Molecular strategies for studies of natural populations of sulphate-reducing microorganisms

Sulphate-Reducing Bacteria: Environmental and Engineered Systems

Volumn , Issue , 2007, Pages 39-116

  Stahl, David A ^a   Loy, Alexander ^b   Wagner, Michael ^b  

^a UNIVERSITY OF WASHINGTON   (United States)

^b UNIVERSITY OF VIENNA   (Austria)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 58149120370     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1017/CBO9780511541490.003     Document Type: Chapter

References (135)

1. Adamczyk, J., Hesselsoe, M., Iversen, N. et al. (2003). The isotope array, a newtool that employs substrate-mediated labeling of rRNA for determination of microbial community structure and function. Appl. Environ. Microbiol., 69, 6875-6887.
2. Alm, E.W., Oerther, D. B., Larsen, N., Stahl, D. A. and Raskin, L. (1996). The oligonucleotide probe database. Appl. Environ. Microbiol., 62, 3557-3559.
3. Alm, E. W. and Stahl, D. A. (2000). Critical factors influencing the recovery and integrity of rRNA extracted from environmental samples: use of an optimized protocol to measure depth-related biomass distribution in freshwater sediments. J. Microbiol. Methods, 40, 153-162.
4. Alm, E.W., Zheng, D. and Raskin, L. (2000). The presence ofhumic substances and DNA in RNA extracts affects hybridization results. Appl. Environ. Microbiol., 66, 4547-4554.
5. Amann, R. and Schleifer, K.-H. (2001). Nucleic acid probes and their application in environmental microbiology. In G. M. Garrity (ed.), Bergey's Manual of Systematic Bacteriology. 2nd edn. New York: Springer.
6. Amann, R. I., Binder, B. J., Olson, R. J. et al. (1990). Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Appl. Environ. Microbiol., 56, 1919-1925.
7. Amann, R. I., Stromley, J., Devereux, R., Key, R. and Stahl, D. A. (1992). Molecular and microscopic identification of sulphate-reducing bacteria in multispecies biofilms. Appl. Environ. Microbiol., 58, 614-623.
8. Baker, B.J., Moser, D. P., MacGregor, B. J. et al. (2003). Related assemblages of sulphate-reducing bacteria associated with ultradeep gold mines of South Africa and deep basalt aquifers of Washington State. Environ. Microbiol., 5, 267-277.
9. Beller, H. R., Chain, P. S., Letain, T. E. et al. (2006). The genome sequence of the obligately chemolithoautotrophic, facultatively anaerobic bacterium Thiobacillus denitrificans. J. Bacteriol., 188, 1473-188.
10. Blazejak, A., Erseus, C., Amann, R. and Dubilier, N. (2005). Coexistence of bacterial sulfide oxidizers, sulphate reducers, and spirochetes in a gutless worm (Oligochaeta) from the Peru margin. Appl. Environ. Microbiol., 71, 1553-1561.
11. Bodrossy, L. and Sessitsch, A. (2004). Oligonucleotide microarrays in microbial diagnostics. Curr. Opin. Microbiol., 7, 245-254.
12. Boetius, A., Ravenschlag, K., Schubert, C. J. et al. (2000). A marine microbial consortium apparently mediating anaerobic oxidation of methane. Nature, 407, 623-626.
13. Brosius, J., Dull, T. L., Sleeter, D. D. and Noller, H. F. (1981). Gene organization and primary structure of a ribosomal operon from Escherichia coli. J. Mol. Biol., 148, 107-127.
14. Castro, H., Newman, S., Reddy, K. R. and Ogram, A. (2005). Distribution and stability of sulphate-reducing prokaryotic and hydrogenotrophic methanogenic assemblages in nutrient-impacted regions of the Florida Everglades. Appl. Environ. Microbiol., 71, 2695-2704.
15. Castro, H., Reddy, K. R. and Ogram, A. (2002). Composition and function of sulphate-reducing prokaryotes in eutrophic and pristine areas ofthe Florida Everglades. Appl. Environ. Microbiol., 68, 6129-6137.
16. Chang, Y. J., Peacock, A. D., Long, P. E. et al. (2001). Diversity and characterization of sulphate-reducing bacteria in groundwater at a uranium mill tailings site. Appl. Environ. Microbiol., 67, 3149-3160.
