1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 71, Issue 6

sp. nov., a novel actinobacterium isolated from the root of pumpkin () No Access

Abstract

A novel acidophilic actinobacterium, designated strain NEAU-YB345, was isolated from a pumpkin root collected from Mudanjiang, Heilongjiang Province, northeast PR China. Based on 16S rRNA gene sequence similarity and chemotaxonomic and morphological properties, the isolate was assigned to the genus , with the high 16S rRNA gene sequence similarities to JCM 16224 (99.2 %), JCM 16223 (99.1 %) and JCM 12277 (98.7 %). Its cell wall contained -diaminopimelic acid as the major diamino acid. Rhamnose, ribose, glucose and galactose were the detected sugars from the whole-cell hydrolysates. The phospholipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside and an unidentified phospholipid. The menaquinones were MK-9(H) and MK-9(H). Major fatty acids were C, iso-C, iso-C and anteiso-C. Phylogenetic analysis using 16S rRNA gene and whole-genome sequences placed the strain in distinct clades but within the genus . The DNA G+C content was 71.2 mol%. Based on DNA–DNA relatedness and physiological and biochemical data, the isolate could be distinguished from its closest relatives. Therefore, strain NEAU-YB345 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is NEAU-YB345 (=CCTCC AA 2020030=JCM 33976).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): 16S rRNA gene , genome , pumpkin and Streptacidiphilus fuscans sp. nov.
Funding
This study was supported by the:
  • the National Natural Youth Science Foundation of China (Award 31772240)
    • Principle Award Recipient: XiangjingWang
© 2021 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004824
2021-06-09
2024-04-25
Loading full text...

Full text loading...

