In situ detection of novel Acidobacteria in microbial mats from a chemolithoautotrophically based cave ecosystem (Lower Kane Cave, WY, USA)

Environmental Microbiology

Volumn 9, Issue 6, 2007, Pages 1523-1534

  Meisinger, Daniela B ^a   Zimmermann, Johannes ^a   Ludwig, Wolfgang ^a   Schleifer, Karl Heinz ^a   Wanner, Gerhard ^b   Schmid, Michael ^c   Bennett, Philip C ^d   Engel, Annette S ^e   Lee, Natuschka M ^a  

^a TECHNICAL UNIVERSITY OF MUNICH   (Germany)

^b UNIVERSITY OF MUNICH   (Germany)

^c Natl Res Ctr Environ and Hlth   (Germany)

^d UNIVERSITY OF TEXAS AT AUSTIN   (United States)

^e LOUISIANA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CARBON; FRESH WATER; RNA 16S;

ARTICLE; BACTERIUM; BIOFILM; CLASSIFICATION; ECOSYSTEM; ENVIRONMENT; FLUORESCENCE IN SITU HYBRIDIZATION; GENETICS; GEOLOGY; GROWTH, DEVELOPMENT AND AGING; ISOLATION AND PURIFICATION; METABOLISM; MICROBIOLOGY; UNITED STATES;

BACTERIA; BIOFILMS; CARBON; ECOSYSTEM; ENVIRONMENT; FRESH WATER; GEOLOGY; IN SITU HYBRIDIZATION, FLUORESCENCE; RNA, RIBOSOMAL, 16S; WATER MICROBIOLOGY; WYOMING;

ACIDOBACTERIA; EPSILONPROTEOBACTERIA; OTUS;

EID: 34248597469     PISSN: 14622912     EISSN: 14622920     Source Type: Journal    
DOI: 10.1111/j.1462-2920.2007.01271.x     Document Type: Article

References (51)

