Geobacillus toebil subsp. decanicus subsp. nov., a hydrocarbon-degrading, heavy metal resistant bacterium from hot compost

Journal of General and Applied Microbiology

Volumn 52, Issue 4, 2006, Pages 223-234

  Poli, Annarita ^a   Romano, Ida ^a   Caliendo, Gaetano ^c   Nicolaus, Giancarlo ^b   Orlando, Pierangelo ^a   de Falco, Antonio ^c   Lama, Licia ^a   Gambacorta, Agata ^a   Nicolaus, Barbara ^a  

^a CNR   (Italy)

^b IRBM   (Italy)

^c Pomigliano Ambiente spa   (Italy)

Author keywords

Alkanes; DNA DNA hybridization; Fatty acid; Geobacillus; Heavy metals; Hot compost; Lipid; PCR finger print; Thermozymes

Indexed keywords

ALPHA GALACTOSIDASE; ALPHA GLUCOSIDASE; BACTERIAL DNA; BACTERIAL RNA; DECANE; FATTY ACID; HEAVY METAL; HYDROCARBON; RNA 16S;

ARTICLE; BACTERIAL GROWTH; BACTERIAL STRAIN; BACTERIUM IDENTIFICATION; BACTERIUM ISOLATE; CARBON SOURCE; COMPOST; CONTROLLED STUDY; CULTURE MEDIUM; DNA CONTENT; DNA DETERMINATION; DNA DNA HYBRIDIZATION; DNA POLYMORPHISM; ENERGY RESOURCE; ENZYME ACTIVITY; FATTY ACID ANALYSIS; GENE CLUSTER; GENE SEQUENCE; GEOBACILLUS; GEOBACILLUS DECANIUS; GEOBACILLUS TOEBII; ITALY; NEW SPECIES; NONHUMAN; NUCLEOTIDE SEQUENCE; PHENOTYPE; PHYLOGENY; POLYMERASE CHAIN REACTION; PROTEIN ANALYSIS; TAXONOMIC IDENTIFICATION; TEMPERATURE SENSITIVITY; BACILLACEAE; DRUG EFFECT; GENETICS; ISOLATION AND PURIFICATION; METABOLISM; METHODOLOGY; MICROBIOLOGY; RANDOM AMPLIFIED POLYMORPHIC DNA; SOIL;

BACTERIA (MICROORGANISMS); GEOBACILLUS; GEOBACILLUS TOEBII; POSIBACTERIA;

BACILLACEAE; FATTY ACIDS; HYDROCARBONS; METALS, HEAVY; PHYLOGENY; RANDOM AMPLIFIED POLYMORPHIC DNA TECHNIQUE; RNA, RIBOSOMAL, 16S; SOIL; SOIL MICROBIOLOGY;

EID: 38049102891     PISSN: 00221260     EISSN: 13498037     Source Type: Journal    
DOI: 10.2323/jgam.52.223     Document Type: Article

References (57)

