Delftia litopenaei sp. nov., a poly-β-hydroxybutyrate- accumulating bacterium isolated from a freshwater shrimp culture pond

International Journal of Systematic and Evolutionary Microbiology

Volumn 62, Issue 10, 2012, Pages 2315-2321

  Chen, Wen Ming ^a   Lin, Yang Shun ^a   Sheu, Der Shyan ^a   Sheu, Shih Yi ^a  

^a NATIONAL KAOHSIUNG UNIVERSITY OF APPLIED SCIENCES   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; CARDIOLIPIN; FATTY ACID; FRESH WATER; ISOPRENOID QUINONE; PHOSPHATIDYLETHANOLAMINE; PHOSPHATIDYLGLYCEROL; PHOSPHOLIPID; POLY(3 HYDROXYBUTYRIC ACID); POLYHYDROXYALKANOATE SYNTHASE; QUINONE DERIVATIVE; RIBOSOME RNA; UNCLASSIFIED DRUG;

ARTICLE; BACTERIAL GENETICS; BACTERIUM ISOLATION; BURKHOLDERIALES; CHEMOTAXONOMY; DELFTIA; DELFTIA ACIDOVORANS; DELFTIA LACUSTRIS; DELFTIA LITOPENAEI; DELFTIA TSURUHATENSIS; DNA BASE COMPOSITION; GENE SEQUENCE; GENOTYPE; GRAM NEGATIVE BACTERIUM; LIPID ANALYSIS; NONHUMAN; NUCLEOTIDE SEQUENCE; PHENOTYPE; PHYLOGENY; POND; PRIORITY JOURNAL; SHRIMP; TAIWAN;

ANIMALS; BACTERIAL TYPING TECHNIQUES; BASE COMPOSITION; DELFTIA; DNA, BACTERIAL; FATTY ACIDS; HYDROXYBUTYRATES; MOLECULAR SEQUENCE DATA; PENAEIDAE; PHYLOGENY; POLYESTERS; PONDS; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; TAIWAN; WATER MICROBIOLOGY;

BACTERIA (MICROORGANISMS); BURKHOLDERIALES; DECAPODA (CRUSTACEA); DELFTIA; DELFTIA ACIDOVORANS; DELFTIA TSURUHATENSIS; NEGIBACTERIA;

EID: 84863720189     PISSN: 14665026     EISSN: None     Source Type: Journal    
DOI: 10.1099/ijs.0.037507-0     Document Type: Article

References (36)