1. Alm, E.W., Oerther, D.B., Larsen, N., Stahl, D.A. Raskin, L. (1996) The oligonucleotide probe data base. Appl Environ Microbiol 62 : 3557 3559.
2. Amann, R. (1995) In situ identification of micro-organisms by whole cell hybridization with rRNA-targeted nucleic acid probes. In Molecular Microbial Ecology Manual. Akkermanns, A.D.L., van Elsas, J. D., de Brujin, F.J. (eds). Dordrecht, The Netherlands : Kluwer Academic Publishers, 3.3.6, pp. 1 15.
3. Amann, R., Binder, B.J., Olson, R.J., Chisholm, S.W., Devereux, R. Stahl, D.A. (1990) Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Appl Environ Microbiol 56 : 1919 1925.
4. Baker, B.J. Banfield, J.F. (2003) Microbial communities in acid mine drainage. FEMS Microbiol Ecol 44 : 139 152.
5. Barns, S.M., Takala, S.L. Kuske, C.R. (1999) Wide distribution and diversity of members of the bacterial kingdom Acidobacterium in the environment. Appl Environ Microbiol 65 : 1731 1737.
6. Behr, T., Koob, C., Schedl, M., Mehlen, A., Meier, H., Knopp, D., et al. (2000) A nested array of rRNA targeted probes for the detection and identification of Enterococci by reverse hybridization. Syst Appl Microbiol 23 : 563 572.
7. Brosius, J., Dull, T.J., Sleeter, D.D. Noller, H.F. (1981) Gene organization and primary structure of a ribosomal RNA operon from Escherichia coli. J Mol Biol 148 : 107 127.
8. Caccavo, J.R.F., Lonergan, D.J., Lovley, D.R., Davis, M., Stolz, J.F. McInerney, M.J. (1994) Geobacter sulfurreducens sp. nov., a hydrogen- and acetate-oxidizing dissimilatory metal-reducing microorganism. Appl Environ Microbiol 60 : 3752 3759.
9. Chelius, M.K. Moore, J.C. (2004) Molecular phylogenetic analysis of Archaea and Bacteria in Wind Cave, South Dakota. Geomicrobiol J 21 : 123 134.
10. Coates, J.D., Ellis, D., Gaw, C.W. Lovley, D.R. (1999) Geothrix fermentans gen. nov., sp. nov., a novel Fe(III)-reducing bacterium from a hydrocarbon-contaminated aquifer. Int J Syst Bacteriol 49 : 1615 1622.
11. Dhillon, A., Teske, A., Dillion, J., Stahl, D.A. Sogin, M.L. (2003) Molecular characterization of sulphate-reducing bacteria in the Guaymas Basin. Appl Environ Micorbiol 69 : 2765 2772.
12. Egemeier, S.J. (1981) Cavern development by thermal waters. Nat Speleol Soc Bull 43 : 31 51.
13. Engel, A.S., Lee, N., Porter, M.L., Stern, L.A., Bennett, P.C. Wagner, M. (2003) Filamentous 'Epsilonproteobacteria' dominate microbial mats from sulfidic cave springs. Appl Environ Microbiol 69 : 5503 5511.
14. Engel, A.S., Porter, M.L., Stern, L.A., Quinlan, S. Bennett, P.C. (2004a) Bacterial diversity and ecosystem function of filamentous microbial mats from aphotic (cave) sulfidic springs dominated by chemolithoautotrophic 'Epsilonproteobacteria'. FEMS Microbiol Ecol 51 : 31 53.
15. Engel, A.S., Stern, L.A. Bennett, P.C. (2004b) Microbial contributions to cave formation: new insights into sulfuric acid speleogenesis. Geology 32 : 369 372.
16. Griffiths, R.I., Whiteley, A.S., O'Donnell, A.G. Bailey, M.J. (2000) Rapid method for coextraction of DNA and RNA from natural environments for analysis of ribosomal DNA- and rRNA-based microbial community composition. Appl Environ Microbiol 66 : 5488 5491.
17. Holmes, A.J., Tujula, N.A., Holley, M., Contos, A., James, J.M., Rogers, P. Gillings, M.R. (2001) Phylogenetic structure of unusual aquatic microbial formations in Nullarbor caves, Australia. Environ Microbiol 3 : 256 264.
18. Hugenholtz, P., Pitulle, C., Hershberger, K.L. Pace, N.R. (1998a) Novel division level bacterial diversity in a Yellowstone hot spring. J Bacteriol 180 : 366 376.
19. Hugenholtz, P., Goebel, B.M. Pace, N.R. (1998b) Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J Bacteriol 180 : 4765 4774.
20. Hutchens, E., Radajewski, S., Dumont, M.G., McDonald, I.R. Murrell, J.C. (2004) Analysis of methanotrophic bacteria in Movile Cave by stable isotope probing. Environ Microbiol 6 : 111 120.
21. Janssen, P.H., Yates, P.S., Grinton, B.E., Taylor, P.M. Sait, M. (2002) Improved culturability of soil bacteria and isolation in pure culture of novel members of the divisions Acidobacteria, Actinobacteria, Proteobacteria and Verrucomicrobia. Appl Environ Microbiol 68 : 2391 2396.
22. Joseph, S.J., Hugenholtz, P., Sangwan, P., Osborne, C.A. Janssen, P.H. (2003) Laboratory cultivation of widespread and previously uncultured soil bacteria. Appl Environ Microbiol 69 : 7210 7215.
23. Juretschko, S., Loy, A., Lehner, A. Wagner, M. (2002) The microbial community composition of a nitrifying/denitrifying activated sludge from an industrial sewage treatment plant analyzed by the full-cycle rRNA approach. Syst Appl Microbiol 25 : 84 99.
24. Kanagawa, T., Kamagata, Y., Aruga, S., Kohno, T., Horn, M. Wagner, M. (2000) Phylogenetic analysis of and oligonucleotide probe development for eikelboom type 021N filamentous bacteria isolated from bulking activated sludge. Appl Environ Microbiol 66 : 5043 5052.
25. Kishimoto, N., Kosako, Y. Tano, T. (1991) Acidobacterium capsulatum gen. nov., sp. nov. an acidophilic, chemoorganotrophic bacterium containing menaquinone from acidic mineral environment. Curr Microbiol 22 : 1 7.
26. Knittel, K., Boetius, A., Lemke, A., Eilers, H., Lochte, K., Pfannkuche, O., et al. (2003) Activity, distribution, and diversity of sulfate reducers and other bacteria in sediments above gas hydrate (Cascadia Margin, OR). Geomicrobiol J 20 : 269 294.
