1887

Abstract

A Gram-stain-positive, non-motile, creamy-white actinobacterium, which has an elementary branching rod-coccus life cycle was isolated from the rhizosphere soil of rice ( L.) collected from Northeast Agricultural University in Harbin, Heilongjiang province, north-east PR China, and its taxonomic status was examined by using a polyphasic approach. Results from the 16S rRNA gene sequence study showed that the isolate, designated strain NEAU-CX67, belonged to the genus and formed a cluster with DSM 44675, NEAU-ML12 and JCM 11308 (98.3, 98.1 and 97.7% gene sequence similarity, respectively). The major fatty acids were C, 10-methyl C, C ω9 and C ω7. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannoside. The major isoprenoid quinone was MK-8(H). Whole-cell hydrolysates contained -diaminopimelic acid. Arabinose, galactose and ribose were detected as diagnostic sugars from whole-cell hydrolysates. Mycolic acids were detected. The genomic DNA G+C content of strain NEAU-CX67 was 64.6 mol%. Strain NEAU-CX67 exhibited low average nucleotide identity and digital DNA–DNA hybridization values with DSM 44675 (92.1 and 45.4 %) and JCM 11308 (81.9 and 24.4 %). On the basis of results of phylogenetic, genotypic, physiological and chemotaxonomic analysis, strain NEAU-CX67 is considered to represent a novel species of the genus for which the name sp. nov. is proposed. The type strain is NEAU-CX67 (=DSM 107701=CCTCC AB 2018233).

Funding
This study was supported by the:
  • Junwei Zhao , the National Natural Youth Science Foundation of China , (Award 31701858)
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2020-04-28
2020-06-04
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References