17. Chhabra, S. R., He, Q., Huang, K. H. et al. (2006). Global analysis of heat shock response in Desulfovibrio vulgaris Hildenborough. J. Bacteriol., 188, 1817-1828.
18. Dahl, C., Engels, S., Pott-Sperling, A. S. et al. (2005). Novel genes of the dsr gene cluster and evidence for close interaction of Dsr proteins during sulfur oxidation in the phototrophic sulfur bacterium Allochromatium vinosum. J. Bacteriol., 187, 1392-1404.
19. Daims, H., Nielsen, P. H., Nielsen, J. L., Juretschko, S. and Wagner, M. (2000). Novel Nitrospira-like bacteria as dominant nitrite-oxidizers in biofilms from wastewater treatment plants: diversity and in situ physiology. Wat. Sci. Tech., 41, 85-90.
20. Daims, H., Stoecker, K. and Wagner, M. (2005). Fluorescence in situ hybridization for the detection of prokaryotes. In Osborn, A. M. and Smith C. J. (eds) Advanced Methods in Molecular Microbial Ecology. Abingdon, UK: BIOS Scientific Publishers.
21. Daly, K., Sharp, R. J. and McCarthy, A. J. (2000). Development of oligonucleotide probes and PCR primers for detecting phylogenetic subgroups of sulphate-reducing bacteria. Microbiology, 146, 1693-1705.
22. Dar, S. A., Kuenen, J. G. and Muyzer, G. (2005). Nested PCR-denaturing gradient gel electrophoresis approach to determine the diversity ofsulphate-reducing bacteria in complex microbial communities. Appl. Environ. Microbiol., 71, 2325-2330.
23. Davies, M.J., Shah, A. and Bruce, I.J. (2000). Synthesis of fluorescently labelled oligonucleotides and nucleic acids. Chem. Soc. Rev., 29, 97-107.
24. de Bok, F. A., Harmsen, H. J., Plugge, C. M. et al. (2005). The first true obligately syntrophic propionate-oxidizing bacterium, Pelotomaculum schinkii sp. nov., co-cultured with Methanospirillum hungatei, and emended description ofthe genus Pelotomaculum. Int. J. Syst. Evol. Microbiol., 55, 1697-1703.
25. Deplancke, B., Hristova, K. R., Oakley, H. A. et al. (2000). Molecular ecological analysis of the succession and diversity of sulphate-reducing bacteria in the mouse gastrointestinal tract. Appl. Environ. Microbiol., 66, 2166-2174.
26. Detmers, J., Strauss, H., Schulte, U. et al. (2004). FISH shows that Desulfotomaculum sare the dominating sulphate-reducing bacteria in a pristine aquifer. Microb. Ecol., 47, 236-242.
27. Devereux, R., Delaney, M., Widdel, F. and Stahl, D. A. (1989). Natural relationships among sulphate-reducing eubacteria. J. Bacteriol., 171, 6689-6695.
28. Devereux, R., Kane, M. D., Winfrey, J. and Stahl, D. A. (1992). Genus- and group-specific hybridization probes for determinative and environmental studies of sulphate-reducing bacteria. Syst. Appl. Microbiol., 15, 601-609.
29. Devereux, R., Winfrey, M. R., Winfrey, J. and Stahl, D. A. (1996). Depth profile of sulphate-reducing bacterial ribosomal RNA and mercury methylation in an estuarine sediment. FEMS Microbiol. Ecol., 20, 23-31.
30. Dhillon, A., Goswami, S., Riley, M., Teske, A. and Sogin, M. (2005). Domain evolution and functional diversification of sulfite reductases. Astrobiology, 5, 18-29.
31. Dhillon, A., Teske, A., Dillon, J., Stahl, D. A. and Sogin, M. L. (2003). Molecular characterization of sulphate-reducing bacteria in the Guaymas Basin. Appl. Environ. Microbiol., 69, 2765-72.
32. Dubilier, N., Mulders, C., Ferdelman, T. et al. (2001). Endosymbiotic sulphate-reducing and sulphide-oxidizing bacteria in an oligochaete worm. Nature, 411, 298-302.
33. Eisen, J. A., Nelson, K. E., Paulsen, I.T. et al. (2002). The complete genome sequence of Chlorobium tepidum TLS, a photosynthetic, anaerobic, green-sulfur bacterium. Proc. Natl. Acad. Sci. USA, 99, 9509-9514.