1. Ahmad, S., Scopes, R. K., Rees, G. N., and Patel, B. K. C. (2000) Saccharococcus caldoxylosilyticus sp. nov., an obligately thermophilic, xylose-utilizing, endospore-forming bacterium. Int. J. Syst Evol. Microbiol., 50, 517-523.
2. Ash, C., Farrow, J. A. E., Wallbanks, S., and Collins, M. D. (1991) Phylogenetic heterogeneity of the genus Bacillus revealed by comparative analysis of small-subunilt-ribosomal RNA. Lett. Appl. Microbiol., 13, 202-206.
3. Beffa, T., Blanc, M., Lyon, P. F., Vogt, G., Marciani, M., Fisher, J. L., and Aragno, M. (1996) Isolation of Thermus strain from hot composts (60-80°C). Appl. Environ. Microbiol., 62, 1723-1727.
4. Blanc, M., Marilley, L., Beffa, T., and Aragno, M. (1999) Thermophilic bacterial communities in hot composts as revealed by most probable number counts and molecular (16S rDNA) methods. FEMS Microbiol. Ecol., 28, 141-149.
5. Bradford, M. M. (1976) A rapid and sensitive method for quantitation of microgram quantities of protein using the principles of protein-dye binding. Anal. Biochem., 72, 248-254.
6. Gaccamo, D., Gugliandolo, C., Stackebrandt, E., and Maugeri, T. L. (2000) Bacillus vulcani sp. nov., a novel thermophilic species isolated from a shallow marine hydrothermal vent. Int. J. Syst. Evol. Microbiol., 50, 2009-2012.
7. Cashion, P., Hodler-Franklin, M. A., McCully, J., and Franklin, M. (1977) A rapid method for base ratio determination of bacterial DNA. Anal, Biochem., 81, 461-466.
8. Chen, X. G., Stabnikova, O., Tay, J. H., Wang, J. Y., and Tay, S. T. L. (2004) Thermoactive extracellular proteases of Geobacillus caldoproteolyticus, sp. nov., from sewage sludge. Extremophiles, 8, 489-498.
9. AL. In Bergey's Manual of Systematic Bacteriology, ed. by Sneath, P. H. A., Mair, N. S., Sharpe, M. E., Holt, J. G., Williams & Wilkins, Baltimore, Vol. 2, pp. 1105-1139.
10. De Ley, J., Cattoir, H., and Reynaerts, A. (1970) Ther quantitative measurement of DNA hybridization from renaturation rates. Eur. J. Biochem., 12, 133-142.
11. Felsenstein, J. (1993) PHYLIP Phylogeny Inference Package, version 3.5.1. Department of Geinetics, University of Washington, Seattle, USA.
12. Fortina, M. G., Mora, D., Schumann, P., Parini, C., Manichini, P. L., and Stackebrandt, E. (2001a) Reclassification of Saccharococcus caldoxylosilyticus as Geobacillus caldoxylosilyticus (Ahmad et al. 2000) comb. nov. Int. J. Syst. Evol. Microbiol., 51, 2063-2071.
13. Fortina, M. G., Pukall, R., Schumann, P., Mora, D., Parini, C., Manichini, P. L., and Stackebrandt, E. (2001b) Ureibacillus gen. nov., a new genus to accommodate Bacillus thermosphaericus (Andersson et al. 1995), emendation of Ureibacillus thermosphaericus and description of Ureibacillus terrenus sp. nov. Int. J. Syst. Evol. Microbiol., 51, 447-455.
14. Fugio, Y. and Kume, S. J. (1991) Isolation and identification of thermophilic bacteria from sewage sludge compost. J. Ferment. Bioeng., 72, 334-337.
15. Golovacheva, R. S., Loginova, L. G., Salikhov, T. A., Kolesnikov, A.-A., and Zaitseva, G. N. (1975) A new thermophilic species Bacillus, thermocatenulatus sp. nov. Microbiology (English translation of Mikrobiologiya), 44, 230-233.
16. Gugliandolo, C., Maugeri, T., Caccamo, D., and Stackebrandt, E. (2003) Bacillus aeolius sp. nov. a novel thermophilic halophilic marine Bacillus species from Eolian Islands (Italy). Syst. Appl. Microbiol., 26, 172-176.
17. Higgins, D. G., Bleasby, A. T., and Fuchs, R. (1992) Clustal W: improved software for multiple sequence alignment. CABIOS, 8, 189-191.
18. Hudson, J. A., Morgan, H. W., and Daniel, R. M. (1986) A numerical classification of some Thermus isolates. J. Gen. Microbiol., 13, 532-540.
19. Huss, V. A. R., Festi, H., and Schleifer, K. H. (1983) Studies on the spectrophotometric determination of DNA hybridization from renaturation rates. Syst. Appl. Microbiol., 4, 184-192.
20. Jukes, T. H. and Cantor, C. R. (1969) Evolution of protein molecules. In Mammalian Protein Metabolism, ed. by Munro, H. N., Academic Press, New York, pp. 21-132.
