Thiofaba tepidiphila gen. nov., sp. nov., a novel obligately chemolithoautotrophic, sulfur-oxidizing bacterium of the Gammaproteobacteria isolated from a hot spring

International Journal of Systematic and Evolutionary Microbiology

Volumn 58, Issue 8, 2008, Pages 1885-1891

  Mori, Koji ^a   Suzuki, Ken Ichiro ^a  

^a NATIONAL INSTITUTE OF TECHNOLOGY AND EVALUATION   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

RNA 16S; BACTERIAL DNA; RIBOSOME DNA; SULFUR;

ARTICLE; BACTERIAL GENE; BACTERIAL GROWTH; BACTERIAL STRAIN; BACTERIUM CULTURE; BACTERIUM IDENTIFICATION; BACTERIUM ISOLATION; CONTROLLED STUDY; GENE SEQUENCE; GRAM NEGATIVE BACTERIUM; NONHUMAN; NUCLEOTIDE SEQUENCE; PHENOTYPE; PHYLOGENY; PRIORITY JOURNAL; SEQUENCE ANALYSIS; STRAIN DIFFERENCE; THIOFABA TEPIDIPHILA; CHEMOAUTOTROPHY; CLASSIFICATION; DNA SEQUENCE; GAMMAPROTEOBACTERIA; GENETICS; ISOLATION AND PURIFICATION; JAPAN; METABOLISM; MICROBIOLOGY; MOLECULAR GENETICS; OXIDATION REDUCTION REACTION; PHYSIOLOGY; RNA GENE; SPECIES DIFFERENCE; THERMAL SPRING;

BACTERIA (MICROORGANISMS); GAMMAPROTEOBACTERIA; HALOTHIOBACILLACEAE; HALOTHIOBACILLUS; NEGIBACTERIA; THIOVIRGA;

BACTERIAL TYPING TECHNIQUES; CHEMOAUTOTROPHIC GROWTH; DNA, BACTERIAL; DNA, RIBOSOMAL; GAMMAPROTEOBACTERIA; GENES, RRNA; HOT SPRINGS; JAPAN; MOLECULAR SEQUENCE DATA; OXIDATION-REDUCTION; PHENOTYPE; PHYLOGENY; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY; SULFUR;

EID: 54749128605     PISSN: 14665026     EISSN: None     Source Type: Journal    
DOI: 10.1099/ijs.0.65754-0     Document Type: Article

References (54)