34. Fishbain, S., Dillon, J. G., Gough, H. L. and Stahl, D. A. (2003). Linkage of high rates of sulphate reduction in Yellowstone hot springs to unique sequence types in the dissimilatory sulphate respiration pathway. Appl. Environ. Microbiol., 69, 3663-3667.
35. Fitz-Gibbon, S.T., Ladner, H., Kim, U. J. et al. (2002). Genome sequence of the hyperthermophilic crenarchaeon Pyrobaculum aerophilum. Proc. Natl. Acad. Sci. USA, 99, 984-989.
36. Friedrich, M. W. (2002). Phylogenetic analysis reveals multiple lateral transfers of adenosine-5'-phosphosulphate reductase genes among sulphate-reducing microorganisms. J. Bacteriol., 184, 278-289.
37. Fukui, M., Suwa, Y. and Urushigawa, Y. (1996). High survival efficiency and ribosomal RNA decaying pattern of Desulfobacter latus, a highly specific acetate-utilizing organism, during starvation. FEMS Microbiol. Ecol., 19, 17-25.
38. Fukui, M., Teske, A., Assmus, B., Muyzer, G. and Widdel, F. (1999). Physiology, phylogenetic relationships, and ecology of filamentous sulphate-reducing bacteria (genus Desulfonema). Arch. Microbiol., 172, 193-203.
39. Geets, J., Borremans, B., Diels, L. et al. (2006). DsrB gene-based DGGE for community and diversity surveys ofsulphate-reducing bacteria. J. Microbiol. Methods, 66, 194-205.
40. Gibson, A. H., Jenkins, B. D., Wilkerson, F. P., Short, S. M. and Zehr, J. P. (2006). Characterization of cyanobacterial glnA gene diversity and gene expression in marine environments. FEMS Microbiol. Ecol., 55, 391-402.
41. Greene, E. A. and Voordouw, G. (2003). Analysis of environmental microbial communities by reverse sample genome probing. J. Microbiol. Methods, 53, 211-219.
42. Heidelberg, J. F., Seshadri, R., Haveman, S. A. et al. (2004). The genome sequence of the anaerobic, sulphate-reducing bacterium Desulfovibrio vulgaris Hildenborough. Nat. Biotechnol., 22, 554-559.
43. Hipp, W. M., Pott, A. S., Thum-Schmitz, N. et al. (1997). Towards the phylogeny of APS reductases and sirohaem sulfite reductases in sulphate-reducing and sulfur-oxidizing prokaryotes. Microbiology, 143, 2891-2902.
44. Hristova, K. R., Mau, M., Zheng, D. et al. (2000). Desulfotomaculum genus- and subgenus-specific 16S rRNA hybridization probes for environmental studies. Environ. Microbiol., 2, 143-159.
45. Imachi, H., Sekiguchi, Y., Kamagata, Y. et al. (2002). Pelotomaculum thermopropionicum gen. nov., sp. nov., an anaerobic, thermophilic, syntrophic propionate-oxidizing bacterium. Int. J. Syst. Evol. Microbiol., 52, 1729-1735.
46. Imachi, H., Sekiguchi, Y., Kamagata, Y. et al. (2006). Non-sulphate-reducing, syntrophic bacteria affiliated with Desulfotomaculum cluster I are widely distributed in methanogenic environments. Appl. Environ. Microbiol., 72, 2080-2091.
47. Imachi, H., Sekiguchi, Y., Kamagata, Y., Ohashi, A. and Harada, H. (2000). Cultivation and in situ detection of a thermophilic bacterium capable of oxidizing propionate in syntrophic association with hydrogenotrophic methanogens in a thermophilic methanogenic granular sludge. Appl. Environ. Microbiol., 66, 3608-3615.
48. Ito, T., Nielsen, J. L., Okabe, S., Watanabe, Y. and Nielsen, P. H. (2002). Phylogenetic identification and substrate uptake patterns of sulphate- reducing bacteria inhabiting an oxic-anoxic sewer biofilm determined by combining microautoradiography and fluorescent in situ hybridization. Appl. Environ. Microbiol., 68, 356-364.
49. Kane, M. D., Poulsen, L. K. and Stahl, D. A. (1993). Monitoring the enrichment and isolation of sulphate-reducing bacteria by using oligonucleotide hybridization probes designed from environmentally derived 16S rRNA sequences. Appl. Environ. Microbiol., 59, 682-686.
