Bacillus oceanisediminis sp. nov., isolated from marine sediment

International Journal of Systematic and Evolutionary Microbiology

Volumn 60, Issue 12, 2010, Pages 2924-2929

  Zhang, Jianli ^a   Wang, Jiewei ^a   Fang, Caiyuan ^a   Song, Fei ^a   Xin, Yuhua ^b   Qu, Lei ^a   Ding, Kai ^a  

^a BEIJING INSTITUTE OF TECHNOLOGY   (China)

^b INSTITUTE OF MICROBIOLOGY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

AMINOPHOSPHOLIPID; BACTERIAL DNA; BACTERIAL RNA; CARDIOLIPIN; GENOMIC DNA; MESODIAMINOPIMELIC ACID; PEPTIDOGLYCAN; PHOSPHATIDYLETHANOLAMINE; PHOSPHATIDYLGLYCEROL; PIMELIC ACID; QUINONE DERIVATIVE; RNA 16S; UNCLASSIFIED DRUG; DIAMINOPIMELIC ACID; FARNOQUINONE; FATTY ACID; SEA WATER; VITAMIN MK 7;

ARTICLE; BACILLUS; BACILLUS OCEANISEDIMINIS; BACTERIAL CELL WALL; BACTERIAL GROWTH; BACTERIAL STRAIN; BACTERIUM ISOLATE; BACTERIUM ISOLATION; CHINA; NONHUMAN; NUCLEOTIDE SEQUENCE; PH; PHYLOGENY; PRIORITY JOURNAL; RNA SEQUENCE; SEDIMENT; SEQUENCE HOMOLOGY; ANALOGS AND DERIVATIVES; BACTERIUM IDENTIFICATION; CHEMISTRY; CLASSIFICATION; DNA BASE COMPOSITION; DNA SEQUENCE; GENETICS; ISOLATION AND PURIFICATION; MICROBIOLOGY; MOLECULAR GENETICS; NUCLEIC ACID HYBRIDIZATION; SEA;

BACILLUS (BACTERIUM); BACILLUS FIRMUS; BACTERIA (MICROORGANISMS);

BACILLUS; BACTERIAL TYPING TECHNIQUES; BASE COMPOSITION; CHINA; DIAMINOPIMELIC ACID; DNA, BACTERIAL; FATTY ACIDS; GEOLOGIC SEDIMENTS; MOLECULAR SEQUENCE DATA; NUCLEIC ACID HYBRIDIZATION; OCEANS AND SEAS; PEPTIDOGLYCAN; PHYLOGENY; RNA, RIBOSOMAL, 16S; SEAWATER; SEQUENCE ANALYSIS, DNA; VITAMIN K 2;

EID: 78650224483     PISSN: 14665026     EISSN: None     Source Type: Journal    
DOI: 10.1099/ijs.0.019851-0     Document Type: Article

References (57)

