gen. nov., sp. nov., a member of the family isolated from soil No Access

Abstract

A polyphasic taxonomic study was carried out on an actinobacterial strain (AN110305) isolated from soil sampled in the Republic of Korea. Cells of the strain were Gram-stain-positive, aerobic, non-motile and rod-shaped. Comparative 16S rRNA gene sequence studies showed a clear affiliation of strain AN110305 with , with highest pairwise sequence similarities to DSM 43935 (97.6%), MK27-91F2 (97.0%), NBRC 110610 (96.9%), A-T 1846 (96.8%), YIM 2047X (96.8%), NRRL B-24060 (96.7%) and NRRL B-16115 (96.6%). Cells of strain AN110305 formed pale-yellow colonies on Reasoner's 2A agar. MK-9 (H) (68%) and MK-10 (H) (32%) were the predominant menaquinones. Diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethyl ethanolamine, hydroxy-phosphatidylethanolamine, an unidentified aminolipid and an unidentified aminophospholipid were major polar lipids. Iso-C (24.5%), anteiso-C (19.3%), anteiso-C (15.7%) and iso-C (15.2%) were the major fatty acids and -diaminopimelic acid was the pepdidoglycan. The cell-wall sugars were composed of galactose, glucose, mannose and ribose. The genomic DNA G+C content was 70.7 mol%. Based on genotypic and phenotypic data, strain AN110305 could be distinguished from all genera within the family and represents a novel genus and species named gen. nov., sp nov. The type strain is AN110305 (=KCTC 39307 =DSM 103572).

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2022-02-25
2024-03-28
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References

  1. Embley MT, Smida J, Stackebrandt E. The phylogeny of mycolate-less wall chemotype IV actinomycetes and description of Pseudonocardiaceae fam. nov. Syst Appl Microbiol 1988; 11:44–52 [View Article]
    [Google Scholar]
  2. Stackebrandt E, Rainey FA, Ward-rainey NL. Proposal for a new hierarchic classification system, Actinobacteria classis nov. Int J Syst Bacteriol 1997; 47:479–491 [View Article]
    [Google Scholar]
  3. Zhi X-Y, Li W-J, 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]
  4. Labeda DP, Goodfellow M, Chun J, Zhi X-Y, Li W-J. Reassessment of the systematics of the suborder Pseudonocardineae: transfer of the genera within the family Actinosynnemataceae Labeda and Kroppenstedt 2000 emend. Zhi et al. 2009 into an emended family Pseudonocardiaceae Embley et al. 1989 emend. Zhi et al. 2009. Int J Syst Evol Microbiol 2011; 61:1259–1264 [View Article] [PubMed]
    [Google Scholar]
  5. Parte AC, Sardà Carbasse J, Meier-Kolthoff JP, Reimer LC, Göker M. List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. Int J Syst Evol Microbiol 2020; 70:5607–5612 [View Article] [PubMed]
    [Google Scholar]
  6. Tamura T, Zhiheng L, Yamei Z, Hatano K. Actinoalloteichus cyanogriseus gen. nov., sp. nov. Int J Syst Evol Microbiol 2000; 50:1435–1440 [View Article] [PubMed]
    [Google Scholar]
  7. Yuan L-J, Zhang Y-Q, Yu L-Y, Liu H-Y, Guan Y et al. Alloactinosynnema album gen. nov., sp. nov., a member of the family Actinosynnemataceae isolated from soil. Int J Syst Evol Microbiol 2010; 60:39–43 [View Article] [PubMed]
    [Google Scholar]
  8. Mao J, Wang J, Dai H-Q, Zhang Z-D, Tang Q-Y et al. Yuhushiella deserti gen. nov., sp. nov., a new member of the suborder Pseudonocardineae. Int J Syst Evol Microbiol 2011; 61:621–630 [View Article] [PubMed]
    [Google Scholar]
  9. Moshtaghi Nikou M, Ramezani M, Harirchi S, Makzoom S, Amoozegar MA et al. Salinifilum gen. nov., with description of Salinifilum proteinilyticum sp. nov., an extremely halophilic actinomycete isolated from Meighan wetland, Iran, and reclassification of Saccharopolyspora aidingensis as Salinifilum aidingensis comb. nov. and Saccharopolyspora ghardaiensis as Salinifilum ghardaiensis comb. nov. Int J Syst Evol Microbiol 2017; 67:4221–4227 [View Article] [PubMed]