  1. Fuhrmann C, Soedarmanto I, Lämmler C. Studies on the rod-coccus life cycle of Rhodococcus equi . Zentralbl Veterinarmed B 1997; 44:287–294 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  2. Zopf W. Über ausscheidung von fettfarbstoffen (Lipochromen) seitens gewisser spaltpilze. Ber Dtsch Bot Ges 1891; 9:22–28
    [Google Scholar]
  3. Tsukamura M. A further numerical taxonomic study of the Rhodochrous group. Jpn J Microbiol 1974; 18:37–44 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  4. Ramaprasad EVV, Mahidhara G, Sasikala C, Ramana CV. Rhodococcus electrodiphilus sp. nov., a marine electro active actinobacterium isolated from coral reef. Int J Syst Evol Microbiol 2018; 68:2644–2649 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  5. Chaudhary DK, Kim J. Rhodococcus olei sp. nov., with the ability to degrade petroleum oil, isolated from oil-contaminated soil. Int J Syst Evol Microbiol 2018; 68:1749–1756 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  6. Guo Q-Q, Ming H, Meng X-L, Duan Y-Y, Gao R et al. Rhodococcus agglutinans sp. nov., an actinobacterium isolated from a soil sample. Antonie van Leeuwenhoek 2015; 107:1271–1280 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  7. Yassin AF. Rhodococcus triatomae sp. nov., isolated from a blood-sucking bug. Int J Syst Evol Microbiol 2005; 55:1575–1579 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  8. Kämpfer P, Dott W, Martin K, Glaeser SP. Rhodococcus defluvii sp. nov., isolated from wastewater of a bioreactor and formal proposal to reclassify [Corynebacterium hoagii] and Rhodococcus equi as Rhodococcus hoagii comb. nov. Int J Syst Evol Microbiol 2014; 64:755–761 [CrossRef]
    [Google Scholar]
  9. Ko KS, Kim Y, Seong CN, Lee SD. Rhodococcus antrifimi sp. nov., isolated from dried bat dung of a cave. Int J Syst Evol Microbiol 2015; 65:4043–4048 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  10. Nguyen TM, Kim J. Rhodococcus pedocola sp. nov. and Rhodococcus humicola sp. nov., two antibiotic-producing actinomycetes isolated from soil. Int J Syst Evol Microbiol 2016; 66:2362–2369 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  11. Atlas RM. Handbook of microbiological media. Q Rev Biol 2006; 2:364–365
    [Google Scholar]
  12. 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 Pt 6:2031–2036 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  13. Lane DJ. 16S/23S rRNA sequencing. In Stackebrandt E, Goodfellow M. (editors) Nucleic Acid Techniques in Bacterial Systematics New York, USA: Wiley; 1991 pp 115–175
    [Google Scholar]
  14. 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 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  15. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  16. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  17. Kluge AG, Farris JS. Quantitative Phyletics and the evolution of anurans. Syst Zool 1969; 18:1–32 [CrossRef]
    [Google Scholar]
  18. 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][PubMed]
    [Google Scholar]
  19. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  20. 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][PubMed]
    [Google Scholar]
  21. Wang L, Zhang L, Zhang X, Zhang S, Yang L et al. Rhodococcus daqingensis sp. nov., isolated from petroleum-contaminated soil. Antonie van Leeuwenhoek 2019; 112:695–702 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  22. 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][PubMed]
    [Google Scholar]
  23. Li R, Li Y, Kristiansen K, Wang J. Soap: short oligonucleotide alignment program. Bioinformatics 2008; 24:713–714 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  24. 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 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  25. Lee I, Chalita M, Ha S-M, Na S-I, Yoon S-H et al. ContEst16S: an algorithm that identifies contaminated prokaryotic genomes using 16S RNA gene sequences. Int J Syst Evol Microbiol 2017; 67:2053–2057 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  26. Chandra R, Tjandrawati M, Joachim W. Biosynthesis of Polyketides in Streptomyces . Microorganisms 2019; 7:124
    [Google Scholar]
  27. Singh HP, Batish DR, Kaur S, Arora K, Kohli RK. alpha-Pinene inhibits growth and induces oxidative stress in roots. Ann Bot 2006; 98:1261–1269 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  28. Guan X, Liu C, Zhao J, Fang B, Zhang Y et al. Streptomyces maoxianensis sp. nov., a novel actinomycete isolated from soil in Maoxian, China. Antonie van Leeuwenhoek 2015; 107:1119–1126 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  29. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966; 16:313–340 [CrossRef]
    [Google Scholar]
  30. Waksman SA. The Actinomycetes A summary of current knowledge, New York: Ronald; 1967
    [Google Scholar]
  31. Jones KL. Fresh isolates of actinomycetes in which the presence of sporogenous aerial mycelia is a fluctuating characteristic. J Bacteriol 1949; 57:141–145 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  32. Waksman SA. The Actinomycetes, Vol. 2, Classification, Identification and Descriptions of Genera and Species Baltimore: Williams and Wilkins; 1961
    [Google Scholar]
  33. Sezonov G, Joseleau-Petit D, D'Ari R. Escherichia coli physiology in Luria-Bertani broth. J Bacteriol 2007; 189:8746–8749 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  34. Kelly KL. Inter-society colour council-national Bureau of standards colour-name charts illustrated with centroid colours published in US; 1964
  35. 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 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  36. 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]
  37. Yokota A, Tamura T, Hasegawa T, Huang LH. Catenuloplanes japonicasjaponicus gen. nov., sp. nov., nom. rev., a new genus of the order Actinomycetales . Int J Syst Bacteriol 1993; 43:805–812 [CrossRef]
    [Google Scholar]
  38. Smibert RM, Krieg NR. Phenotypic characterisation. In Gerhardt P, R. G. E Murray, Wood WA, Krieg NR. (editors) Methods for General and Molecular Bacteriology American Society for Microbiology; 1994 pp 607–654
    [Google Scholar]
  39. 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][PubMed]
    [Google Scholar]
  40. Lechevalier MP, Lechevalier HA. The chemotaxonomy of actinomycetes. In Dietz A, Thayer DW. (editors) Actinomycete Taxonomy Special Publication. Society of Industrial Microbiology 1986 pp 227–291
    [Google Scholar]
  41. 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]
  42. 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]
  43. Wu C, Lu X, Qin M, Wang Y, Ruan J. Analysis of menaquinone compound in microbial cells by HPLC. Microbiology [English translation of Microbiology (Beijing)] 1989; 16:176–178
    [Google Scholar]
  44. Qu Z, Ruan JS, Hong K. Application of high performance liquid chromatography and gas chromatography in the identification of Actinomyces. Biotechnology Bulletin [English translation of Biotechnology Bulletin] 2009; s1:79–82
    [Google Scholar]
  45. 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][PubMed]
    [Google Scholar]
  46. 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][PubMed]
    [Google Scholar]
  47. Zhao JW, Yu B, Han CY, Cao P, ZY Y et al. Microbispora fusca sp. nov., a novel actinomycete isolated from the ear of wheat (Triticum aestivum L.). Int J Syst Evol Microbiol 2019
    [Google Scholar]
  48. Kämpfer P, Dott W, Martin K, Glaeser SP. Rhodococcus defluvii sp. nov., isolated from wastewater of a bioreactor and formal proposal to reclassify [Corynebacterium hoagii] and Rhodococcus equi as Rhodococcus hoagii comb. nov. Int J Syst Evol Microbiol 2014; 64:755–761 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  49. 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 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  50. 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][PubMed]
    [Google Scholar]
  51. 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][PubMed]
    [Google Scholar]
  52. 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]
  53. 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 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  54. 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 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  55. Zhang J, Zhang Y, Xiao C, Liu Z, Goodfellow M. Rhodococcus maanshanensis sp. nov., a novel actinomycete from soil. Int J Syst Evol Microbiol 2002; 52:2121–2126 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  56. Liu H, Zhang Y, Liu C, Fang B, Li C et al. Rhodococcus kronopolitis sp. nov., a novel actinobacterium isolated from a millipede (Kronopolites svenhedind Verhoeff). Antonie van Leeuwenhoek 2014; 106:1207–1214 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  57. Matsuyama H, Yumoto I, Kudo T, Shida O. Rhodococcus tukisamuensis sp. nov., isolated from soil. Int J Syst Evol Microbiol 2003; 53:1333–1337 [CrossRef][PubMed][PubMed]
    [Google Scholar]
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