1887

Abstract

A novel cellulase-producing actinobacterium, designated strain NEAU-L178, was isolated from soil sample collected from Qiqihaer, Heilongjiang Province, PR China. A polyphasic study was carried out to determine the taxonomic status of the strain. On the basis of 16S rRNA gene sequence analysis, strain NEAU-L178 should be classified into the genus and is closely related to SYSU K10005 (99.31 % 16S rRNA gene sequence similarity), NEAU-BB2C19 (98.75 %), NEAU-ZJ3 (98.75 %) and ‘’ NEAU-mq18 (98.34 %). The digital DNA–DNA hybridization values between them are 27.1, 26.1, 42.0 and 30.9 %, and the whole-genome average nucleotide identity values between them are 83.1, 82.3, 90.3 and 85.8 %, respectively. The whole-cell hydrolysates contained glucose, ribose, arabinose and madurose. The menaquinones were identified as MK-9(H), MK-9(H) and MK-9(H). The major fatty acids were C, iso-C and C 10-methyl. The detected polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, hydroxy-phosphatidylethanolamine, phosphatidylinositol and three unidentified phospholipids. The genomic DNA G+C content was 69.7 mol%. In addition, whole-genome analysis indicated that strain NEAU-L178 had the potential to degrade cellulose. Based on the phenotypic, genotypic, chemotaxonomic and phylogenetic data, strain NEAU-L178 can be differentiated from its close phylogenetic relatives and represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is NEAU-L178 (=JCM 34799=CGMCC 4.7741).

Funding
This study was supported by the:
  • the National Natural Science Foundation of China (Award 31972291)
    • Principle Award Recipient: XiangjingWang
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005411
2022-06-06
2022-07-06
Loading full text...

Full text loading...