    [Google Scholar]
  10. Xia ZF, Guan TW, Ruan JS, Huang Y, Zhang LL. Longimycelium tulufanense gen. nov., sp. nov., a filamentous actinomycete of the family Pseudonocardiaceae. Int J Syst Evol Microbiol 2013; 63:2813–2818 [View Article] [PubMed]
    [Google Scholar]
  11. Lai H, Jiang Y, Chen X, Li Q, Jiang C et al. Haloactinomyces albus gen. nov., sp. nov., isolated from the Dead Sea. Int J Syst Evol Microbiol 2017; 67:1163–1168 [View Article] [PubMed]
    [Google Scholar]
  12. Kaewkla O, Franco CMM. Pseudonocardia adelaidensis sp. nov., an endophytic actinobacterium isolated from the surface-sterilized stem of a grey box tree (Eucalyptus microcarpa. Int J Syst Evol Microbiol 2010; 60:2818–2822 [View Article] [PubMed]
    [Google Scholar]
  13. Chu X, Liu B-B, Gao R, Zhang Z-Y, Duan Y-Q et al. Umezawaea endophytica sp. nov., isolated from tobacco root samples. Antonie Van Leeuwenhoek 2015; 108:667–672 [View Article] [PubMed]
    [Google Scholar]
  14. Liu J-M, Habden X, Guo L, Tuo L, Jiang Z-K et al. Prauserella endophytica sp. nov., an endophytic actinobacterium isolated from Tamarix taklamakanensis. Antonie van Leeuwenhoek 2015; 107:1401–1409 [View Article] [PubMed]
    [Google Scholar]
  15. Zhang C-F, Ai M-J, Wang J-X, Liu S-W, Zhao L-L et al. Herbihabitans rhizosphaerae gen. nov., sp. nov., a member of the family Pseudonocardiaceae isolated from rhizosphere soil of the herb Limonium sinense (Girard). Int J Syst Evol Microbiol 2016; 66:4156–4161 [View Article] [PubMed]
    [Google Scholar]
  16. Snipes CE, Duebelbeis DO, Olson M, Hahn DR, Dent WH 3rd et al. The ansacarbamitocins: polar ansamitocin derivatives. J Nat Prod 2007; 70:1578–1581 [View Article] [PubMed]
    [Google Scholar]
  17. Tamura T, Ishida Y, Otoguro M, Hatano K, Suzuki K. Classification of “Streptomyces tenebrarius” Higgins and Kastner as Streptoalloteichus tenebrarius nom. rev., comb. nov., and emended description of the genus Streptoalloteichus. Int J Syst Evol Microbiol 2008; 58:688–691 [View Article] [PubMed]
    [Google Scholar]
  18. Tang B, Zhao W, Zheng H, Zhuo Y, Zhang L et al. Complete genome sequence of Amycolatopsis mediterranei S699 based on de novo assembly via a combinatorial sequencing strategy. J Bacteriol 2012; 194:5699–5700 [View Article] [PubMed]
    [Google Scholar]
  19. Butbunchu N, Pathom-Aree W. Actinobacteria as promising candidate for polylactic acid type bioplastic degradation. Front Microbiol 2019; 10:2834 [View Article] [PubMed]
    [Google Scholar]
  20. Vértesy L, Barbone FP, Cashmen E, Decker H, Ehrlich K et al. Pluraflavins, potent antitumor antibiotics from Saccharothrix sp. DSM 12931. J Antibiot 2001; 54:718–729
    [Google Scholar]
  21. Labeda DP, Kroppenstedt RM. Goodfellowia gen. nov., a new genus of the Pseudonocardineae related to Actinoalloteichus, containing Goodfellowia coeruleoviolacea gen. nov., comb. nov. Int J Syst Evol Microbiol 2006; 56:1203–1207 [View Article] [PubMed]
    [Google Scholar]
  22. Labeda DP, Kroppenstedt RM, Euzéby JP, Tindall BJ. Proposal of Goodfellowiella gen. nov. to replace the illegitimate genus name Goodfellowia Labeda and Kroppenstedt 2006. Int J Syst Evol Microbiol 2008; 58:1047–1048 [View Article] [PubMed]
    [Google Scholar]
  23. Gregersen T. Rapid method for distinction of Gram-negative from Gram-positive bacteria. European J Appl Microbiol Biotechnol 1978; 5:123–127 [View Article]
    [Google Scholar]
  24. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966; 16:313–340 [View Article]
    [Google Scholar]
  25. Kovacs N. Identification of Pseudomonas pyocyanea by the oxidase reaction. Nature 1956; 178:703 [View Article] [PubMed]