27. Lane, D.J. (1991) 16S/23S rRNA sequencing. In Nucleid Acid Techniques in Bacterial Systematics. Stackebrandt, E. Goodfellow, M. (eds). Chichester, UK : J. Wiley and Sons, pp. 115 175.
28. Liesack, W., Bak, F., Kreft, U. Stackebrandt, E. (1994) Holophaga foetida gen. nov., spec. nov., a new, homoacetogenic bacterium degrading methoxylated aromatic compounds. Arch Microbiol 162 : 85 90.
29. Ludwig, W., Kirchhof, G., Klugbauer, N., Weizenegger, M., Betzl, D., Ehrmann, M., et al. (1992) Complete 23S ribosomal RNA sequences of Gram-positive bacteria with a low DNA content. Syst Appl Microbiol 15 : 487 501.
30. Ludwig, W., Bauer, S.H., Bauer, M., Held, I., Kirchhof, G., Schulze, R., et al. (1997) Detection and in situ identification of representatives of a widely distributed new bacterial phylum. FEMS Microbiol Lett 153 : 181 190.
31. Ludwig, W., Strunk, O., Klugbauer, S., Klugbauer, N., Weizenegger, M., Neumaier, J., et al. (1998) Bacterial phylogeny based on comparative sequence analysis. Electrophoresis 19 : 554 568.
32. Ludwig, W., Strunk, O., Westram, R., Richter, L., Meier, H., Yadhukumar, et al. (2004) ARB: a software environment for sequence data. Nucleic Acids Res 32 : 1363 1371.
33. Manz, W., Amann, R., Ludwig, W., Wagner, M. Schleifer, K.-H. (1992) Phylogenetic oligodeoxynucleotide probes for the major subclasses of proteobacteria: problems and solutions. Syst Appl Microbiol 15 : 593 600.
34. Ravenschlag, K., Sahm, K., Pernthaler, J. Amann, R. (1999) High bacterial diversity in permanently cold marine sediments. Appl Env Microbiol 65 : 3982 3989.
35. de Rijk, P., Van de Peer, Y., Van den Broeck, I. de Wachter, R. (1995) Evolution according to large ribosomal subunit RNA. J Mol Evol 41 : 366 375.
36. Rosselló-Mora, R. Amann, R. (2001) The species concept for prokaryotes. FEMS Microbiol Rev 25 : 39 67.
37. Sait, M., Hugenholtz, P. Janssen, P.J. (2002) Cultivation of globally distributed soil bacteria from phylogenetic lineages previously only detected in cultivation-independent surveys. Environ Microbiol 4 : 654 666.
38. Sait, M., Davis, K.E.R. Janssen, P.H. (2006) Effect of pH on isolation and distribution of members of subdivision 1 of the phylum Acidobacteria occurring in soil. Appl Env Microbiol 72 : 1852 1857.
39. Schabereiter-Gurtner, C., Saiz-Jimenez, C., Piñar, G., Lubitz, R. Roelleke, C. (2002a) Altamira cave Paleolithic paintings harbor partly unknown bacterial communities. FEMS Microbiol Let 211 : 7 11.
40. Schabereiter-Gurtner, C., Saiz-Jimenez, C., Piñar, G., Lubitz, R. Roelleke, C. (2002b) Phylogenetic 16S rRNA analysis reveals the presence of complex and partly unknown bacterial communities in Tito Bustillo cave, Spain, and on its Paleolithic paintings. Environ Microbiol 4 : 392 400.
41. Schabereiter-Gurtner, C., Piñar, G., Lubitz, R., Roelleke, C. Saiz-Jimenez, C. (2003) Acidobacteria in paleolithic painting caves. In Molecular Biology and Cultural Heritage. Saiz-Jimenez, C. (ed.). Lisse, The Netherlands : Swets & Zeitlinger, pp. 23 28.
42. Schabereiter-Gurtner, C., Saiz-Jimenez, C., Piñar, G., Lubitz, R. Roelleke, C. (2004) Phylogenetic diversity of bacteria associated with paleolithic paintings and surrounding rock walls in two Spanish caves (Llonín and La Garma). FEMS Microbiol Ecol 47 : 235 247.
43. Sogin, M.L., Morrison, H.G., Huber, J.A., Welch, D.M., Huse, S.M., Neal, P.R., et al. (2006) Microbial diversity in the deep sea and the underexplored 'rare biosphere'. PNAS 103 : 12115 12120.
44. Spring, S., Schulze, R., Overmann, J. Schleifer, K.-H. (2000) Identification and characterization of ecologically significant prokaryotes in the sediment of freshwater lakes: molecular and cultivation studies. FEMS Microbiol Rev 24 : 573 590.
45. Stevenson, B.S., Eichorst, S.A., Wertz, J.T., Schmidt, T.M. Breznak, J.A. (2004) New strategies for cultivation and detection of previously uncultured microbes. Appl Environ Microbiol 70 : 4748 4755.
46. von Wintzingerode, F., Selent, B., Hegemann, W. Göbel, U.B. (1999) Phylogenetic analysis of an anaerobic, trichlorobenzene-transforming microbial consortium. Appl Environ Microbiol 65 : 283 286.
47. Zimmermann, J. (2002) Oligo- und Polynukleotidsonden-gestützte Charakterisierung und Anreicherung bisher nicht kultivierbarer Acidobacteria. Dissertation. Munich, Germany: Technische Universität München. [WWW document]. URL http://tumb1.biblio.tu-muenchen.de/publ/diss/ch/2002/zimmermann. html.
48. Zimmermann, J., Ludwig, W. Schleifer, K.-H. (2001) DNA polynucleotide probes generated from representatives of the genus Acinetobacter and their application in fluorescence in situ hybridization of environmental samples. Syst Appl Microbiol 24 : 238 244.
49. Zimmermann, J., Gonzalez, J., Ludwig, W. Saiz-Jimenez, C. (2005a) Detection and phylogenetic relationships of highly diverse uncultured acidobacterial communities in Altamira Cave using 23S rRNA sequence analyses. Geomicrobiol J 22 : 379 388.
50. Zimmermann, J., Gonzalez, J. Saiz-Jimenez, C. (2005b) Epilithic biofilms in Saint Callixtus catacombs (Rome) harbour a broad spectrum of Acidobacteria. Antonie Van Leeuwenhoek 89 : 203 208.
51. Zwirglmaier, K. (2005) Fluorescence in situ hybridisation (FISH) - the next generation. FEMS Microbiol Lett 246 : 151 158.