Microbial evolution, diversity, and ecology: A decade of ribosomal RNA analysis of uncultivated microorganisms

Microbial Ecology

Volumn 35, Issue 1, 1998, Pages 1-21

  Head, I M ^a   Saunders, J R ^b   Pickup, R W ^c  

^a NEWCASTLE UNIVERSITY   (United Kingdom)

^b UNIVERSITY OF LIVERPOOL   (United Kingdom)

^c CENTRE FOR ECOLOGY AND HYDROLOGY   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

EVOLUTION; MICROBIAL DIVERSITY; MOLECULAR GENETICS; RIBOSOMAL RNA ANALSYIS;

EID: 0031982528     PISSN: 00953628     EISSN: None     Source Type: Journal    
DOI: 10.1007/s002489900056     Document Type: Article

References (141)

1. Amann RT (1995) Fluorescently labelled, rRNA-targeted oligonucleotide probes in the study of microbial ecology. Mol Ecol 4:543-554
2. Amann RJ, Binder B, Olson RI, Chisholm SW, Devereux R, Stahl DA (1990) Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Appl Environ Microbiol 56:1919-1925
3. Amman R, Springer N, Ludwig W, Görtz H-D, Schleifer K-H (1991) Identification and phylogeny of uncultured bacterial endosymbionts. Nature 351:161-164
4. Amann RI, Zarda B, Stahl DA, Schleifer K-H (1992) Identification of individual prokaryotic cells with enzyme-labelled rRNA-targeted oligonucleotide probes. Appl Environ Microbiol 58:3007-3011
5. Amann RI, Ludwig W, Schleifer K-H (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59:143-169
6. Angert ER, Clements KD, Pace NR (1993) The largest bacterium. Nature 362:239-241
7. Beimfohr C, Krause A, Amann R, Ludwig W, Schleifer K-H (1993) In situ identification of lactococci, enterococci, and streptococci. Syst Appl Microbiol 16:450-456
8. Belser LW (1979) Population ecology of nitrifying bacteria. Ann Rev Microbiol 33:309-333
9. Blackall LL, Seviour EM, Cunningham MA, Seviour RJ, Hugenholz P (1994) "Microthrix parvicella" a novel deep branching member of the actinomyces subphylum. System Appl Microbiol 17:513-518
10. Blackall LL, Stratton H, Bradford D, Del Dot T, Sjörup C, Seviour EM, Seviour RJ (1996) "Candidatus Microthrix parvicella" a filamentous bacterium from activated sludge sewage treatment plants. Int J Syst Bacteriol 46:344-346
11. Blakemore RP (1975) Magnetotactic bacteria. Science 190:377-379
12. Blumer M, Chase T, Watson SW (1969) Fatty acids in the lipids of marine and terrestrial nitrifying bacteria. J Bacteriol 99:366-370
13. Bock E, Koops H-P, Harms H (1986) Cell biology of nitrifying bacteria. In: Prosser JI (ed) Nitrification. IRL Press, Oxford, pp 17-38
14. Britschgi TB, Giovannoni SJ (1991) Phylogenetic analysis of a natural marine bacterioplankton population by rRNA gene cloning and sequencing. Appl Environ Microbiol 57:1707-1713
15. Brock TD (1987) The study of microorganisms in situ: progress and problems. Symp Soc Gen Microbiol 41:1-17
16. Bruce KD, Hiorns WD, Hobman JL, Osborn AM, Strike P, Ritchie DA (1992) Amplification of DNA from native populations of soil bacteria by using the polymerase chain reaction. Appl Environ Microbiol 58:3413-3416
17. Cary SC, Giovannoni SJ (1993) Transovarial inheritance of endosymbiotic bacteria in clams inhabiting deep-sea hydrothermal vents and cold seeps. Proc Natl Acad Sci USA 90:5695-5699
18. Cary SC, Warren WD, Anderson E, Giovannoni SJ (1993) Identification and localization of bacterial endosymbionts in hydrothermal vent taxa with symbiont specific PCR amplification and in situ hybridization techniques. Marine Mol Biol Biotechnol 2:51-62
19. Clayton RA, Sutton G, Hinkle Jr PS, Bult C, Fields C (1995) Intraspecific variation in small-subunit rRNA sequences in GenBank: why single sequences may not adequately represent prokaryotic taxa. Int J Syst Bacteriol 45:595-599
20. Clements KD, Bullivant S (1991) An unusual symbiont from the gut of surgeonfishes may be the largest known prokaryote. J Bacteriol 171:5359-5362
21. Cole ST, Girons IS (1994) Bacterial genomics. FEMS Microbiol Rev 14:139-160
22. de Boer WE, La Riviere JWM, Schmidt K (1971) Some properties of Achromatium oxaliferum. Ant van Leeuwen 37:553-563
23. Degrange V, Bardin R (1995) Detection and counting of Nitrobacter populations in soil by PCR. Appl Environ Microbiol 61:2093-2098
24. DeLong EF, Wickham GS, Pace NR (1989) Phylogenetic stains: ribosomal RNA-based probes for the identification of single microbial cells. Science 243:1360-1363
25. DeLong EF, Frankel RB, Bazylinski DA (1993) Multiple evolutionary origins of magnetotaxis in bacteria. Science 259:803-806