1. Adachi, J. & Hasegawa, M. (1995). Improved dating of the human/chimpanzee separation in the mitochondrial DNA tree: heterogeneity among amino acid sites. J Mol Evol 40, 622-628.
2. Durand, P., Reysenbach, A. L., Prieur, D. & Pace, N. (1993). Isolation and characterization of Thiobacillus hydrothermalis sp. nov., a mesophilic obligately chemolithoautotrophic bacterium isolated from a deep-sea hydrothermal vent in Fiji Basin. Arch Microbiol 159, 39-44.
3. Elshahed, M. S., Senko, J. M., Najar, F. Z., Kenton, S. M., Roe, B. A., Dewers, T. A., Spear, J. R. & Krumholz, L. R. (2003). Bacterial diversity and sulfur cycling in a mesophilic sulfide-rich spring. Appl Environ Microbiol 69, 5609-5621.
4. Götz, D., Banta, A., Beveridge, T. J., Rushdi, A. I., Simoneit, B. R. & Reysenbach, A. L. (2002). Persephonella marina gen. nov., sp. nov. and Persephonella guaymasensis sp. nov., two novel, thermophilic, hydrogen-oxidizing microaerophiles from deep-sea hydrothermal vents. Int J Syst Evol Microbiol 52, 1349-1359.
5. Grosskopf, R., Janssen, P. H. & Liesack, W. (1998). Diversity and structure of the methanogenic community in anoxic rice paddy soil microcosms as examined by cultivation and direct 16S rRNA gene sequence retrieval. Appl Environ Microbiol 64, 960-969.
6. Hallberg, K. B. & Lindström, E. B. (1994). Characterization of Thiobacillus caldus sp. nov., a moderately thermophilic acidophile. Microbiology 140, 3451-3456.
7. Hasegawa, M., Kishino, H. & Yano, T. (1985). Dating of the humanape splitting by a molecular clock of mitochondrial DNA. J Mol Evol 22, 160-174.
8. Hattori, S., Kamagata, Y., Hanada, S. & Shoun, H. (2000). Thermacetogenium phaeum gen. nov., sp. nov., a strictly anaerobic, thermophilic, syntrophic acetate-oxidizing bacterium. Int J Syst Evol Microbiol 50, 1601-1609.
9. Hiraishi, A., Umezawa, T., Yamamoto, H., Kato, K. & Maki, Y. (1999). Changes in quinone profiles of hot spring microbial mats with a thermal gradient. Appl Environ Microbiol 65, 198-205.
10. Hirayama, H., Takai, K., Inagaki, F., Nealson, K. H. & Horikoshi, K. (2005). Thiobacter subterraneus gen. nov., sp. nov., an obligately chemolithoautotrophic, thermophilic, sulfur-oxidizing bacterium from a subsurface hot aquifer. Int J Syst Evol Microbiol 55, 467-472.
11. Huber, H. & Prangishvili, D. (2006). Sulfolobales. In The Prokaryotes. A Handbook on the Biology of Bacteria, 3rd edn, vol. 3, pp. 23-51. Edited by M. Dworkin, S. Falkow, E. Rosenberg, K.-H. Schleifer & E. Stackebrandt. New York: Springer.
12. Huber, G. & Stetter, K. O. (1991). Sulfolobus metallicus, sp. nov., a novel strictly chemolithoautotrophic thermophilic archaeal species of metal-mobilizers. Syst Appl Microbiol 14, 372-378.
13. Huber, R., Wilharm, T., Huber, D., Trincone, A., Burggraf, S., König, H., Rachel, R., Rockinger, I., Fricke, H. & Stetter, K. O. (1992). Aquifex pyrophilus gen. nov., sp. nov., represents a novel group of marine hyperthermophilic hydrogen-oxidizing bacteria. Syst Appl Microbiol 15, 340-351.
14. Huber, R., Eder, W., Heldwein, S., Wanner, G., Huber, H., Rachel, R. & Stetter, K. O. (1998). Thermocrinis ruber gen. nov., sp. nov., a pink-filament-forming hyperthermophilic bacterium isolated from Yellowstone National Park. Appl Environ Microbiol 64, 3576-3583.
15. Hutchinson, M., Johnstone, K. I. & White, D. (1965). The taxonomy of certain thiobacilli. J Gen Microbiol 41, 357-366.
16. Hutchinson, M., Johnstone, K. I. & White, D. (1969). Taxonomy of the genus Thiobacillus: the outcome of numerical taxonomy applied to the group as a whole. J Gen Microbiol 57, 397-410.
17. Inaga, S., Katsumoto, T., Tanaka, K., Kameie, T., Nakane, H. & Naguro, T. (2007). Platinum blue as an alternative to uranyl acetate for staining in transmission electron microscopy. Arch Histol Cytol 70, 43-49.
18. Ito, T., Sugita, K. & Okabe, S. (2004). Isolation, characterization, and in situ detection of a novel chemolithoautotrophic sulfur-oxidizing bacterium in wastewater biofilms growing under microaerophilic conditions. Appl Environ Microbiol 70, 3122-3129.
