1887

Abstract

A novel actinobacterium, designated strain NEAU-THZ27, was isolated from soil collected from the Cornel peak in Jiaozuo, Henan Province, PR China and characterized using a polyphasic approach. Morphological and chemotaxonomic characteristics of the strain coincided with those of members of the genus. The results of 16S rRNA gene sequence analysis showed that strain NEAU-THZ27 belongs to the genus and was most closely related to YPL1 (98.96 %), Q41 (98.89 %), HKI 0478 (98.86%) and S1.4 (98.85 %), similarities to other type strains of species of the genus were found to be less than 98.7 %. Phylogenetic analyses using the 16S rRNA gene sequence and multilocus sequence analysis using the concatenated gene sequences of the , , , and genes all showed that the strain formed a separate branch in the genus . The cell wall contained -diaminopimelic acid as the major diamino acid and the whole-cell hydrolysates were ribose and glucose. The major polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol and phosphatidylinositol. The predominant menaquinone was MK-9(H). Major fatty acids were iso-C, iso-C and anteiso-C, these chemotaxonomic data supported the affiliation of strain NEAU-THZ27 to the genus . The DNA G+C content was 68.0 mol%. Furthermore, the strain could be clearly distinguished by concatenated gene genetic distances, the combination of DNA–DNA hybridization results and some phenotypic characteristics. Therefore, it is proposed that strain NEAU-THZ27 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is NEAU-THZ27 (=CGMCC 4.7504=DSM 105535).

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2019-11-01
2019-12-12
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References

