Paenibacillus marinisediminis sp. nov., a bacterium isolated from marine sediment

Journal of Microbiology

Volumn 51, Issue 3, 2013, Pages 312-317

  Lee, Hae Won ^a,b   Roh, Seong Woon ^a   Yim, Kyung June ^b   Shin, Na Ri ^a   Lee, Jina ^a   Whon, Tae Woong ^a   Kim, Joon Yong ^a   Hyun, Dong Wook ^a   Kim, Daekyung ^b   Bae, Jin Woo ^a  

^a Kyung Hee University   (South Korea)

^b Korea Basic Science Institute (KBSI)   (South Korea)

Author keywords

bacterial taxonomy; marine sediment; Paenibacillus marinisediminis sp. nov.

Indexed keywords

DIAMINOPIMELIC ACID; PHOSPHATIDYLETHANOLAMINE; PHOSPHATIDYLGLYCEROL; PHOSPHOLIPID; RNA 16S; SPERMIDINE;

ARTICLE; CLASSIFICATION; DNA BASE COMPOSITION; GENETICS; METABOLISM; MICROBIOLOGY; PAENIBACILLUS; PHYLOGENY; SEDIMENT;

BASE COMPOSITION; DIAMINOPIMELIC ACID; GEOLOGIC SEDIMENTS; PAENIBACILLUS; PHOSPHATIDYLETHANOLAMINES; PHOSPHATIDYLGLYCEROLS; PHOSPHOLIPIDS; PHYLOGENY; RNA, RIBOSOMAL, 16S; SPERMIDINE;

BACTERIA (MICROORGANISMS); NEGIBACTERIA; PAENIBACILLUS;

EID: 84879667981     PISSN: 12258873     EISSN: 19763794     Source Type: Journal    
DOI: 10.1007/s12275-013-3198-2     Document Type: Article

References (30)

