes Family Thermomonosporaceae. In Identification Manual of Actinomycetes Tokyo: Business Center for Academic Societies; 2001 pp 281–291
     [Google Scholar]
  6. Zhao J, Guo L, Sun P, Han C, Bai L et al. Actinomadura jiaoheensis sp. nov. and Actinomadura sporangiiformans sp. nov., two novel actinomycetes isolated from muddy soil and emended description of the genus Actinomadura. Antonie van Leeuwenhoek 2015; 108:1331–1339 [View Article] [PubMed]
     [Google Scholar]
  7. Stackebrandt E, Rainey FA, Ward-Rainey NL. Proposal for a new hierarchic classification system, Actinobacteria classis nov. Int J Syst Evol Microbiol 1997; 47:479–491 [View Article]
     [Google Scholar]
  8. Tamura T, Ishida Y, Nozawa Y, Otoguro M, Suzuki K-I. Transfer of Actinomadura spadix Nonomura and Ohara 1971 to Actinoallomurus spadix gen. nov., comb. nov., and description of Actinoallomurus amamiensis sp. nov., Actinoallomurus caesius sp. nov., Actinoallomurus coprocola sp. nov., Actinoallomurus fulvus sp. nov., Actinoallomurus iriomotensis sp. nov., Actinoallomurus luridus sp. nov., Actinoallomurus purpureus sp. nov. and Actinoallomurus yoronensis sp. nov. Int J Syst Evol Microbiol 2009; 59:1867–1874 [View Article] [PubMed]
     [Google Scholar]
  9. Iinuma S, Yokota A, Hasegawa T, Kanamaru T. Actinocorallia gen. nov., a new genus of the order Actinomycetales. Int J Syst Evol Microbiol 1994; 44:230–234 [View Article]
     [Google Scholar]
  10. Couch JN. Some new genera and species of the Actinoplanaceae. J Elisha Mitchell Sci Soc 1963; 79:53–70
     [Google Scholar]
  11. Henssen A. Beiträge zur Morphologie und Systematik der thermophilen Actinomyceten. Arch Microbiol 1957; 26:373–414 [View Article]
     [Google Scholar]
  12. Trujillo ME, Goodfellow M. Genus III. Actinomadura Lechevalier and Lechevalier 1970A, 400AL emend. Kroppenstedt, Stackebrandt and Goodfellow 1990, 156. Goodfellow M, Kämpfer P, Busse H-J, Trujillo ME, Suzuki K-i. eds In Bergey’s Manual of Systematic Bacteriology Vol 5 2012 pp 1940–1959
     [Google Scholar]
  13. Benndorf R, Martin K, Küfner M, de Beer ZW, Vollmers J et al. Actinomadura rubteroloni sp. nov. and Actinomadura macrotermitis sp. nov., isolated from the gut of the fungus growing-termite Macrotermes natalensis. Int J Syst Evol Microbiol 2020; 70:5255–5262 [View Article] [PubMed]
     [Google Scholar]
  14. Zhuang X, Peng C, Wang Z, Zhao J, Shen Y et al. Actinomadura physcomitrii sp. nov., a novel actinomycete isolated from moss [Physcomitrium sphaericum (Ludw) Fuernr]. Antonie van Leeuwenhoek 2020; 113:677–685 [View Article] [PubMed]
     [Google Scholar]
  15. Rachniyom H, Matsumoto A, Inahashi Y, Take A, Takahashi Y et al. Actinomadura barringtoniae sp. nov., an endophytic actinomycete isolated from the roots of Barringtonia acutangula (L.) Gaertn. Int J Syst Evol Microbiol 2018; 68:1584–1590 [View Article] [PubMed]
     [Google Scholar]
  16. Ay H. Genomic insight into a novel actinobacterium, Actinomadura rubrisoli sp. nov., reveals high potential for bioactive metabolites. Antonie van Leeuwenhoek 2021; 114:195–208 [View Article] [PubMed]
     [Google Scholar]
  17. Cao P, Xu X, Li C, Han L, Mu W et al. Actinomadura litoris sp. nov., an actinobacterium isolated from sandy soil in Sanya. Int J Syst Evol Microbiol 2021; 71:004708 [View Article]
     [Google Scholar]
  18. Shi L, Han L, Guo X, Zhao J, Wang J et al. Actinomadura logoneensis sp. nov., a novel actinomycete isolated from the soil. Int J Syst Evol Microbiol 2019; 69:2914–2920 [View Article] [PubMed]
     [Google Scholar]
  19. Shin B, Kim B-. Y, Cho E, Oh K-. B, Shin J et al. Actinomadurol, an antibacterial norditerpenoid from a rare actinomycete, Actinomadura sp. KC 191. J Nat Prod 2016; 79:1886–1890 [View Article] [PubMed]
     [Google Scholar]
  20. Simmons L, Kaufmann K, Garcia R, Schwär G, Huch V et al. Bendigoles D–F, bioactive sterols from the marine sponge-derived Actinomadura sp. SBMs009. Bioorg Med Chem 2011; 19:6570–6575 [View Article] [PubMed]