References

  1. Kim SB, Lonsdale J, Seong CN, Goodfellow M. Streptacidiphilus gen. nov., acidophilic actinomycetes with wall chemotype I and emendation of the family Streptomycetaceae (Waksman and Henrici (1943) AL) emend. Rainey et al. 1997. Antonie van Leeuwenhoek 2003; 83:107–116 [View Article][PubMed]
     [Google Scholar]
  2. Nouioui I, Klenk HP, Igual JM, Gulvik CA, Lasker BA. Streptacidiphilus bronchialis sp. nov., a ciprofloxacin-resistant bacterium from a human clinical specimen; reclassification of Streptomyces griseoplanus as Streptacidiphilus griseoplanus comb. nov. and emended description of the genus Streptacidiphilus . Int J Syst Evol Microbiol 2019; 69:1047–1056 [View Article][PubMed]
     [Google Scholar]
  3. Golinska P, Dahm H, Goodfellow M. Streptacidiphilus toruniensis sp. nov., isolated from a pine forest soil. Antonie van Leeuwenhoek 2016; 109:1583–1591 [View Article][PubMed]
     [Google Scholar]
  4. Williams ST, Davies FL, Mayfield CI, Khan MR. Studies on the ecology of actinomycetes in soil. II. the pH requirements of streptomycetes from two acid soils. Soil Biol Biochem 1971; 3:187–195 [View Article]
     [Google Scholar]
  5. Williams ST, Goodfellow M, Alderson G, Wellington EMH, Sneath PHA. Numerical classification of Streptomyces and related genera. J Gen Microbiol 1983; 129:1743–1813 [View Article][PubMed]
     [Google Scholar]
  6. Williams ST, Lanning S, Wellington EMH. Ecology of actinomycetes. Goodfellow M, Mordarski M, Williams S. eds In The Biology of Actinomycetes London: Academic Press; 1984 pp 481–528
     [Google Scholar]
  7. Wang L, Huang Y, Liu Z, Goodfellow M, Rodríguez C. Streptacidiphilus oryzae sp. nov., an actinomycete isolated from rice-field soil in Thailand. Int J Syst Evol Microbiol 2006; 56:1257–1261 [View Article][PubMed]
     [Google Scholar]
  8. Wang XJ, Zhao JW, Liu CX, Wang JD, Shen Y. Nonomuraea solani sp. nov., a novel actinomycete isolated from eggplant root (Solanum melongena L. Int J Syst Evol Microbiol 2013; 63:2418–2423 [View Article][PubMed]
     [Google Scholar]
  9. Atlas RM. Handbook of microbiological media. Parks L. eds In Microbiology Boca Raton: CRC Press; 1993
     [Google Scholar]
  10. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966; 16:313–340 [View Article]
     [Google Scholar]
  11. Jin LY, Zhao Y, Song W, Duan LP, Jiang SW. Streptomyces inhibens sp. nov., a novel actinomycete isolated from rhizosphere soil of wheat (Triticum aestivum L.). Int J Syst Evol Microbiol 2019; 69:688–695 [View Article][PubMed]
     [Google Scholar]
  12. Waksman SA. The Actinomycetes. A Summary of Current Knowledge New York: Ronald; 1967
     [Google Scholar]
  13. 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]
  14. Waksman SA. The Actinomycetes, vol. 2, Classification, Identification and Descriptions of Genera and Species Baltimore: Williams and Wilkins; 1961
     [Google Scholar]
  15. Kelly KL. Inter-society Color Council-national Bureau of Standards Color-name Charts Illustrated with Centroid Colors Published in US 1964
     [Google Scholar]
  16. Zhao JW, Han LY, MY Y, Cao P, DM L. Characterization of Streptomyces sporangiiformans sp. nov., a novel soil actinomycete with antibacterial activity against Ralstonia solanacearum. Microorganisms 2019; 7:360
     [Google Scholar]
  17. Cao P, CX L, Tan KF, Liu CZ, Xu X. Characterization, phylogenetic analyses and pathogenicity of enterobacter cloacae on rice seedlings in Heilongjiang Province, China. Plant Disease 2020 [View Article]
     [Google Scholar]
  18. Smibert RM, Krieg NR. Phenotypic characterisation. Gerhardt P, R. G. E Murray, Wood WA, Krieg NR. eds In Methods for General and Molecular Bacteriology American Society for Microbiology; 1994 pp 607–654
     [Google Scholar]
  19. Gordon RE, Barnett DA, Handerhan JE, Pang C. Nocardia coeliaca, Nocardia autotrophica, and the nocardin strain. Int J Syst Bacteriol 1974; 24:54–63 [View Article]
     [Google Scholar]
  20. Yokota A, Tamura T, Hasegawa T, Huang LH. Catenuloplanes japonicas 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]
  21. McKerrow J, Vagg S, McKinney T, Seviour EM, Maszenan AM. A simple HPLC method for analysing diaminopimelic acid diastereomers in cell walls of Gram-positive bacteria. Lett Appl Microbiol 2000; 30:178–182 [View Article][PubMed]
     [Google Scholar]
  22. Lechevalier MP, Lechevalier HA. The chemotaxonomy of actinomycetes. Dietz A, Thayer D. eds In Actinomycete Taxonomy Special Publication, Society of Industrial Microbiology Vol 6 1980 pp 227–291
     [Google Scholar]
  23. Minnikin DE, O’Donnell AG, Goodfellow M, Alderson G, Athalye M. An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 1984; 2:233–241
     [Google Scholar]
  24. Collins MD. Isoprenoid quinone analyses in bacterial classification and identification. Goodfellow M, Minnikin D. eds In Chemical Methods in Bacterial Systematics London: Academic Press; 1985 pp 267–284
     [Google Scholar]
  25. Wu C, Lu X, Qin M, Wang Y, Ruan J. Analysis of Menaquinone Compound in Microbial Cells by HPLC Microbiology [English translation of Microbiology (Beijing)]; 1989 pp 176–178
     [Google Scholar]
  26. Gao R, Liu C, Zhao J, Jia F, Yu C et al. Micromonospora jinlongensis sp. nov., isolated from muddy soil in China and emended description of the genus Micromonospora . . Antonie van Leeuwenhoek 2014; 105:307–315 [View Article][PubMed]
     [Google Scholar]
  27. Xiang WS, Liu CX, Wang XJ, Du J, LJ X. Actinoalloteichus nanshanensis sp. nov., isolated from the rhizosphere of a fig tree (ficus religiosa. Int J Syst Evol Microbiol 2011; 61:1165–1169 [View Article]
     [Google Scholar]
  28. Kim SB, Brown R, Oldfield C, Gilbert SC, Iliarionov S. Gordonia amicalis sp. nov., a novel dibenzothiophene-desulphurizing actinomycete. Int J Syst Evol Microbiol 2000; 50:2031–2036 [View Article]
     [Google Scholar]
  29. Yoon SH, SM H, Kwon S, Lim J, Kim Y. Introducing EzBioCloud: A taxonomically united database of 16S rRNA and whole genome assemblies. Int J Syst Evol Microbiol 2017; 67:1613–1617
     [Google Scholar]
  30. 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]
  31. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
     [Google Scholar]
  32. 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][PubMed]
     [Google Scholar]
  33. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:83–791 [View Article]
     [Google Scholar]
  34. 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]
  35. 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]
  36. Nikodinovic J, Barrow KD, Chuck JA. High yield preparation of genomic DNA from Streptomyces . Biotechniques 2003; 35:932–934 [View Article][PubMed]
     [Google Scholar]
  37. 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]
  38. Li R, Li Y, Kristiansen K, Wang J. Soap: Short oligonucleotide alignment program. Bioinformatics 2008; 24:713–714 [View Article][PubMed]
     [Google Scholar]
  39. Yoon SH, SM H, Lim J, Kwon S, Chun J. A large scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek 2017; 10:1281–1286
     [Google Scholar]
  40. Meier-Kolthoff JP, Auch AF, Klenk HP, Goker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinform 2013; 14:60
     [Google Scholar]
  41. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O. International Committee on Systematic Bacteriology. Report of the AD Hoc committee on Reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 1987; 37:463–464
     [Google Scholar]
  42. Richter M, Rossello-Mora R. Shifting the genomic gold standard for the prokaryotic species defifinition. Proc Natl Acad Sci USA 2009; 106:19126–19131
     [Google Scholar]
  43. Chun J, Rainey FA. Integrating genomics into the taxonomy and systematics of the bacteria and archaea. Int J Syst Evol Microbiol 2014; 64:316–324 [View Article][PubMed]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004824
Loading
Streptacidiphilus fuscans sp. nov., a novel actinobacterium isolated from the root of pumpkin (Cucurbita moschata)
Int J Syst Evol Microbiol 71, 004824 (2021); https://doi.org/10.1099/ijsem.0.004824
/content/journal/ijsem/10.1099/ijsem.0.004824
/content/journal/ijsem/10.1099/ijsem.0.004824
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