50. Karkhoff-Schweizer, R. R., Huber, D. P. and Voordouw, G. (1995). Conservation of the genes for dissimilatory sulfite reductase from Desulfovibrio vulgaris and Archaeoglobus fulgidus allows their detection by PCR. Appl. Environ. Microbiol., 61, 290-296.
51. Karnachuk, O. V., Pimenov, N. V., Yusupov, S. K. et al. (2006). Distribution, diversity, and activity of sulphate-reducing bacteria in the water column in Gek-Gel Lake, Azerbaijan. Microbiologiya, 75, 101-109.
52. Kjeldsen, K. U., Loy, A., Thomsen, T. R., et al. (2007). Diversity of sulfate-reducing bacteria from an extreme hypersaline sediment, Great Salt Lake (Utah, USA). FEMS Microbiol. Ecol., in press.
53. Kleikemper, J., Schroth, M. H., Sigler, W. V. et al. (2002). Activity and diversity of sulphate-reducing bacteria in a petroleum hydrocarbon-contaminated aquifer. Appl. Environ. Microbiol., 68, 1516-1523.
54. Klein, M., Friedrich, M., Roger, A. J. et al. (2001). Multiple lateral transfers of dissimilatory sulfite reductase genes between major lineages of sulphate-reducing prokaryotes. J. Bacteriol., 183, 6028-6035.
55. Klenk, H.-P., Clayton, R. A., Tomb, J.-F. et al. (1997). The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus. Nature, 390, 364-370.
56. Koizumi, Y., Kojima, H. and Fukui, M. (2004). Dominant microbial composition and its vertical distribution in saline meromictic Lake Kaiike (Japan) as revealed by quantitative oligonucleotide probe membrane hybridization. Appl. Environ. Microbiol., 70, 4930-4940.
57. Kusel, K., Pinkart, H. C., Drake, H. L. and Devereux, R. (1999). Acetogenic and sulphate-reducing bacteria inhabiting the rhizoplane and deep cortex cells of the sea grass Halodule wrightii. Appl. Environ. Microbiol., 65, 5117-5123.
58. Larsen, O., Lien, T. and Birkeland, N. K. (1999). Dissimilatory sulfite reductase from Archaeoglobus profundus and Desulfotomaculum thermocisternum: phylogenetic and structural implications from gene sequences. Extremophiles, 3, 63-70.
59. Laue, H., Friedrich, M., Ruff, J. and Cook, A. M. (2001). Dissimilatory sulfite reductase (desulfoviridin) of the taurine-degrading, non-sulphate-reducing bacterium Bilophila wadsworthia RZATAU contains a fused DsrB-DsrD subunit. J. Bacteriol, 183, 1727-1733.
60. Lie, T. J., Godchaux, W. and Leadbetter, E. R. (1999). Sulfonates as terminal electron acceptors for growth of sulfite-reducing bacteria (Desulfitobacterium) and sulphate-reducing bacteria: effects of inhibitors of sulfidogenesis. Appl. Environ. Microbiol., 65, 4611-4617.
61. Lin, C., Flesher, B., Capman, W. C., Amann, R. I. and Stahl, D. A. (1994). Taxon specific hybridization probes for fiber-digesting bacteria suggest novel gut-associated Fibrobacter. Syst. Appl. Microbiol., 17, 418-424.
62. Liu, W.T., Marsh, T. L., Cheng, H. and Forney, L. J. (1997). Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA. Appl. Environ. Microbiol., 63, 4516-4522.
63. Llobet-Brossa, E., Rabus, R., Bottcher, M. E. et al. (2002). Community structure and activity of sulphate-reducing bacteria in an intertidal surface sediment: a multi-method approach. Aquatic Microbial Ecology, 29, 211-226.
64. Loy, A. and Bodrossy, L. (2006). Highly parallel microbial diagnostics using oligonucleotide microarrays. Clin. Chim. Acta, 363, 106-119.
65. Loy, A., Horn, M. and Wagner, M. (2003). probeBase: an online resource for rRNA-targeted oligonucleotide probes. Nucleic Acids Res., 31, 514-516.