    [Google Scholar]
  26. Williams ST, Goodfellow M, Alderson G. Genus Streptomyces Waksman and Henrici 1943, 339AL. In Williams ST, Sharpe ME, Holt JG. eds Manual of Systematic Bacteriology vol. 4 Williams & Wilkins, Baltimore: 1989 pp 2452
    [Google Scholar]
  27. 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]
  28. Tindall BJ. A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Applied Microbiol 1990; 13:128–130 [View Article]
    [Google Scholar]
  29. Hasegawa T, Takizawa M, Tanida S. A rapid analysis for chemical grouping of aerobic actinomycetes. J Gen Appl Microbiol 1983; 29:319–322 [View Article]
    [Google Scholar]
  30. Komagata K, Suzuki KI. Lipid and cell wall analysis in bacterial systematics. Methods Microbiol 1987; 19:161–207
    [Google Scholar]
  31. Lane DJ. 16S/23S rRNA sequencing. In Stackebrandt E, Goodfellow M. eds Nucleic Acid Techniques in Bacterial Systematics New York: John Wiley & Sons; p 1991
    [Google Scholar]
  32. Anzai Y, Kim H, Park JY, Wakabayashi H, Oyaizu H. Phylogenetic affiliation of the pseudomonads based on 16S rRNA sequence. Int J Syst Evol Microbiol 2000; 50 Pt 4:1563–1589 [View Article] [PubMed]
    [Google Scholar]
  33. 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]
  34. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997; 25:4876–4882 [View Article] [PubMed]
    [Google Scholar]
  35. Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser 1999; 4:95–98
    [Google Scholar]
  36. 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]
  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. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Systematic Biology 1971; 20:406–416 20-4-406 [View Article]
    [Google Scholar]
  40. Felsenstein J. Phylogenies and the comparative method. American Naturalist 1985; 125:1–15 [View Article]
    [Google Scholar]
  41. 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]
  42. Qi J, Wang B, Hao BI. Whole proteome prokaryote phylogeny without sequence alignment: a K-string composition approach. J Mol Evol 2004; 58:1–11 [View Article] [PubMed]
    [Google Scholar]
  43. Zuo G. CVTree: A parallel alignment-free phylogeny and taxonomy tool based on composition vectors of genomes. Genomics Proteomics Bioinformatics 2021; 10:S1672–S0229 [PubMed]
    [Google Scholar]
  44. Wattam AR, Davis JJ, Assaf R, Boisvert S, Brettin T et al. Improvements to PATRIC, the all-bacterial bioinformatics database and analysis resource center. Nucleic Acids Res 2017; 45:D535–D542 [View Article]
    [Google Scholar]
  45. Lee I, Ouk Kim Y, Park S-C, Chun J. OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2016; 66:1100–1103 [View Article] [PubMed]
    [Google Scholar]
  46. Blin K, Shaw S, Steinke K, Villebro R, Ziemert N et al. AntiSMASH 5.0: updates to the secondary metabolite genome mining pipeline. Nucleic Acids Res 2019; 47:W81–W87 [View Article]
    [Google Scholar]
  47. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007; 57:81–91 [View Article] [PubMed]
    [Google Scholar]
  48. 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]
  49. Kim M, Oh H-S, Park S-C, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014; 64:346–351 [View Article] [PubMed]
    [Google Scholar]
  50. Luo C, Rodriguez-R LM, Konstantinidis KT. MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences. Nucleic acids Res 2014; 42:e73 [PubMed]
    [Google Scholar]
  51. Konstantinidis KT, Rosselló-Móra R, Amann R. Uncultivated microbes in need of their own taxonomy. ISME J 2017; 11:2399–2406 [View Article] [PubMed]
    [Google Scholar]
