Pelagicoccus mobilis gen. nov., sp. nov., Pelagicoccus albus sp. nov. and Pelagicoccus litoralis sp. nov., three novel members of subdivision 4 within the phylum 'Verrucomicrobia', isolated from seawater by in situ cultivation

International Journal of Systematic and Evolutionary Microbiology

Volumn 57, Issue 7, 2007, Pages 1377-1385

  Yoon, Jaewoo ^a   Yasumoto Hirose, Mina ^b,c   Matsuo, Yoshihide ^b   Nozawa, Midori ^b   Matsuda, Satoru ^b   Kasai, Hiroaki ^b   Yokota, Akira ^a  

^a UNIVERSITY OF TOKYO   (Japan)

^b MARINE BIOTECHNOLOGY INSTITUTE   (Japan)

^c Japan Science and Technology Agency   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; BACTERIAL RNA; DIAMINOPIMELIC ACID; FATTY ACID; MENAQUINONE; MURAMIC ACID; PEPTIDOGLYCAN; RNA 16S;

AMINO ACID ANALYSIS; ANTIBIOTIC SENSITIVITY; ARTICLE; BACTERIAL CELL; BACTERIAL GENE; BACTERIAL STRAIN; BACTERIUM ISOLATION; CELL WALL; DNA CONTENT; DNA DNA HYBRIDIZATION; GENE SEQUENCE; GENETIC SIMILARITY; GRAM NEGATIVE BACTERIUM; IN SITU HYBRIDIZATION; JAPAN; NEW GENUS; NEW SPECIES; NONHUMAN; NUCLEOTIDE SEQUENCE; PALAU; PELAGICOCCUS ALBUS; PELAGICOCCUS LITORALIS; PELAGICOCCUS MOBILIS; PHYLOGENY; PHYLUM; PRIORITY JOURNAL; SPECIES DIFFERENCE; TAXONOMIC RANK; VERRUCOMICROBIA;

ANTI-BACTERIAL AGENTS; BACTERIA; BASE COMPOSITION; CELL WALL; DIAMINOPIMELIC ACID; DNA, BACTERIAL; DNA, RIBOSOMAL; FATTY ACIDS; GENES, RRNA; JAPAN; MICROBIAL SENSITIVITY TESTS; MICROSCOPY, ELECTRON, TRANSMISSION; MOLECULAR SEQUENCE DATA; MURAMIC ACIDS; NUCLEIC ACID HYBRIDIZATION; PALAU; PHYLOGENY; RNA, BACTERIAL; RNA, RIBOSOMAL, 16S; SEAWATER; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY, NUCLEIC ACID; VITAMIN K 2;

NEGIBACTERIA; OPITUTACEAE; VERRUCOMICROBIA;

EID: 34547406175     PISSN: 14665026     EISSN: None     Source Type: Journal    
DOI: 10.1099/ijs.0.64970-0     Document Type: Article

References (34)

