1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 73, Issue 5

sp. nov., a novel actinobacterium isolated from soils of weathering dolomite No Access

Abstract

Strain KLBMP 9083, a novel actinobacterium, was isolated from weathered soils collected from a karst area in Anshun, Guizhou Province, PR China. The taxonomic position of strain KLBMP 9083 was studied using the polyphasic approach. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain KLBMP 9083 formed a stabilized monophyletic clade with its closest relative strain CGMCC 1.13856 (98.4 % 16S rRNA gene sequence similarity). The peptidoglycan hydrolysates contained alanine, glutamic acid, threonine and lysine. The polar lipids were composed of diphosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside, an unidentified phosphoglycolipid, an unidentified phospholipid and an unidentified glycolipid. The predominant menaquinones were MK-9(H) (87.1 %), MK-9(H) (7.3 %) and MK-9(H) (5.6 %). The major fatty acids (>10 %) were anteiso-C and iso-C. The genomic DNA G+C content was 72.3 mol%. The digital DNA–DNA hybridization and average nucleotide identity values between strain KLBMP 9083 and CGMCC 1.13856 were 23.4 and 79.9 %, respectively. On the basis of morphological, chemotaxonomic and phylogenetic characteristics, strain KLBMP 9083 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is KLBMP 9083 (=CGMCC 4.7737=NBRC 115577).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): karstic soils , polyphasic taxonomy , Promicromonosporaceae and whole-genome analysis
Funding
This study was supported by the:
  • Transformation Program of Scientific and Technological Achievements of Jiangsu Province (Award KYCX21_2609)
    • Principle Award Recipient: YaZhang
  • the Key Research Plan of Modern Agriculture of Xuzhou City (Award KC20049)
    • Principle Award Recipient: Cheng-LiangCao
  • State Key Laboratory for Management and Control of Complex Systems (Award SKLEG2020207)
    • Principle Award Recipient: Cheng-LiangCao
  • the National Natural Science Foundation of China (Award 32030072)
    • Principle Award Recipient: JihongJiang
© 2023 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005771
2023-05-16
2024-04-28
Loading full text...

Full text loading...

