Nocardioides gilvus sp. nov., isolated from Namtso Lake

Abstract

A Gram-stain positive, facultatively anaerobic, non-motile and rod to coccoid-shaped bacterium, designated XZ17T, was isolated from Namtso Lake of Tibet, China. Strain XZ17T grew optimally at pH 8.0–9.0, at 30–33 °C and in the presence of 0–1.0 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences demonstrated that strain XZ17T belongs to the genus Nocardioides in the family Nocardioidaceae. Strain XZ17T shared pairwise 16S rRNA gene sequence similarities of 97.2, 96.8, 96.5, 96.4 and <96.0 % to Nocardioides solisilvae KCTC 39528T, Nocardioides daejeonensis JCM 16922T, Nocardioides jensenii NCIB 9770T, Nocardioides dubius KCTC 9992T and other Nocardioides species, respectively. It contained MK-8 (H4) as the predominant menaquinone and C17:1 ω8c, C15:0, C17:0 and C18:1 ω9c as the major fatty acid. The strain had cell wall peptidoglycan based on ll-2,6-diaminopimelic acid. The polar lipids of strain XZ17T comprised diphosphatidylglycerol, phosphatidylglycerol, three unidentified phospholipids, three unidentified glycolipids and two unidentified lipids. The DNA G+C content of strain XZ17T was 68.9 mol%. Based on distinctive phenotypic characteristics, phylogenetic analysis and chemotaxonomic data, it can be concluded that strain XZ17T represents a novel species within the genus Nocardioides, for which the name Nocardioides gilvus sp. nov. is proposed. The type strain is strain XZ17T (=KCTC 39561T = MCCC 1H00114T).

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References

  1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410

    CAS  Article  PubMed  Google Scholar 

  2. Bligh EG, Dyer WJ (1959) A rapid method of total lipid extraction and purification. Can J Biochem Physiol 37:911–917

    CAS  Article  PubMed  Google Scholar 

  3. Cho Y, Jang GI, Cho BC (2013) Nocardioides marinquilinus sp. nov., isolated from coastal seawater. Int J Syst Evol Microbiol 63:2594–2599

    CAS  Article  PubMed  Google Scholar 

  4. Collins MD (1985) Isoprenoid quinone analyses in bacterial classification and identification. Society for Applied Bacteriology: Technical, pp 267–287

  5. Du HJ, Wei YZ, Su J, Liu HY, Ma BP, Guo BL, Zhang YQ, Yu LY (2013) Nocardioides perillae sp. nov., isolated from surface-sterilized roots of Perilla frutescens. Int J Syst Evol Microbiol 63:1068–1072

    CAS  Article  PubMed  Google Scholar 

  6. Du ZJ, Wang Y, Dunlap C, Rooney AP, Chen GJ (2014) Draconibacterium orientale gen. nov., sp. nov., isolated from two distinct marine environments, and proposal of Draconibacteriaceae fam. nov. Int J Syst Evol Microbiol 64:1690–1696

    CAS  Article  PubMed  Google Scholar 

  7. Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376

    CAS  Article  PubMed  Google Scholar 

  8. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791

    Article  Google Scholar 

  9. Fitch WM (1971) Towards defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20:406–416

    Article  Google Scholar 

  10. Han JH, Kim TS, Joung Y, Kim MN, Shin KS, Bae T (2013) Nocardioides endophyticus sp. nov. and Nocardioides conyzicola sp. nov., isolated from herbaceous plant roots. Int J Sys Evol Microbiol 63:4730–4734

    CAS  Article  Google Scholar 

  11. Kim KH, Roh SW, Chang HW, Nam YD, Yoon JH, Jeon CO, Oh HM, Bae JW (2009) Nocardioides basaltis sp. nov., isolated from black beach sand. Int J Syst Evol Microbiol 59:42–47

    CAS  Article  PubMed  Google Scholar 

  12. Kim OS, Cho YJ, Lee K, Yoon SH, Kim M, NaH Park SC, Jeon YS, Lee JH, Yi H, Won S, Chun J (2012) Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 62:716–721

    CAS  Article  PubMed  Google Scholar 

  13. Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120

    CAS  Article  PubMed  Google Scholar 

  14. Komagata K, Suzuki KI (1988) 4 Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 19:161–207

    Article  Google Scholar 

  15. Kroppenstedt RM (1982) Separation of bacterial menaquinones by HPLC using reverse phase (RP18) and a silver loaded ion exchanger as stationary phases. J Liq Chromatogr 5:2359–2367

    CAS  Article  Google Scholar 

  16. Lane DJ (1991) 16S/23S rRNA sequencing. In: Stackebrandt E, Goodfellow M (eds) Nucleic acid techniques in bacterial systematic. Wiley, Chichester, pp 115–175

    Google Scholar 

  17. Lee DW, Hyun CG, Lee SD (2007) Nocardioides marinisabuli sp. nov., a novel actinobacterium isolated from beach sand. Int J Syst Evol Microbiol 57:2960–2963

    CAS  Article  PubMed  Google Scholar 

  18. Lee DW, Lee SY, Yoon JH, Lee SD (2011) Nocardioides ultimimeridianus sp. nov. and Nocardioides maradonensis sp. nov., isolated from rhizosphere soil. Int J Syst Evol Microbiol 61:1933–1937