19. Ito, T., Sugita, K., Yumoto, I., Nodasaka, Y. & Okabe, S. (2005). Thiovirga sulfuroxydans gen. nov., sp. nov., a chemolithoautotrophic sulfur-oxidizing bacterium isolated from a microaerobic waste-water biofilm. Int J Syst Evol Microbiol 55, 1059-1064.
20. Kamagata, Y. & Mikami, E. (1991). Isolation and characterization of a novel thermophilic Methanosaeta strain. Int J Syst Bacteriol 41, 191-196.
21. Kelly, D. P. & Wood, A. P. (2000). Reclassification of some species of Thiobacillus to the newly designated genera Acidithiobacillus gen. nov., Halothiobacillus gen. nov. and Thermithiobacillus gen. nov. Int J Syst Evol Microbiol 50, 511-516.
22. Kelly, D. P. & Wood, A. P. (2005). Family III. Halothiobacillaceae fam. nov. Kelly and Wood 2003. In Bergey's Manual of Systematic Bacteriology, vol. 2, pp. 58-59. Edited by D. J. Brenner, N. R. Krieg, J. T. Staley & G. M. Garrity. New York: Springer.
23. Kelly, D. P., Stackebrandt, E., Burghardt, J. & Wood, A. P. (1998). Confirmation that Thiobacillus halophilus and Thiobacillus hydrothermalis are distinct species within the gamma-subclass of the Proteobacteria. Arch Microbiol 170, 138-140.
24. Lane, D. J. (1991). 16S/23S rRNA sequencing. In Nucleic Acid Techniques in Bacterial Systematics, pp. 115-175. Edited by E. Stackebrandt & M. Goodfellow. Chichester: Wiley.
25. La Rivière, J. W. M. & Schmidt, K. (2006). Morphologically conspicuous sulfur-oxidizing eubacteria. In The Prokaryotes, vol. 7, pp. 941-954. Edited by M. Dworkin, S. Falkow, E. Rosenberg, K.-H. Schleifer & E. Stackebrandt. New York: Springer.
26. Ludwig, W., Strunk, O., Westram, R., Richter, L., Meier, H., Yadhukumar, Buchner, A., Lai, T., Steppi, S. & other authors (2004). ARB: a software environment for sequence data. Nucleic Acids Res 32, 1363-1371.
27. Macalady, J. L., Lyon, E. H., Koffman, B., Albertson, L. K., Meyer, K., Galdenzi, S. & Mariani, S. (2006). Dominant microbial populations in limestone-corroding stream biofilms, Frasassi cave system, Italy. Appl Environ Microbiol 72, 5596-5609.
28. McDonald, I. R., Kelly, D. P., Murrell, J. C. & Wood, A. P. (1997). Taxonomic relationships of Thiobacillus halophilus, Thiobacillus aquesulis, and other species of Thiobacillus, as determined using 16S rRNA sequencing. Arch Microbiol 166, 394-398.
29. Mori, K., Kim, H., Kakegawa, T. & Hanada, S. (2003). A novel lineage of sulfate-reducing microorganisms: Thermodesulfobiaceae fam. nov., Thermodesulfobium narugense, gen. nov., sp. nov., a new thermophilic isolate from a hot spring. Extremophiles 7, 283-290.
30. Nakagawa, Y. & Yamasato, K. (1993). Phylogenetic diversity of the genus Cytophaga revealed by 16S rRNA sequencing and menaquinone analysis. J Gen Microbiol 139, 1155-1161.
31. Nakagawa, S., Nakamura, S., Inagaki, F., Takai, K., Shirai, N. & Sako, Y. (2004). Hydrogenivirga caldilitoris gen. nov., sp. nov., a novel extremely thermophilic, hydrogen- and sulfur-oxidizing bacterium from a coastal hydrothermal field. Int J Syst Evol Microbiol 54, 2079-2084.
32. NBRC (2005). NBRC Catalogue of Biological Resources: Microorganisms, Genomic DNA Clones, and cDNAs, 1st edn. Chiba, Japan: National Institute of Technology and Evaluation (NITE).
33. Reysenbach, A. L., Wickham, G. S. & Pace, N. R. (1994). Phylogenetic analysis of the hyperthermophilic pink filament community in Octopus Spring, Yellowstone National Park. Appl Environ Microbiol 60, 2113-2119.
34. Robertson, L. & Kuenen, J. (2006). The genus Thiobacillus. In The Prokaryotes, 3rd edn, vol. 5, pp. 812-827. Edited by M. Dworkin, S. Falkow, E. Rosenberg, K.-H. Schleifer & E. Stackebrandt. New York: Springer.
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. Schulz, H. N., Brinkhoff, T., Ferdelman, T. G., Mariné, M. H., Teske, A. & Jørgensen, B. B. (1999). Dense populations of a giant sulfur bacterium in Namibian shelf sediments. Science 284, 493-495.
38. Segerer, A., Neuner, A., Kristjansson, J. K. & Stetter, K. O. (1986). Acidianus infernus gen. nov., sp. nov., and Acidianus brierleyi comb. nov.: facultatively aerobic, extremely acidophilic thermophilic sulfur-metabolizing archaebacteria. Int J Syst Bacteriol 36, 559-564.