66. Loy, A., Kusel, K., Lehner, A., Drake, H. L. and Wagner, M. (2004). Microarray and functional gene analyses of sulphate-reducing prokaryotes in low sulphate, acidic fens reveal co-occurence of recognized genera and novel lineages. Appl. Environ. Microbiol., 70, 6998-7009.
67. Loy, A., Lehner, A., Lee, N., Adamczyk, J. et al. (2002). Oligonucleotide microarray for 16S rRNA gene-based detection of all recognized lineages of sulphate-reducing prokaryotes in the environment. Appl. Environ. Microbiol., 68, 5064-5081.
68. Loy, A., Taylor, M. W., Bodrossy, L. and Wagner, M. (2006). Applications of nucleic acid microarrays in soil microbial ecology. In J. E. Cooper and J. R. Rao (eds.), Molecular approaches to soil, rhizosphere and plant microorganism analysis. Wallingford, UK: CABI Publishing.
69. Lueders, T., Pommerenke, B. and Friedrich, M.W. (2004). Stable-isotope probing of microorganisms thriving at thermodynamic limits: syntrophic propionate oxidation in flooded soil. Appl. Environ. Microbiol., 70, 5778-5786.
70. Liimann, H., Arth, I. and Liesack, W. (2000). Spatial changes in the bacterial community structure along a vertical oxygen gradient in flooded paddy soil cores. Appl. Environ. Microbiol., 66, 754-762.
71. Mansfield, E. S., Worley, J.M., McKenzie, S. E. et al. (1995). Nucleic-acid detection using nonradioactive labeling methods. Mol. Cell. Probes, 9, 145-156.
72. Manz, W., Eisenbrecher, M., Neu, T. R. and Szewzyk, U. (1998). Abundance and spatial organization of Gram-negative sulphate-reducing bacteria in activated sludge investigated by in situ probing with specific 16S rRNA targeted oligonucleotides. FEMS Microbiol. Ecol., 25, 43-61.
73. Martin-Laurent, F., Philippot, L., Hallet, S. et al. (2001). DNA extraction from soils: old bias for new microbial diversity analysis methods. Appl. Environ. Microbiol., 67, 2354-2359.
74. Matsui, G. Y., Ringelberg, D. B. and Lovell, C. R. (2004). Sulphate-reducing bacteria in tubes constructed by the marine infaunal polychaete Diopatra cuprea. Appl. Environ. Microbiol., 70, 7053-7065.
75. Maukonen, J., Saarela, M. and Raaska, L. (2006). Desulfovibrionales-related bacteria in a paper mill environment as detected with molecular techniques and culture. J. Ind. Microbiol. Biotechnol., 33, 45-54.
76. Minz, D., Fishbain, S., Green, S. J. et al. (1999). Unexpected population distribution in a microbial mat community: sulphate-reducing bacteria localized to the highly oxic chemocline in contrast to a eukaryotic preference for anoxia. Appl. Environ. Microbiol., 65, 4659-4665.
77. Minz, D., Flax, J. L., Green, S. J. et al. (1999). Diversity of sulphate-reducing bacteria in oxic and anoxic regions of a microbial mat characterized by comparative analysis of dissimilatory sulfite reductase genes. Appl. Environ. Microbiol., 65, 4666-4671.
78. Molitor, M., Dahl, C., Molitor, I. et al. (1998). A dissimilatory sirohaem-sulfite- reductase-type protein from the hyperthermophilic archaeon Pyrobaculum islandicum. Microbiology, 144, 529-541.
79. Mussmann, M., Ishii, K., Rabus, R. and Amann, R. (2005). Diversity and vertical distribution of cultured and uncultured Deltaproteobacteria in an intertidal mud flat of the Wadden Sea. Environ. Microbiol., 7, 405-418.
80. Mussmann, M., Richter, M., Lombardot, T. et al. (2005). Clustered genes related to sulphate respiration in uncultured prokaryotes support the theory of their concomitant horizontal transfer. J. Bacteriol., 187, 7126-7137.
81. Nakagawa, T., Ishibashi, J., Maruyama, A. et al. (2004). Analysis of dissimilatory sulfite reductase and 16S rRNA gene fragments from deep-sea hydrothermal sites of the Suiyo Seamount, Izu-Bonin Arc, Western Pacific. Appl. Environ. Microbiol., 70, 393-403.