    CAS  Article  PubMed  Google Scholar 

  19. Meier-Kolthoff JP, Alexander FA, Klenk HP, G#ker M (2013) Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinform 14:60

    Article  Google Scholar 

  20. Mesbah M, Premachandran U, Whitman WB (1989) Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Bacteriol 39:159–167

    CAS  Article  Google Scholar 

  21. Park SC, Baik KS, Kim MS, Chun J, Seong CN (2008) Nocardioides dokdonensis sp. nov., an actinomycete isolated from sand sediment. Int J Syst Evol Microbiol 58:2619–2623

    CAS  Article  PubMed  Google Scholar 

  22. Prauser H (1976) Nocardioides, a new genus of the order Actinomycetales. Int J Syst Evol Microbiol 26:58–65

    Google Scholar 

  23. Prauser H (1984) Nocardioides luteus spec. nov. Zeitschrift Für Allgemeine Mikrobiologie 24:647–648

    Article  Google Scholar 

  24. Qin S, Yuan B, Zhang YJ, Bian GK, Tamura T, Sun BZ, Li WJ, Jiang JH (2012) Nocardioides panzhihuaensis sp. nov., a novel endophytic actinomycete isolated from medicinal plant Jatropha curcas L. Antonie Van Leeuwenhoek 102:353–360

    CAS  Article  PubMed  Google Scholar 

  25. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425

    CAS  PubMed  Google Scholar 

  26. Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids. MIDI Inc, Newark

    Google Scholar 

  27. Singh H, Yin CS (2016) Nocardioides flava sp. nov., isolated from rhizosphere of poppy plant, Republic of Korea. Arch Microbiol 198:279–285

    CAS  Article  PubMed  Google Scholar 

  28. Smibert RM, Krieg NR (1994) Phenotypic characterization. In: Gerhardt P, Murray RGE, Wood WA, Krieg NR (eds) Methods for general and molecular bacteriology. American Society for Microbiology, Washington, DC, pp 607–654

    Google Scholar 

  29. Srinivasan S, Lee SS, Lee JJ, Kim MK (2014) Nocardioides soli sp. nov., a bacterium isolated from a mountain soil. Antonie Van Leeuwenhoek 106:271–278

    CAS  Article  PubMed  Google Scholar 

  30. Stackebrandt E, Goebel BM (1994) Place for DNA-DNA Reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 44:846–849

    CAS  Article  Google Scholar 

  31. Sultanpuram VR, Mothe T, Mohammed F (2015) Nocardioides solisilvae sp. nov., isolated from a forest soil. Antonie Van Leeuwenhoek 107:1599–1606

    CAS  Article  PubMed  Google Scholar 

  32. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  33. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  34. Tindall BJ, Sikorski J, Smibert RM, Kreig NR (2007) Phenotypic characterization and the principles of comparative systematics. In: Reddy CA, Beveridge TJ, Breznak JA, Marzluf G, Schmidt TM, Snyder LR (eds) Methods for general and molecular microbiology, 3rd edn. ASM Press, Washington DC, pp 330–393

    Google Scholar 

  35. Wang FQ, Xie ZH, Zhao JX, Chen GJ, Du ZJ (2015) Mesonia sediminis sp. nov., isolated from a sea cucumber culture pond. Antonie Van Leeuwenhoek 108:1205–1212

    CAS  Article  PubMed  Google Scholar 

  36. Woo SG, Srinivasan S, Yang J, Jung YA, Kim MK, Lee M (2012) Nocardioides daejeonensis sp. nov., a denitrifying bacterium isolated from sludge in a sewage-disposal plant. Int J Syst Evol Microbiol 62:1199–1203

    CAS  Article  PubMed  Google Scholar 

  37. Yoon JH, Rhee SK, Lee JS, Park YH, Lee ST (1997) Nocardioides pyridinolyticus sp. nov., a pyridine-degrading bacterium isolated from the oxic zone of an oil shale column. Int J Syst Bacteriol 47:933–938

    CAS  Article  PubMed  Google Scholar 

  38. Yoon JH, Cho YG, Lee ST, Suzuki KI, Nakase T, Park YH (1999) Nocardioides nitrophenolicus sp. nov., a p-nitrophenol-degrading bacterium. Int J Syst Bacteriol 49:675–680

    CAS  Article  PubMed  Google Scholar 

  39. Yoon JH, Kim IG, Lee MH, Lee CH, Oh TK (2005) Nocardioides alkalitolerans sp. nov., isolated from an alkaline serpentinite soil in Korea. Int J Syst Evol Microbiol 55:809–814

    CAS  Article  PubMed  Google Scholar 

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Acknowledgments

This work was supported by the National Natural Science Foundation of China (31370057, 31290231) and 2013 Shandong Provincial Second Group Projects on Resource Platforms for Marine Economic and Innovative Development Regions: Marine Microorganisms Preservation Platform (2150299).

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Correspondence to Zong-Jun Du.

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The GenBank accession number for the 16S rRNA gene sequence of strain XZ17T is KR534267.

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Zhang, HX., Wang, K., Xu, ZX. et al. Nocardioides gilvus sp. nov., isolated from Namtso Lake. Antonie van Leeuwenhoek 109, 1367–1374 (2016). https://doi.org/10.1007/s10482-016-0735-0

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Keywords

  • Nocardioides gilvus sp. nov.
  • 16S rRNA gene
  • Namtso Lake