1. Chin, K.-J., Liesack, W. & Janssen, P. H. (2001). Opitutus terrae gen. nov., sp. nov., to accommodate novel strain of the division 'Verrucomicrobia' isolated from rice paddy soil. Int J Syst Evol Microbiol 51, 1965-1968.
2. Dedysh, S. N., Pankratov, T. A., Belova, S. E., Kulichevskaya, I. S. & Liesack, W. (2006). Phylogenetic analysis and in situ identification of bacteria community composition in an acidic Sphagnum peat bog. Appl Environ Microbiol 72, 2110-2117.
3. Ezaki, T., Hashimoto, Y. & Yabuuchi, E. (1989). Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in micro-dilution 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.
4. Felsenstein, J. (1985). Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783-791.
5. Harper, J. J. & Davis, G. H. G. (1979). Two-dimensional thin-layer chromatography for amino acid analysis of bacterial cell walls. Int J Syst Bacteriol 29, 56-58.
6. Haukka, K., Heikkinen, E., Kairesalo, T., Karjalainen, H. & Sivonen, K. (2005). Effect of humic material on the bacterioplankton community composition in boreal lakes and mesocosms. Environ Microbiol 7, 620-630.
7. Haukka, K., Kolmonen, E., Hyder, R., Hietala, J., Vakkilainen, K., Kairesalo, T., Haario, H. & Sivonen, K. (2006). Effect of nutrient loading on bacterioplankton community composition in lake mesocosms. Microb Ecol 51, 137-146.
8. Hayakawa, M. & Nonomura, H. (1987). Humic acid-vitamin agar, a new medium for the selective isolation of soil actinomycetes. J Ferment Technol 65, 501-509.
9. Hedlund, B. P., Gosink, J. J. & Staley, J. T. (1997). Verrucomicrobia div. nov., a new division of the bacteria containing three new species of Prosthecobacter. Antonie van Leeuwenhoek 72, 29-38.
10. Hugenholtz, P., Goebel, B. M. & Pace, N. R. (1998). Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J Bacteriol 180, 4765-4774.
11. Joseph, S. J., Hugenholtz, P., Sangwan, P., Osborne, C. A. & Janssen, P. H. (2003). Laboratory cultivation of widespread and previously uncultured soil bacteria. Appl Environ Microbiol 69, 7210-7215.
12. Kanokratana, P., Chanapan, S., Pootanakit, K. & Eurwilaichitr, L. (2004). Diversity and abundance of Bacteria and Archaea in the Bor Khlueng hot spring in Thailand. J Basic Microbiol 44, 430-444.
13. Katsuta, A., Adachi, K., Matsuda, S., Shizuri, Y. & Kasai, H. (2005). Ferrimonas marina sp. nov. Int J Syst Evol Microbiol 55, 1851-1855.
14. Kumar, S., Tamura, K. & Nei, M. (2004). MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 5, 150-163.
15. Lyman, J. & Fleming, R. H. (1940). Composition of sea water. J Mar Res 3, 134-146.
16. Marmur, J. (1961). A procedure for the isolation of deoxyribonucleic acid from micro-organisms. J Mol Biol 3, 208-218.
17. Mesbah, M., Premachandran, U. & 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.
18. 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, DC: American Society for Microbiology.
19. Polymenakou, P. N., Bertilsson, S., Tselepides, A. & Stephanou, E. G. (2005). Bacterial community composition in different sediments from the Eastern Mediterranean Sea: a comparison of four 16S ribosomal DNA clone libraries. Microb Ecol 50, 447-462.
20. Rappé, M. S. & Giovannoni, S. J. (2003). The uncultured microbial majority. Annu Rev Microbiol 57, 369-394.
21. Sakai, T., Ishizuka, K. & Kato, I. (2003). Isolation and characterization of a fucoidan-degrading marine bacterium. Mar Biotechnol (NY) 5, 409-416.
22. Sangwan, P., Chen, X, Hugenholtz, P. & Janssen, P. H. (2004). Chthoniobacter flavus gen. nov., sp. nov., the first pure-culture representative of subdivision two, Spartobacteria classis nov., of the phylum Verrucomicrobia. Appl Environ Microbiol 70, 5875-5881.
23. Scheuermayer, M., Guider, T. A. M., Bringmann, G. & Hentschel, U. (2006). Rubritalea marina gen. nov., sp. nov., a marine representative of the phylum 'Verrucomicrobia', isolated from a sponge (Porifera). Int J Syst Evol Microbiol 56, 2119-2124.
24. Schleifer, K. H. & Kandler, O. (1972). Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 36, 407-477.
25. Shieh, W. Y. & Jean, W. D. (1998). Alterococcus agarolyticus, gen. nov., sp. nov., a halophilic thermophilic bacterium capable of agar degradation. Can J Microbiol 44, 637-645.
26. Sikes, D. S. & Lewis, P. O. (2001). Beta software, version 1. PAUPR at: PAUP implementation of the parsimony ratchet. Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs.
27. Swofford, D. L. (2002). PAUP*: Phylogenetic Analysis Using Parsimony (*and other methods). Sunderland, MA: Sinauer Associates.
28. 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.
29. Vandekerckhove, T. T. M., Willems, A., Gillis, M. & Coomans, A. (2000). Occurrence of novel verrucomicrobial species, endosymbiotic and associated with parthenogenesis in Xiphinema americanum-group species (Nematoda, Longidoridae). Int J Syst Evol Microbiol 50, 2197-2205.
30. 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.
31. Weisburg, W. G., Barns, S. M., Pelletier, D. A. & Lane, D. J. (1991). 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173, 697-703.
32. Yasumoto-Hirose, M., Nishijima, M., Ngirchechol, M. K., Kanoh, K., Shizuri, Y. & Mikl, W. (2006). Isolation of marine bacteria by in situ culture on media-supplemented polyurethane foam. Mar Biotechnol (NY) 8, 227-237.
33. Yokota, A., Tamura, T., Nishii, T. & Hasegawa, T. (1993). Kineococcus aurantiacus gen. nov., sp. nov., a new aerobic, gram-positive, motile coccus with meso-diaminopimelic acid and arabinogalactan in the cell wall. Int J Syst Bacteriol 43, 52-57.
34. Yoon, J., Yasumoto-Hirose, M., Katsuta, A., Sekiguchi, H., Matsuda, S., Kasai, H. & Yokota, A. (2007). Coraliomargarita akajimensis gen. nov., sp. nov., a novel member of the phylum 'Verrucomicrobia' isolated from seawater in Japan. Int J Syst Evol Microbiol 57, 959-963.