1887

Abstract

A novel actinobacterial strain, designated NCCP-696, was isolated from the Thal desert in Punjab, Pakistan, and characterized by using a polyphasic taxonomy approach. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain NCCP-696 belongs to the genus Nocardioides and showed the highest level of sequence similarity with respect to Nocardioides panacisoli Gsoil 346 (98.2 %) and less than 96.4 % to the strains of other species of the genus Nocardioides . Cells of strain NCCP-696 were Gram-positive, aerobic, non-motile rods and formed cream-coloured colonies. The strain was positive for oxidase and catalase. Growth occurred at 20–42 °C (optimum 30–37 °C) at pH 5.5–9.0 (optimum pH 7.0) and with 0–4 % NaCl (optimum 0–2 %, w/v). Strain NCCP-696 contained Iso-C16 : 0, C18 : 1ω9c, C17 : 1ω8c and C17 : 0 as the predominant fatty acids and was found to have LL-2,6-diaminopimelic acid in the cell-wall peptidoglycan. The polar lipid profile consisted of phosphatidylinositol, phosphatidylglycerol and one unknown phospholipid. The major menaquinone was MK-8(H4) (98.7 %) while a minor amount (1.3 %) of MK-9(H2) was also detected. The DNA G+C content of the genomic DNA was 71.6 mol%. The DNA–DNA hybridization value of the isolate against the closely related type strain Nocardioides panacisoli Gsoil 346 was 56.3±1.4. On the basis of the phylogenetic inference, chemotaxonomic characteristics and phenotypic data, strain NCCP-696 should be classified as a novel species, for which the name Nocardioides thalensis sp. nov. is proposed. The type strain is NCCP-696 (=DSM 103833=CCTCC AB 2016296).

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2017-08-30
2019-09-21
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References