References

  1. Zhang Z, Wang Y, Ruan J. Reclassification of Thermomonospora and Microtetraspora. Int J Syst Bacteriol 1998; 48:411–422 [View Article] [PubMed]
    [Google Scholar]
  2. Chiba S, Suzuki M, Ando K. Taxonomic re-evaluation of “Nocardiopsis” sp. K-252T (= NRRL 15532T): a proposal to transfer this strain to the genus Nonomuraea as Nonomuraea longicatena sp. nov. Int J Syst Bacteriol 1999; 49:1623–1630 [View Article] [PubMed]
    [Google Scholar]
  3. Nonomura H, Ohara Y. Distribution of actinomycetes in soil. XI. Some new species of the genus Actinomadura Lechevalier et al. . J Ferment Technol 1971; 49:904–912
    [Google Scholar]
  4. Cao P, Wang Y, Sun P, Li C, Zhao J et al. Nonomuraea lactucae sp. nov., a novel actinomycete isolated from rhizosphere soil of lettuce (Lactuca sativa). Int J Syst Evol Microbiol 2019; 69:316–321 [View Article] [PubMed]
    [Google Scholar]
  5. Sripreechasak P, Phongsopitanun W, Supong K, Pittayakhajonwut P, Kudo T et al. Nonomuraea rhodomycinica sp. nov., isolated from peat swamp forest soil. Int J Syst Evol Microbiol 2017; 67:1683–1687 [View Article] [PubMed]
    [Google Scholar]
  6. Wu H, Liu B. Nonomuraea thermotolerans sp. nov., a thermotolerant actinomycete isolated from mushroom compost. Int J Syst Evol Microbiol 2016; 66:894–900 [View Article] [PubMed]
    [Google Scholar]
  7. Qin S, Zhao G-Z, Klenk H-P, Li J, Zhu W-Y et al. Nonomuraea antimicrobica sp. nov., an endophytic actinomycete isolated from a leaf of Maytenus austroyunnanensis. Int J Syst Evol Microbiol 2009; 59:2747–2751 [View Article] [PubMed]
    [Google Scholar]
  8. Rachniyom H, Matsumoto A, Indananda C, Duangmal K, Takahashi Y et al. Nonomuraea syzygii sp. nov., an endophytic actinomycete isolated from the roots of a jambolan plum tree (Syzygium cumini L. Skeels). Int J Syst Evol Microbiol 2015; 65:1234–1240 [View Article] [PubMed]
    [Google Scholar]
  9. Zhang Y, Zhao J, Liu C, Shen Y, Jia F et al. Nonomuraea shaanxiensis sp. nov., a novel actinomycete isolated from a soil sample. Antonie van Leeuwenhoek 2014; 105:57–64 [View Article] [PubMed]
    [Google Scholar]
  10. Wang X, Zhao J, Liu C, Wang J, Shen Y et al. Nonomuraea solani sp. nov., an actinomycete isolated from eggplant root (Solanum melongena L.). Int J Syst Evol Microbiol 2013; 63:2418–2423 [View Article] [PubMed]
    [Google Scholar]
  11. Fang B-Z, Hua Z-S, Han M-X, Zhang Z-T, Wang Y-H et al. Nonomuraea cavernae sp. nov., a novel actinobacterium isolated from a karst cave sample. Int J Syst Evol Microbiol 2017; 67:4692–4697 [View Article] [PubMed]
    [Google Scholar]
  12. Peng C, Zhuang X, Wang Z, Gao C, Zhao J et al. Nonomuraea typhae sp. nov., an endophytic actinomycete isolated from the root of cattail pollen (Typha angustifolia L.). Int J Syst Evol Microbiol 2020; 70:3845–3851 [View Article] [PubMed]
    [Google Scholar]
  13. Lipun K, Teo WFA, Suksaard P, Pathom-aree W, Duangmal K. Nonomuraea antri sp. nov., an actinomycete isolated from cave soil in Thailand. Int J Syst Evol Microbiol 2020; 70:5296–5303 [View Article]
    [Google Scholar]
  14. Ay H. Nonomuraea terrae sp. nov., isolated from arid soil. Arch Microbiol 2020; 202:2197–2205 [View Article]
    [Google Scholar]
  15. Atlas RM. Handbook of Microbiological Media, 2nd edn. CRC Press; 2006 pp 364–365
    [Google Scholar]
  16. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966; 16:313–340 [View Article]
    [Google Scholar]
  17. 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]
  18. 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]
  19. Waksman SA. The Actinomycetes. A Summary of Current Knowledge New York: Ronald Press; 1967
    [Google Scholar]
  20. Waksman SA. The Actinomycetes Baltimore: Williams and Wilkins;1961; [View Article]
    [Google Scholar]
  21. Kelly KL, Judd DB. ISCC-NBS color-name charts illustrated with centroid colors. U.S. National Bureau of Standards; 1965
  22. 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]
    [Google Scholar]
  23. 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]
  24. 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]
    [Google Scholar]
  25. Smibert RM, 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]
  26. 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]
  27. 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]
  28. 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]
  29. 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]
  30. Lechevalier MP, Lechevalier HA. Chemical composition as a criterion in the classification of aerobic actinomycetes. Int J Syst Bacteriol 1970; 20:435–443 [View Article]
    [Google Scholar]
  31. 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]
  32. 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]
  33. 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]
  34. 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]
  35. 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]
  36. Monteiro M, Moreira N, Pinto J, Pires-Luís AS, Henrique R et al. GC-MS metabolomics-based approach for the identification of a potential VOC-biomarker panel in the urine of renal cell carcinoma patients. J Cell Mol Med 2017; 21:2092–2105 [View Article] [PubMed]
    [Google Scholar]
  37. 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]
  38. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
    [Google Scholar]
  39. 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]
  40. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
    [Google Scholar]
  41. Kimura M. The Neutral Theory of Molecular Evolution Cambridge University Press; 1983
    [Google Scholar]
  42. 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]
  43. Nikodinovic J, Barrow KD, Chuck JA. High yield preparation of genomic DNA from Streptomyces. Biotechniques 2003; 35:932–934 [View Article] [PubMed]
    [Google Scholar]
  44. Li R, Li Y, Kristiansen K, Wang J. SOAP: short oligonucleotide alignment program. Bioinformatics 2008; 24:713–714 [View Article] [PubMed]
    [Google Scholar]
  45. 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]
  46. 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]
  47. 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]
  48. 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]
  49. 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]
  50. Henrissat B, Claeyssens M, Tomme P, Lemesle L, Mornon JP. Cellulase families revealed by hydrophobic cluster analysis. Gene 1989; 81:83–95 [View Article] [PubMed]
    [Google Scholar]
  51. Zhang H, Yohe T, Huang L, Entwistle S, Wu P et al. dbCAN2: a meta server for automated carbohydrate-active enzyme annotation. Nucleic Acids Res 2018; 46:W95–W101 [View Article] [PubMed]
    [Google Scholar]
  52. Tatusov RL, Galperin MY, Natale DA, Koonin EV et al. The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res 2000; 28:33–36 [View Article] [PubMed]
    [Google Scholar]
  53. Kanehisa M, Goto S, Sato Y, Furumichi M, Tanabe M et al. KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res 2012; 40:D109–14 [View Article] [PubMed]
    [Google Scholar]
  54. Li Z, Song W, Zhao J, Zhuang X, Zhao Y et al. Nonomuraea glycinis sp. nov., a novel actinomycete isolated from the root of black soya bean [Glycine max (L.) Merr]. Int J Syst Evol Microbiol 2017; 67:5026–5031 [View Article] [PubMed]
    [Google Scholar]
  55. Wang S, Liu C, Zhang Y, Zhao J, Zhang X et al. Nonomuraea guangzhouensis sp. nov., and Nonomuraea harbinensis sp. nov., two novel actinomycetes isolated from soil. Antonie van Leeuwenhoek 2014; 105:109–118 [View Article]
    [Google Scholar]
  56. Zhao J, Mu S, Zhao Q, Jiang S, Cao P et al. Nonomuraea rhizosphaerae sp. nov., an actinomycete isolated from the rhizosphere soil of a rubber tree (Hevea brasiliensis Muell. Arg). Antonie van Leeuwenhoek 2018; 111:2009–2016 [View Article] [PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.005411
Loading
/content/journal/ijsem/10.1099/ijsem.0.005411
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited this month 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