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Abstract

Strain NL19 is a Gram-stain-negative, aerobic bacterium that was isolated from sludge of a deactivated uranium mine in Portugal. 16S rRNA gene sequence analysis revealed that strain NL19 is a member of the genus and closely related to the strains MTCC 6384, DSM 14825, DSM 19036 and DSM 19033. It had a DNA G+C content of 40.8 mol%, which agreed with the genus description. The main fatty acids included Cω7, Cω5, C, iso-C, iso-C 3-OH, C, anteiso-C and iso-C 3-OH. The main lipids present were phospholipids (60 %) and sphingolipids (35 %). The most abundant phospholipids included phosphatidylethanolamine, phosphatidylinositol and phosphatidylcholine. Menaquinone-7 (MK-7) was the only isoprenoid quinone detected. DNA–DNA hybridization similarities between strain NL19 and MTCC 6384, DSM 14825, DSM 19036 and DSM 19033 were 15.3 , 16.2 , 11.5 and 16.0 %, respectively. Strain NL19 can also be distinguished from these four species based on and intergenic transcribed spacers (ITS) sequences and by some phenotypic traits such as NaCl tolerance, pH, growth temperature and carbon source utilization. Strain NL19represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is NL19 (=LMG 29220=CECT 9028). An amended description of is also included.

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2017-05-01
2024-03-29
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References

  1. Steyn PL, Segers P, Vancanneyt M, Sandra P, Kersters K et al. Classification of heparinolytic bacteria into a new genus, Pedobacter, comprising four species: Pedobacter heparinus comb. nov., Pedobacter piscium comb. nov., Pedobacter africanus sp. nov. and Pedobacter saltans sp. nov. proposal of the family Sphingobacteriaceae fam. nov. Int J Syst Bacteriol 1998; 48 Pt 1:165–177 [View Article][PubMed]
    [Google Scholar]
  2. Du J, Singh H, Ngo HT, Won KH, Kim KY et al. Pedobacter daejeonensis sp. nov. and Pedobacter trunci sp. nov., isolated from an ancient tree trunk, and emended description of the genus Pedobacter. Int J Syst Evol Microbiol 2015; 65:1241–1246 [View Article][PubMed]
    [Google Scholar]
  3. Farfán M, Montes MJ, Marqués AM. Reclassification of Sphingobacterium antarcticum Shivaji et al. 1992 as Pedobacter antarcticus comb. nov. and Pedobacter piscium (Takeuchi and Yokota 1993) Steyn et al. 1998 as a later heterotypic synonym of Pedobacter antarcticus. Int J Syst Evol Microbiol 2014; 64:863–868 [View Article][PubMed]
    [Google Scholar]
  4. Gallego V, García MT, Ventosa A. Pedobacter aquatilis sp. nov., isolated from drinking water, and emended description of the genus Pedobacter. Int J Syst Evol Microbiol 2006; 56:1853–1858 [View Article][PubMed]
    [Google Scholar]
  5. Hwang CY, Choi DH, Cho BC. Pedobacter roseus sp. nov., isolated from a hypertrophic pond, and emended description of the genus Pedobacter. Int J Syst Evol Microbiol 2006; 56:1831–1836 [View Article][PubMed]
    [Google Scholar]
  6. Vanparys B, Heylen K, Lebbe L, de Vos P. Pedobacter caeni sp. nov., a novel species isolated from a nitrifying inoculum. Int J Syst Evol Microbiol 2005; 55:1315–1318 [View Article][PubMed]
    [Google Scholar]
  7. Zhou Z, Jiang F, Wang S, Peng F, Dai J et al. Pedobacter arcticus sp. nov., a facultative psychrophile isolated from Arctic soil, and emended descriptions of the genus Pedobacter, Pedobacter heparinus, Pedobacter daechungensis, Pedobacter terricola, Pedobacter glucosidilyticus and Pedobacter lentus. Int J Syst Evol Microbiol 2012; 62:1963–1969 [View Article][PubMed]
    [Google Scholar]
  8. Qiu X, Qu Z, Jiang F, Ren L, Chang X et al. Pedobacter huanghensis sp. nov. and Pedobacter glacialis sp. nov., isolated from Arctic glacier foreland. Int J Syst Evol Microbiol 2014; 64:2431–2436 [View Article][PubMed]
    [Google Scholar]
  9. Euzéby JP. List of bacterial names with standing in nomenclature: a folder available on the internet. Int J Syst Bacteriol 1997; 47:590–592 [View Article][PubMed]
    [Google Scholar]
  10. Takeuchi M, Yokota A. Proposals of Sphingobacterium faecium sp. nov., Sphingobacterium piscium sp. nov., Sphingobacterium heparinum comb. nov., Sphingobacterium thalpophilum comb. nov. and two genospecies of the genus Sphingobacterium, and synonymy of Flavobacterium yabuuchiae and Sphingobacterium spiritivorum. J Gen Appl Microbiol 1992; 38:465–482 [View Article]
    [Google Scholar]
