Design of 16S rRNA-targeted oligonucleotide probes for detecting cultured and uncultured archaeal lineages in high-temperature environments

Environmental Microbiology

Volumn 6, Issue 2, 2004, Pages 170-182

  Nercessian, Olivier ^a,d   Prokofeva, Maria ^b   Lebedinski, Alexander ^b   L'Haridon, Stéphane ^a   Cary, Craig ^c   Prieur, Daniel ^a   Jeanthon, Christian ^a  

^a UNIVERSITÉ DE BRETAGNE OCCIDENTALE   (France)

^b RUSSIAN ACADEMY OF SCIENCES   (Russian Federation)

^c UNIVERSITY OF DELAWARE   (United States)

^d University of Washington   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARCHAEAL DNA; ARCHAEAL RNA; RNA 16S;

ARCHAEBACTERIUM; ARTICLE; CLASSIFICATION; ECOSYSTEM; ENVIRONMENT; GENETICS; HEAT; ISOLATION AND PURIFICATION; METABOLISM; OLIGONUCLEOTIDE PROBE; PHYLOGENY;

ARCHAEA; DNA, ARCHAEAL; ECOSYSTEM; ENVIRONMENT; HEAT; OLIGONUCLEOTIDE PROBES; PHYLOGENY; RNA, ARCHAEAL; RNA, RIBOSOMAL, 16S;

ARCHAEA; ARCHAEOGLOBUS; CRENARCHAEOTA; DESULFUROCOCCALES; IGNICOCCUS; KORARCHAEOTA; METHANOCALDOCOCCACEAE; METHANOPYRUS; PYRODICTIACEAE; SULFOLOBALES; THERMOCOCCALES; THERMOPROTEACEAE;

EID: 1142281824     PISSN: 14622912     EISSN: None     Source Type: Journal    
DOI: 10.1046/j.1462-2920.2003.00560.x     Document Type: Article

References (67)