References

  1. Zhang L-Y, Fang B-Z, Jiao J-Y, Zhang X-T, Liu L et al. Antribacter gilvus gen. nov., sp. nov., a new member of the family Promicromonosporaceae from a karstic cavern. Int J Syst Evol Microbiol 2019; 69:3792–3799 [View Article]
     [Google Scholar]
  2. 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 [View Article]
     [Google Scholar]
  3. Zhi XY, Li WJ, Stackebrandt E. An update of the structure and 16S rRNA gene sequence-based definition of higher ranks of the class Actinobacteria, with the proposal of two new suborders and four new families and emended descriptions of the existing higher taxa. Int J Syst Evol Microbiol 2009; 59:589–608 [View Article] [PubMed]
     [Google Scholar]
  4. Qiu D, Ruan J, Huang Y. Selective isolation and rapid identification of members of the genus Micromonospora. Appl Environ Microbiol 2008; 74:5593–5597 [View Article] [PubMed]
     [Google Scholar]
  5. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966; 16:313–340 [View Article]
     [Google Scholar]
  6. Li W-J, Xu P, Schumann P, Zhang Y-Q, Pukall R et al. Georgenia ruanii sp. nov., a novel actinobacterium isolated from forest soil in Yunnan (China), and emended description of the genus Georgenia. Int J Syst Evol Microbiol 2007; 57:1424–1428 [View Article] [PubMed]
     [Google Scholar]
  7. 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]
  8. 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]
  9. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
     [Google Scholar]
  10. 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]
  11. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article]
     [Google Scholar]
  12. Kumar S, Stecher G, Tamura K. MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article]
     [Google Scholar]
  13. Lim HJ, Lee EH, Yoon Y, Chua B, Son A. Portable lysis apparatus for rapid single-step DNA extraction of Bacillus subtilis. J Appl Microbiol 2016; 120:379–387 [View Article] [PubMed]
     [Google Scholar]
  14. Li R, Zhu H, Ruan J, Qian W, Fang X et al. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res 2010; 20:265–272 [View Article] [PubMed]
     [Google Scholar]
  15. Li R, Li Y, Kristiansen K, Wang J. SOAP: short oligonucleotide alignment program. Bioinformatics 2008; 24:713–714 [View Article] [PubMed]
     [Google Scholar]
  16. 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]
  17. Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJM et al. ABySS: a parallel assembler for short read sequence data. Genome Res 2009; 19:1117–1123 [View Article] [PubMed]
     [Google Scholar]
  18. Lee I, Ouk Kim Y, Park SC, Chun J. OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2016; 66:1100–1103 [View Article]
     [Google Scholar]
  19. Blin K, Shaw S, Steinke K, Villebro R, Ziemert N et al. antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline. Nucleic Acids Res 2019; 47:W81–W87 [View Article] [PubMed]
     [Google Scholar]
  20. Hardy MA, Dalton HP, Allison MJ. Laboratory identification and epidemiology of streptococcal hospital isolates. J Clin Microbiol 1978; 8:534–544 [View Article] [PubMed]
     [Google Scholar]
  21. Stokes EJ. A guide to the identification of the genera of bacteria. Q Rev Biol 1959; 36(2):870
     [Google Scholar]
  22. Gerhardt P, Wood WA, Krieg NR, Murray R. Methods for general and molecular bacteriology. ASM 1994
     [Google Scholar]
  23. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966; 16:313–340 [View Article]
     [Google Scholar]
  24. Waksman SA. eds The Actinomycetes. A summary of Current Knowledge New York: Ronald Press; 1967
     [Google Scholar]
  25. Atlas RM. eds Handbook of Microbiological Media, 4th. edn Boca Raton, FL: CRC Press; 2010 p 719
     [Google Scholar]
  26. KL K. Inter-Society Colour Council-National Bureau of Standards Colour-Name Charts Illustrated With Centroid Colours Published in US 1964
     [Google Scholar]
  27. Xu P, Li W-J, Tang S-K, Zhang Y-Q, Chen G-Z et al. Naxibacter alkalitolerans gen. nov., sp. nov., a novel member of the family “Oxalobacteraceae” isolated from China. Int J Syst Evol Microbiol 2005; 55:1149–1153 [View Article]
     [Google Scholar]
  28. Kamlage B. Methods for general and molecular bacteriology. Mol Nutr Food Res 2010; 40:103 [View Article]
     [Google Scholar]
  29. Kurup PV, Schmitt JA. Numerical taxonomy of Nocardia. Can J Microbiol 1973; 19:1035–1048 [View Article] [PubMed]
     [Google Scholar]
  30. Smibert RA, Krieg NR. Phenotypic characterization. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. eds Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994 pp 607–654
     [Google Scholar]
  31. Gordon RE, Barnett DA, Handerhan JE, Pang C-N. Nocardia coeliaca, Nocardia autotrophica, and the Nocardin strain. Int J Syst Bacteriol 1974; 24:54–63 [View Article]
     [Google Scholar]
  32. 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]
  33. Tang S-K, Wang Y, Chen Y, Lou K, Cao L-L et al. Zhihengliuella alba sp. nov., and emended description of the genus Zhihengliuella. Int J Syst Evol Microbiol 2009; 59:2025–2031 [View Article] [PubMed]
     [Google Scholar]
  34. 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]
  35. 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]
  36. Kroppenstedt RM. Separation of bacterial menaquinones by HPLC using reverse phase (RP18) and a silver loaded ion exchanger as stationary phases. J Liq Chromatogr 1982; 5:2359–2367 [View Article]
     [Google Scholar]
  37. Sasser M. Technical Note 101: Identification of bacteria by gas chromatography of cellular fatty acids. Newark, DE: MIDI; 1990
  38. 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]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.005771
Loading
Antribacter soli sp. nov., a novel actinobacterium isolated from soils of weathering dolomite
Int J Syst Evol Microbiol 73, 005771 (2023); https://doi.org/10.1099/ijsem.0.005771
/content/journal/ijsem/10.1099/ijsem.0.005771
/content/journal/ijsem/10.1099/ijsem.0.005771
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