  11. Ten LN, Liu QM, Im WT, Lee M, Yang DC et al. Pedobacter ginsengisoli sp. nov., a DNase-producing bacterium isolated from soil of a ginseng field in South Korea. Int J Syst Evol Microbiol 2006; 56:2565–2570 [View Article][PubMed]
    [Google Scholar]
  12. Muurholm S, Cousin S, Päuker O, Brambilla E, Stackebrandt E. Pedobacter duraquae sp. nov., Pedobacter westerhofensis sp. nov., Pedobacter metabolipauper sp. nov., Pedobacter hartonius sp. nov. and Pedobacter steynii sp. nov., isolated from a hard-water rivulet. Int J Syst Evol Microbiol 2007; 57:2221–2227 [View Article][PubMed]
    [Google Scholar]
  13. Roh SW, Quan ZX, Nam YD, Chang HW, Kim KH et al. Pedobacter agri sp. nov., from soil. Int J Syst Evol Microbiol 2008; 58:1640–1643 [View Article][PubMed]
    [Google Scholar]
  14. Hoang VA, Kim YJ, Nguyen NL, Min JW, Yang DC. Pedobacter ginsengiterrae sp. nov., isolated from soil of a ginseng field. Int J Syst Evol Microbiol 2013; 63:1273–1279 [View Article][PubMed]
    [Google Scholar]
  15. Won KH, Kook M, Yi TH. Pedobacter bambusae sp. nov., isolated from soil of a bamboo plantation. Antonie van Leeuwenhoek 2015; 107:565–573 [View Article][PubMed]
    [Google Scholar]
  16. Pereira A, Neves L, Dias JMM, Barbosa SVT. Evaluation of radionuclide contamination in the vicinity of the cunha baixa and quinta do bispo old uranium mines (Central portugal). Radioproteccao (S. Joao Da Talha) 2004; 2:103–117
    [Google Scholar]
  17. Lanyi B. Classical and rapid identification methods for medically important Bacteria. Methods Microbiol 1988; 19:1–67 [View Article]
    [Google Scholar]
  18. Cowan ST, Steel KJ, Barrow G I, Feltham RKA. (editors) Cowan and Steel’s Manual for the Identification of Medical Bacteria, 3rd ed. Cambridge: Cambridge University Press; 1993 pp. 331
    [Google Scholar]
  19. Wilson K. Preparation of genomic DNA from bacteria. Curr Protoc Mol Biol 2001; Chapter 2:Unit 2.4 [View Article][PubMed]
    [Google Scholar]
  20. Cleenwerck I, Vandemeulebroecke K, Janssens D, Swings J. Re-examination of the genus Acetobacter, with descriptions of Acetobacter cerevisiae sp. nov. and Acetobacter malorum sp. nov. Int J Syst Evol Microbiol 2002; 52:1551–1558 [View Article][PubMed]
    [Google Scholar]
  21. 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]
  22. EUCAST European Committee on Antimicrobial Susceptibility Testing. Break- point tables for interpretation of MICs and zonediameters. Version 5.0; 2015 www.eucast.org
  23. Andrews JM. Determination of minimum inhibitory concentrations. J Antimicrob Chemother 2001; 48:5–16 [View Article][PubMed]
    [Google Scholar]
  24. Clinical and Laboratory StandardsInstitute Performance standards for antimicrobial susceptibility testing 23rd Informational Supplement Document M100-S23 Wayne, PA: CLSI; 2015
    [Google Scholar]
  25. Kook M, Park Y, Yi TH. Pedobacter jejuensis sp. nov., isolated from soil of a pine grove, and emended description of the genus Pedobacter. Int J Syst Evol Microbiol 2014; 64:1789–1794 [View Article][PubMed]
    [Google Scholar]
  26. 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]
  27. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees; 1987; 4406–425 [View Article]
  28. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
    [Google Scholar]
  29. 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]
  30. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 2013; 30:2725–2729 [View Article][PubMed]
    [Google Scholar]
  31. Shivaji S, Chaturvedi P, Reddy GS, Suresh K. Pedobacter himalayensis sp. nov., from the hamta glacier located in the himalayan mountain ranges of India. Int J Syst Evol Microbiol 2005; 55:1083–1088 [View Article][PubMed]
    [Google Scholar]
  32. Margesin R, Spröer C, Schumann P, Schinner F. Pedobacter cryoconitis sp. nov., a facultative psychrophile from alpine glacier cryoconite. Int J Syst Evol Microbiol 2003; 53:1291–1296 [View Article][PubMed]
    [Google Scholar]
  33. Stackebrand E. Molecular taxonomic parameters. Microbiol Aust 2011; 32:59–61
    [Google Scholar]
  34. Meier-Kolthoff JP, Göker M, Spröer C, Klenk HP. When should a DDH experiment be mandatory in microbial taxonomy?. Arch Microbiol 2013; 195:413–418 [View Article][PubMed]
    [Google Scholar]
  35. Cashion P, Holder-Franklin MA, Mccully J, Franklin M. A rapid method for the base ratio determination of bacterial DNA. Anal Biochem 1977; 81:461–466 [View Article][PubMed]