82. Neretin, L. N., Schippers, A., Pernthaler, A. et al. (2003). Quantification of dissimilatory (bi)sulphite reductase gene expression in Desulfobacterium autotrophicum using real-time RT-PCR. Environ. Microbiol., 5, 660-671.
83. Nielsen, J. L. and Nielsen, P. H. (2002). Quantification of functional groups in activated sludge by microautoradiography. Water Sci. Technol., 46, 389-395.
84. Okabe, S., Itoh, T., Satoh, H. and Watanabe, Y. (1999). Analyses of spatial distributions of sulphate-reducing bacteria and their activity in aerobic wastewater biofilms. Appl. Environ. Microbiol., 65, 5107-5116.
85. Okabe, S., Santegoeds, C. M., Watanabe, Y. and de Beer, D. (2002). Successional development of sulphate-reducing bacterial populations and their activities in an activated sludge immobilized agar gel film. Biotechnol. Bioengineering, 78, 119-130.
86. Omelchenko, M. V., Makarova, K. S., Wolf, Y. I., Rogozin, I. B. and Koonin, E. V. (2003). Evolution of mosaic operons by horizontal gene transfer and gene displacement in situ. Genome Biol., 4, R55.
87. Orphan, V. J., House, C. H., Hinrichs, K. U., McKeegan, K. D. and DeLong, E. F. Methane-consuming archaea revealed by directly coupled isotopic and phylogenetic analysis. Science, 293, 484-487.
88. Orphan, V. J., House, C. H., Hinrichs, K. U., McKeegan, K. D. and DeLong, E. F.. Multiple archaeal groups mediate methane oxidation in anoxic cold seep sediments. Proc. Natl. Acad. Sci. USA, 99, 7663-7668.
89. Overmann, J., Coolen, M. J. L. and Tuschak, C. (1999). Specific detection of different phylogenetic groups of chemocline bacteria based on PCR and denaturing gradient gel electrophoresis of 16S rRNA gene fragments. Arch. Microbiol., 172, 83-94.
90. Palmer, C., Bik, E. M., Eisen, M. B. et al. (2006). Rapid quantitative profiling of complex microbial populations. Nucleic Acids Res., 34, e5.
91. Palumbo, A. V., Schryver, J.C., Fields, M.W. et al. (2004). Coupling of functional gene diversity and geochemical data from environmental samples. Appl. Environ. Microbiol., 70, 6525-6534.
92. Perez-Jimenez, J. R. and Kerkhof, L. J. (2005). Phylogeography of sulphate- reducing bacteria among disturbed sediments, disclosed by analysis ofthe dissimilatory sulfite reductase genes (dsrAB). Appl. Environ. Microbiol., 71, 1004-1011.
93. Pernthaler, A. and Amann, R. (2004). Simultaneous fluorescence in situ hybridization of mRNA and rRNA in environmental bacteria. Appl. Environ. Microbiol., 70, 5426-5433.
94. Pernthaler, A., Pernthaler, J. and Amann, R. (2002). Fluorescence in situ hybridization and catalyzed reporter deposition for the identification of marine bacteria. Appl. Environ. Microbiol., 68, 3094-3101.
95. Poulsen, L. K., Ballard, G. and Stahl, D. A. (1993). Use of rRNA fluorescence in situ hybridization for measuring the activity of single cells in young and established biofilms. Appl. Environ. Microbiol., 59, 1354-1360.
96. Rabus, R., Fukui, M., Wilkes, H. and Widdle, F. (1996). Degradative capacities and 16S rRNA-targeted whole-cell hybridization of sulphate-reducing bacteria in an anaerobic enrichment culture utilizing alkylbenzenes from crude oil. Appl. Environ. Microbiol., 62, 3605-3613.
97. Rabus, R., Hansen, T. and Widdel, F. (2000). Dissimilatory sulphate- and sulfur-reducing prokaryotes. In M. Dworkin, S. Falkow, E. Rosenberg, K.-H. Schleifer and E. Stackebrandt (eds.), The Prokaryotes: An evolving electronic resource for the microbiological community. 3rd ed. New York: Springer-Verlag.
98. Rabus, R., Ruepp, A., Frickey, T. et al. (2004). The genome of Desulfotalea psychrophila, a sulphate-reducing bacterium from permanently cold Arctic sediments. Environ. Microbiol., 6, 887-902.
