sp. nov., a difficultly cultivable bacterium that grows on solid but not in liquid medium, isolated from an abandoned lead–zinc mine Free

Abstract

A difficult to cultivate bacterial strain, designated 1PNM-26, isolated from a lead–zinc mine, was investigated using a polyphasic taxonomic approach. The strain was able to grow on solid medium but not in liquid medium. Cells were Gram-reaction-negative, aerobic, non-spore-forming, non-motile and rod-shaped. It showed positive reactions for catalase and oxidase and hydrolysis of aesculin. The results of phylogenetic analyses based on 16S rRNA gene sequences indicated that strain 1PNM-26 represents a member of the genus and forms a stable cluster with KCTC 42183, JCM 16711 and NBRC 105508. The major fatty acids were summed feature 8 (Cω7 and/or Cω6), summed feature 3 (Cω7 and/or Cω6) and C. C 2-OH was present as the major hydroxyl fatty acid. The major polyamine was -homospermidine, and ubiquinone 10 (Q-10) was the predominant respiratory quinone. The genomic DNA G+C content of strain 1PNM-26 was determined to be 66.3±0.3 mol%, and the polar lipids consisted of sphingoglycolipid, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidyldimethylethanolamine, phosphatidylmonomethylethanolamine, an unidentified glycolipid, three unidentified aminolipids and three unidentified lipids. The phenotypic, phylogenetic and chemotaxonomic results strongly supported the hypothesis that strain 1PNM-26 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is 1PNM-26 (=GDMCC 1.664=KCTC 42758=DSM 27573).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.002461
2017-12-01
2024-03-28
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/67/12/5273.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.002461&mimeType=html&fmt=ahah

