Zhizhongheella caldifontis gen. nov., sp. nov., a novel member of the family Comamonadaceae

Antonie van Leeuwenhoek, International Journal of General and Molecular Microbiology

Volumn 105, Issue 4, 2014, Pages 755-761

  Dong, Lei ^a   Ming, Hong ^a,b   Liu, Lan ^a   Zhou, En Min ^a   Yin, Yi Rui ^a   Duan, Yan Yan ^c   Nie, Guo Xing ^c   Feng, Hui Geng ^b   Li, Wen Jun ^a  

^a YUNNAN UNIVERSITY   (China)

^b XINXIANG MEDICAL UNIVERSITY   (China)

^c HENAN NORMAL UNIVERSITY   (China)

Author keywords

Family Comamonadaceae; Hehua hot spring; Polyphasic taxonomy; Zhizhongheella caldifontis sp. nov.; Zhizhongheella gen. nov.

Indexed keywords

BACTERIAL DNA; BACTERIAL RNA; CYTOSINE; GENOMIC DNA; GUANINE; RNA 16S; SODIUM CHLORIDE; UBIQUINONE;

16S RRNA GENE; AEROBIC BACTERIUM; ARTICLE; BACTERIAL GENE; BACTERIAL GROWTH; BACTERIAL STRAIN; BACTERIUM COLONY; BACTERIUM ISOLATION; BETAPROTEOBACTERIA; CHINA; CLUSTER ANALYSIS; COMAMONADACEAE; CONTROLLED STUDY; GENE SEQUENCE; GENOTYPE; GRAM NEGATIVE BACTERIUM; HEAT TOLERANCE; NONHUMAN; NUCLEOTIDE SEQUENCE; PH; PHENOTYPE; PHYLOGENY; PRIORITY JOURNAL; PROTEIN CONTENT; STRAIN DIFFERENCE; THERMAL SPRING; WATER SAMPLING; ZHIZHONGHEELLA CALDIFONTIS;

BACTERIA (MICROORGANISMS); BETAPROTEOBACTERIA; COMAMONADACEAE;

BACTERIAL TYPING TECHNIQUES; BASE COMPOSITION; CHINA; CLUSTER ANALYSIS; COMAMONADACEAE; DNA, BACTERIAL; DNA, RIBOSOMAL; FATTY ACIDS; HOT SPRINGS; MOLECULAR SEQUENCE DATA; PHYLOGENY; QUINONES; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA;

EID: 84896494210     PISSN: 00036072     EISSN: 15729699     Source Type: Journal    
DOI: 10.1007/s10482-014-0131-6     Document Type: Article

References (36)