  52. Nicholson AC, Gulvik CA, Whitney AM, Humrighouse BW, Bell ME et al. Division of the genus Chryseobacterium: Observation of discontinuities in amino acid identity values, a possible consequence of major extinction events, guides transfer of nine species to the genus Epilithonimonas, eleven species to the genus Kaistella, and three species to the genus Halpernia gen. nov., with description of Kaistella daneshvariae sp. nov. and Epilithonimonas vandammei sp. nov. derived from clinical specimens. Int J Syst Evol Microbiol 2020; 70:4432–4450 [View Article] [PubMed]
    [Google Scholar]
  53. Labeda DP, Kroppenstedt RM. Proposal of Umezawaea gen. nov., a new genus of the Actinosynnemataceae related to Saccharothrix, and transfer of Saccharothrix tangerinus Kinoshita et al. 2000 as Umezawaea tangerina gen. nov., comb. nov. Int J Syst Evol Microbiol 2007; 57:2758–2761 [View Article] [PubMed]
    [Google Scholar]
  54. Chu X, Liu B-B, Gao R, Zhang Z-Y, Duan Y-Q et al. Umezawaea endophytica sp. nov., isolated from tobacco root samples. Antonie van Leeuwenhoek 2015; 108:667–672 [View Article] [PubMed]
    [Google Scholar]
  55. Ningsih F, Yokota A, Sakai Y, Nanatani K, Yabe S et al. Gandjariella thermophila gen. nov., sp. nov., a new member of the family Pseudonocardiaceae, isolated from forest soil in a geothermal area. Int J Syst Evol Microbiol 2019; 69:3080–3086 [View Article]
    [Google Scholar]
  56. Chanama M, Thongkrachang N, Suriyachadkun C, Chanama S. Kutzneria chonburiensis sp. nov., isolated from soil. Int J Syst Evol Microbiol 2015; 65:4169–4174 [View Article] [PubMed]
    [Google Scholar]
  57. Stackebrandt E, Kroppenstedt RM, Kemmerling C, Gürtler H. Transfer of Streptosporangium viridogriseum (Okuda et al. 1966), Streptosporangium viridogriseum subsp. kofuense (Nonomura and Ohara 1969), and Streptosporangium albidum (Furumai et al. 1968) to Kutzneria gen. nov. as Kutzneria viridogrisea comb. nov., Kutzneria kofuensis comb. nov., and Kutzneria albida comb. nov., respectively, and emendation of the genus Streptosporangium. Int J Syst Evol Microbiol 1994; 44:265
    [Google Scholar]
  58. Suriyachadkun C, Ngaemthao W, Chunhametha S, Tamura T, Sanglier JJ. Kutzneria buriramensis sp. nov., isolated from soil, and emended description of the genus Kutzneria. Int J Syst Evol Microbiol 2013; 63:47–52 10.1099/ijs.0.036533-0
    [Google Scholar]
  59. Labeda DP, Kroppenstedt RM. Phylogenetic analysis of Saccharothrix and related taxa: proposal for Actinosynnemataceae fam. nov. Int J Syst Evol Microbiol 2000; 50:331–336 [View Article] [PubMed]
    [Google Scholar]
  60. Li Y-Q, Liu L, Cheng C, Shi X-H, Lu C-Y et al. Saccharothrix lopnurensis sp. nov., a filamentous actinomycete isolated from sediment of Lop Nur. Antonie van Leeuwenhoek 2015; 108:975–981 [View Article] [PubMed]
    [Google Scholar]
  61. Bouznada K, Bouras N, Mokrane S, Chaabane Chaouch F, Zitouni A et al. Saccharothrix isguenensis sp. nov., an actinobacterium isolated from desert soil. Int J Syst Evol Microbiol 2016; 66:4785–4790 [View Article] [PubMed]
    [Google Scholar]
  62. Bouznada K, Bouras N, Mokrane S, Chaabane Chaouch F, Zitouni A et al. Saccharothrix ghardaiensis sp. nov., an actinobacterium isolated from Saharan soil. Antonie van Leeuwenhoek 2017; 110:399–405 [View Article] [PubMed]
    [Google Scholar]
  63. Ibeyaima A, Singh AK, Lal R, Gupta S, Goodfellow M et al. Saccharothrix tharensis sp. nov., an actinobacterium isolated from the Thar Desert, India. Antonie van Leeuwenhoek 2018; 111:2141–2147 [View Article] [PubMed]
    [Google Scholar]
  64. Liu J, Sun Y, Liu J, Wu Y, Cao C et al. Saccharothrix deserti sp. nov., an actinomycete isolated from desert soil. Int J Syst Evol Microbiol 2020; 70:1882–1887 [View Article] [PubMed]
    [Google Scholar]
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