1887

Abstract

A Gram-stain-negative, aerobic, non-spore-forming and rod-shaped bacterium, designated YIM 730274, was isolated from a sediment sample collected from a hot spring located in Tibet, PR China, and was characterized by using a polyphasic taxonomy approach. Cells were motile by means of a polar flagellum. The strain was oxidase- and catalase-positive, and contained polyalkanoates and polyphosphate as storage polymers. Growth occurred at 25–50 °C, at pH 6.0–8.5 and with 0.5–1.0 % NaCl. The major fatty acids (>10 %) were summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c), summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C16 : 0. The known polar lipids comprised of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylserine. The isoprenoid quinone was Q-8. The G+C content of genomic DNA was 70.7 mol%. The results of phylogenetic analyses based on 16S rRNA gene sequences indicated that the strain forms a monophyletic branch at the periphery of the evolutionary radiation occupied by the genus Aquabacterium in the class Betaproteobacteria . The most closely related phylogenetic neighbours were Aquabacterium limnoticum ABP-4 (97.8 % 16S rRNA gene sequence identity) and Aquabacterium commune B8 (97.2 % 16SrRNA gene sequence identity). DNA–DNA relatedness values between YIM 730274 and A. limnoticum KCTC 23306 (46.4±0.4 %) and A. commune DSM 11901 (42.2±1.2 %) were well below the 70 % limit for species identification. YIM 730274 was distinguishable from other members of the genus Aquabacterium by the differences in phenotypic, chemotaxonomic and genotypic characteristics. YIM 730274 merits recognition as a representative of a novel species of the genus Aquabacterium . It is proposed that the isolate should be classified in the genus Aquabacterium as representing a novel species, Aquabacterium tepidiphilum sp. nov. The type strain is YIM 730274 (=KCTC 52716=CCTCC AB 2016295).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.003103
2018-11-07
2019-10-17
Loading full text...

Full text loading...

References

  1. Kalmbach S, Manz W, Wecke J, Szewzyk U. Aquabacterium gen. nov., with description of Aquabacterium citratiphilum sp. nov., Aquabacterium parvum sp. nov. and Aquabacterium commune sp. nov., three in situ dominant bacterial species from the Berlin drinking water system. Int J Syst Bacteriol 1999;49:769–777 [CrossRef][PubMed]
    [Google Scholar]
  2. Lin MC, Jiang SR, Chou JH, Arun AB, Young CC et al. Aquabacterium fontiphilum sp. nov., isolated from spring water. Int J Syst Evol Microbiol 2009;59:681–685 [CrossRef][PubMed]
    [Google Scholar]
  3. Chen WM, Cho NT, Yang SH, Arun AB, Young CC et al. Aquabacterium limnoticum sp. nov., isolated from a freshwater spring. Int J Syst Evol Microbiol 2012;62:698–704 [CrossRef][PubMed]
    [Google Scholar]
  4. Pham VH, Jeong SW, Kim J. Aquabacterium olei sp. nov., an oil-degrading bacterium isolated from oil-contaminated soil. Int J Syst Evol Microbiol 2015;65:3597–3602 [CrossRef][PubMed]
    [Google Scholar]
  5. Buck JD. Nonstaining (KOH) method for determination of Gram reactions of marine bacteria. Appl Environ Microbiol 1982;44:992–993[PubMed]
    [Google Scholar]
  6. 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]
  7. 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]
  8. Mergaert J, Cnockaert MC, Swings J. Fulvimonas soli gen. nov., sp. nov., a γ-proteobacterium isolated from soil after enrichment on acetylated starch plastic. Int J Syst Evol Microbiol 2002;52:1285–1289 [CrossRef][PubMed]
    [Google Scholar]
  9. Kovacs N. Identification of Pseudomonas pyocyanea by the oxidase reaction. Nature 1956;178:703–704 [CrossRef][PubMed]
    [Google Scholar]
  10. Macfaddin JF. Biochemical Tests for Identification of Medical Bacteria Williams & Wilkins Co; 1976
    [Google Scholar]
  11. 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]
  12. 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]
  13. 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]
  14. 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]
  15. 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]
  16. 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]
  17. 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]
  18. 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]
  19. 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]
  20. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987;4:406–425 [CrossRef][PubMed]
    [Google Scholar]
  21. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981;17:368–376 [CrossRef][PubMed]
    [Google Scholar]
  22. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971;20:406–416 [CrossRef]
    [Google Scholar]
  23. 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]
  24. 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]
  25. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985;39:783–791 [CrossRef][PubMed]
    [Google Scholar]
  26. 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]
  27. 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]
  28. 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]
  29. Harrison P. SPADES - a process algebra for discrete event simulation. J Logic Comput 2000;10:3–42 [CrossRef]
    [Google Scholar]
  30. Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010;11:119 [CrossRef][PubMed]
    [Google Scholar]
  31. 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]
  32. Stackebrandt E, Goebel BM. Taxonomic Note: a place for DNA–DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Evol Microbiol 1994;44:846–849 [CrossRef]
    [Google Scholar]
  33. Stackebrandt E, Ebers J. Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 2006;33:152–155
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.003103
Loading
/content/journal/ijsem/10.1099/ijsem.0.003103
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF

Most Cited This Month

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error