Use of the 16S-23S ribosomal genes spacer region for the molecular typing of sphingomonads

Canadian Journal of Microbiology

Volumn 54, Issue 8, 2008, Pages 668-676

  Tokajian, Sima ^a   Al Medawar, Siba ^a   Hashwa, Fuad ^a  

^a LEBANESE AMERICAN UNIVERSITY   (Lebanon)

Author keywords

16S rDNA; Fingerprinting; ITS; Sphingomonads

Indexed keywords

AMPLIFICATION; POTABLE WATER;

16S RDNA; BANDING PATTERNS; COLONY MORPHOLOGY; DRINKING WATER; FINGERPRINTING; ITS; MOLECULAR TYPING; OPPORTUNISTIC INFECTIONS; REFERENCE STRAINS; RESTRICTION DIGESTION; RIBOSOMAL GENES; SPHINGOMONADS; TRANSCRIBED SPACER;

INTELLIGENT VEHICLE HIGHWAY SYSTEMS;

DNA 16S; DNA 23S; DRINKING WATER; SPACER DNA;

BACTERIAL DISEASE; DNA FINGERPRINTING; DRINKING WATER; GENE EXPRESSION; MOLECULAR ANALYSIS;

ARTICLE; BACTERIAL COLONIZATION; BACTERIAL STRAIN; CONTROLLED STUDY; DNA POLYMORPHISM; GENE AMPLIFICATION; MOLECULAR TYPING; MORPHOLOGY; NONHUMAN; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN ISOLATION; PROTEIN PURIFICATION; REPRODUCIBILITY; SPHINGOMONAS;

DNA, BACTERIAL; DNA, RIBOSOMAL SPACER; FRESH WATER; MOLECULAR SEQUENCE DATA; RIBOTYPING; RNA, RIBOSOMAL, 16S; RNA, RIBOSOMAL, 23S; SPHINGOMONADACEAE;

EID: 49449086182     PISSN: 00084166     EISSN: None     Source Type: Journal    
DOI: 10.1139/W08-054     Document Type: Article

References (36)