1. Ash, C., Priest, F. G., and Collins, M. D. 1993. Molecular identification of rRNA group 3 bacilli (Ash, Farrow, Wallbanks and Collins) using a PCR probe test. Proposal for the creation of a new genus Paenibacillus. Antonie van Leeuwenhoek64, 253-260.
2. Ash, C., Priest, F. G., and Collins, M. D. 1994. Paenibacillus gen. nov and Paenibacillus polymyxa comb. nov. In Validation of the Publication of New Names and New Combinations Previously Effectively Published Outside the IJSB, List no. 51. Int. J. Syst. Bacteriol. 44, 582.
3. Benson, H. J. 2002. Microbiological applications: a laboratory manualzin general microbiology. McGraw-Hill New York, N. Y., USA.
4. Busse, J. and Auling, G. 1988. Polyamine pattern as a chemotaxonomic marker within the Proteobacteria. Syst. Appl. Microbiol. 11, 1-8.
5. Collins, M. D. and Jones, D. 1981. Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implication. Microbiol. Rev. 45, 316-354.
6. De Vos, P., Ludwig, W., Schleifer, K.-H., and Whitman, W. B. 2009. Family IV. Paenibacillaceae fam. nov. Bergey's Manual of Systematic Bacteriology, 2nd edn, vol. 3 (The Firmicutes), pp. 269. In De Vos, P., Garrity, G. M., Jones, D., Krieg, N. R., Ludwig, W., Rainey, F. A., Schleifer, K.-H., and Whitman, W. B. (eds.). Springer, New York, N. Y., USA.
7. Ezaki, T., Hashimoto, Y., and 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. Evol. Microbiol. 39, 224-229.
8. Felsenstein, J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17, 368-376.
9. Gonzalez, C., Gutierrez, C., and Ramirez, C. 1978. Halobacterium vallismortis sp. nov. An amylolytic and carbohydrate-metabolizing, extremely halophilic bacterium. Can. J. Microbiol. 24, 710-715.
10. Gonzalez, J. M. and Saiz-Jimenez, C. 2002. A fluorimetric method for the estimation of G+C mol% content in microorganisms by thermal denaturation temperature. Environ. Microbiol. 4, 770-773.
11. Judicial Commission of the International Committee for Systematics of Prokaryotes. 2005. The type species of the genus Paenibacillus Ash et al. 1994 is Paenibacillus polymyxa. Opinion 77. Int. J. Syst. Evol. Microbiol. 55, 513.
12. Kim, O. S., Cho, Y. J., Lee, K., Yoon, S. H., Kim, M., Na, H., Park, S. C., Jeon, Y. S., Lee, J. H., Yi, H., andet al. 2012. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int. J. Syst. Evol. Microbiol. 62, 716-721.
13. Kluge, A. G. and Farris, F. S. 1969. Quantitative phyletics and the evolution of anurans. Syst. Zool. 18, 1-32.
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 sequences for phylogenetic analyses. Proc. Natl. Acad. Sci. USA82, 6955-6959.
15. Lee, F. L., Kuo, H. P., Tai, C. J., Yokota, A., and Lo, C. C. 2007. Paenibacillus taiwanensis sp. nov., isolated from soil in Taiwan. Int. J. Syst. Evol. Microbiol. 57, 1351-1354.
16. MIDI. 1999. Sherlock Microbial Identification System Operating Manual, version 3. 0. MIDI, Inc., Newark, DE, USA.
17. Minnikin, D. E., O'Donnell, A. G., and Goodfellow, M. 1984. An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J. Microbiol. Methods2, 233-241.
18. Nakamura, L. K. 1996. Paenibacillus apiarius sp. nov. Int. J. Syst. Bacteriol. 46, 688-693.
19. Percival Zhang, Y. H., Himmel, M. E., and Mielenz, J. R. 2006. Outlook for cellulase improvement: screening and selection strategies. Biotechnol. Adv. 24, 452-481.
20. Pruesse, E., Peplies, J., and Glockner, F. O. 2012. SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics28, 1823-1829.
21. Roh, S. W., Sung, Y., Nam, Y. D., Chang, H. W., Kim, K. H., Yoon, J. H., Jeon, C. O., Oh, H. M., and Bae, J. W. 2008. Arthrobacter soli sp. nov., a novel bacterium isolated from wastewater reservoir sediment. J. Microbiol. 46, 40-44.
22. Saha, P., Mondal, A. K., Mayilraj, S., Krishnamurthi, S., Bhattacharya, A., and Chakrabarti, T. 2005. Paenibacillus assamensis sp. nov., a novel bacterium isolated from a warm spring in Assam, India. Int. J. Syst. Evol. Microbiol. 55, 2577-2581.
23. Saitou, N. and Nei, M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4, 406-425.
24. Schaeffer, A. B. and Fulton, M. D. 1933. A simplified method of staining endospores. Science77, 194.
25. Shida, O., Takagi, H., Kadowaki, K., Nakamura, L. K., and Komagata, K. 1997. Transfer of Bacillus alginolyticus, Bacillus chondroitinus, Bacillus curdlanolyticus, Bacillus glucanolyticus, Bacillus kobensis, and Bacillus thiaminolyticus to the genus Paenibacillus and emended description of the genus Paenibacillus. Int. J. Syst. Bacteriol. 47, 289-298.
26. Suzuki, M. T. and Giovannoni, S. J. 1996. Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl. Environ. Microbiol. 62, 625-630.
27. 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.
28. Tcherpakov, M., Ben-Jacob, E., and Gutnick, D. L. 1999. Paenibacillus dendritiformis sp. nov., proposal for a new pattern-forming species and its localization within a phylogenetic cluster. Int. J. Syst. Bacteriol. 49, 239-246.
29. Tittsler, R. P. and Sandholzer, L. A. 1936. The use of semi-solid agar for the detection of bacterial motility. J. Bacteriol. 31, 575-580.
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., Stackebrandt, E., andet al. 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.