21. Koneman, E. W., Allen, S. D., Dowell, V. R., and Sommers, H. M. (1984) Colour Atlas and Textbook of Diagnostic Microbiology, ed. by Lippincott JB Company, Philadelphia, Toronto.
22. Logan, N. A. and Berkeley, R. C. W. (1984) Identification of Bacillus strains using the API system. J. Gen. Microbiol., 130, 1871-1882.
23. Lyon, P. F., Beffa, T., Blanc, M., Auling, G., and Aragno, M. (2000) Isolation and characterization of highly thermophilic xylanolytic Thermus thermophilus strains from hot composts. Can. J. Microbiol., 46, 1029-1035.
24. Maidak, B. L., Cole, J. R., Parker, C. T., Garrity, G. M., Larsen, N., Li, B., Liburn, I G., McCaughey, M. J., Olsen, G. J., Overbeek, R., Pramanik, S., Schmidt, T. M., Tiedje, J. M., and Woese, C. R. (1999) A new version of the RDP (Ribosomal Database Project). Nucleic Acids Res., 27, 171-173.
25. Manichini, P. L., Mora, D., Nicastro, G., Parini, C., Stackebrandt, E., Pukall, R., and Fortina, M. G. (2000) Bacillus thermo-denitrificans sp. nov., nom. rev. Int. J. Syst. Evol. Microbiol., 50, 1331-1337.
26. Maugeri, T. L., Gugliandolo, C., Caccamo, D., and Stackebrandt, E. (2001) A polyphasic taxonomic study of thermophilic bacilli from shallow marine vents. Syst. Appl. Microbiol., 24, 572-587.
27. Maugeri, T. L., Gugliandolo, C., Caccamo, D., Panico, A., Lama, L., Gambacorta, A., and Nicolaus, B. (2002) A halophilic thermotolerant Bacillus isolated from a marine hot spring able to produce a new exopolysaccharide. Biotechnol. Lett., 24, 515-519.
28. Mesbah, M., Premachandran, U., and Whitman, W. (1989) Precise measurement of the G+C content of deoxyribonucleic acid by high performance liquid chromatography. Int. J. Syst Bacteriol., 39, 159-167.
29. Miller, F. G. (1996) Composting of municipal solid waste and its components. In Microbiology of Solid Waste, ed. by Palmisano, A. C. and Barlaz, N. A., CRC Press, Boca Raton, Fla., pp. 115-154.
30. Nazina, T. N., Lebedeva, E. V., Poltaraus. A. B., Tourova, T. P., Grigoryan, A. A., Sokolova, D. S., Lysenko, A. M., and Osipov, G. A. (2004) Geobacillus gargensis sp. nov., a novel thermophile from a hot spring, and the reclassification of Bacillus vulcani as Geobacillus vulcani (Caccamo et al., 2000) comb. nov. Int. J. Syst. Evol. Microbiol., 54, 2019-2024.
31. Nazina, T. N., Sokolova, D. S., Grigoryan, A. A., Shestakova, N. M., Mikhailova, E. M., Poltaraus, A. B., Tourova, T. P., Lysenko, A. M., Osipov, G. A., and Belyaev, S. S. (2005) Geobacillus jurassicus sp. nov., a new thermophilic bacterium isolated from a high-temperature petroleum reservoir and validation of the Geobacillus species. Syst. Appl. Microbiol., 28, 43-53.
32. 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., Belyaev, S. S., and Ivanov, M. V. (2001) Taxonomic study of aerobic thermophilic bacilli: Description of Geobacillus subterraneus gen. nov., sp. nov. and Geobaacillus 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. thermecatenulatus, G. thermoleovorans, G. kaustophilus, G. thermoglucosidasius and G. thermodenitrificans. Int. J. Syst. Evol. Microbiol., 5, 433-446.
33. Nicolaus, B., Improta, R., Manca, M. C., Lama, L., Esposito, E., and Gambacorta, A. (1998) Alicyclobacilli from an unexplored geothermal soil in Antarctica: Mount Rittmann. Polar Biol., 19, 133-141.
34. Nicolaus, B., Lama, L., Esposito, E., Manca, M. C., Di Prisco, G., and Gambacorta, A. (1996) "Bacillus thermoantarcticus" sp. nov., from Mount Melbourne, Antarctica: A novel thermophilic species. Polar Biol., 16, 101-104.
35. Nicolaus, B., Manca, M. C., Lama, L., Esposito, E., and Gambacorta, A. (2001) Lipid modulation by environmental stresses in two models of extremophiles isolated from Antarctica. Polar Biol., 24, 1-8.
36. Nicolaus, B., Panico, A., Manca, M. C., Lama, L., Gambacorta, A., Maugeri, T., Gugliandolo, C., and Caccamo, D. (2000) A thermophilic Bacillus isolated from an eolian shallow hydrothermal vent, able to produce exopolysaccharides. Syst. Appl. Microbiol., 23, 426-432.
37. Nystrand, R.. (1984) Saccharococcus thermophilus gen. nov., sp. nov. isolated from beet sugar extraction. Syst Appl. Microbiol., 5, 204-219.