1. Albert, R. A., Archambault, J., Rosselló-Mora, R., Tindall, B. J. & Matheny, M. (2005). Bacillus acidicola sp. nov., a novel mesophilic, acidophilic species isolated from acidic Sphagnum peat bogs in Wisconsin. Int J Syst Evol Microbiol 55, 2125-2130.
2. Albert, R. A., Archambault, J., Lempa, M., Hurst, B., Richardson, C., Gruenloh, S., Duran, M., Worliczek, H. L., Huber, B. E. & other authors (2007). Proposal of Viridibacillus gen. nov. and reclassification of Bacillus arvi, Bacillus arenosi and Bacillus neidei as Viridibacillus arvi gen. nov., comb. nov., Viridibacillus arenosi comb. nov. and Viridibacillus neidei comb. nov. Int J Syst Evol Microbiol 57, 2729-2737.
3. Ash, C., Farrow, J. A. E., Wallbanks, S. & Collins, M. D. (1991). Phylogenetic heterogeneity of the genus Bacillus revealed by comparative analysis of small-subunit-ribosomal RNA sequences. Lett Appl Microbiol 13, 202-206.
4. Ash, C., Priest, F. G. & 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 Leeuwenhoek 64, 253-260. (Pubitemid 24151590)
5. Carrasco, I. J., Márquez, M. C., Xue, Y., Ma, Y., Cowan, D. A., Jones, B. E., Grant, W. D. & Ventosa, A. (2007). Bacillus chagannorensis sp. nov., a moderate halophile from a soda lake in Inner Mongolia, China. Int J Syst Evol Microbiol 57, 2084-2088.
6. Collins, M. D., Howarth, O. W., Grund, E. & Kroppenstedt, R. M. (1987). Isolation and structural determination of new members of the vitamin K2 series in Nocardia brasiliensis. FEMS Microbiol Lett 41, 35-39.
7. De Ley, J., Cattoir, H. & Reynaerts, A. (1970). The quantitative measurements of DNA hybridization from renaturation rates. Eur J Biochem 12, 133-142.
8. Felsenstein, J. (1985). Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783-791.
9. Gerhardt, P., Murray, R. G. E., Costilow, R. N., Nester, E. W., Wood, W. A., Krieg, N. R. & Phillips, G. B. (editors) (1981). Manual of Methods for General Bacteriology. Washington, DC: American Society for Microbiology.
10. Goodfellow, M. & Orchard, V. A. (1974). Antibiotic sensitivity of some nocardioform bacteria and its value as a criterion for taxonomy. J Gen Microbiol 83, 375-387.
11. Goodfellow, M., Stainsby, F. M., Davenport, R., Chun, J. & Curtis, T. (1998). Activated sludge foaming: the true extent of actinomycete diversity. Water Sci Technol 37, 511-519. (Pubitemid 28246256)
12. Gordon, R. E. & Mihm, J. M. (1957). A comparative study of some strains received as nocardiae. J Bacteriol 73, 15-27.
13. Gordon, R. E., Haynes, W. C. & Pang, C. H.-N. (1973). The Genus Bacillus. US Department of Agriculture Handbook no. 427. Washington, DC: Agricultural Research Service.
14. Gordon, R. E., Barnett, D. A., Handerhan, J. E. & Pang, C. H.-N. (1974). Nocardia coeliaca, Nocardia autotrophica, and the nocardin strain. Int J Syst Bacteriol 24, 54-63.
15. Gordon, R. E., Hyde, J. L. & Moore, J. A., Jr (1977). Bacillus firmus-Bacillus lentus: a series or one species? Int J Syst Bacteriol 27, 256-262.
16. Heyrman, J., Vanparys, B., Logan, N. A., Balcaen, A., Rodriguez-Diaz, M., Felske, A. & De Vos, P. (2004). Bacillus novalis sp. nov., Bacillus vireti sp. nov., Bacillus soli sp. nov., Bacillus botaviensis sp. nov. and Bacillus drentensis sp. nov., from the Drentse A grasslands. Int J Syst Evol Microbiol 54, 47-57. (Pubitemid 38181270)
17. Huß, V. A. R., Festl, H. & Schleifer, K. H. (1983). Studies on the spectrophotometric determination of DNA hybridization from renaturation rates. Syst Appl Microbiol 4, 184-192.
18. Jahnke, K. D. (1992). BASIC computer program for evaluation of spectroscopic DNA renaturation data from Gilford System 2600 spectrophotometer on a PC/XT/AT type personal computer. J Microbiol Methods 15, 61-73.
19. Kämpfer, P. (1994). Limits and possibilities of total fatty acid analysis for classification and identification of Bacillus species. Syst Appl Microbiol 17, 86-98.