1. Blackall LL, Crocetti GR, Saunders AM, Bond PL (2002) A review and update of the microbiology of enhanced biological phosphorus removal in wastewater treatment plants. Antonie Van Leeuwenhoek 81:681-691 (Pubitemid 35314650)
2. Cerny G (1978) Studies on aminopeptidase for the distinction of Gram-negative from Gram-positive bacteria. Appl Microbiol Biotechnol 5:113-122
3. Chou YJ, Sheu SY, Sheu DS, Wang JT, Chen WM (2006) Schlegelella aquatica sp. nov., a novel thermophilic bacterium isolated from a hot spring. Int J Syst Evol Microbiol 56:2793-2797
4. Collins MD, Pirouz T, Goodfellow M, Minnikin DE (1977) Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 100:221-230 (Pubitemid 8122111)
5. Dubinina GA, Grabovich MY (1984) Isolation, cultivation, and characteristics of Macromonas bipunctata. Microbiology (English translation of Microbiologia) 53:610-617
6. Elbanna K, Lütke-Eversloh T, van Trappen S, Mergaert J, Swings J, Steinbüchel A (2003) Schlegelella thermodepolymerans gen. nov., sp. nov., a novel thermophilic bacterium that degrades poly(3-hydroxybutyrate-co-3- mercaptopropionate). Int J Syst Evol Microbiol 53:1165-1168 (Pubitemid 36896532)
7. Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368-376
8. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783-791
9. Fitch WM (1971) Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20:406-416
10. Ginige MP, Hugenholtz P, Daims H, Wagner M, Keller J, Blackall LL (2004) Use of stable-isotope probing, fullcycle rRNA analysis, and fluorescence in situ hybridization-microautoradiography to study a methanol-fed denitrifying microbial community. Appl Environ Microbiol 70:588-596 (Pubitemid 38090252)
11. Gonzalez C, Gutierrez C, Ramirez C (1978) Halobacterium vallismortis sp. nov., an amylolytic and carbohydrate-metabolizing, extremely halophilic bacterium. Can J Microbiol 24:710-715 (Pubitemid 8380304)
12. Grabovich M, Gavrish E, Kuever J, Lysenko AM, Podkopaeva D, Dubinina G (2006) Proposal of Giesbergeria voronezhensis gen. nov., sp. nov. and G. kuznetsovii sp. nov. and reclassification of [Aquaspirillum] anulus, [A.] sinuosum and [A.] giesbergeri as Giesbergeria anulus comb. nov., G. sinuosa comb. nov. and G. giesbergeri comb. nov., and [Aquaspirillum] metamorphum and [A .] psychrophilum as Simplicispira metamorpha gen. nov., comb. nov. and S. psychrophila comb. nov. Int J Syst Evol Microbiol 56:569-576
13. Heylen K, Lebbe L, De Vos P (2008) Acidovorax caeni sp. nov., a denitrifying species with genetically diverse isolates from activated sludge. Int J Syst Evol Microbiol 58:73-77 (Pubitemid 351843541)
14. Hiraishi A, Shin YK, Sugiyama J (1995) Brachymonas denitrificans gen, nov, sp, nov, an aerobic chemoorganotrophic bacterium which contains rhodoquinones, and evolutionary relationships of rhodoquinone producers to bacterial species with various quinone classes. J Gen Appl Microbiol 41:99-117
15. Juretschko S, Loy A, Lehner A, Wagner M (2002) The microbial community composition of a nitrifying-denitrifying activated sludge from an industrial sewage treatment plant analyzed by the full-cycle rRNA approach. Syst Appl Microbiol 25:84-99 (Pubitemid 34602149)
16. Kim OS, Cho YJ, Lee K, Yoon SH, Kim M, Na H, 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. doi:10.1099/ijs.0.038075-0
17. 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
18. 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 5:2359-2387
19. Lee N, Nielsen PH, Aspegren H, Henze M, Schleifer KH, la Cour Jansen J (2003) Long-term population dynamics and in situ physiology in activated sludge systems with enhanced biological phosphorus removal operated with and without nitrogen removal. Syst Appl Microbiol 26:211-227
20. Li WJ, Xu P, Schumann P, Zhang YQ, Pukall R, Xu LH, Stackebrandt E, Jiang CL (2007) 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 57:1424-1428 (Pubitemid 47162982)
21. Locci R (1989) Streptomyces and related genera. In: Williams ST, Sharpe ME, Holt JG (eds) Bergey's manual of systematic bacteriology, vol 4. Williams & Wilkins, Baltimore, pp 2451-2508
22. 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
23. Ming H, Nie GX, Jiang HC, Yu TT, Zhou EM, Feng HG, Tang SK, Li WJ (2012) Paenibacillus frigoriresistens sp. nov., a novel psychrotroph isolated from a peat bog in Heilongjiang. Northern China. Antonie van Leeuwenhoek 102:297-305
24. Purkhold U, Pommerening-Röser A, Juretschko S, Schmid MC, Koops HP, Wagner M (2000) Phylogeny of all recognized species of ammonia oxidizers based on comparative 16S rRNA and amoA sequence analysis: implications for molecular diversity surveys. Appl Environ Microbiol 66:5368-5382 (Pubitemid 32217144)
25. Rouvière PE, Chen MW (2003) Isolation of Brachymonas petroleovorans CHX, a novel cyclohexane-degrading β-proteobacterium. FEMS Microbiol Lett 227:101-106 (Pubitemid 41123327)
26. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406-425
27. Shirling EB, Gottlieb D (1966) Methods for characterization of Streptomyces species. Int J Syst Bacteriol 16:313-340
28. Spring S, Wagner M, Schumann P, Kämpfer P (2005) Malikia granosa gen. nov., sp. nov., a novel polyhydroxyalkanoate- and polyphosphate- accumulating bacterium isolated from activated sludge, and reclassification of Pseudomonas spinosa as Malikia spinosa comb. nov. Int J Syst Evol Microbiol 55:621-629 (Pubitemid 40485043)
29. Takeda M, Kamagata Y, Ghiorse WC, Hanada S, Koizumi J (2002) Caldimonas manganoxidans gen. nov., sp. nov., a poly(3-hydroxybutyrate)-degrading, manganese-oxidizing thermophile. Int J Syst Evol Microbiol 52:895-900 (Pubitemid 34591217)
30. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731-2739
31. 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 (Pubitemid 28022245)
32. Williams ST, Goodfellow M, Alderson G (1989) Genus Streptomyces Waksman and Henrici 1943, 339AL. In: Williams ST, Sharpe ME, Holt JG (eds) Bergey's manual of systematic bacteriology, vol. 4. Williams & Wilkins, Baltimore, pp 2463-2468
33. Willems A, Pot B, Falsen E, Vandamme P, Gillis M, Kersters K, De Ley J (1991) Polyphasic taxonomic study of the emended genus Comamonas: relationship to Aquaspirillum aquaticum, E. Falsen group 10, and other clinical isolates. Int J Syst Bacteriol 41:427-444
34. Yu XY, Li YF, Zheng JW, Li Y, Li L, He J, Li SP (2011) Comamonas zonglianii sp. nov., isolated from phenol-contaminated soil. Int J Syst Evol Microbiol 61:255-258
35. Yu TT, Zhou EM, Yin YR, Yao JC, Ming H, Dong L, Li S, Nie GX & Li WJ (2013) Vulcaniibacterium tengchongense gen. nov., sp. nov. isolated from a geothermally heated soil sample, and reclassification of Lysobacter thermophilus Wei et al. 2012 as Vulcaniibacterium thermophilum comb. nov. Antonie van Leeuwenhoek: 1-8
36. Zhang WY, Fang MX, Zhang WW, Xiao C, Zhang XQ, Yu ZP, Zhu XF, Wu M (2012) Extensimonas vulgaris gen. nov., sp. nov., a member of the family Comamonadaceae. Int J Syst Evol Microbiol 63:2062-2068