1. Alm, E.W., Oerther, D.B., Larsen, N., Stahl, D.A., and Raskin, L. (1996) The Oligonucleotide Probe Database. Appl Environ Microbiol 65: 270-277.
2. Balch, W.E., Fox, G.E., Magrum, C.J., Woese, C.R., and Wolfe, R.S. (1979) Methanogens: reevaluation of a unique biological group. Microbiol Rev 43: 260-296.
3. Barns, S.M., Fundyga, R.E., Jeffries, M.W., and Pace, N.R. (1994) Remarkable archaeal diversity detected in a Yellowstone National Park hot spring environment. Proc Natl Acad Sci USA 91: 1609-1613.
4. Barns, S.M., Delwiche, C.F., Palmer, J.D., and Pace, N.R. (1996) Perspectives on archaeal diversity, thermophily and monophyly from environmental rRNA sequences. Proc Natl Acad Sci USA 93: 9188-9193.
5. Bintrim, S.B., Donohue, T.J., Handelsman, J., Roberts, G.P., and Goodman, R.M. (1997) Molecular phylogeny of Archaea from soil. Proc Natl Acad Sci USA 94: 277-282.
6. Blochl, E., Rachel, R., Burggraf, S., Hafenbradl, D., Jannasch, H.W., and Stetter, K.O. (1997) Pyrolobus fumarii, gen. and sp. nov., represents a novel group of Archaea, extending the upper temperature limit for life to 113 degrees C. Extremophiles 1: 14-21.
7. Boone, D.R., Castenholz, R.W., and Garrity, G.M. (2001) Bergey's Manual of Systematic Bacteriology, Vol. 1, 2nd edn. New York: Springer-Verlag.
8. 2, and S(-II) in porewaters of marine and freshwater sediments. Environ Sci Technol 29: 751-761.
9. Brosius, J., Palmer, J.L., Kennedy, J.P., and Noller, H.F. (1978) Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia coli. Proc Natl Acad Sci USA 75: 4801-4805.
10. Burggraf, S., Fricke, H., Neuner, A., Kristjansson, J., Rouvier, P., Mandelco, L., et al. (1990a) Methanococcus igneus sp. nov., a novel hyperthermophilic methanogen from a shallow submarine hydrothermal system. Syst Appl Microbiol 13: 263-269.
11. Burggraf, S., Jannasch, H.W., Nicolaus, B., and Stetter, K.O. (1990b) Archaeoglobus profundus, sp. nov., represents a new species within the sulfate-reducing archaebacteria. Syst Appl Microbiol 13: 24-28.
12. Burggraf, S., Heyder, P., and Eis, N. (1997) A pivotal Archaea group. Nature 385: 780.
13. Charbonnier, F., Forterre, P., Erauso, G., and Prieur, D. (1995) Purification of plasmids from thermophilic and hyperthermophilic Archaea. In Thermophiles, Archaea a Laboratory Manual. Robb, F.T., and Place, A.R. (eds). Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press, pp. 87-90.
14. DeLong, E.F. (1992) Archaea in coastal marine environments. Proc Natl Acad Sci USA 89: 5685-5689.
15. Di Meo, C.A., Wakefield, J.R., and Cary, S.C. (1999) A new device for sampling small volumes of water from marine micro-environments. Deep-Sea Res I 46: 1279-1287.
16. Erauso, G., Reysenbach, A.L., Godfroy, A., Meunier, J.R., Crump, B., Partensky, F., et al. (1993) Pyrococcus abyssi sp. nov., a new hyperthermophilic archaeon isolated from a deep-sea hydrothermal vent. Arch Microbiol 160: 338-349.
17. Esnault, G., Caumette, P., and Garcia, J.L. (1988) Characterization of Desulfovibrio giganteus sp. nov., a sulfate reducing bacterium isolated from a brackish coastal lagoon. Syst Appl Microbiol 10: 147-151.
18. Fiala, G., Stetter, K.O., Jannasch, H.W., Langworthy, T.A., and Madon, J. (1986) Staphylothermus marinus sp. nov. represents a novel genus of extremely thermophilic submarine heterotrophic archaebacteria growing up to 98°C. Syst Appl Microbiol 8: 106-113.
19. Garrity, G.M., and Holt, J.G. (2001) The road map to the manual. In Bergey's Manual of Systematic Bacteriology, Vol. 1, 2nd edn. Boone, D.R., Castenholz, R.W., and Garrity, G.M. (eds). New York: Springer-Verlag, pp. 119-166.
20. Grogan, D., Palm, P., and Zillig, W. (1990) Isolate B12, which harbours a virus-like element, represents a new species of the archaebacterial genus Sulfolobus, Sulfolobus shibatae, sp. nov. Arch Microbiol 154: 594-599.
21. Hafenbradl, D., Keller, M., Dirmeier, R., Rachel, R., Rossnagel, P., Burggraf, S., et al. (1996) Ferroglobus placidus gen. nov., sp. nov., a novel hyperthermophilic archaeum that oxidizes Fe2+ at neutral pH under anoxic conditions. Arch Microbiol 166: 308-314.
22. Huber, G., Spinnler, C., Gambacorta, A., and Stetter, K.O. (1989) Metallosphaera sedula gen. and sp. nov. represents a new genus of aerobic, metal-mobilizing, thermoacetophilic archaebacteria. Syst Appl Microbiol 12: 38-47.
23. Huber, H., Thomm, M., König, H., Thies, G., and Stetter, K.O. (1982) Methanococcus thermolithotrophicus a novel thermophilic lithotrophic methanogen. Arch Microbiol 132: 47-50.
24. Huber, H., Burggraf, S., Mayer, T., Wyschkony, I., Rachel, R., and Stetter, K.O. (2000) Ignicoccus gen. nov., a novel genus of hyperthermophilic, chemolithoautotrophic Archaea, represented by two new species, Ignicoccus islandicus sp. nov. and Ignicoccus pacificus sp. nov. Int J Syst Evol Microbiol 50: 2093-2100.