1. Anzai, Y., Kudo, Y. & Oyaizu, H. (1997). The phylogeny of the genera Chryseomonas, Flavimonas, and Pseudomonas supports synonymy of these three genera. Int J Syst Bacteriol 47, 249-251.
2. Bowman, J. P. (2000). Description of Cellulophaga algicola sp. nov., isolated from the surfaces of Antarctic algae, and reclassification of Cytophaga uliginosa (ZoBell and Upham 1944) Reichenbach 1989 as Cellulophaga uliginosa comb. nov. Int J Syst Evol Microbiol 50, 1861-1868.
3. Breznak, J. A. & Costilow, R. N. (1994). Physicochemical factors in growth. In Methods for General and Molecular Bacteriology, pp. 137-154. Edited by P. Gerhardt, R. G. E. Murray, W. A. Wood & N. R. Krieg. Washington, D.C.: American Society for Microbiology.
4. Cai, L., Liu, G., Rensing, C. & Wang, G. (2009). Genes involved in arsenic transformation and resistance associated with different levels of arsenic-contaminated soils. BMC Microbiol 9, 4.
5. Chen, W. M., Laevens, S., Lee, T. M., Coenye, T., De Vos, P., Mergeay, M. & Vandamme, P. (2001). Ralstonia taiwanensis sp. nov., isolated from root nodules of Mimosa species and sputum of a cystic fibrosis patient. Int J Syst Evol Microbiol 51, 1729-1735.
6. Chun, J., Lee, J.-H., Jung, Y., Kim, M., Kim, S., Kim, B. K. & Lim, Y. W. (2007). EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences. Int J Syst Evol Microbiol 57, 2259-2261.
7. Collins, M. D. (1985). Isoprenoid quinone analysis in classification and identification. In Chemical Methods in Bacterial Systematics, pp. 267-287. Edited by M. Goodfellow & D. E. Minnikin. London: Academic Press.
8. Embley, T. M. & Wait, R. (1994). Structural lipids of eubacteria. In Chemical Methods in Prokaryotic Systematics, pp. 121-161. Edited by M. Goodfellow & A. G. O'Donnell. Chichester: John Wiley.
9. Ezaki, T., Hashimoto, Y. & Yabuuchi, E. (1989). 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 39, 224-229.
10. Felsenstein, J. (1981). Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17, 368-376.
11. Felsenstein, J. (1993). PHYLIP (phylogeny inference package), version 3.5c. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle, USA.
12. Hall, T. A. (1999). BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41, 95-98.
13. Jørgensen, N. O. G., Brandt, K. K., Nybroe, O. & Hansen, M. (2009). Delftia lacustris sp. nov., a peptidoglycan-degrading bacterium from fresh water, and emended description of Delftia tsuruhatensis as a peptidoglycan-degrading bacterium. Int J Syst Evol Microbiol 59, 2195-2199.
14. Kimura, M. (1983). The Neutral Theory of Molecular Evolution. Cambridge: Cambridge University Press.
15. Kluge, A. G. & Farris, F. S. (1969). Quantitative phyletics and the evolution of anurans. Syst Zool 18, 1-32.
16. Loo, C.-Y. & Sudesh, K. (2007). Biosynthesis and native granule characteristics of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) in Delftia acidovorans. Int J Biol Macromol 40, 466-471.
17. Maidak, B. L., Cole, J. R., Lilburn, T. G., Parker, C. T., Jr, Saxman, P. R., Farris, R. J., Garrity, G. M., Olsen, G. J., Schmidt, T. M. & Tiedje, J. M. (2001). The RDP-II (Ribosomal Database Project). Nucleic Acids Res 29, 173-174.
18. Mesbah, M., Premachandran, U. & Whitman, W. B. (1989). Precise measurement of the G+C content of deoxyribonucleic acid by highperformance liquid chromatography. Int J Syst Bacteriol 39, 159-167.
19. Murray, R. G. E., Doetsch, R. N. & Robinow, C. F. (1994). Determinative and cytological light microscopy. In Methods for General and Molecular Bacteriology, pp. 21-41. Edited by P. Gerhardt, R. G. E. Murray, W. A. Wood & N. R. Krieg. Washington, D.C.: American Society for Microbiology.
20. Nokhal, T. H. & Schlegel, H. G. (1983). Taxonomic study of Paracoccus denitrificans. Int J Syst Bacteriol 33, 26-37.
21. Pelz, O., Cifuentes, L. A., Hammer, B. T., Kelley, C. A. & Coffin, R. B. (1998). Tracing the assimilation of organic compounds using d13C analysis of unique amino acids in the bacterial peptidoglycan cell wall. FEMS Microbiol Ecol 25, 229-240.
22. Powers, E. M. (1995). Efficacy of the Ryu nonstaining KOH technique for rapidly determining gram reactions of food-borne and waterborne bacteria and yeasts. Appl Environ Microbiol 61, 3756-3758.
23. Saitou, N. & Nei, M. (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406-425.
24. Sasser, M. (1990). Identification of bacteria by gas chromatography of cellular fatty acids. Newark, DE: MIDI Inc.
25. Schlegel, H. G., Lafferty, R. & Krauss, I. (1970). The isolation of mutants not accumulating poly-b-hydroxybutyric acid. Arch Mikrobiol 71, 283-294.
26. Sheu, D. S., Wang, Y. T. & Lee, C. Y. (2000). Rapid detection of polyhydroxyalkanoate-accumulating bacteria isolated from the environment by colony PCR. Microbiology 146, 2019-2025.
27. Shigematsu, T., Yumihara, K., Ueda, Y., Numaguchi, M., Morimura, S. & Kida, K. (2003). Delftia tsuruhatensis sp. nov., a terephthalateassimilating bacterium isolated from activated sludge. Int J Syst Evol Microbiol 53, 1479-1483.
28. Siew, E. L., Rajab, N. F., Osman, A. B., Sudesh, K. & Inayat-Hussain, S. H. (2009). Mutagenic and clastogenic characterization of poststerilized poly(3-hydroxybutyrate-co-4-hydroxybutyrate) copolymer biosynthesized by Delftia acidovorans. J Biomed Mater Res A 91, 786-794.
29. Smibert, R. M. & Krieg, N. R. (1994). Phenotypic characterization. In Methods for General and Molecular Bacteriology, pp. 607-654. Edited by P. Gerhardt, R. G. E. Murray, W. A. Wood & N. R. Krieg. Washington, DC: American Society for Microbiology.
30. Spiekermann, P., Rehm, B. H. A., Kalscheuer, R., Baumeister, D. & Steinbüchel, A. (1999). A sensitive, viable-colony staining method using Nile red for direct screening of bacteria that accumulate polyhydroxyalkanoic acids and other lipid storage compounds. Arch Microbiol 171, 73-80.
31. 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.
32. Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F. & Higgins, D. G. (1997). The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25, 4876-4882.
33. Wayne, L. G., Brenner, D. J., Colwell, R. R., Grimont, P. A. D., Kandler, O., Krichevsky, M. I., Moore, L. H., Moore, W. E.C., Murray, R. G. E. & other authors (1987). International Committee on Systematic Bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37, 463-464.
34. Wen, A., Fegan, M., Hayward, C., Chakraborty, S. & Sly, L. I. (1999). Phylogenetic relationships among members of the Comamonadaceae, and description of Delftia acidovorans (den Dooren de Jong 1926 and Tamaoka et al. 1987) gen. nov., comb. nov. Int J Syst Bacteriol 49, 567-576.
35. Wen, C. M., Tseng, C. S., Cheng, C. Y. & Li, Y. K. (2002). Purification, characterization and cloning of a chitinase from Bacillus sp. NCTU2. Biotechnol Appl Biochem 35, 213-219.
36. 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.