39. Segerer, A. H., Trincone, A., Gahrtz, M. & Stetter, K. O. (1991). Stygiolobus azoricus gen. nov., sp. nov. represents a novel genus of anaerobic, extremely thermoacidophilic archaebacteria of the order Sulfolobales. Int J Syst Bacteriol 41, 495-501.
40. Sievert, S. M., Heidorn, T. & Kuever, J. (2000). Halothiobacillus kellyi sp. nov., a mesophilic, obligately chemolithoautotrophic, sulfur-oxidizing bacterium isolated from a shallow-water hydrothermal vent in the Aegean Sea, and emended description of the genus Halothiobacillus. Int J Syst Evol Microbiol 50, 1229-1237.
41. Skirnisdottir, S., Hreggvidsson, G. O., Hjörleifsdottir, S., Marteinsson, V. T., Petursdottir, S. K., Holst, O. & Kristjansson, J. K. (2000). Influence of sulfide and temperature on species composition and community structure of hot spring microbial mats. Appl Environ Microbiol 66, 2835-2841.
42. Smith, A. L. & Kelly, D. P. (1979). Competition in the chemostat between an obligately and a facultatively chemolithotrophic Thiobacillus. J Gen Microbiol 115, 377-384.
43. Sorokin, D. Yu., Banciu, H., Robertson, L. A. & Kuenen, J. G. (2006). Haloalkaliphilic sulfur-oxidizing bacteria. In The Prokaryotes, 3rd edn, vol. 2, pp. 969-984. Edited by M. Dworkin, S. Falkow, E. Rosenberg, K.-H. Schleifer & E. Stackebrandt. New York: Springer.
44. Stahl, D. A. & Amann, R. (1991). Development and application of nucleic acid probes in bacterial systematics. In Nucleic Acid Techniques in Bacterial Systematics, pp. 205-248. Edited by E. Stackebrandt & M. Goodfellow. Chichester: Wiley.
45. Takai, K., Inagaki, F., Nakagawa, S., Hirayama, H., Nunoura, T., Sako, Y., Nealson, K. H. & Horikoshi, K. (2003a). Isolation and phylogenetic diversity of members of previously uncultivated epsilon-Proteobacteria in deep-sea hydrothermal fields. FEMS Microbiol Lett 218, 167-174.
46. Takai, K., Kobayashi, H., Nealson, K. H. & Horikoshi, K. (2003b). Sulfurihydrogenibium subterraneum gen. nov., sp. nov., from a subsurface hot aquifer. Int J Syst Evol Microbiol 53, 823-827.
47. Takai, K., Hirayama, H., Nakagawa, T., Suzuki, Y., Nealson, K. H. & Horikoshi, K. (2004). Thiomicrospira thermophila sp. nov., a novel microaerobic, thermotolerant, sulfur-oxidizing chemolithomixotroph isolated from a deep-sea hydrothermal fumarole in the TOTO caldera, Mariana Arc, Western Pacific. Int J Syst Evol Microbiol 54, 2325-2333.
48. Takai, K., Miyazaki, M., Nunoura, T., Hirayama, H., Oida, H., Furushima, Y., Yamamoto, H. & Horikoshi, K. (2006). Sulfurivirga caldicuralii gen. nov., sp. nov., a novel microaerobic, thermophilic, thiosulfate-oxidizing chemolithoautotroph, isolated from a shallow marine hydrothermal system occurring in a coral reef, Japan. Int J Syst Evol Microbiol 56, 1921-1929.
49. 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.
50. Visser, J. M., Stefess, G. C., Robertson, L. A. & Kuenen, J. G. (1997). Thiobacillus sp. W5, the dominant autotroph oxidizing sulfide to sulfur in a reactor for aerobic treatment of sulfidic wastes. Antonie Van Leeuwenhoek 72, 127-134.
51. Wood, A. P. & Kelly, D. P. (1985). Physiological characteristics of a new thermophilic obligately chemolithotrophic Thiobacillus species, Thiobacillus tepidarius. Int J Syst Bacteriol 35, 434-437.
52. Wood, A. P. & Kelly, D. P. (1988). Isolation and characterisation of Thiobacillus aquaesulis sp. nov., a novel facultatively autotrophic moderate thermophile. Arch Microbiol 149, 339-343.
53. Wood, A. P. & Kelly, D. P. (1991). Isolation and characterisation of Thiobacillus halophilus sp. nov., a sulfur-oxidising autotrophic eubacterium from a Western Australian hypersaline lake. Arch Microbiol 156, 277-280.
54. Yamamoto, H., Hiraishi, A., Kato, K., Chiura, H. X., Maki, Y. & Shimizu, A. (1998). Phylogenetic evidence for the existence of novel thermophilic bacteria in hot spring sulfur-turf microbial mats in Japan. Appl Environ Microbiol 64, 1680-1687.