25. Huber, J.A., Butterfield, D.A., and Baross, J.A. (2002) Temporal changes in archaeal diversity and chemistry in a mid-ocean ridge subseafloor habitat. Appl Environ Microbiol 68: 1585-1594.
26. Huber, R., Kristjansson, J.K., and Stetter, K.O. (1987) Pyrobaculum gen. nov., a new genus of neutrophilic, rod-shaped archaebacteria from continental solfataras growing optimally at 100°C. Arch Microbiol 149: 95-101.
27. Hugenholtz, P. (2002) Exploring prokaryotic diversity in the genomic area. Genome Biol 3: 1-8.
28. Itoh, T., Suzuki, K., and Nakase, T. (1998) Thermocladium modestius gen. nov., sp. nov., a new genus of rod-shaped, extremely thermophilic crenarchaeote. Int J Syst Bacteriol 48: 879-887.
29. Itoh, T., Suzuki, K., and Nakase, T. (2002) Vulcanisaeta distributa gen. nov., sp. nov. and Vulcanisaeta souniana sp. nov., novel hyperthermophilic, rod-shaped crenarchaeotes isolated from hot springs in Japan. Int J Syst Evol Microbiol 52: 1097-1104.
30. Jannasch, H.W. (1995) Microbial interactions with hydrothermal fluids. In Seafloor Hydrothermal Systems: Physical, Chemical, Biological, and Geological Interactions. Humphris, S.E., Zierenberg, R.A., Mullineaux, L.S., and Thomson, R.E. (eds). Washington: American Geophysical Union, pp. 273-296.
31. Jones, W.J., Leigh, J.A., Mayer, F., Woese, C.R., and Wolfe, R.S. (1983) Methanococcus jannaschii sp. nov., an extremely thermophilic methanogen from a submarine hydrothermal vent. Arch Microbiol 136: 254-261.
32. Jukes, T.H., and Cantor, C.R. (1969) Evolution of protein molecules. In Mammalian Protein Metabolism. Munro, H.N. (ed.). New York: Academic Press, pp. 21-132.
33. Karner, M.B., DeLong, E.F., and Karl, D.M. (2001) Archaeal dominance in the mesopelagic zone of the Pacific Ocean. Nature 409: 507-510.
34. Kashefi, K., Tor, J.M., Holmes, D.E., Gaw Van Praagh, C.V., Reysenbach, A.L., and Lovley, D.R. (2002) Geoglobus ahangari gen. nov., sp. nov., a novel hyperthermophilic archaeon capable of oxidizing organic acids and growing autotrophically on hydrogen with Fe(III) serving as the sole electron acceptor. Int J Syst Evol Microbiol 52: 719-728.
35. Kobayashi, T., Kwak, Y.S., Akiba, T., Kudo, T., and Horikoshi, K. (1994) Thermococcus profundus sp. nov., a new hyperthermophilic archaeon isolated from a deep-sea hydrothermal vent. Syst Appl Microbiol 17: 232-236.
36. Kurr, M., Huber, R., König, H., Jannasch, H.W., Fricke, H., Trincone, A., et al. (1991) Methanopyrus kandleri, gen. and sp. nov. represents a novel group of hyperthermophilic methanogens, growing at 110°C. Arch Microbiol 156: 239-247.
37. Luther, G.W., Glazer, B.T., Hohmann, L., Popp, J.I., Taillefert, M., Rozan, T.F., et al. (2001) Sulfur speciation monitored in situ with solid state gold amalgam voltammetric microelectrodes: polysulfides as a special case in sediments, microbial mats and hydrothermal vent waters. J Environ Monit 3: 61-66.
38. Marteinsson, V.T., Kristjansson, J.K., Kristmannsdottir, H., Dahlkvist, M., Saemundsson, K., Hannington, M., et al. (2001) Discovery and description of giant submarine smectite cones on the seafloor in Eyjafjordur, northern Iceland, and a novel thermal microbial habitat. Appl Environ Microbiol 67: 827-833.
39. Massana, R., DeLong, E.F., and Pedros-Alio, C. (2000) A few cosmopolitan phylotypes dominate planktonic archaeal assemblages in widely different oceanic provinces. Appl Environ Microbiol 66: 1777-1787.
40. Moyer, C.L., Tiedje, J.M., Dobbs, F.C., and Karl, D.M. (1998) Diversity of deep-sea hydrothermal vent Archaea from Loihi Seamount, Hawaii. Deep-Sea Res II 45: 303-317.
41. Nercessian, O., Reysenbach, A.L., Prieur, D., and Jeanthon, C. (2003) Archaeal diversity associated with in situ samplers deployed on hydrothermal vents on the East Pacific Rise (13°N). Environ Microbiol 5: 492-502.
42. Orphan, V.J., Taylor, L.T., Hafenbradl, D., and Delong, E.F. (2000) Culture-dependent and culture-independent characterization of microbial assemblages associated with high-temperature petroleum reservoirs. Appl Environ Microbiol 66: 700-711.
43. Paterek, J.R., and Smith, P.H. (1985) Isolation and characterization of a halophilic methanogen from Great Salt Lake. Appl Environ Microbiol 50: 877-881.
44. Pley, U., Schipka, A., Gambacorta, A., Jannasch, H.W., Fricke, H., Rachel, R., and Stetter, K.O. (1991) Pyrodictium abyssi, sp. nov. represents a novel heterotrophic marine archaeal hyperthermophile growing at 110°C. Syst Appl Microbiol 14: 245-253.