References

  1. Yabuuchi E, Yano I, Oyaizu H, Hashimoto Y, Ezaki T et al. Proposals of Sphingomonas paucimobilis gen. nov. and comb. nov., Sphingomonas parapaucimobilis sp. nov., Sphingomonas yanoikuyae sp. nov., Sphingomonas adhaesiva sp. nov., Sphingomonas capsulata comb. nov., and two genospecies of the genus Sphingomonas. Microbiol Immunol 1990; 34:99–119 [View Article][PubMed]
    [Google Scholar]
  2. Takeuchi M, Hamana K, Hiraishi A. Proposal of the genus Sphingomonas sensu stricto and three new genera, Sphingobium, Novosphingobium and Sphingopyxis, on the basis of phylogenetic and chemotaxonomic analyses. Int J Syst Evol Microbiol 2001; 51:1405–1417 [View Article][PubMed]
    [Google Scholar]
  3. Busse HJ, Denner EB, Buczolits S, Salkinoja-Salonen M, Bennasar A et al. Sphingomonas aurantiaca sp. nov., Sphingomonas aerolata sp. nov. and Sphingomonas faeni sp. nov., air- and dustborne and Antarctic, orange-pigmented, psychrotolerant bacteria, and emended description of the genus Sphingomonas. Int J Syst Evol Microbiol 2003; 53:1253–1260 [View Article][PubMed]
    [Google Scholar]
  4. Feng GD, Yang SZ, Wang YH, Zhang XX, Zhao GZ et al. Description of a Gram-negative bacterium, Sphingomonas guangdongensis sp. nov. Int J Syst Evol Microbiol 2014; 64:1697–1702 [View Article][PubMed]
    [Google Scholar]
  5. Feng GD, Yang SZ, Wang YH, Zhao GZ, Deng MR et al. Sphingomonas gimensis sp. nov., a novel Gram-negative bacterium isolated from abandoned lead–zinc ore mine. Antonie van Leeuwenhoek 2014; 105:1091–1097 [View Article][PubMed]
    [Google Scholar]
  6. Feng GD, Yang SZ, Xiong X, Li HP, Zhu HH. Sphingomonas metalli sp. nov., isolated from an abandoned lead–zinc mine. Int J Syst Evol Microbiol 2016; 66:2046–2051 [View Article][PubMed]
    [Google Scholar]
  7. Feng GD, Yang SZ, Xiong X, Li HP, Zhu HH. Sphingomonas spermidinifaciens sp. nov., a novel bacterium containing spermidine as the major polyamine, isolated from an abandoned lead–zinc mine and emended descriptions of the genus Sphingomonas and the species Sphingomonas yantingensis and Sphingomonas japonica. Int J Syst Evol Microbiol 2017; 67:2160–2165 [View Article][PubMed]
    [Google Scholar]
  8. Weisburg WG, Barns SM, Pelletier DA, Lane DJ. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 1991; 173:697–703 [View Article][PubMed]
    [Google Scholar]
  9. 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]
  10. 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]
  11. 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]
  12. Rzhetsky A, Nei M. Theoretical foundation of the minimum-evolution method of phylogenetic inference. Mol Biol Evol 1993; 10:1073–1095[PubMed]
    [Google Scholar]
  13. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
    [Google Scholar]
  14. 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]
  15. 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 Bacteriol 1987; 37:463–464 [View Article]
    [Google Scholar]
  16. Kim M, Oh HS, Park SC, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014; 64:346–351 [View Article][PubMed]
    [Google Scholar]
  17. van der Linde K, Lim BT, Rondeel JM, Antonissen LP, de Jong GM. Improved bacteriological surveillance of haemodialysis fluids: a comparison between Tryptic soy agar and Reasoner's 2A media. Nephrol Dial Transplant 1999; 14:2433–2437 [View Article][PubMed]
    [Google Scholar]
  18. Busse HJ, Hauser E, Kämpfer P. Description of two novel species, Sphingomonas abaci sp. nov. and Sphingomonas panni sp. nov. Int J Syst Evol Microbiol 2005; 55:2565–2569 [View Article][PubMed]
    [Google Scholar]
  19. Buck JD. Nonstaining (KOH) method for determination of Gram reactions of marine bacteria. Appl Environ Microbiol 1982; 44:992–993[PubMed]
    [Google Scholar]
  20. Tindall BJ, Sikorski J, Smibert RA, Krieg NR. Phenotypic characterization and the principles of comparative systematics. In Reddy CA, Beveridge TJ, Breznak JA, Marzluf GA, Schmidt TM et al. (editors) Methods for General and Molecular Microbiology, 3rd ed. Washington, DC: ASM Press; 2007 pp. 330–393
    [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. Scherer P, Kneifel H. Distribution of polyamines in methanogenic bacteria. J Bacteriol 1983; 154:1315–1322[PubMed]
    [Google Scholar]
  23. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
    [Google Scholar]
  24. 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]
  25. Hiraishi A, Ueda Y, Ishihara J, Mori T. Comparative lipoquinone analysis of influent sewage and activated sludge by high-performance liquid chromatography and photodiode array detection. J Gen Appl Microbiol 1996; 42:457–469 [View Article]
    [Google Scholar]
  26. Chen H, Jogler M, Rohde M, Klenk HP, Busse HJ et al. Reclassification and emended description of Caulobacter leidyi as Sphingomonas leidyi comb. nov., and emendation of the genus Sphingomonas. Int J Syst Evol Microbiol 2012; 62:2835–2843 [View Article][PubMed]
    [Google Scholar]
  27. Luo YR, Tian Y, Huang X, Kwon K, Yang SH et al. Sphingomonas polyaromaticivorans sp. nov., a polycyclic aromatic hydrocarbon-degrading bacterium from an oil port water sample. Int J Syst Evol Microbiol 2012; 62:1223–1227 [View Article][PubMed]
    [Google Scholar]
  28. Han SI, Lee JC, Ohta H, Whang KS. Sphingomonas oligoaromativorans sp. nov., an oligotrophic bacterium isolated from a forest soil. Int J Syst Evol Microbiol 2014; 64:1679–1684 [View Article][PubMed]
    [Google Scholar]
  29. Liu Y, Yao S, Lee YJ, Cao Y, Zhai L et al. Sphingomonas morindae sp. nov., isolated from Noni (Morinda citrifolia L.) branch. Int J Syst Evol Microbiol 2015; 65:2817–2823 [View Article][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.002461
Loading
/content/journal/ijsem/10.1099/ijsem.0.002461
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF

Most cited Most Cited RSS feed