99. Ramsing, N. B., Fossing, H., Ferdelman, T. G., Andersen, F. and Thamdrup, B. (1996). Distribution ofbacterial populations in a stratified fjord (Mariager Fjord, Denmark) quantified by in situ hybridization and related to chemical gradients in the water column. Appl. Environ. Microbiol., 62, 1391-1404.
100. Ramsing, N. B., Kuhl, M. and J0rgensen, B. B. (1993). Distribution of sulphate-reducing bacteria, O2, and H2S in photosynthetic biofilms determined by oligonucleotide probes and microelectrodes Appl. Environ. Microbiol., 59, 3840-3849.
101. Raskin, L., Capman, W. C., Kane, M. D., Rittmann, B. E. and Stahl, D. A. (1996). Critical evaluation of membrane supports for use in quantitative hybridizations. Appl. Environ. Microbiol., 62, 300-303.
102. Raskin, L., Rittmann, B. E. and Stahl, D. A. (1996). Competition and coexistence of sulphate-reducing and methanogenic populations in anaerobic biofilms. Appl. Environ. Microbiol., 62, 3847-3857.
103. 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.
104. Ravenschlag, K., Sahm, K., Knoblauch, C., J0rgensen, B. B. and Amann, R. (2000). Community structure, cellular rRNA content, and activity of sulphate-reducing bacteria in marine arctic sediments. Appl. Environ. Microbiol., 66, 3592-3602.
105. Ricke, P., Kolb, S. and Braker, G. (2005). Application of a newly developed ARB software-integrated tool for in silico terminal restriction fragment length polymorphism analysis reveals the dominance of a novel pmoA cluster in a forest soil. Appl. Environ. Microbiol., 71, 1671-1673.
106. Risatti, J. B., Capman, W. C. and Stahl, D. A. (1994). Community structure of a microbial mat: the phylogenetic dimension. Proc. Natl. Acad. Sci., 91, 10173-1017.
107. Sabehi, G., Loy, A., Jung, K. H. et al. (2005). New insights into metabolic properties of marine bacteria encoding proteorhodopsins. PLoS Biol., 3, e273.
108. Sahm, K., Knoblauch, C. and Amann, R. (1999). Phylogenetic affiliation and quantification of psychrophilic sulphate-reducing isolates in marine arctic sediments. Appl. Environ. Microbiol., 65, 3976-3981.
109. Santegoeds, C. M., Ferdelman, T. G., Muyzer, G. and de Beer, D. (1998). Structural and functional dynamics of sulphate-reducing populations in bacterial biofilms. Appl. Environ. Microbiol., 64, 3731-3739.
110. Schadt, C. W., Liebich, J., Chong, S. C. et al. (2005). Design and use of functional gene microarrays (FGAs) for the characterization of microbial communities. Methods Microbiol., 34, 331-368.
111. Schedel, M. and Triiper, H. G. (1980). Anaerobic oxidation of thiosulphate and elemental sulfur in Thiobacillus denitrificans. Arch. Microbiol., 124, 205-210.
112. Scheid, D. and Stubner, S. (2001). Structure and diversity of Gram-negative sulphate-reducing bacteria on rice roots. FEMS Microbiol. Ecol., 36, 175-183.
113. Schwenn, J. D. and Biere, M. (1979). APS-reductase activity in the chromatophores of Chromatium vinosum strain D. FEMS Microbiol. Lett., 6, 19-22.
114. Stackebrandt, E., Sproer, C., Rainey, F. A. et al. (1997). Phylogenetic analysis of the genus Desulfotomaculum: evidence for the misclassification of Desulfotomaculum guttoideum and description ofDesulfotomaculum orientis as Desulfosporosinus orientis gen. nov., comb. nov. Int. J. Syst. Bacteriol., 47, 1134-1139.
115. Stahl, D. A. (2004). High-throughput techniques for analyzing complex bacterial communities. Adv. Exp. Med. Biol., 547, 5-17.
116. Stahl, D. A. and Amann, R. (1991). Development and application of nucleic acid probes. In E. Stackebrandt and M. Goodfellow (eds.), Nucleic acid techniques in bacterial systematics. Chichester, UK: John Wiley & Sons Ltd.
117. Stahl, D. A., Flesher, B., Mansfield, H. R. and Montgomery, L. (1988). Use of phylogenetically based hybridization probes for studies of ruminal microbial ecology. Appl. Environ. Microbiol., 54, 1079-1084.
