1887

Abstract

A novel ligninase-producing actinomycete, designated strain NEAU-G4, was isolated from a soil sample and subjected to a polyphasic taxonomic study to establish its status. According to 16S rRNA gene sequence comparisons, the isolate was identified as a member of the genus , with the highest sequence similarity to DSM 44496 (99.2 %). The whole-cell sugars contained galactose and arabinose. The amino acid of the cell wall was determined to be -diaminopimelic acid. The major fatty acids (>10 %) were C, C 9, C and C 7. The predominant menaquinone was identified as MK-8(H, ω-cycl). The major polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol. Strain NEAU-G4 had a draft genome size of 6 405 167 bp, annotated with 5815 protein-coding genes. The DNA G+C content was 67.6 mol%. Phylogenetic analysis using the 16S rRNA gene and whole-genome sequences showed that strain NEAU-G4 formed a stable phyletic line with DSM 44496. The digital DNA–DNA hybridization and average nucleotide identity values between them were 63.7 % (60.8–66.5 %) and 95.5 %, respectively. Moreover, genomic analysis indicated that strain NEAU-G4 had the potential to degrade lignin and produce bioactive compounds. On the basis of genotypic analysis, physiological data, as well as phenotypic and chemotaxonomic characterizations, it is concluded that the organism be classified as representing a novel species of the genus , for which the name sp. nov. is proposed. The type strain is NEAU-G4 (=CCTCC AA 2020038=DSM 111936).

Funding
This study was supported by the:
  • “Academic Backbone” Project of Northeast Agricultural University (Award 19XG18)
    • Principle Award Recipient: JiaSong
  • National Natural Science Foundation of China (Award 31972291)
    • Principle Award Recipient: XiangjingWang
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005416
2022-06-10
2022-07-06
Loading full text...

Full text loading...