20. Kämpfer, P. & Kroppenstedt, R. M. (1996). Numerical analysis of fatty acid patterns of coryneform bacteria and related taxa. Can J Microbiol 42, 989-1005.
21. Kämpfer, P., Rosselló -Mora, R., Falsen, E., Busse, H.-J. & Tindall, B. J. (2006). Cohnella thermotolerans gen. nov., sp. nov. and classification of 'Paenibacillus hongkongensis' as Cohnella hongkongensis sp. nov. Int J Syst Evol Microbiol 56, 781-786.
22. Kimura, M. (1980). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16, 111-120.
23. Ko, K. S., Oh, W. S., Lee, M. Y., Lee, J. H., Lee, H., Peck, K. R., Lee, N. Y. & Song, J.-H. (2006). Bacillus infantis sp. nov. and Bacillus idriensis sp. nov., isolated from a patient with neonatal sepsis. Int J Syst Evol Microbiol 56, 2541-2544. (Pubitemid 44782450)
24. Kumar, S., Tamura, K. & Nei, M. (2004). MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 5, 150-163.
25. Lim, J.-M., Jeon, C. O. & Kim, C.-J. (2006a). Bacillus taeanensis sp. nov., a halophilic Gram-positive bacterium from a solar saltern in Korea. Int J Syst Evol Microbiol 56, 2903-2908.
26. Lim, J.-M., Jeon, C. O., Lee, S.-M., Lee, J.-C., Xu, L.-H., Jiang, C.-L. & Kim, C.-J. (2006b). Bacillus salarius sp. nov., a halophilic sporeforming bacterium isolated from a salt lake in China. Int J Syst Evol Microbiol 56, 373-377.
27. Lu, Z., Liu, Z., Wang, L., Zhang, Y., Qi, W. & Goodfellow, M. (2001). Saccharopolyspora flava sp. nov. and Saccharopolyspora thermophila sp. nov., novel actinomycetes from soil. Int J Syst Evol Microbiol 51, 319-325.
28. Marmur, J. & Doty, P. (1962). Determination of base composition of deoxyribonucleic acid from its denaturation temperature. J Mol Biol 5, 109-118.
29. Minnikin, D. E., O'Donnell, A. G., Goodfellow, M., Alderson, G., Athalye, M., Schaal, A. & Parlett, J. H. (1984). An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2, 233-241.
30. Nazina, T. N., Tourova, T. P., Poltaraus, A. B., Novikova, E. V., Grigoryan, A. A., Ivanova, A. E., Lysenko, A. M., Petrunyaka, V. V., Osipov, G. A. & other authors (2001). Taxonomic study of aerobic thermophilic bacilli: descriptions of Geobacillus subterraneus gen. nov., sp. nov. and Geobacillus uzenensis sp. nov. from petroleum reservoirs and transfer of Bacillus stearothermophilus, Bacillus thermocatenulatus, Bacillus thermoleovorans, Bacillus kaustophilus, Bacillus thermoglucosidasius and Bacillus thermodenitrificans to Geobacillus as the new combinations G. stearothermophilus, G. thermocatenulatus, G. thermoleovorans, G. kaustophilus, G. thermoglucosidasius and G. thermodenitrificans. Int J Syst Evol Microbiol 51, 433-446.
31. Nielsen, P., Rainey, F. A., Outtrup, H., Priest, F. G. & Fritze, D. (1994). Comparative 16S rDNA sequence analysis of some alkaliphilic bacilli and the establishment of a sixth rRNA group within the genus Bacillus. FEMS Microbiol Lett 117, 61-66. (Pubitemid 2058501)
32. Nielsen, P., Fritze, D. & Priest, F. G. (1995). Phenetic diversity of alkaliphilic Bacillus strains: proposal for nine new species. Microbiology 141, 1745-1761.
33. Priest, F. G., Goodfellow, M. & Todd, C. (1988). A numerical classification of the genus Bacillus. J Gen Microbiol 134, 1847-1882.
34. Rainey, F. A., Ward-Rainey, N., Kroppenstedt, R. M. & Stackebrandt, E. (1996). The genus Nocardiopsis represents a phylogenetically coherent taxon and a distinct actinomycete lineage: proposal of Nocardiopsiaceae fam. nov. Int J Syst Bacteriol 46, 1088-1092. (Pubitemid 26339237)
35. Saitou, N. & Nei, M. (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406-425.
36. Sasser, M. (1990). Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101. Newark, DE: MIDI Inc.
37. Schleifer, K. H. (1985). Analysis of the chemical composition and primary structure of murein. Methods Microbiol 18, 123-156.
38. Schlesner, H., Lawson, P. A., Collins, M. D., Weiss, N., Wehmeyer, U., Völker, H. & Thomm, M. (2001). Filobacillus milensis gen. nov., sp. nov., a new halophilic spore-forming bacterium with Orn-D-Glu-type peptidoglycan. Int J Syst Evol Microbiol 51, 425-431. (Pubitemid 32266686)