1. Amy, P.S., Haldeman, D.L., Ringelberg, D., Hall, D.H., and Russell, C. 1992. Comparison of identification systems for classification of bacteria isolated from water and endolithic habitats within deep subsurfaces. Appl. Environ. Microbiol. 58: 3367-3373. PMID:16348791.
2. Barbeau, J., Tanguay, R., Faucher, E., Avezard, C., Trudel, L., Côté, L., and Prévost, A.P. 1996. Multiparametric analysis of waterline contamination in dental units. Appl. Environ. Microbiol. 62: 3954-3959. PMID:8899982.
3. Condon, C., Squires, C., and Squires, C.L. 1995. Control of rRNA transcription in Escherichia coli. Microbiol. Rev. 59: 623-645. PMID:8531889.
4. Fegatella, F., and Cavicchioli, R. 2000. Physiological responses to starvation in the marine oligotrophic ultramicrobacterium Sphingomonas sp. strain RB2256. Appl. Environ. Microbiol. 66: 2037-2044. doi:10.1128/AEM.66.5.2037-2044.2000. PMID:10788378.
5. Fegatella, F., Lim, J., Kjelleberg, S., and Cavicchioli, R. 1998. Implications of rRNA operon copy number and ribosome content in the marine oligotrophic ultramicrobacterium Sphingomonas sp. strain RB2256. Appl. Environ. Microbiol. 64: 4433-4438. PMID:9797303.
6. Fujii, K., Urano, N., Ushio, H., Satomi, M., Iida, H., Ushio-Sata, N., and Kimura, S. 2000. Profile of a nonylphenol-degrading microflora and its potential for bioremedial applications. J. Biochem. 128: 909-916. PMID:11098132.
7. Garcia-Martinez, J., Acinas, S.G., Anton, A.I., and Rodriguez-Valera, F. 1999. Use of the 16S-23S ribosomal genes spacer region in studies of prokaryotic diversity. J. Microbiol. Methods, 36: 55-64. doi:10.1016/S0167-7012(99) 00011-1. PMID:10353800.
8. Garcia-Martinez, J., Bescos, I., Rodriguez-Sala, J., and Rodriguez-Valera, F. 2001. RISSC: a novel database for ribosomal 16S-23S RNA genes spacer region. Nucleic Acids Res. 29: 178-180. doi:10.1093/nar/29. 1.178. PMID:11125084.
9. Hsueh, P.R., Teng, L.J., Yang, P.C., Chen, Y.C., Pan, H.J., Ho, S.W., and Luh, K.T. 1998. Nosocomial infections caused by Sphingomonas paucimobilis: clinical features and microbiological characteristics. Clin. Infect. Dis. 26: 676-681. doi:10.1086/514595. PMID:9524843.
10. Jensen, M.A., Webster, J.A., and Straus, N. 1993. Rapid identification of bacteria on the basis of polymerase chain reaction-amplified ribosomal DNA spacer polymorphisms. Appl. Environ. Microbiol. 59: 945-952. PMID:8476298.
11. Kabadjova, P., Dousset, X., Le Cam, V., and Prevost, H. 2002. Differentiation of closely related Carnobacterium food isolates based on 16S-23S ribosomal DNA intergenic spacer region polymorphism. Appl. Environ. Microbiol. 68: 5358-5366. PMID:12406725.
12. Kelley, S.T., Theisen, U., Angenent, L.T., Amand, A., and Pace, N.R. 2004. Molecular analysis of shower curtain biofilm microbes. Appl. Environ. Microbiol. 70: 4187-4192. doi:10.1128/AEM.70.7.4187-4192.2004. PMID:15240300.
13. Kwon, H.-R., and Kim, Y.-C. 2007. Nucleotide sequence and secondary structure of 5S rRNA from Sphingobium chungbukense DJ77. J. Microbiol. 45: 79-82. PMID:17342061.
14. Lane, D.J., Pace, B., Olsen, G.J., Stahl, D.A., Sogin, M.L., and Pace, N.R. 1985. Rapid determination of 16S ribosomal RNA sequence for phylogenetic analyses. Proc. Natl. Acad. Sci. U.S.A. 82: 6955-6959. doi:10.1073/pnas.82.20.6955. PMID:2413450.
15. Lee, J.S., Kook, S.Y., Yoon, J.H., Takeuchi, M., Pyun, Y.R., and Park, Y.H. 2001. Sphingomonas aquatilis sp. nov., Sphingomonas koreensis sp. nov., and Sphingomonas taejonensis sp. nov., yellow-pigmented bacteria isolated from natural mineral water. Int. J. Syst. Evol. Microbiol. 51: 1491-1498. PMID:11491350.
16. Lemaitre, D., Elaichouni, A., Hunhausen, M., Glaeys, G., Vanhaesebrouck, P., Vaneechoutte, M., and Verschaegen, G. 1996. Tracheal colonization with Sphingomonas paucimobilis in mechanically ventilated neonates due to contaminated ventilator temperature probes. J. Hosp. Infect. 32: 199-206. doi:10.1016/S0195-6701(96)90146-2. PMID:8690883.
17. Leys, N.M., Ryngaert, A., Bastiaens, L., Verstraete, W., Top, E.M., and Springael, D. 2004. Occurrence and phylogenetic diversity of Sphingomonas strains in soils contaminated with polycyclic aromatic hydrocarbons. Appl. Environ. Microbiol. 70: 1944-1955. doi:10.1128/AEM.70.4.1944-1955.2004. PMID:15066784.
18. Matar, G.M., Swaminathan, B., Hunter, S.B., Slater, L.N., and Welch, D. 1993. Polymerase chain reaction-based restriction fragment length polymorphism analysis of a fragment of ribosomal operon from Rochalimaea species for subtyping. J. Clin. Microbiol. 31: 1730-1734. PMID:8102375.