    [Google Scholar]
  36. de Ley J, Cattoir H, Reynaerts A. The quantitative measurement of DNA hybridization from renaturation rates. Eur J Biochem 1970; 12:133–142 [View Article][PubMed]
    [Google Scholar]
  37. Huss VA, Festl H, Schleifer KH. Studies on the spectrophotometric determination of DNA hybridization from renaturation rates. Syst Appl Microbiol 1983; 4:184–192 [View Article][PubMed]
    [Google Scholar]
  38. 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]
  39. Rodríguez-Alcalá LM, Castro-Gómez P, Felipe X, Noriega L, Fontecha J. Effect of processing of cow milk by high pressures under conditions up to 900 MPa on the composition of neutral, polar lipids and fatty acids. LWT - Food Sci Technol 2015; 62:265–270 [View Article]
    [Google Scholar]
  40. Matyash V, Liebisch G, Kurzchalia TV, Shevchenko A, Schwudke D. Lipid extraction by methyl-tert-butyl ether for high-throughput lipidomics. J Lipid Res 2008; 49:1137–1146 [View Article][PubMed]
    [Google Scholar]
  41. Tindall BJ. A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol 1990a; 13:128–130 [View Article]
    [Google Scholar]
  42. Tindall BJ. Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett 1990b; 66:199–202 [View Article]
    [Google Scholar]
  43. Tindall BJ, Sikorski J, Smibert RA, Krieg NR et al. In Marzluf GA, Reddy CA, Beveridge TJ, Schmidt TM, Snyder LR, Breznak JA. (editors) Methods for General and Molecular Microbiology, 3rd ed. American Society of Microbiology; 2007 [View Article]
    [Google Scholar]
  44. Chun J, Kang JY, Jahng KY. Pedobacter pituitosus sp. nov., isolated from a waterfall. Int J Syst Evol Microbiol 2014; 64:3838–3843 [View Article][PubMed]
    [Google Scholar]
  45. Derichs J, Kämpfer P, Lipski A. Pedobacter nutrimenti sp. nov., isolated from chilled food. Int J Syst Evol Microbiol 2014; 64:1310–1316 [View Article][PubMed]
    [Google Scholar]
  46. Kang H, Kim H, Joung Y, Joh K. Pedobacter rivuli sp. nov., isolated from a freshwater stream. Int J Syst Evol Microbiol 2014; 64:4073–4078 [View Article][PubMed]
    [Google Scholar]
  47. Zeng Y, Feng H, Huang Y. Pedobacter xixiisoli sp. nov., isolated from bank soil. Int J Syst Evol Microbiol 2014; 64:3683–3689 [View Article][PubMed]
    [Google Scholar]
  48. Rodríguez-Alcalá LM, C, Pimentel LL, Pestana D, Teixeira D et al. Endocrine disruptor DDE associated with a high-fatdiet enhances the impairment of liver fatty acid composition in rats. J Agric Food Chem 2015; 63:9341–9348 [View Article][PubMed]
    [Google Scholar]
  49. das S, Dash HR, Mangwani N, Chakraborty J, Kumari S. Understanding molecular identification and polyphasic taxonomic approaches for genetic relatedness and phylogenetic relationships of microorganisms. J Microbiol Methods 2014; 103:80–100 [View Article][PubMed]
    [Google Scholar]
  50. Liu W, Li L, Khan MA, Zhu F. Popular molecular markers in bacteria. Mol Genet Microbiol Virol 2012; 27:103–107 [View Article]
    [Google Scholar]
  51. Patwardhan A, Ray S, Roy A. Molecular markers in phylogenetic studies-a review. J Phylogenetics Evol Biol 2014; 2:1–9 [View Article]
    [Google Scholar]
  52. Kostman JR, Alden MB, Mair M, Edlind TD, Lipuma JJ et al. A universal approach to bacterial molecular epidemiology by polymerase chain reaction ribotyping. J Infect Dis 1995; 171:204–208 [View Article][PubMed]
    [Google Scholar]
  53. Chanter N, Collin N, Holmes N, Binns M, Mumford J. Characterization of the lancefield group C Streptococcus 16S-23S RNA gene intergenic spacer and its potential for identification and sub-specific typing. Epidemiol Infect 1997; 118:125–135 [View Article][PubMed]
    [Google Scholar]
  54. Sambrook J, Russel DW. A Laboratory Manual vol. 1, 2, 3 Cold Spring Harbour, New York: Cold Spring Harbour Laboratory Press; 2001
    [Google Scholar]
  55. Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 1997; 25:955–964 [View Article][PubMed]
    [Google Scholar]
  56. Liolios K, Sikorski J, Lu M, Nolan M, Lapidus A et al. Complete genome sequence of the gliding, heparinolytic Pedobacter saltans type strain (113T). Stand Genomic Sci 2011; 5:30–40 [View Article][PubMed]
    [Google Scholar]
  57. Santos T, Cruz A, Caetano T, Covas C, Mendo S. Draft genome sequence of Pedobacter sp. strain NL19, a producer of potent antibacterial compounds. Genome Announc 2015; 3:e00184-15 [View Article][PubMed]
    [Google Scholar]
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