  1. Prauser H. Nocardioides, a new genus of the order Actinomycetales. Int J Syst Bacteriol 1976;26:58–65 [CrossRef]
    [Google Scholar]
  2. Evtushenko LI, Krausova VI, Yoon JH.Nocardioides. In Bergey’s Manual of Systematics of Archaea and Bacteria New York: Wiley; 2015
    [Google Scholar]
  3. Ahn JH, Lim JM, Kim SJ, Song J, Kwon SW et al. Nocardioides paucivorans sp. nov. isolated from soil. J Microbiol 2014;52:990–994 [CrossRef][PubMed]
    [Google Scholar]
  4. Kim HM, Choi DH, Hwang CY, Cho BC. Nocardioides salarius sp. nov., isolated from seawater enriched with zooplankton. Int J Syst Evol Microbiol 2008;58:2056–2064 [CrossRef][PubMed]
    [Google Scholar]
  5. Wang L, Li J, Zhang G. Nocardioides rotundus sp. nov., isolated from deep seawater. Int J Syst Evol Microbiol 2016;66:1932–1936 [CrossRef][PubMed]
    [Google Scholar]
  6. Lee SD, Lee DW. Nocardioides rubroscoriae sp. nov., isolated from volcanic ash. Antonie van Leeuwenhoek 2014;105:1017–1023 [CrossRef][PubMed]
    [Google Scholar]
  7. Lin SY, Wen CZ, Hameed A, Liu YC, Hsu YH et al. Nocardioides echinoideorum sp. nov., isolated from sea urchins (Tripneustes gratilla). Int J Syst Evol Microbiol 2015;65:1953–1958 [CrossRef][PubMed]
    [Google Scholar]
  8. Tuo L, Dong YP, Habden X, Liu JM, Guo L et al. Nocardioides deserti sp. nov., an actinobacterium isolated from desert soil. Int J Syst Evol Microbiol 2015;65:1604–1610 [CrossRef][PubMed]
    [Google Scholar]
  9. Yoon JH, Kim IG, Kang KH, Oh TK, Park YH. Nocardioides aquiterrae sp. nov., isolated from groundwater in Korea. Int J Syst Evol Microbiol 2004;54:71–75 [CrossRef][PubMed]
    [Google Scholar]
  10. Lee DW, Hyun CG, Lee SD. Nocardioides marinisabuli sp. nov., a novel actinobacterium isolated from beach sand. Int J Syst Evol Microbiol 2007;57:2960–2963 [CrossRef][PubMed]
    [Google Scholar]
  11. Liu Q, Liu HC, Zhang JL, Zhou YG, Xin YH. Nocardioides glacieisoli sp. nov., isolated from a glacier. Int J Syst Evol Microbiol 2015;65:4845–4849 [CrossRef][PubMed]
    [Google Scholar]
  12. Srinivasan S, Lee SS, Lee JJ, Kim MK. Nocardioides soli sp. nov., a bacterium isolated from a mountain soil. Antonie van Leeuwenhoek 2014;106:271–278 [CrossRef][PubMed]
    [Google Scholar]
  13. Sultanpuram VR, Mothe T, Mohammed F. Nocardioides solisilvae sp. nov., isolated from a forest soil. Antonie van Leeuwenhoek 2015;107:1599–1606 [CrossRef][PubMed]
    [Google Scholar]
  14. Dastager SG, Lee JC, Ju YJ, Park DJ, Kim CJ. Nocardioides sediminis sp. nov., isolated from a sediment sample. Int J Syst Evol Microbiol 2009;59:280–284 [CrossRef][PubMed]
    [Google Scholar]
  15. Zhao Y, Liu Q, Kang MS, Jin F, Yu H et al. Nocardioides ungokensis sp. nov., isolated from lake sediment. Int J Syst Evol Microbiol 2015;65:4857–4862 [CrossRef][PubMed]
    [Google Scholar]
  16. Qin S, Yuan B, Zhang YJ, Bian GK, Tamura T et al. Nocardioides panzhihuaensis sp. nov., a novel endophytic actinomycete isolated from medicinal plant Jatropha curcas L. Antonie van Leeuwenhoek 2012;102:353–360 [CrossRef][PubMed]
    [Google Scholar]
  17. Xu H, Zhang S, Cheng J, Asem MD, Zhang MY et al. Nocardioides ginkgobilobae sp. nov., an endophytic actinobacterium isolated from the root of the living fossil Ginkgo biloba L. Int J Syst Evol Microbiol 2016;66:2013–2018 [CrossRef][PubMed]
    [Google Scholar]
  18. Kämpfer P, Glaeser SP, Mcinroy JA, Busse HJ. Nocardioides zeicaulis sp. nov., an endophyte actinobacterium of maize. Int J Syst Evol Microbiol 2016;66:1869–1874 [CrossRef][PubMed]
    [Google Scholar]
  19. Cerny G. Studies on the aminopeptidase test for the distinction of Gram-negative from Gram-positive bacteria. Eur J Appl Microbiol Biotechnol 1978;5:113–122 [CrossRef]
    [Google Scholar]
  20. Xu P, Li WJ, Tang SK, Zhang YQ, Chen GZ et al. Naxibacter alkalitolerans gen. nov., sp. nov., a novel member of the family 'Oxalobacteraceae' isolated from China. Int J Syst Evol Microbiol 2005;55:1149–1153 [CrossRef][PubMed]
    [Google Scholar]
  21. 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]
  22. Mergaert J, Cnockaert MC, Swings J. Fulvimonas soli gen. nov., sp. nov., a gamma-proteobacterium isolated from soil after enrichment on acetylated starch plastic. Int J Syst Evol Microbiol 2002;52:1285–1289 [CrossRef][PubMed]
    [Google Scholar]
  23. Kovacs N. Identification of Pseudomonas pyocyanea by the oxidase reaction. Nature 1956;178:703 [CrossRef][PubMed]
    [Google Scholar]
  24. Macfaddin JF. Biochemical Tests for Identification of Medical Bacteria Williams & Wilkins Co; 1976
    [Google Scholar]
  25. Gonzalez C, Gutierrez C, Ramirez C. Halobacterium vallismortis sp. nov. an amylolytic and carbohydrate-metabolizing, extremely halophilic bacterium. Can J Microbiol 1978;24:710–715 [CrossRef][PubMed]
    [Google Scholar]
  26. Smibert R, Krieg NR. Phenotypic characterization. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994; pp.607–654
    [Google Scholar]
  27. Minnikin DE, Collins MD, Goodfellow M. Fatty acid and polar lipid composition in the classification of Cellulomonas, Oerskovia and related taxa. J Appl Bacteriol 1979;47:87–95 [CrossRef]
    [Google Scholar]
  28. Collins MD, Jones D. Lipids in the classification and identification of coryneform bacteria containing peptidoglycans based on 2, 4-diaminobutyric acid. J Appl Bacteriol 1980;48:459–470 [CrossRef]
    [Google Scholar]
  29. Collins MD, Pirouz T, Goodfellow M, Minnikin DE. Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 1977;100:221–230 [CrossRef][PubMed]
    [Google Scholar]
  30. Kroppenstedt RM. Separation of bacterial menaquinones by HPLC using reverse phase (RP18) and a silver loaded Ion exchanger as stationary phases. J Liq Chromatogr 1982;5:2359–2367 [CrossRef]
    [Google Scholar]
  31. Mesbah M, Premachandran U, Whitman WB. Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Bacteriol 1989;39:159–167 [CrossRef]
    [Google Scholar]
  32. Cui XL, Mao PH, Zeng M, Li WJ, Zhang LP et al. Streptimonospora salina gen. nov., sp. nov., a new member of the family Nocardiopsaceae. Int J Syst Evol Microbiol 2001;51:357–363 [CrossRef][PubMed]
    [Google Scholar]
  33. Li WJ, Xu P, Schumann P, Zhang YQ, Pukall R et al. Georgenia ruanii sp. nov., a novel actinobacterium isolated from forest soil in Yunnan (China), and emended description of the genus Georgenia. Int J Syst Evol Microbiol 2007;57:1424–1428 [CrossRef][PubMed]
    [Google Scholar]
  34. 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]
  35. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987;4:406–425[PubMed]
    [Google Scholar]
  36. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981;17:368–376 [CrossRef][PubMed]
    [Google Scholar]
  37. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971;20:406–416 [CrossRef]
    [Google Scholar]
  38. Tamura K, Peterson D, Peterson N, Stecher G, Nei M et al. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 2011;28:2731–2739 [CrossRef][PubMed]
    [Google Scholar]
  39. 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]
  40. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985;39:783–791 [CrossRef][PubMed]
    [Google Scholar]
  41. Ezaki T, Hashimoto Y, Yabuuchi E. Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int J Syst Bacteriol 1989;39:224–229 [CrossRef]
    [Google Scholar]
  42. Christensen H, Angen O, Mutters R, Olsen JE, Bisgaard M. DNA-DNA hybridization determined in micro-wells using covalent attachment of DNA. Int J Syst Evol Microbiol 2000;50:1095–1102 [CrossRef][PubMed]
    [Google Scholar]
  43. Li SH, Yu XY, Park DJ, Hozzein WN, Kim CJ et al. Rhodococcus soli sp. nov., an actinobacterium isolated from soil using a resuscitative technique. Antonie van Leeuwenhoek 2015;107:357–366 [CrossRef][PubMed]
    [Google Scholar]
  44. Wayne LG, Moore WEC, Stackebrandt E, Kandler O, Colwell RR et al. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Evol Microbiol 1987;37:463–464 [CrossRef]
    [Google Scholar]
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