Characterization of Rhizobium naphthalenivorans sp. nov. with special emphasis on aromatic compound degradation and multilocus sequence analysis of housekeeping genes

Journal of General and Applied Microbiology

Volumn 58, Issue 3, 2012, Pages 211-224

  Kaiya, Shinichi ^a   Rubaba, Owen ^a   Yoshida, Naoko ^a   Yamada, Takeshi ^a   Hiraishi, Akira ^a  

^a TOYOHASHI UNIVERSITY OF TECHNOLOGY   (Japan)

Author keywords

Multilocus sequence analysis; Naphthalene degradation; Rhizobium naphthalenivorans

Indexed keywords

AROMATIC COMPOUND; DNA 16S; DNA 23S; DNA TOPOISOMERASE (ATP HYDROLYSING) B; FATTY ACID; NAPHTHALENE; PROTEIN DNAK; RECA PROTEIN; RNA 16S; UBIDECARENONE;

ARTICLE; ATPD GENE; BACTERIAL STRAIN; BACTERIUM IDENTIFICATION; BACTERIUM ISOLATE; CARBON SOURCE; DNA BASE COMPOSITION; DNA DNA HYBRIDIZATION; DNAK GENE; ENERGY RESOURCE; FATTY ACID ANALYSIS; GLNLL GENE; GYRB GENE; HOUSEKEEPING GENE; MICROMORPHOLOGY; MOLECULAR PHYLOGENY; MULTILOCUS SEQUENCE TYPING; NONHUMAN; NUCLEOTIDE SEQUENCE; RECA GENE; RHIZOBIUM; RHIZOBIUM NAPHTHALENIVORANS; SEQUENCE ANALYSIS; UNINDEXED SEQUENCE;

AEROBIOSIS; BASE COMPOSITION; BIOTRANSFORMATION; CARBON; CLUSTER ANALYSIS; DNA, BACTERIAL; DNA, RIBOSOMAL; DNA, RIBOSOMAL SPACER; FATTY ACIDS; FLAGELLA; GENES, BACTERIAL; GENES, ESSENTIAL; LOCOMOTION; MOLECULAR SEQUENCE DATA; MULTILOCUS SEQUENCE TYPING; NAPHTHALENES; NUCLEIC ACID HYBRIDIZATION; PHYLOGENY; QUINONES; RHIZOBIUM; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA;

EID: 84865089522     PISSN: 00221260     EISSN: 13498037     Source Type: Journal    
DOI: 10.2323/jgam.58.211     Document Type: Article

References (44)