References

  1. Trevisan V. I Generi E Le Specie Delle Bacteriaceae Milan: Zanaboni & Gabuzzi; 1889
    [Google Scholar]
  2. Goodfellow M, Jones AL et al. Order V. Corynebacteriales ord. nov. In Goodfellow M, Kämpfer P, Busse HJ. eds Bergey’s Manual of Systematic Bacteriology, 2nd edn. New York: Springer; 2012 pp 235–243
    [Google Scholar]
  3. Goodfellow M, Lechevalier MP. Genus Nocardia Trevisan 1889, 9 AL. In Williams ST, ME S, Holt JG. eds Bergey’s Manual of Systematic Bacteriology vol 4 Baltimore: Williams & Wilkins; 1989 pp 2348–2361
    [Google Scholar]
  4. Isik K, Chun J, Hah YC, Goodfellow M. Nocardia salmonicida nom. rev., a fish pathogen. Int J Syst Bacteriol 1999; 49:833–837 [View Article] [PubMed]
    [Google Scholar]
  5. Kageyama A, Yazawa K, Mukai A, Kohara T, Nishimura K et al. Nocardia araoensis sp. nov. and Nocardia pneumoniae sp. nov., isolated from patients in Japan. Int J Syst Evol Microbiol 2004; 54:2025–2029 [View Article] [PubMed]
    [Google Scholar]
  6. Kaewkla O, Franco CMM. Nocardia callitridis sp. nov., an endophytic actinobacterium isolated from a surface-sterilized root of an Australian native pine tree. Int J Syst Evol Microbiol 2010; 60:1532–1536 [View Article] [PubMed]
    [Google Scholar]
  7. 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]
  8. Camas M, Veyisoglu A, Sahin N. Nocardia sungurluensis sp. nov., isolated from soil. Int J Syst Evol Microbiol 2014; 64:1629–1634 [View Article] [PubMed]
    [Google Scholar]
  9. Thawai C, Rungjindamai N, Klanbut K, Tanasupawat S. Nocardia xestospongiae sp. nov., isolated from a marine sponge in the Andaman Sea. Int J Syst Evol Microbiol 2017; 67:1451–1456 [View Article] [PubMed]
    [Google Scholar]
  10. Goodfellow M, Maldonado LA. Genus I. Nocardia Trevisan 1889AL. In Goodfellow M, Kämpfer P, Busse HJ, Trujillo ME, Suzuki KI. eds Bergey’s Manual of Systematic Bacteriology, 2nd edn. vol 5 New York: Springer; 2012 pp 376–419
    [Google Scholar]
  11. Andlar M, Rezić T, Marđetko N, Kracher D, Ludwig R et al. Lignocellulose degradation: An overview of fungi and fungal enzymes involved in lignocellulose degradation. Eng Life Sci 2018; 18:768–778 [View Article] [PubMed]
    [Google Scholar]
  12. Hayakawa M, Tamura T, Nonomura H. Selective isolation of Actinoplanes and Dactylosporangium from soil by using γ-collidine as the chemoattractant. J Ferment Bioeng 1991; 72:426–432 [View Article]
    [Google Scholar]
  13. Liu C, Zhuang X, Yu Z, Wang Z, Wang Y et al. Community structures and antifungal activity of root-associated endophytic actinobacteria of healthy and diseased soybean. Microorganisms 2019; 7:243 [View Article] [PubMed]
    [Google Scholar]
  14. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966; 16:313–340 [View Article]
    [Google Scholar]
  15. 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]
  16. Waksman SA. The Actinomycetes Baltimore: Williams and Wilkins; 1961
    [Google Scholar]
  17. 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]
  18. Waksman SA. The Actinomycetes. A Summary of Current Knowledge New York: Ronald Press; 1967
    [Google Scholar]
  19. Kelly KL. Inter-society Colour Council-national Bureau of Standards Colour-name Charts Illustrated with Centroid Colours Washington, DC: US Government Printing Office; 1964
    [Google Scholar]
  20. 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]
  21. 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]
  22. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966; 16:313–340 [View Article]
    [Google Scholar]
  23. Athalye M, Goodfellow M, Lacey J, White RP. Numerical classification of Actinomadura and Nocardiopsis. Int J Syst Bacteriol 1985; 35:86–98 [View Article]
    [Google Scholar]
  24. Nie GX, Ming H, Li S, Zhou EM, Cheng J et al. Amycolatopsis dongchuanensis sp. nov., a novel actinobacterium isolated from dry-hot valley in Tunnan, south-west China. Int J Syst Evol Microbiol 2012; 62:2650–2656 [View Article]
    [Google Scholar]
  25. 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]
  26. Williams ST, Goodfellow M, Alderson G. Genus Streptomyces Waksman and Henrici 1943, 339AL. In Williams ST, Sharpe ME, Holt JG. eds Bergey’s Manual of Systematic Bacteriology vol 4 Baltimore: Williams and Willkins; 1989 pp 2453–2492
    [Google Scholar]
  27. Goldschmidt MC, Fung DY, Grant R, White J, Brown T. New aniline blue dye medium for rapid identification and isolation of Candida albicans. J Clin Microbiol 1991; 29:1095–1099 [View Article] [PubMed]
    [Google Scholar]
  28. 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]
  29. Lechevalier MP, Lechevalier HA. The chemotaxonomy of actinomycetes. In Dietz A, Thayer DW. eds Actinomycete Taxonomy Special Publication vol 6 Arlington: Society of Industrial Microbiology; 1980 pp 227–291
    [Google Scholar]
  30. 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]
  31. Collins MD. Isoprenoid quinone analyses in bacterial classification and identification. In Goodfellow M, Minnikin DE. eds Chemical Methods in Bacterial Systematics London: Academic Press; 1985 pp 267–284
    [Google Scholar]
  32. 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]
  33. Song J, Qiu S, Zhao J, Han C, Wang Y et al. Pseudonocardia tritici sp. nov., a novel actinomycete isolated from rhizosphere soil of wheat (Triticum aestivum L.). Antonie van Leeuwenhoek 2019; 112:765–773 [View Article] [PubMed]
    [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. 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]
  37. Yoon SH, Ha SM, 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]
  38. 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]
  39. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
    [Google Scholar]
  40. 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]
  41. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
    [Google Scholar]
  42. Nikodinovic J, Barrow KD, Chuck JA. High yield preparation of genomic DNA from Streptomyces. Biotechniques 2003; 35:932–934 [View Article] [PubMed]
    [Google Scholar]
  43. Li R, Li Y, Kristiansen K, Wang J. SOAP: short oligonucleotide alignment program. Bioinformatics 2008; 24:713–714 [View Article] [PubMed]
    [Google Scholar]
  44. 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]
  45. 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]
  46. Medema MH, Blin K, Cimermancic P, de Jager V, Zakrzewski P et al. antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences. Nucleic Acids Res 2011; 39:W339–46 [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. 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
    [Google Scholar]
  49. Levasseur A, Drula E, Lombard V, Coutinho PM, Henrissat B. Expansion of the enzymatic repertoire of the CAZy database to integrate auxiliary redox enzymes. Biotechnol Biofuels 2013; 6:41 [View Article] [PubMed]
    [Google Scholar]
  50. Blánquez A, Ball AS, González-Pérez JA, Jiménez-Morillo NT, González-Vila F et al. Laccase SilA from Streptomyces ipomoeae CECT 3341, a key enzyme for the degradation of lignin from agricultural residues?. PLoS One 2017; 12:e0187649 [View Article] [PubMed]
    [Google Scholar]
  51. 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.0.005416
Loading
/content/journal/ijsem/10.1099/ijsem.0.005416
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