     [Google Scholar]
  21. Yan J-X, Chevrette MG, Braun DR, Harper MK, Currie CR et al. Madurastatin D1 and D2, oxazoline containing siderophores isolated from an Actinomadura sp. Org Lett 2019; 21:6275–6279 [View Article] [PubMed]
     [Google Scholar]
  22. Lee SR, Lee D, Yu JS, Benndorf R, Lee S et al. Natalenamides A–C, cyclic tripeptides from the termite-associated Actinomadura sp. RB99. Molecules 2018; 23:3003 [View Article]
     [Google Scholar]
  23. Igarashi Y, Matsuoka N, In Y, Kataura T, Tashiro E et al. Nonthmicin, a polyether polyketide bearing a halogen-modified tetronate with neuroprotective and antiinvasive activity from Actinomadura sp. Org Lett 2017; 19:1406–1409 [View Article] [PubMed]
     [Google Scholar]
  24. Wieme AD, Gosselé F, Snauwaert C, Cleenwerck I, Vandamme P. Actinomadura roseirufa sp. nov., producer of semduramicin, a polyether ionophore. Int J Syst Evol Microbiol 2019; 69:3068–3073 [View Article] [PubMed]
     [Google Scholar]
  25. Bonifaz A, Tirado-Sánchez A, Vázquez-González D, Fierro-Arias L, Araiza J et al. Actinomycetoma by Actinomadura madurae. Clinical and therapeutic characteristics of 18 cases with two treatment modalities. J Dermatolog Treat 20201–5 [View Article] [PubMed]
     [Google Scholar]
  26. van de Sande WW. Global burden of human mycetoma: a systematic review and meta-analysis. PLoS Negl Trop Dis 2013; 7:e2550 [View Article] [PubMed]
     [Google Scholar]
  27. McNeil M, Brown J, Scalise G, Piersimoni C. Nonmycetomic Actinomadura madurae infection in a patient with AIDS. J Clin Microbiol 1992; 30:1008–1010 [View Article] [PubMed]
     [Google Scholar]
  28. Siddig EE, Nyuykonge B, Ahmed MT, Hassan R, Saad ESA et al. Human actinomycetoma caused by Actinomadura mexicana in Sudan: the first report. Trans R Soc Trop Med Hyg 2021; 115:406–410 [View Article] [PubMed]
     [Google Scholar]
  29. Saricaoglu S, Saygin H, Topkara AR, Gencbay T, Guven K et al. Nonomuraea basaltis sp. nov., a siderophore-producing actinobacteria isolated from surface soil of basaltic parent material. Arch Microbiol 2020; 202:1535–1543 [View Article] [PubMed]
     [Google Scholar]
  30. Tan GYA, Ward AC, Goodfellow M. Exploration of Amycolatopsis diversity in soil using genus-specific primers and novel selective media. Syst Appl Microbiol 2006; 29:557–569 [View Article] [PubMed]
     [Google Scholar]
  31. Weisburg WG, Barns SM, Pelletier DA, Lane DJ. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 1991; 173:697–703 [View Article] [PubMed]
     [Google Scholar]
  32. Lane DJ. 16S/23S rRNA sequencing. Stackebrandt E, Goodfellow M. eds In Nucleic Acid Techniques in Bacterial Systematics New York: John Wiley and Sons; 1991 pp 115–175
     [Google Scholar]
  33. 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]
  34. 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]
  35. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
     [Google Scholar]
  36. Jukes T, Cantor C. Evolution of protein molecules. Munro HN. eds In Mammalian Protein Metabolism New York: Academic Press; 1969 pp 21–132
     [Google Scholar]
  37. 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]
  38. Stackebrandt E, Ebers J. Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 2006; 33:152–155
     [Google Scholar]
  39. 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]
  40. Wattam AR, Davis JJ, Assaf R, Boisvert S, Brettin T et al. Improvements to PATRIC, the all-bacterial bioinformatics database and analysis resource center. Nucleic Acids Res 2017; 45:D535–D542 [View Article] [PubMed]
     [Google Scholar]
  41. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T et al. The RAST Server: rapid annotations using subsystems technology. BMC Genomics 2008; 9:75 [View Article] [PubMed]
     [Google Scholar]
  42. 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]
  43. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article] [PubMed]