19. Momma, K., Hashimoto, W., Miyake, O., Yoon, H.-J., Kawai, S., Mishima, Y., et al. 1999. Special cell surface structure, and novel macromolecule transport/depolymerization system of Sphingomonas sp. A1. J. Ind. Microbiol. Biotechnol. 23: 425-435. doi:10.1038/sj.jim.2900719. PMID:11423964.
20. Mossel, D.A., and Struijk, C.B. 2004. Assessment of the microbial integrity, sensu G.S. Wilson, of piped and bottled drinking water in the condition as ingested. Int. J. Food Microbiol. 92: 375-390. doi:10.1016/j.ijfoodmicro.2003.08.015. PMID:15145596.
21. Perola, O., Nousiainen, T., Suomalainen, S., Aukee, S., Karkkainen, U.M., Kauppinen, J., et al. 2002. Recurrent Sphingomonas paucimobilis-bacteraemia associated with a multi-bacterial water-borne epidemic among neutropenic patients. J. Hosp. Infect. 50: 196-201. doi:10.1053/jhin. 2001.1163. PMID:11886195.
22. Pollock, T.J. 1993. Gellan-related polysaccharides and the genus Sphingomonas. J. Gen. Microbiol. 139: 1939-1945.
23. Pollock, T.J., and Armentrout, R.W. 1999. Planktonic/sessile dimorphism of polysacharride incapsulated sphingomonads. J. Ind. Microbiol. Biotechnol. 23: 436-441. doi:10.1038/sj.jim.2900710. PMID:11423965.
24. Reasoner, D.J., and Geldreich, E.E. 1985. A new medium for the enumeration and subculture of bacteria from potable water. Appl. Environ. Microbiol. 49: 1-7. PMID:3883894.
25. Sørensen, S.R., Ronen, Z., and Aamand, J. 2001. Isolation from agricultural soil and characterization of a Sphingomonas sp. able to mineralize the phenyl urea herbicide isoproturon. Appl. Environ. Microbiol. 67: 5403-5409. doi:10.1128/AEM.67.12.5403-5409.2001. PMID:11722885.
26. Tabata, K., Kasuya, K., Abe, H., Masuda, K., and Doi, Y. 1999. Poly (aspartic acid) degradation by a Sphingomonas sp. isolated from freshwater. Appl. Environ. Microbiol. 65: 4268-4270. PMID:10473451.
27. Takeuchi, M., Sakane, T., Yanagi, M., Yamasato, K., Hamana, K., and Yokota, A. 1995. Taxonomic study of bacteria isolated from plants: proposal of Sphingomonas rosa sp. nov., Sphingomonas pruni sp. nov., Sphingomonas asaccharolytica sp. nov., and Sphingomonas mali sp. nov. Int. J. Syst. Bacteriol. 45: 334-341. PMID:7537068.
28. Takeuchi, M., Hamana, K., and Hiraishi, A. 2001. 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. 51: 1405-1417. PMID:11491340.
29. Tokajian, S., and Hashwa, F. 2004a. Microbiological quality and genotypic speciation of heterotrophic bacteria isolated from potable water stored in household tanks. Water Qual. Res. J. Can. 19: 64-73.
30. Tokajian, S., and Hashwa, F. 2004b. Incidence of antibiotic resistance in coliforms from drinking water and their identification using the Biolog and the API identification systems. J. Chemother. 16: 45-50. doi:10.1159/000076619. PMID:15077998.
31. Tokajian, S., and Hashwa, F. 2004c. Phenotypic and genotypic identification of Aeromonas spp. isolated from a chlorinated intermittent water distribution system in Lebanon. J. Water Health, 2: 115-122. PMID:15387135.
32. Tokajian, S.T., Hashwa, F.A., Hancock, I.C., and Zalloua, P.A. 2005. Phylogenetic assessment of heterotrophic bacteria from a water distribution system using 16S rDNA sequencing. Can. J. Microbiol. 51: 325-335. doi:10.1139/w05-007. PMID:15980895.
33. White, D.C., Sutton, S.D., and Ringelberg, D.B. 1996. The genus Sphingomonas: physiology and ecology. Curr. Opin. Biotechnol. 7: 301-306. doi:10.1016/S0958-1669(96)80034-6. PMID:8785434.
34. Yabuuchi, E., Yano, I., Oyaizu, H., Hashimoto, Y., Ezaki, T., and Yamamoto, H. 1990. 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. 34: 99-119. PMID:2111872.
35. Yabuuchi, E., Kosako, Y., Fujiwara, N., Naka, T., Matsunaga, I., Ogura, H., and Kobayashi, K. 2002. Emendation of the genus Sphingomonas and junior objective synonymy of the species of three genera, Sphingobium, Novosphingobium and Sphingopyxis, in conjunction with Blastomonas ursincola. Int. J. Syst. Evol. Microbiol. 52: 1485-1496. doi:10.1099/ijs.0.01868-0. PMID:12361250.
36. Yang, D.C., Im, W.T., Kim, M.K., Ohta, H., and Lee, S.T. 2006. Sphingomonas soli sp. nov., a beta-glucosidase-producing bacterium in the family Sphingomonadaceae in the alpha-4 subgroup of the Proteobacteria. Int. J. Syst. Evol. Microbiol. 56: 703-707. doi:10.1099/ijs.0.63839-0. PMID:16585680. Can. J. Microbiol. 54: 595-599 (2008)