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Volume 67, Issue 11

sp. nov., isolated from desert soil Free

Abstract

A novel bacterial strain, designated YIM 73061, was isolated from the Cholistan desert in Punjab, Pakistan, and characterized by using a polyphasic taxonomic approach. 16S rRNA gene sequence analysis revealed the highest levels of sequence similarity with respect to FWC21 (97.6 %), FaiI3 (97.4 %), 4T-6 (97.0 %) and W2-3-4 (96.8 %). Cells were Gram-stain-negative, aerobic and motile rods that formed orange colonies. The strain was oxidase- and catalase-positive. Growth occurred at 20–40 °C (optimum, 30–37 °C) at pH 5.0–8.0 (optimum, pH 7.0) and with 0–1 % (w/v) NaCl (optimum, 0–0.5 %). The major cellular fatty acids (>10 %) were summed feature 8 (comprising Cω7 and/or Cω6) and C The polar lipid profile consisted of phosphatidylglycerol and four unidentified glycolipids. The major isoprenoid quinone was ubiquinone-10 (Q-10). The G+C content of the genomic DNA was 66.8 mol%. Strain YIM 73061 showed low levels of DNA–DNA relatedness to FWC21 (27.2±2.6 %), FaiI3 (24.6±1.1 %) and 4T-6 (18.4±3.1 %). On the basis of phylogenetic inference, chemotaxonomic characteristics and phenotypic data, strain YIM 73061 should be classified as representing a novel species, for which the name sp. nov. is proposed. The type strain is YIM 73061 (=DSM 103871=CCTCC AB 2016297).

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Keyword(s): Cholistan desert , Pakistan , Phenylobacterium deserti sp. nov. and polyphasic taxonomy
© 2017 IUMS
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2017-11-01
2024-04-19
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References

  1. Lingens F, Blecher R, Blecher H, Blobel F, Eberspacher J et al. Phenylobacterium immobile gen. nov., sp. nov., a gram-negative bacterium that degrades the herbicide chloridazon. Int J Syst Bacteriol 1985; 35:26–39 [View Article]
     [Google Scholar]
  2. Oh YS, Roh DH. Phenylobacterium muchangponense sp. nov., isolated from beach soil, and emended description of the genus Phenylobacterium. Int J Syst Evol Microbiol 2012; 62:977–983 [View Article][PubMed]
     [Google Scholar]
  3. Kanso S, Patel BK. Phenylobacterium lituiforme sp. nov., a moderately thermophilic bacterium from a subsurface aquifer, and emended description of the genus Phenylobacterium. Int J Syst Evol Microbiol 2004; 54:2141–2146 [View Article][PubMed]
     [Google Scholar]
  4. Tiago I, Mendes V, Pires C, Morais PV, Verśsimo A. Phenylobacterium falsum sp. nov., an Alphaproteobacterium isolated from a nonsaline alkaline groundwater, and emended description of the genus Phenylobacterium. Syst Appl Microbiol 2005; 28:295–302 [View Article][PubMed]
     [Google Scholar]
  5. Abraham WR, Macedo AJ, Lünsdorf H, Fischer R, Pawelczyk S et al. Phylogeny by a polyphasic approach of the order Caulobacterales, proposal of Caulobacter mirabilis sp. nov., Phenylobacterium haematophilum sp. nov. and Phenylobacterium conjunctum sp. nov., and emendation of the genus Phenylobacterium. Int J Syst Evol Microbiol 2008; 58:1939–1949 [View Article][PubMed]
     [Google Scholar]
  6. Aslam Z, Im WT, Ten LN, Lee ST. Phenylobacterium koreense sp. nov., isolated from South Korea. Int J Syst Evol Microbiol 2005; 55:2001–2005 [View Article][PubMed]
     [Google Scholar]
  7. Weon HY, Kim BY, Kwon SW, Go SJ, Koo BS et al. Phenylobacterium composti sp. nov., isolated from cotton waste compost in Korea. Int J Syst Evol Microbiol 2008; 58:2301–2304 [View Article][PubMed]
     [Google Scholar]
  8. 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 [View Article]
     [Google Scholar]
  9. 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 [View Article][PubMed]
     [Google Scholar]
  10. 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 [View Article]
     [Google Scholar]
  11. 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 [View Article][PubMed]
     [Google Scholar]
  12. Kovacs N. Identification of Pseudomonas pyocyanea by the oxidase reaction. Nature 1956; 178:703 [View Article][PubMed]
     [Google Scholar]
  13. Macfaddin JF. Biochemical Tests for Identification of Medical Bacteria Philadelphia: Williams & Wilkins Co; 1976
     [Google Scholar]
  14. 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 [View Article][PubMed]
     [Google Scholar]
  15. Smibert RM, 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]
  16. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. USFCC Newsl 1990; 20:16
     [Google Scholar]
  17. 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 [View Article]
     [Google Scholar]
  18. 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 [View Article]
     [Google Scholar]
  19. Collins MD, Pirouz T, Goodfellow M, Minnikin DE. Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 1977; 100:221–230 [View Article][PubMed]
     [Google Scholar]
  20. 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 [View Article]
     [Google Scholar]
  21. 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 [View Article][PubMed]
     [Google Scholar]
  22. 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 [View Article][PubMed]
     [Google Scholar]
  23. 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 [View Article][PubMed]
     [Google Scholar]
  24. 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]
  25. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
     [Google Scholar]
  26. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406–416 [View Article]
     [Google Scholar]
  27. 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 [View Article][PubMed]
     [Google Scholar]
  28. 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]
  29. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
     [Google Scholar]
  30. 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 [View Article]
     [Google Scholar]
  31. 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 [View Article][PubMed]
     [Google Scholar]
  32. 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 [View Article][PubMed]
     [Google Scholar]
  33. 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 [View Article]
     [Google Scholar]
  34. 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 [View Article]
     [Google Scholar]
  35. Chu C, Yuan C, Liu X, Yao L, Zhu J et al. Phenylobacterium kunshanense sp. nov., isolated from the sludge of a pesticide manufacturing factory. Int J Syst Evol Microbiol 2015; 65:325–330 [View Article][PubMed]
     [Google Scholar]
  36. Farh ME, Kim YJ, Singh P, Hoang VA, Yang DC. Phenylobacterium panacis sp. nov., isolated from the rhizosphere of rusty mountain ginseng. Int J Syst Evol Microbiol 2016; 66:2691–2696 [View Article][PubMed]
     [Google Scholar]
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Phenylobacterium deserti sp. nov., isolated from desert soil
Int J Syst Evol Microbiol 67, 4722 (2017); https://doi.org/10.1099/ijsem.0.002366
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