1887

Abstract

A Gram-stain-positive, aerobic actinobacterium, designated strain NEAU-24, was isolated from saline-alkali soil collected from Daqing City, Heilongjiang Province, PR China. Strain NEAU-24 was found to produce abundant substrate mycelia but no aerial hyphae. The substrate mycelia formed irregular pseudosporangia consisting of nuciform spores, and the surface of the spores was smooth. 16S rRNA gene sequence analysis showed that strain NEAU-24 clustered with 3-44-a(19), subsp. DSM 44103 and subsp. DSM 43634 within the family and was most closely related to 3-44-a(19) (99.17 %). The strain contained -diaminopimelic acid as the cell-wall diamino acid and MK-9(H) as the menaquinone. The whole cell sugar profile consisted of glucose, galactose, xylose and arabinose. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, an unidentified phospholipid, phosphatidylinositol and an unidentified lipid. The major fatty acids were summarized as C, C, C, iso-C and iso-C. The low digital DNA–DNA hybridization and average nucleotide identity values could differentiate strain NEAU-24 from its related type strains. The phenotypic, genetic and chemotaxonomic data also indicated that strain NEAU-24 occupied a branch separated from those of known genera in the family . In addition, genomic analysis confirmed that strain NEAU-24 had the potential to produce chitinase. Therefore, strain NEAU-24 represents a novel species of a new genus and species in the family , for which the name gen. nov., sp. nov. is proposed. The type strain of is NEAU-24 (=CCTCC AA 2020016=JCM 33973).

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.0.005421
2022-06-09
2024-06-16
Loading full text...

Full text loading...

References

  1. Krasil’nikov NA. Ray fungi and related organisms actinomycetales. Izdatel’stvo Akademii Nauk SSSR 1938
    [Google Scholar]
  2. Goodfellow M, Stanton LJ, Simpson KE, Minnikin DE. Numerical and chemical classification of Actinoplanes and some related actinomycetes. J Gen Microbiol 1990; 136:19–36 [View Article]
    [Google Scholar]
  3. Koch C, Kroppenstedt RM, Rainey FA, Stackebrandt E. 16S ribosomal DNA analysis of the genera Micromonospora, Actinoplanes, Catellatospora, Catenuloplanes, Couchioplanes, Dactylosporangium, and Pilimelia and emendation of the family Micromonosporaceae . Int J Syst Bacteriol 1996; 46:765–768 [View Article] [PubMed]
    [Google Scholar]
  4. Stackebrandt E, Rainey FA, Ward-Rainey NL. Proposal for a new hierarchic classification sNew Hierarchic Classification System, Actinobacteria classis nov. Int J Syst Bacteriol 1997; 47:479–491 [View Article]
    [Google Scholar]
  5. 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]
  6. Ara I, Matsumoto A, Bakir MA, Kudo T, Omura S et al. Pseudosporangium ferrugineum gen. nov., sp. nov., a new member of the family micromonosporaceae. Int J Syst Bacteriol 2008; 58:1644–1652
    [Google Scholar]
  7. Tamura T, Nakagaito Y, Nishii T, Hasegawa T, Stackebrandt E et al. A new genus of the order Actinomycetales, Couchioplanes gen. nov., with descriptions of Couchioplanes caeruleus (Horan and Brodsky 1986) comb. nov. and Couchioplanes caeruleus subsp. azureus subsp. nov. Int J Syst Bacteriol 1994; 44:193–203 [View Article] [PubMed]
    [Google Scholar]
  8. Ara I, Kudo T. Krasilnikovia gen. nov., a new member of the family Micromonosporaceae and description of Krasilnikovia cinnamonea sp. nov. Actinomycetologica 2007; 21:1–10 [View Article]
    [Google Scholar]
  9. Atlas RM. Handbook of microbiological media. Q Rev Biol 2006; 2:364–365
    [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 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]
  12. Waksman SA. The Actinomycetes. A Summary of Current Knowledge Ronald Press; 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 Williams and Wilkins; 1961
    [Google Scholar]
  15. Kelly KL. ISCC-NBS Color-Name Charts Illustrated with Centroid Colors Washington, DC: US National Bureau of Standards; 1964
    [Google Scholar]
  16. 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:E360 [View Article] [PubMed]
    [Google Scholar]
  17. 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]
  18. Smibert RM, Krieg NR. Phenotypic characterization. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. eds 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-N. 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 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]
  21. Singh AK, Chhatpar HS. Purification and characterization of chitinase from Paenibacillus sp. D1. Appl Biochem Biotechnol 2011; 164:77–88 [View Article] [PubMed]
    [Google Scholar]
  22. Staneck JL, Roberts GD. Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol 1974; 28:226–231 [View Article] [PubMed]
    [Google Scholar]
  23. 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]
  24. 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]
  25. Collins MD, Faulkner M, Keddie RM. Menaquinone composition of some sporeforming actinomycetes. Syst Appl Microbiol 1984; 5:20–29 [View Article]
    [Google Scholar]
  26. 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]
  27. 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]
  28. Zhuang X, Peng C, Wang Z, Zhao J, Shen Y et al. Actinomadura physcomitrii sp. nov., a novel actinomycete isolated from moss [Physcomitrium sphaericum (Ludw) Fuernr]. Antonie van Leeuwenhoek 2020; 113:677–685 [View Article]
    [Google Scholar]
  29. 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]
  30. 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]
  31. 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]
  32. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
    [Google Scholar]
  33. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Systematic Zoology 1971; 20:406 [View Article]
    [Google Scholar]
  34. 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]
  35. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
    [Google Scholar]
  36. 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]
  37. Tamura K, Nei M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 1993; 10:512–526 [View Article] [PubMed]
    [Google Scholar]
  38. Mahmoud H, Jose L, Eapen S. Grimontia sedimenti sp. nov., isolated from benthic sediments near coral reefs south of Kuwait. Int J Syst Evol Microbiol 2019; 71: [View Article]
    [Google Scholar]
  39. 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]
  40. 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]
  41. Li R, Li Y, Kristiansen K, Wang J. SOAP: Short Oligonucleotide Alignment Program. Bioinformatics 2008; 24:713–714 [View Article] [PubMed]
    [Google Scholar]
  42. 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]
  43. 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]
  44. 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]
  45. 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]
  46. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009; 106:19126–19131 [View Article] [PubMed]
    [Google Scholar]
  47. 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]
  48. Benini S. Carbohydrate-active enzymes: structure, activity, and reaction products. Int J Mol Sci 2020; 21:E2727 [View Article] [PubMed]
    [Google Scholar]
  49. Oliveira ST, Azevedo MIG, Cunha RMS, Silva CFB, Muniz CR et al. Structural and functional features of a class VI chitinase from cashew (Anacardium occidentale L.) with antifungal properties. Phytochemistry 2020; 180:112527 [View Article] [PubMed]
    [Google Scholar]
  50. Lombard V, Golaconda Ramulu H, Drula E, Coutinho PM, Henrissat B. The carbohydrate-active enzymes database (CAZy) in 2013. Nucleic Acids Res 2014; 42:D490–5 [View Article] [PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.005421
Loading
/content/journal/ijsem/10.1099/ijsem.0.005421
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF
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