1. Ben Said, O., Goni-Urriza, M. S., El Bour, M., Dellali, M., Aissa, P., and Duran, R. (2008) Characterization of aerobic polycyclic aromatic hydrocarbon-degrading bacteria from Bizerte lagoon sediments, Tunisia. J. Appl. Microbiol., 104, 987-997.
2. Bernaerts, M. and DeLey, J. (1963) A biochemical test for crown gal bacteria. Nature, 197, 406-407.
3. Felsenstein, J. (1985) Confidence limits on phylogenies: An approach using the bootstrap. Evolution, 39, 783-791.
4. Field, J. A. and Sierra-Alvarez, R. (2008) Microbial degradation of chlorinated dioxins. Chemosphere, 71, 1005-1018.
5. Futamata, H., Uchida, T., Yoshida, N., Yonemitsu, Y., and Hiraishi, A. (2004) Distribution of dibenzofuran-degrading bacteria in soils polluted with different levels of polychlorinated dioxins. Microbes Environ., 19, 172-177.
6. Hiraishi, A. (2003) Biodiversity of dioxin-degrading microorganisms and potential utilization in bioremediation. Microbes Environ., 18, 105-125.
7. Hiraishi, A. (2008) Biodiversity of dehalorespiring bacteria with special emphasis on polychlorinated biphenyl/dioxin dechlorinators. Microbes Environ., 23, 1-12.
8. Hiraishi, A. and Hoshino, Y. (1984) Distribution of rhodoquinone in Rhodospirillaceae and its taxonomic implications. J. Gen. Appl. Micrbiol., 30, 435-448.
9. Hiraishi, A., Kaiya, S., Miyakoda, H., and Futamata, H. (2005) Biotransformation of polychlorinated dioxins and microbial community dynamics in sediment microcosms at different contamination levels. Microbes Environ., 20, 227-242.
10. Hiraishi, A. and Kitamura, H. (1984) Distribution of phototrophic purple nonsulfur bacteria in activated sludge systems and other aquatic environments. Bull. Jpn. Soc. Sci. Fish., 50, 1929-1937.
11. Hiraishi, A., Kamagata, Y., and Nakamura, K. (1995) Polymerase chain reaction amplification and restriction fragment length polymorphism analysis of 16S rRNA genes from methanogens. J. Ferment. Bioeng., 79, 523-529.
12. Hiraishi, A., Ueda, Y., Ishihara, J., and Mori, T. (1996) Comparative lipoquinone analysis of influent sewage and activated sludge by high-performance liquid chromatography and photodiode array detection. J. Gen. Appl. Microbiol., 42, 457-469.
13. Hiraishi, A., Yonemitsu, Y., Matsushita, M., Shin, Y. K., Kuraishi, H., and Kawahara, K. (2002) Characterization of Porphyrobacter sanguineus sp. nov., an aerobic bacteriochlorophyll- containing bacterium capable of degrading biphenyl and dibenzofuran. Arch. Microbiol., 178, 45-52.
14. Hunter, W. J., Kuykendall, L. D., and Manter, D. K. (2007) Rhizobium selenireducens sp. nov.: A selenite-reducing alpha- Proteobacteria isolated from a bioreactor. Curr. Microbiol., 55, 455-460.
15. Jobb, G., von Haeseler, A., and Strimmer, K. (2004) TREEFINDER: A powerful graphical analysis environment for molecular phylogenetics. BMC Evol. Biol., 4,18.
16. Kaiya, S., Utsunomiya, S., Suzuki, S., Yoshida, N., Futamata, H., Yamada, T., and Hiraishi, A. (2012) Isolation and functional gene analyses of aromatic-hydrocarbon-degrading bacteria from a polychlorinated-dioxin-dechlorinating process. Microbes Environ., 29 (in press).
17. Kauer, J., Verma, M., and Lal, R. (2011) Rhizobium rosettiformans sp. nov., isolated from a hexachlorocyclohexane dump site, and reclassification of Blastobacter aggregatus Hirsch and Müller 1986 as Rhizobium aggregatum comb. nov. Int. J. Syst. Evol. Microbiol., 61, 1218-1225.
18. Kubota, M., Kawahara, K., Sekiya, K., Uchida, T., Hattori, Y., Futamata, H., and Hiraishi, A. (2005) Nocardioides aromaticivorans sp. nov., a dibenzofuran-degrading bacterium isolated from dioxin-polluted environments. Syst. Appl. Microbiol., 28, 165-174.
19. AL. In Bergey's Manual of Systematic Bacteriology, 2nd ed., Vol. 2, The Proteobacteria, Part C, The Alpha-, Beta-, Delta-, and Epsilonproteobacteria, ed. by Brenner, D. J., Krieg, N. R., Staley, J. T., and Garrity, G. M. (Editor-in-Chief), Springer, New York, pp.325-340.
20. Laguerre, G., Nour, S. M., Macheret, V., Sanjuan, J., Drouin, P., and Amarger, N. (2001) Classification of rhizobia based on nodC and nifH gene analysis reveals a close phylogenetic relationship among Phaseolus vulgaris symbionts. Microbiology, 147, 981-993.
21. Lane, D. J. (1991) 16S/23S rRNA sequencing. In Nucleic Acid Techniques in Bacterial Systematics, ed. by Stackebrandt, E. and Goodfellow, M., Wiley, New York, pp. 115-175.
22. Leifson, E. (1930) A method of staining bacterial flagella and capsules together with a study of the origin of flagella. J. Bacteriol., 20, 203-211.