118. Stubner, S. and Meuser, K. (2000). Detection of Desulfotomaculum in an Italian rice paddy soil by 16S ribosomal nucleic acid analyses. FEMS Microbiol. Ecol., 34, 73-80.
119. Tonolla, M., Bottinelli, M., Demarta, A., Peduzzi, R. and Hahn, D. (2005). Molecular identification of an uncultured bacterium (“morphotype R”) in meromictic Lake Cadagno, Switzerland. FEMS Microbiol. Ecol., 53, 235-244.
120. Tonolla, M., Demarta, A., Peduzzi, S., Hahn, D. and Peduzzi, R. (2000). In situ analysis of sulphate-reducing bacteria related to Desulfocapsa thiozymogenes in the chemocline of meromictic Lake Cadagno (Switzerland). Appl. Environ. Microbiol., 66, 820-824.
121. van der Maarel, M. J. E. C., Artz, R. R. E., Haanstra, R. and Forney, L. J. (1998). Association of marine Archaea with the digestive tracts of two marine fish species. Appl. Environ. Microbiol., 64, 2894-2898.
122. Wagner, M., Horn, M. and Daims, H. (2003). Fluorescence in situ hybridisation for the identification and characterisation of prokaryotes. Curr. Opin. Microbiol., 6, 302-309.
123. Wagner, M., Loy, A., Klein, M. et al. (2005). Functional marker genes for identification of sulphate-reducing prokaryotes. Methods Enzymol., 397, 469-489.
124. Wagner, M., Nielsen, P. H., Loy, A., Nielsen, J. L. and Daims, H. (2006). Linking microbial community structure with function: fluorescence in situ hybridization-microautoradiography and isotope arrays. Curr. Opin. Biotechnol., 17, 1-9.
125. Wagner, M., Roger, A. J., Flax, J. L., Brusseau, G. A. and Stahl, D. A. (1998). Phylogeny of dissimilatory sulfite reductases supports an early origin of sulphate respiration. J. Bacteriol., 180, 2975-2982.
126. Wagner, M., Schmid, M., Juretschko, S. et al. (1998b). In situ detection of a virulence factor mRNA and 16S rRNA in Listeria monocytogenes. FEMS Microbiol. Lett., 160, 159-168.
127. Wagner, M., Smidt, H., Loy, A. and Jizhong, Z. (2007). Unravelling microbial communities with DNA-microarrays: challenges and future directions. Microb. Ecol., in press.
128. Watras, C. J., Morrison, K. A., Kent, A. et al. (2005). Sources of methylmercury to a wetland-dominated lake in northern Wisconsin. Environ. Sci. Technol., 39, 4747-4758.
129. Wawer, C., Jetten, M. S. and Muyzer, G. (1997). Genetic diversity and expression of the NiFe hydrogenase large-subunit gene of Desulfovibrio sin environmental samples. Appl. Environ. Microbiol., 63, 4360-4369.
130. Wawer, C. and Muyzer, G. (1995). Genetic diversity of Desulfovibrio sIn environmental samples analyzed by denaturing gradient gel electrophoresis of NiFe hydrogenase gene fragments. Appl. Environ. Microbiol., 61, 2203-2210.
131. Wawrik, B., Paul, J. H. and Tabita, F. R. (2002). Real-time PCR quantification of rbcL (ribulose-1,5-bisphosphate carboxylase/oxygenase) mRNA in diatoms and pelagophytes. Appl. Environ. Microbiol., 68, 3771-3779.
132. Wieland, A., Kuhl, M., McGowan, L. et al. (2003). Microbial mats on the Orkney Islands revisited: microenvironment and microbial community composition. Microb. Ecol., 46, 371-390.
133. Wu, M., Ren, Q., Durkin, A. S. et al. (2005). Life in hot carbon monoxide: the complete genome sequence of Carboxydothermus hydrogenoformans Z-2901. PLoS Genet., 1, e65.
134. Zhou, J. (2003). Microarrays for bacterial detection and microbial community analysis. Curr. Opin. Microbiol., 6, 288-294.
135. Zverlov, V., Klein, M., Liicker, S., Friedrich, M.W., Kellermann, J., Stahl, D. A., Loy, A. and Wagner, M. (2005). Lateral gene transfer of dissimilatory (bi)sulfite reductase revisited. J. Bacteriol., 187, 2203-2208.