  1. Park YH, Yoon JH, Shin YK, Suzuki K, Kudo T et al. Classification of 'Nocardioides fulvus' IFO 14399 and Nocardioides sp. ATCC 39419 in Kribbella gen. nov., as Kribbella flavida sp. nov. and Kribbella sandramycini sp. nov. Int J Syst Bacteriol 1999;49:743–752 [CrossRef][PubMed]
    [Google Scholar]
  2. Sohn K, Hong SG, Bae KS, Chun J. Transfer of Hongia koreensis Lee et al. 2000 to the genus Kribbella Park et al. 1999 as Kribbella koreensis comb. nov. Int J Syst Evol Microbiol 2003;53:1005–1007 [CrossRef][PubMed]
    [Google Scholar]
  3. Everest GJ, Curtis SM, de Leo F, Urzì C, Meyers PR. Kribbella albertanoniae sp. nov., isolated from a Roman catacomb, and emended description of the genus Kribbella. Int J Syst Evol Microbiol 2013;63:3591–3596 [CrossRef][PubMed]
    [Google Scholar]
  4. Nouioui I, Carro L, García-López M, Meier-Kolthoff JP, Woyke T et al. Genome-based taxonomic classification of the phylum Actinobacteria. Front Microbiol 2018;9: [CrossRef][PubMed]
    [Google Scholar]
  5. Ozdemir-Kocak F, Saygin H, Saricaoglu S, Cetin D, Guven K et al. Kribbella soli sp. nov., isolated from soil. Antonie Van Leeuwenhoek 2017;110:641–649 [CrossRef][PubMed]
    [Google Scholar]
  6. Ozdemir-Kocak F, Isik K, Saricaoglu S, Saygin H, Inan-Bektas K et al. Kribbella sindirgiensis sp. nov. isolated from soil. Arch Microbiol 2017;199:1399–1407 [CrossRef][PubMed]
    [Google Scholar]
  7. Sun JQ, Xu L, Guo Y, Li WL, Shao ZQ et al. Kribbella deserti sp. nov., isolated from rhizosphere soil of Ammopiptanthus mongolicus. Int J Syst Evol Microbiol 2017;67:692–696 [CrossRef][PubMed]
    [Google Scholar]
  8. Song W, Duan L, Zhao J, Jiang S, Guo X et al. Kribbella monticola sp. nov., a novel actinomycete isolated from soil. Int J Syst Evol Microbiol 2018;68:3441–3446 [CrossRef][PubMed]
    [Google Scholar]
  9. Saygin H, Ay H, Guven K, Sahin N. Kribbella turkmenica sp. nov., isolated from the Karakum Desert. Int J Syst Evol Microbiol 2019; [CrossRef][PubMed]
    [Google Scholar]
  10. Atlas RM. Handbook of microbiological media. Quarterly Review of Biology 2006;2:364–365
    [Google Scholar]
  11. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966;16:313–340 [CrossRef]
    [Google Scholar]
  12. 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 [CrossRef][PubMed]
    [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[PubMed]
    [Google Scholar]
  14. Waksman SA. The Actinomycetes. A Summary of Current Knowledge New York: Ronald; 1967
    [Google Scholar]
  15. Waksman SA. The Actinomycetes, Vol. 2, Classification, Identification and Descriptions of Genera and Species Baltimore: Williams and Wilkins; 1961
    [Google Scholar]
  16. Kelly KL. Inter-society color council-national bureau of standards color-name charts illustrated with centroid colors published in US. 1964
  17. 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 [CrossRef][PubMed]
    [Google Scholar]
  18. Fu Y, Yan R, Liu D, Jiang S, Cui L et al. Trinickia diaoshuihuensis sp. nov., a plant growth promoting bacterium isolated from soil. Int J Syst Evol Microbiol 2019;69:291–296 [CrossRef][PubMed]
    [Google Scholar]
  19. Smibert RM, Krieg NR. Phenotypic characterization. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) Methods for General and Molecular Bacteriology American Society for Microbiology Washington, DC; 1994; pp.607–654
    [Google Scholar]
  20. Gordon RE, Barnett DA, Handerhan JE, Pang CH-N. Nocardia coeliaca, Nocardia autotrophica, and the Nocardin Strain. Int J Syst Bacteriol 1974;24:54–63 [CrossRef]
    [Google Scholar]
  21. 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 [CrossRef]
    [Google Scholar]
  22. 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 [CrossRef][PubMed]
    [Google Scholar]
  23. Lechevalier MP, Lechevalier HA. The chemotaxonomy of actinomycetes. In Dietz A, Thayer DW. (editors) Actinomycete Taxonomy (Special Publication)vol. 6 Arlington: Society of Industrial Microbiology; 1980; pp.227–291
    [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 [CrossRef]
    [Google Scholar]
  25. Collins MD. Isoprenoid quinone analyses in bacterial classification and identification. In Goodfellow M, Minnikin DE. (editors) Chemical Methods in Bacterial Systematics London: Academic Press; 1985; pp.267–284
    [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 [CrossRef][PubMed]
    [Google Scholar]
  28. 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 [CrossRef][PubMed]
    [Google Scholar]
  29. 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 [CrossRef][PubMed]
    [Google Scholar]
  30. 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 [CrossRef][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 [CrossRef][PubMed]
    [Google Scholar]
  32. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981;17:368–376 [CrossRef][PubMed]
    [Google Scholar]
  33. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016;33:1870–1874 [CrossRef][PubMed]
    [Google Scholar]
  34. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985;39:783–791 [CrossRef][PubMed]
    [Google Scholar]
  35. 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 [CrossRef][PubMed]
    [Google Scholar]
  36. 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 [CrossRef][PubMed]
    [Google Scholar]
  37. de Ley J, Cattoir H, Reynaerts A. The quantitative measurement of DNA hybridization from renaturation rates. Eur J Biochem 1970;12:133–142 [CrossRef][PubMed]
    [Google Scholar]
  38. Huss VA, Festl H, Schleifer KH. Studies on the spectrophotometric determination of DNA hybridization from renaturation rates. Syst Appl Microbiol 1983;4:184–192 [CrossRef][PubMed]
    [Google Scholar]
  39. Thomas EA, Alvarez CE, Sutcliffe JG. Evolutionarily distinct classes of S27 ribosomal proteins with differential mRNA expression in rat hypothalamus. J Neurochem 2000;74:2259–2267 [CrossRef][PubMed]
    [Google Scholar]
  40. Curtis SM, Norton I, Everest GJ, Meyers PR. Kribbella podocarpi sp. nov., isolated from the leaves of a yellowwood tree (Podocarpus latifolius). Antonie Van Leeuwenhoek 2018;111:875–882 [CrossRef][PubMed]
    [Google Scholar]
  41. Curtis SM, Meyers PR. Multilocus sequence analysis of the actinobacterial genus Kribbella. Syst Appl Microbiol 2012;35:441–446 [CrossRef][PubMed]
    [Google Scholar]
  42. 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]
  43. 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 [CrossRef][PubMed]
    [Google Scholar]
  44. Li R, Li Y, Kristiansen K, Wang J. SOAP: short oligonucleotide alignment program. Bioinformatics 2008;24:713–714 [CrossRef][PubMed]
    [Google Scholar]
  45. Kirby BM, Le Roes M, Meyers PR. Kribbella karoonensis sp. nov. and Kribbella swartbergensis sp. nov., isolated from soil from the Western Cape, South Africa. Int J Syst Evol Microbiol 2006;56:1097–1101 [CrossRef][PubMed]
    [Google Scholar]
  46. Carlsohn MR, Groth I, Spröer C, Schütze B, Saluz HP et al. Kribbella aluminosa sp. nov., isolated from a medieval alum slate mine. Int J Syst Evol Microbiol 2007;57:1943–1947 [CrossRef][PubMed]
    [Google Scholar]
  47. Everest GJ, Meyers PR. Kribbella hippodromi sp. nov., isolated from soil from a racecourse in South Africa. Int J Syst Evol Microbiol 2008;58:443–446 [CrossRef][PubMed]
    [Google Scholar]
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