     [Google Scholar]
  44. Yoon S-H, Ha S-M, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek 2017; 110:1281–1286 [View Article] [PubMed]
     [Google Scholar]
  45. 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]
  46. Wayne L, Brenner D, Colwell R, Grimont P, Kandler O et al. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Evol Microbiol 1987; 37:463–464 [View Article]
     [Google Scholar]
  47. Cheng C, Pan L, Chen Y, Song H, Qin Y et al. Total synthesis of (±)-marinopyrrole a and its library as potential antibiotic and anticancer agents. J Comb Chem 2010; 12:541–547 [View Article] [PubMed]
     [Google Scholar]
  48. Chu M, Yarborough R, Schwartz J, Patel M, Horan A et al. Sch 47554 and Sch 47555, two novel antifungal antibiotics produced from a Streptomyces sp. J Antibiot 1993; 46:861–865 [View Article]
     [Google Scholar]
  49. McAlpine JB, Bachmann BO, Piraee M, Tremblay S, Alarco A-M et al. Microbial genomics as a guide to drug discovery and structural elucidation: ECO-02301, a novel antifungal agent, as an example. J Nat Prod 2005; 68:493–496 [View Article] [PubMed]
     [Google Scholar]
  50. Staneck JL, Roberts GD. Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Environ Microbiol 1974; 28:226–231 [View Article]
     [Google Scholar]
  51. Lechevalier MP, Lechevalier H. Chemical composition as a criterion in the classification of aerobic actinomycetes. Int J Syst Evol Microbiol 1970; 20:435–443
     [Google Scholar]
  52. Minnikin D, O’Donnell A, 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]
  53. Tindall B. A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol 1990; 13:128–130 [View Article]
     [Google Scholar]
  54. Tindall B. Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett 1990; 66:199–202 [View Article]
     [Google Scholar]
  55. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
     [Google Scholar]
  56. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966; 16:313–340 [View Article]
     [Google Scholar]
  57. Waksman SA. The Actinomycetes. A Summary of Current Knowledge New York: Ronald Press; 1967
     [Google Scholar]
  58. 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] [PubMed]
     [Google Scholar]
  59. Waksman SA. The Actinomycetes.vol. II. Classification, Identification and Descriptions of Genera and Species Baltimore: Williams & Wilkins; 1961
     [Google Scholar]
  60. Williams S, Goodfellow M, Alderson G, Wellington E, Sneath P et al. Numerical classification of Streptomyces and related genera. J Gen Microbiol 1983; 129:1743–1813 [View Article] [PubMed]
     [Google Scholar]
  61. Küster E, Williams S. Selection of media for isolation of streptomycetes. Nature 1964; 202:928–929 [View Article] [PubMed]
     [Google Scholar]
  62. Ay H, Nouioui I, Del Carmen Montero-Calasanz M, Carro L, Klenk H-P et al. Actinomadura alkaliterrae sp. nov., isolated from an alkaline soil. Antonie van Leeuwenhoek 2017; 110:787–794 [View Article] [PubMed]
     [Google Scholar]
  63. Sazak A, Camas M, Spröer C, Klenk H-P, Sahin N. Actinomadura geliboluensis sp. nov., isolated from soil. Int J Syst Evol Microbiol 2012; 62:2011–2017 [View Article] [PubMed]
     [Google Scholar]
  64. 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]
  65. Farris JS. Estimating phylogenetic trees from distance matrices. Am Nat 1972; 106:645–668 [View Article]
     [Google Scholar]
  66. Trujillo ME, Goodfellow M. Actinomadura. In Bergey’s Manual of Systematics of Archaea and Bacteria John Wiley & Sons Inc; 2015 pp 1–32
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.005062
Loading
Actinomadura soli sp. nov., isolated from the top soil layer on basaltic material in Turkey
Int J Syst Evol Microbiol 71, 005062 (2021); https://doi.org/10.1099/ijsem.0.005062
/content/journal/ijsem/10.1099/ijsem.0.005062
/content/journal/ijsem/10.1099/ijsem.0.005062
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