45. Prokofeva, M.I., Miroshnichenko, M.L., Kostrikina, N.A., Chernyh, N.A., Kuznetsov, B.B., Tourova, T.P., and Bonch-Osmolovskaya, E.A. (2000) Acidilobus aceticus gen. nov., sp. nov., a novel anaerobic thermoacidophilic archaeon from continental hot vents in Kamchatka. Int J Syst Evol Microbiol 50: 2001-2008.
46. Raskin, L., Stromley, J.M., Rittmann, B.E., and Stahl, D.A. (1994) Group-specific 16S rRNA hybridization probes to describe natural communities of methanogens. Appl Environ Microbiol 60: 1232-1240.
47. Reysenbach, A.L., Longnecker, K., and Kirshtein, J. (2000) Novel bacterial and archaeal lineages from an in situ growth chamber deployed at a Mid-Atlantic Ridge hydrothermal vent. Appl Environ Microbiol 66: 3798-3806.
48. Romesser, J.A., Wolfe, R.S., Mayer, F., Spiess, E., and Walther-Mauruschat, A. (1979) Methanogenium, a new genus of marine methanogenic Bacteria, and characterization of Methanogenium cariaci sp. nov. and Methanogenium marisnigri sp. nov. Arch Microbiol 121: 147-153.
49. Saitou, N., and Nei, M. (1987) The neighbour joining method: a new tool for reconstructing phylogenetic trees. Mol Biol Evol 4: 406-425.
50. Sako, Y., Nomura, N., Uchida, A., Ishida, Y., Morii, H., Koga, Y., et al. (1996) Aeropyrum pernix gen. nov., sp. nov., a novel aerobic hyperthermophilic archaeon growing at temperatures up to 100 degrees C. Int J Syst Bacteriol 46: 1070-1077.
51. Sambrook, J., Fritsch, E.F., and Maniatis, T. (1989) Molecular Cloning: a Laboratory Manual, 2nd edn. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press.
52. Stahl, D.A., and Amann, R. (1991) Development and application of nucleic acid probes. In Nucleic Acids Techniques in Bacterial Systematics. Stackebrandt, E., and Goodfellow, E. (eds). Chichester: John Wiley & Sons, pp. 205-248.
53. Stookey, L.L. (1970) Ferrozine - a new spectrophotometric reagent for iron. Anal Chem 42: 779-781.
54. Takai, K., and Horikoshi, K. (1999) Genetic diversity of Archaea in deep-sea hydrothermal vent environments. Genetics 152: 1285-1297.
55. Takai, K., and Sako, Y. (1999) A molecular view of archaeal diversity in marine and terrestrial hot water environments. FEMS Microbiol Ecol 28: 177-188.
56. Takai, K., Sugai, A., Itoh, T., and Horikoshi, K. (2000) Palaeococcus ferrophilus gen. nov., sp. nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent. Int J Syst Evol Microbiol 50: 489-500.
57. Takai, K., Moser, D.P., DeFlaun, M., Onstott, T.C., and Frederickson, J.K. (2001a) Archaeal diversity in waters from deep South African gold mines. Appl Environ Microbiol 67: 3618-3629.
58. Takai, K., Komatsu, T., Inagaki, F., and Horikoshi, K. (2001b) Distribution of Archaea in a black smoker chimney structure. Appl Environ Microbiol 67: 3618-3629.
59. Teske, A., Hinrichs, K.U., Edgcomb, V., de Vera Gomez, A., Kysela, D., Sylva, S.P., et al. (2002) Microbial diversity of hydrothermal sediments in the Guaymas Basin: evidence for anaerobic methanotrophic communities. Appl Environ Microbiol 68: 1994-2007.
60. Vetriani, C., Jannasch, H.W., MacGregor, B.J., Stahl, D.A., and Reysenbach, A.L. (1999) Population structure and phylogenetic characterization of marine benthic Archaea in deep-sea sediments. Appl Environ Microbiol 65: 4375-4384.
61. von Wintzingerode, F., Gobel, U.B., and Stackebrandt, E. (1997) Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol Rev 21: 213-229.
62. Woese, C.R., Kandler, O., and Wheelis, M.L. (1990) Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci USA 87: 4576-4579.
63. Zillig, W., Stetter, K.O., Wunderl, S., Schulz, W., Priess, H., and Scholz, I. (1980) The Sulfolobus-'Caldariella' group: taxonomy on the basis of the structure of DNA dependent RNA polymerases. Arch Microbiol 125: 259-269.
64. Zillig, W., Stetter, K.O., Schäfer, W., Janekovic, D., Wunderl, S., Holz, J., and Palm, P. (1981) Thermoproteales: a novel type of extremely thermoacidophilic anaerobic archaebacteria isolated from Icelandic solfataras. Zentbl Bakteriol Mikrobiol Hyg 1 Abt Orig C 2: 205-227.
65. Zillig, W., Stetter, K.O., Prangishvilli, D., Schäfer, W., Wunderl, S., Jankovic, D., et al. (1982) Desulfurococcaceae, the second family of the extremely thermophilic, anaerobic, sulfur-respiring Thermoproteales. Zentbl Bakteriol Hyg Abt Orig C 3: 304-317.
66. Zillig, W., Gierl, A., Schreiber, G., Wunderl, S., Janekovic, D., Stetter, K.O., and Klenk, H.P. (1983a) The archaebacterium Thermofilum pendens represents a novel genus of the thermophilic, anaerobic sulfur respiring Thermoproteales. Syst Appl Microbiol 4: 79-87.
67. Zillig, W., Holz, L., Janekovic, D., Schäfer, W., and Reiter, W.D. (1983b) The archaebacterium Thermococcus celer represents a novel genus within the thermophilic branch of the archaebacteria. Syst Appl Microbiol 4: 88-94.