1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 74, Issue 2

sp. nov., a novel actinomycete isolated from sandy soil No Access

Abstract

A novel mycelium-forming actinomycete, designated strain NEAU-S30, was isolated from the sandy soil of a sea beach in Shouguang city, Shandong province, PR China. The strain developed long chains of non-motile cylindrical spores with smooth surfaces on aerial mycelia. The results of a polyphasic taxonomic study indicated that NEAU-S30 represented a member of the genus . The results of 16S rRNA gene sequence analysis indicated that NEAU-S30 was closely related to ‘Glycomyces ’ (98.97 % sequence similarity), Glycomyces (98.90 %), ‘’ (98.83 %) and (98.76 %). The average nucleotide identity (ANI) values between NEAU-S30 and ‘’ NEAU-A15, DSM 44727, ‘’ NEAU-C2 and DSM 44724 were 87.77, 87.53, 87.41 and 87.80 %, respectively. The digital DNA G+C content of the genomic DNA was 70.5 %. The whole-cell sugars contained ribose and xylose. The predominant menaquinones were MK-10(H), MK-10(H) and MK-10(H). The predominant fatty acids were anteiso-C, iso-C, anteiso-C and iso-C. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphoglycolipid, phosphatidylinositol, phosphatidylinositol mannoside and an unidentified glycolipid. On the basis of the results of comparative analysis of genotypic, phenotypic and chemotaxonomic data, the novel actinomycete strain NEAU-S30 (=JCM 33975=CGMCC 4.7890) represents the type strain of a novel species within the genus , for which the name sp. nov. is proposed.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): 16S rRNA gene , Glycomyces niveus sp. nov. , polyphasic taxonomy and whole genome
Funding
This study was supported by the:
  • Key Programme (Award U22A20483)
    • Principle Award Recipient: XiangjingWang
© 2024 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.006265
2024-02-08
2024-05-20
Loading full text...

Full text loading...