39. Shida, O., Takagi, H., Kadowaki, K. & Komagata, K. (1996). Proposal for two new genera, Brevibacillus gen. nov. and Aneurinibacillus gen. nov. Int J Syst Bacteriol 46, 939-946.
40. 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.
41. Stackebrandt, E. & Goebel, B. M. (1994). Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 44, 846-849.
42. Stackebrandt, E. & Liesack, W. (1993). Nucleic acids and classification. In Handbook of New Bacterial Systematics, pp. 152-189. Edited by M. Goodfellow & A. G. O'Donnell. London: Academic Press.
43. Stackebrandt, E., Fredericksen, W., Garrity, G. M., Grimont, P. A. D., Kämpfer, P., Maiden, M. C. J., Nesme, X., Rosselló-Mora, R., Swings, J. & other authors (2002). Report of the ad hoc committee for the reevaluation of the species definition in bacteriology. Int J Syst Evol Microbiol 52, 1043-1047.
44. 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. (Pubitemid 28022245)
45. Venkateswaran, K., Kempf, M., Chen, F., Satomi, M., Nicholson, W. & Kern, R. (2003). Bacillus nealsonii sp. nov., isolated from a spacecraftassembly facility, whose spores are c-radiation resistant. Int J Syst Evol Microbiol 53, 165-172. (Pubitemid 36285235)
46. Wainø, M., Tindall, B. J., Schumann, P. & Ingvorsen, K. (1999). Gracilibacillus gen. nov., with description of Gracilibacillus halotolerans gen. nov., sp. nov.; transfer of Bacillus dipsosauri to Gracilibacillus dipsosauri comb. nov., and Bacillus salexigens to the genus Salibacillus gen. nov., as Salibacillus salexigens comb. nov. Int J Syst Bacteriol 49, 821-831. (Pubitemid 129755069)
47. 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.
48. Wieser, M., Worliczek, H., Kämpfer, P. & Busse, H.-J. (2005). Bacillus herbersteinensis sp. nov. Int J Syst Evol Microbiol 55, 2119-2123.
49. Wu, C., Lu, X., Qin, M., Wang, Y. & Ruan, J. (1989). Analysis of menaquinone compound in microbial cells by HPLC. Microbiology [English translation of Microbiology (Beijing)] 16, 176-178.
50. Xue, Y., Ventosa, A., Wang, X., Ren, P., Zhou, P. & Ma, Y. (2008). Bacillus aidingensis sp. nov., a moderately halophilic bacterium isolated from Ai-Ding salt lake in China. Int J Syst Evol Microbiol 58, 2828-2832.
51. Yoon, J.-H., Weiss, N., Lee, K.-C., Lee, I.-S., Kang, K.-H. & Park, Y.-H. (2001). Jeotgalibacillus alimentarius gen. nov., sp. nov., a novel bacterium isolated from jeotgal with L-lysine in the cell wall, and reclassification of Bacillus marinus Rüger 1983 as Marinibacillus marinus gen. nov., comb. nov. Int J Syst Evol Microbiol 51, 2087-2093.
52. Yoon, J.-H., Kim, I.-G., Kang, K.-H., Oh, T.-K. & Park, Y.-H. (2004). Bacillus hwajinpoensis sp. nov. and an unnamed Bacillus genomospecies, novel members of Bacillus rRNA group 6 isolated from sea water of the East Sea and the Yellow Sea in Korea. Int J Syst Evol Microbiol 54, 803-808.
53. Zhang, J., Zhang, Y., Xiao, C., Liu, Z. & Goodfellow, M. (2002). Rhodococcus maanshanensis sp. nov., a novel actinomycete from soil. Int J Syst Evol Microbiol 52, 2121-2126. (Pubitemid 36004194)
54. Zhang, J., Wu, D., Zhang, J., Liu, Z. & Song, F. (2008). Saccharopolyspora shandongensis sp. nov., isolated from wheat-field soil. Int J Syst Evol Microbiol 58, 1094-1099.
55. Zhang, J., Song, F., Xin, Y.-H., Zhang, J. & Fang, C. (2009). Microvirga guangxiensis sp. nov., a novel alphaproteobacterium from soil, and emended description of the genus Microvirga. Int J Syst Evol Microbiol 59, 1997-2001.
56. Zhou, Y., Wei, W., Chen, Q., Xu, Y., Wang, X., Huang, X. & Lai, R. (2008). Bacillus pallidus sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 58, 2850-2854.
57. Zhou, Y., Xu, J., Xu, L. & Tindall, B. J. (2009). Falsibacillus pallidus to replace the homonym Bacillus pallidus Zhou et al. 2008. Int J Syst Evol Microbiol 59, 3176-3180.