23. Ludwig, W., Strunk, O., Westram, R., Richter, L., Meier, H., Yadhukumar Buchner, A., Lai, T., Steppi, S., Jobb, G., Foerster, W., Brettske, I., Gerber, S., Ginhart, A. W., Gross, O., Grumann, S., Hermann, S., Jost, R., Koenig, A., Liss, T., Lüssmann, R., May, M., Nonhoff, B., Reichel, B., Strehlow, R., Stamatakis, A., Stuckmann, N., Vilbig, A., Lenke, M., Ludwig, T., Bode, A., and Schleifer, K. H. (2004) ARB: A software environment for sequence data. Nucleic Acids Res., 32, 1363-1371.
24. Marmur, J. (1961) A procedure for the isolation of deoxyribonucleic acid from micro-organisms. J. Mol. Biol., 3, 208-218.
25. Martens, M., Dawyndt, P., Coopman, R., Gillis, M., De Vos, P., and Willems, A. (2008) Advantages of multilocus sequence analysis for taxonomic studies: A case study using 10 housekeeping genes in the genus Ensifer (including former Sinorhizobium). Int. J. Syst. Evol. Microbiol., 58, 200-214.
26. Martens, M., Delaere, M., Coopman, R., De Vos, P., Gillis, M., and Willems, A. (2007) Multilocus sequence analysis of Ensifer and related taxa. Int. J. Syst. Evol. Microbiol., 57, 489-503.
27. Menna, P., Barcellos, F. G., and Hungria M. (2009) Phylogeny and taxonomy of a diverse collection of Bradyrhizobium strains based on multilocus sequence analysis of the 16S rRNA gene, ITS region and glnII, recA, atpD and dnaK genes. Int. J. Syst. Evol. Microbiol., 59, 2934-2950.
28. Mesbah, M., Premachandran, U., and Whitman, W. B. (1989) Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int. J. Syst. Bacteriol., 39, 159-167.
29. Okamura, K., Takata, K., and Hiraishi, A. (2009) Intrageneric relationships of members of the genus Rhodopseudomonas. J. Gen. Appl. Microbiol., 55, 469-478.
30. Quan, Z. X., Bae, H. S., Baek, J. H., Chen, W. F., Im, W. T., and Lee, S. T. (2005) Rhizobium daejeonense sp. nov. isolated from a cyanide treatment bioreactor. Int. J. Syst. Evol. Microbiol., 55, 2543-2549.
31. Rivas, R., Velázquez, E., Willems, A., Vizcaíno, N., Subba-Rao, N. S., Mateos, P. F., Gillis, M., Dazzo, F. B., and Martínez-Molina, E. (2002) A new species of Devosia that forms a unique nitrogen-fixing rootnodule symbiosis with the aquatic legume Neptunia natans (L. f.) Druce. Appl. Environ. Microbiol., 68, 5217-5222.
32. Saitou, N. and Nei, M. (1987) The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol., 4, 406-425.
33. Sanchez, O., Diestra, E., Esteve, I., and Mas, J. (2005) Molecular characterization of an oil-degrading cyanobacterial consortium. Microb. Ecol., 50, 580-588.
34. Sawada, H., Kuykendall, L. D., and Young, J. M. (2003) Changing concepts in the systematics of bacterial nitrogen-fixing legume symbionts. J. Gen. Appl. Microbiol., 49, 155-179.
35. Stackebrandt, E. and Ebers, J. (2006) Taxonomic parameters revised: Tarnished gold standards. Microbiol. Today, 6, 152-155.
36. Suzuki, S. and Hiraishi, A. (2007) Novosphingobium naphthalenivorans sp. nov., a naphthalene-degrading bacterium isolated from polychlorinated-dioxin-contaminated environments. J. Gen. Appl. Microbiol., 53, 221-228.
37. Swofford, D. L. (2002) PAUP* 4 phlyogenetic analysis using parsimony (and other methods), version 4. Sinauer Associates, Sunderland, MA.
38. Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M., and Kumar, S. (2011) MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol., 28, 2731-2739.
39. Tan, Z., Hurek, T., Vinuesa, P., Müller, P., Ladha, J. K., and Reinhold-Hurek, B. (2001) Specific detection of Bradyrhizobium and Rhizobium strains colonizing rice (Oryza sativa) roots by 16S-23S ribosomal DNA intergenic spacer-targeted PCR. Appl. Environ. Microbiol., 67, 3655-3664.
40. Tighe, S. W., De Lajudie, P., Dipietro, K., Lindstroem K., Nick, G., and Jarvis, B. D. W. (2000) Analysis of cellular fatty acids and phenotypic relationships of Agrobacterium, Bradyrhizobium, Mesorhizobium, Sinorhizobium and Rhizobium species using the Sherlock Microbial Identification System. J. Syst. Evol. Microbiol., 50, 787-801.
41. Vinuesa, P., Silva, C., Werner, D., and Martinez-Romero, E. (2005) Population genetics and phylogenetic inference in bacterial molecular systematics: The roles of migration and recombination in Bradyrhizobium species cohesion and delineation. Mol. Phylogenet. Evol., 34, 29-54.
42. Wernegreen, J. J. and Riley, M. A. (1999) Comparison of the evolutionary dynamics of symbiotic and housekeeping loci: A case for the genetic coherence of rhizobial lineages. Mol. Biol. Evol., 16, 98-113.
43. Willems, A., Coopman, R., and Gillis, M. (2001) Comparison of sequence analysis of 16S-23S rDNA spacer regions, AFLP analysis and DNA-DNA hybridizations in Bradyrhizobium. Int. J. Syst. Evol. Microbiol., 51, 623-632.
44. Yoshida, N., Takahashi, N., and Hiraishi, A. (2005) Phylogenetic characterization of a polychlorinated-dioxin-dechlorinating microbial community by use of microcosm studies. Appl. Environ. Microbiol., 71, 4325-4334.