References

  1. Labeda DP, Testa RT, Lechevalier MP, Lechevalier HA. Glycomyces, a new genus of the actinomycetales. Int J Syst Evol Microbiol 1985; 35:417–421 [View Article]
     [Google Scholar]
  2. Labeda DP, Kroppenstedt RM. Emended description of the genus Glycomyces and description of Glycomyces algeriensis sp. nov., Glycomyces arizonensis sp. nov. and Glycomyces lechevalierae sp. nov. Int J Syst Evol Microbiol 2004; 54:2343–2346 [View Article] [PubMed]
     [Google Scholar]
  3. 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] [PubMed]
     [Google Scholar]
  4. Labeda DP, Kroppenstedt RM. Stackebrandtia nassauensis gen. nov., sp. nov. and emended description of the family Glycomycetaceae. Int J Syst Evol Microbiol 2005; 55:1687–1691 [View Article] [PubMed]
     [Google Scholar]
  5. Li W, Liu C, Guo X, Song W, Sun T et al. Glycomyces tritici sp. nov., isolated from rhizosphere soil of wheat (Triticum aestivum L.) and emended description of the genus Glycomyces. Antonie van Leeuwenhoek 2018; 111:1087–1093 [View Article] [PubMed]
     [Google Scholar]
  6. Potekhina NV, Tul’skaya EM, Naumova IB, Shashkov AS, Evtushenko LI. Erythritolteichoic acid in the cell wall of Glycomyces tenuis VKM Ac-1250. Eur J Biochem 1993; 218:371–375 [View Article] [PubMed]
     [Google Scholar]
  7. Potekhina NV, Tul’skaya EM, Shashkov AS, Taran VV, Evtushenko LI et al. Species specificity of teichoic acids in the actinomycete genus Glycomyces. Mikrobiologiya 1998; 67:330–334
     [Google Scholar]
  8. Guan TW, Wang PH, Tian L, Tang SK, Xiang HP. Glycomyces lacisalsi sp. nov., an actinomycete isolated from a hypersaline habitat. Int J Syst Evol Microbiol 2016; 66:5366–5370 [View Article] [PubMed]
     [Google Scholar]
  9. Han X-X, Luo X-X, Zhang L-L. Glycomyces fuscus sp. nov. and Glycomyces albus sp. nov., actinomycetes isolated from a hypersaline habitat. Int J Syst Evol Microbiol 2014; 64:2437–2441 [View Article] [PubMed]
     [Google Scholar]
  10. Duan L, Song W, Jiang S, Qian L, Guo X et al. Glycomyces luteolus sp. nov., a novel actinomycete isolated from rhizosphere soil of wheat (Triticum aestivum L.). Antonie van Leeuwenhoek 2019; 112:703–710 [View Article] [PubMed]
     [Google Scholar]
  11. Zhang X, Ren K, Du J, Liu H, Zhang L. Glycomyces artemisiae sp. nov., an endophytic actinomycete isolated from the roots of Artemisia argyi. Int J Syst Evol Microbiol 2014; 64:3492–3495 [View Article] [PubMed]
     [Google Scholar]
  12. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966; 16:313–340 [View Article]
     [Google Scholar]
  13. Kim SB, Brown R, Oldfield C, Gilbert SC, Iliarionov S et al. Gordonia amicalis sp. nov., a novel dibenzothiophene-desulphurizing actinomycete. Int J Syst Evol Microbiol 2000; 50:2031–2036 [View Article] [PubMed]
     [Google Scholar]
  14. 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]
  15. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994; 22:4673–4680 [View Article] [PubMed]
     [Google Scholar]
  16. 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]
  17. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
     [Google Scholar]
  18. Desper R, Gascuel O. Fast and accurate phylogeny reconstruction algorithms based on the minimum-evolution principle. J Comput Biol 2002; 9:687–705 [View Article] [PubMed]
     [Google Scholar]
  19. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
     [Google Scholar]
  20. 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]
  21. 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]
  22. Nikodinovic J, Barrow KD, Chuck JA. High yield preparation of genomic DNA from Streptomyces. Biotechniques 2003; 35:932–934 [View Article] [PubMed]
     [Google Scholar]
  23. 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]
  24. Li R, Li Y, Kristiansen K, Wang J. SOAP: short oligonucleotide alignment program. Bioinformatics 2008; 24:713–714 [View Article] [PubMed]
     [Google Scholar]
  25. 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]
  26. 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 [View Article] [PubMed]
     [Google Scholar]
  27. Yoon SH, Ha SM, 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]
  28. Rodriguez-R LM, Konstantinidis KT. The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes. PeerJ Preprints 2016 [View Article]
     [Google Scholar]
  29. Blin K, Shaw S, Augustijn HE, Reitz ZL, Biermann F et al. antiSMASH 7.0: new and improved predictions for detection, regulation, chemical structures and visualisation. Nucleic Acids Res 2023; 51:W46–W50 [View Article] [PubMed]
     [Google Scholar]
  30. Kanehisa M, Goto S, Kawashima S, Okuno Y, Hattori M. The KEGG resource for deciphering the genome. Nucleic Acids Res 2004; 32:D277–D280 [View Article] [PubMed]
     [Google Scholar]
  31. Cantarel BL, Coutinho PM, Rancurel C, Bernard T, Lombard V et al. The carbohydrate-active EnZymes database (CAZy): an expert resource for glycogenomics. Nucleic Acids Res 2009; 37:D233–D238 [View Article] [PubMed]
     [Google Scholar]
  32. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O et al. 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 [View Article]
     [Google Scholar]
  33. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 2009; 106:19126–19131 [View Article] [PubMed]
     [Google Scholar]
  34. 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]
  35. Jin L, Zhao Y, Song W, Duan L, Jiang S et al. 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]
  36. 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]
  37. Waksman SA. The Actinomycetes. A Summary of Current Knowledge New York: Ronald; 1967
     [Google Scholar]
  38. Waksman SA. The Actinomycetes. In Classification, Identification and Descriptions of Genera and Species vol 2 Baltimore: Williams and Wilkins; 1961
     [Google Scholar]
  39. Kelly KL. Inter-Society Colour Council-National Bureau of Standards Colour-Name Charts Illustrated with Centroid Colours Published in US 1964
     [Google Scholar]
  40. Jia F, Liu C, Wang X, Zhao J, Liu Q et al. Wangella harbinensis gen. nov., sp. nov., a new member of the family Micromonosporaceae. Antonie van Leeuwenhoek 2013; 103:399–408 [View Article] [PubMed]
     [Google Scholar]
  41. Zhao J, Han L, Yu M, Cao P, Li D et al. Characterization of Streptomyces sporangiiformans sp. nov., a novel soil actinomycete with antibacterial activity against Ralstonia solanacearum. Microorganisms 2019; 7:360 [View Article] [PubMed]
     [Google Scholar]
  42. Cao P, Li C, Tan K, Liu C, Xu X et al. Characterization, phylogenetic analyses, and pathogenicity of Enterobacter cloacae on rice seedlings in Heilongjiang Province, China. Plant Dis 2020; 104:1601–1609 [View Article] [PubMed]
     [Google Scholar]
  43. Smibert RM, Krieg NR. Phenotypic Characterisation. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. eds Methods for General and Molecular Bacteriology. American Society for Microbiology Washington: American Society for Microbiology; 1994 pp 607–654
     [Google Scholar]
  44. 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]
  45. 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]
  46. McKerrow J, Vagg S, McKinney T, Seviour EM, Maszenan AM et al. 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]
  47. Lechevalier MP, Lechevalier HA. The chemotaxonomy of actinomycetes. In Dietz A, Thayer DW. eds Actinomycete Taxonomy Special Publication, Society of Industrial Microbiology vol 6 1980 pp 227–291
     [Google Scholar]
  48. 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]
  49. Collins MD. Isoprenoid quinone analyses in bacterial classification and identification. In Goodfellow M, Minnikin DE. eds Chemical Methods in Bacterial Systematics London: Academic Press; 1999 pp 267–284
     [Google Scholar]
  50. Wu C, Lu X, Qin M, Wang Y, Ruan J. Analysis of menaquinone compound in microbial cells by HPLC. Microbiology 1989; 16:176–178
     [Google Scholar]
  51. 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]
  52. Xiang W, Liu C, Wang X, Du J, Xi L et al. 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] [PubMed]
     [Google Scholar]
  53. Dong G, Bai X, Aimila A, Aisa HA, Maiwulanjiang M. Study on lavender essential oil chemical compositions by GC–MS and improved pGC. Molecules 2020; 25:3166 [View Article] [PubMed]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.006265
Loading
Glycomyces niveus sp. nov., a novel actinomycete isolated from sandy soil
Int J Syst Evol Microbiol 74, 006265 (2024); https://doi.org/10.1099/ijsem.0.006265
/content/journal/ijsem/10.1099/ijsem.0.006265
/content/journal/ijsem/10.1099/ijsem.0.006265
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