38. Oren, h A. and Galinski, E. A. (1994) Hydrolysis of N′-benzoyl-arginine-p-nitroanilide stereoisomers as a phenotypic test: A study of Gram-positive halotolerant bacteria. Syst. Appl. Microbiol., 17, 710-716.
39. Poli, A., Esposito, E., Lama, L., Pelliccione, S., Gambacorta, A., and Nicolaus, B. (2006) Heavy metal effects on Extremophiles and on enzyme biosynthesis in a new Bacillus strain from Mount Rittmann, Antarctica. In Modern Multidisciplinary Applied Microbiology, ed. by Mendez-Vilas, A., Wiley-VCH Verlag GmbH & Co. KgaA, Weinheim, pp. 83-88.
40. Priest, F. G., Goodfellow, M., and Todd, C. (1988) A numerical classification of the genus Bacillus. J. Gen. Microbiol., 134, 1847-1882.
41. Rainey, F. A., Fritze, D., and Stackebrandt, E. (1994) The phylogenetic diversity of thermophilic members of the genus Bacillus as revealed by 16S rDNA analysis. FEMS Microbiol. Lett., 115, 205-212.
42. Rainey, F. A., Ward-Raney, N., Kroppenstedt, R. M., and Stackebrandt, E. (1996) The genus Nocardiopsis represents a phylogenetically coherent taxon and a distinct actinomycete lineage; Proposal of Nocardiopsaceae fam. nov. Int. J. Syst. Bacteriol., 46, 1088-1092.
43. Rhee, S. K., Jeon, C. O., Bae, J. W., and 9 other authors. (2002) Characterization of Symbiobacterium toebii, an obligate commensal thermophile isolated from compost. Extremophiles, 6, 57-64.
44. Ronimus, R. S., Parker, L. E., and Morgan, H. W. (1997) The utilization of RAPD-PCR for identifying thermophilic and mesophilic, Bacillus species. FEMS Microbiol. Lett., 147, 75-79.
45. Saitou, N. and Nei, M. (1987) The neighbour-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol., 4, 406-425.
46. Santos, M. A., Williams, R. A. D., and da Costa, M. S. (1989) Numerical taxonomy of Thermus isolates from hot spring in Portugal. Syst. Appl. Microbiol., 12, 310-315.
47. Stackebrandt, E. and 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.
48. Strom, P. F. (1985a) Effect of temperature on bacterial species diversity in thermophilic solid-waste composting. Appl. Environ. Microbiol., 50, 899-905.
49. Strom, P. F. (1985b) Identification of thermophilic bacteria in solid-waste composting. Appl. Environ. Microbiol., 50, 906-913.
50. Sung, M. H., Kim, H., Bae, J. W., Rhee, S. K., Jeon, C. O., Kim, K., Kim, J. J., Hong, S. P., Lee, S. G., Yoon, J. H., Park, Y. H., and Baek, D. H. (2002) Geobacillus toebii sp. nov., a novel thermophilic bacterium isolated from hay compost. Int. J. Syst. Evol. Microbiol., 52, 2251-2255.
51. Sunna, A., Tokajian, S., Burghardt, J., Raney, F., Antranikian, G., and Hashwa, F. (1997) Identification of Bacillus kaustophilus, Bacillus thermocatenulatus and Bacillus Strain HSR as members of Bacillus thermoleovorans. Syst. Appl. Microbiol., 20, 232-237.
52. Suzuki, Y., Kishigami, T., Inoue, K., Mizoguchi, Y., Eto, N., Takagi, M., and Abe, S. (1983) Bacillus thermoglucosidasius sp. nov., a new species of obligately thermophilic bacilli. Syst. Appl. Microbiol., 4, 487-495.
53. Tamaoka, J. and Komagata, K. (1984) Determination of DNA base composition by reversed-phase-high-performahee liquid chromatography. FEMS Mirobiol. Lett., 25, 125-128.
54. Tomita, K., Ikeda, N., and Ueno, A. (2003) Isolation and characterization of a thermophilic bacterium, Geobacillus thermocatenulatus, degradipg nylon 12 and nylon 66. Biotechnol. Lett., 25, 1743-1746.
55. 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., Starr, M. P., and Trupper, H. G. (1987) Report of the Ad Hoc Committee on reconciliation of approaches to bacterial systematics. Int J. Syst. Bacteriol., 37, 463-464.
56. White, D., Sharp, R. J., and Priest, F. G. (1993) A polyphasic taxonomic study of thermophilic bacilli from a wide geographical area. Antonie van Leeuwenhoek, 64, 357-386.
57. Zarilla, K. A. and Perry, J. J. (1987) Bacillus thermoleovorans, sp. nov., a species of obligately thermophilic hydrocarbon utilizing endospore-forming bacteria. Syst. Appl. Microbiol., 9, 258-264.