26. Distel DL, Wood AP (1992) Characterization of the gill symbiont of Thyasira flexuosa (Thyasiridae: Bivalvia) by use of polymerase chain reaction and 16S rRNA sequence analysis. J Bacteriol 174:6317-6320
27. Distel DL, Lane DL, Olsen GJ, Giovannoni SJ, Pace B, Pace NR, Stahl DA, Felbeck H (1988) Sulfur-oxidizing bacterial endosymbionts: analysis of phylogeny and specificity by 16S rRNA sequences. J Bacteriol 170:2506-2510
28. Distel DL, Felbeck H, Cavanaugh CM (1994) Evidence for phylogenetic congruence among sulfur-oxidizing chemoautotrophic bacterial endosymbionts and their bivalve hosts. J Mol Evol 38:533-542
29. Diviacco S, Norio P, Zentilin L, Menzo S, Clementi M, Biamonti G, Riva S, Falaschi A, Giacca M (1992) A novel procedure for quantitative polymerase chain reaction by co-amplification of competitive templates. Gene 122:313-320
30. Edwards U, Rogall T, Blöcker H, Emde M, Böttger EC (1989) Isolation and direct complete nucleotide determination of entire genes. Characterization of a gene coding for 16S ribosomal RNA. Nucl Acids Res 17:7843-7853
31. Eikelboom DH (1975) Filamentous organisms observed in activated sludge. Water Res 9:365-388
32. Eikelboom DH (1977) Identification of filamentous bacteria in bulking activated sludge. Progress in Water Technol 8:153-162
33. Embley TM, Finlay BJ (1994) The use of small subunit rRNA sequences to unravel the relationships between anaerobic ciliates and their methanogen symbionts. Microbiology 140:225-235
34. Embley TM, Finlay BJ (1994) Phylogenetic diversity of methanogen endosymbionts of anaerobic ciliates. In: Priest FG, Ramos-Cormenzana A, Tindall BJ (eds) Bacterial diversity and systematics. Plenum Press, New York, pp 153-160
35. Embley TM, Finlay BJ, Thomas RH, Dyal PL (1992) The use of rRNA sequences and fluorescent probes to investigate the phylogenetic positions of the anaerobic ciliate Metopus palaeformis and its archaeobacterial endosymbiont. J of Gen Microbiol 138:1479-1487
36. Embley TM, Finlay BJ, Dyal PL, Hirt RP, Wilkinson M, Williams AG (1995) Multiple origins of anaerobic ciliates with hydrogenosomes within the radiation of aerobic ciliates. Proc R Soc London Ser B 262:87-93
37. Farrelly V, Rainey FA, Stackebrandt E (1995) Effect of genome size and rrn gene copy number on PCR amplification of 16S rRNA genes from a mixture of bacterial species. Appl Environ Microbiol 61:2798-2801
38. Fischer SG, Lerman LS (1979) Length-independent separation of DNA restriction fragments in two-dimensional gel electrophoresis. Cell 16:191-200
39. Ferris MJ, Muyzer G, Ward DM (1996) Denaturing gradient gel electrophoresis profiles of 16S rRNA-defined populations inhabiting a hot spring microbial community. Appl Environ Microbiol 62:340-346
40. Fishelson L, Montgomery WL, Myrberg Jr AA (1985) A unique symbiosis in the gut of tropical herbivorous surgeon-fish (Acanthuridae: Teleostei) from the Red Sea. Science 229: 49-51
41. Fuhrman JA, Comeau DE, Hagstrom A, Chan AM (1988) Extraction from natural planktonic microorganisms of DNA suitable for molecular biological studies. Appl Environ Microbiol 54:1426-1429
42. Fuhrman JA, McCallum K, Davis AA (1992) Novel major archaebacterial group from marine plankton. Nature 356:148-149
43. Giannakis C, Miller DJ, Nicholas DJD (1985) Comparative studies on redox proteins from ammonia-oxidizing bacteria. FEMS Microbiol Lett 30:81-85
44. Giovannoni SJ, Cary SC (1993) Probing marine systems with ribosomal RNAs. Oceanography 6:95-104
45. Giovannoni SJ, DeLong EF, Olsen GJ, Pace NR (1988) Phylogenetic group-specific oligodeoxynucleotide probes for identification of single microbial cells. J Bacteriol 170:720-726
46. Giovannoni SJ, Britschgi TB, Moyer CL, Field KG (1990) Genetic diversity in Sargasso Sea bacterioplankton. Nature 345: 60-63
47. Gordon DA, Giovannoni SJ (1996) Detection of stratified microbial populations related to Chlorobium and Fibrobacter species in the Atlantic and Pacific oceans. Appl Environ Microbiol 62:1171-1177
48. Gutell RR, Larsen N, Woese CR (1994) Lessons from an evolving rRNA: 16S and 23S rRNA structures from a comparative perspective. Microbiol Rev 58:10-26
49. Hahn D, Amann RI, Ludwig W, Akkermans ADL, Schleifer K-H (1992) Detection of microorganisms in soil after in situ hybridization with rRNA-targeted, fluorescently labelled oligonucleotides. J Gen Microbiol 138:879-887
50. Hahn D, Amann RI, Zeyer J (1993) Detection of mRNA in Streptomyces cells by in situ hybridization with digoxigenin-labelled probes. Appl Environ Microbiol 59:2753-2757
51. Hall GH (1986) Nitrification in Lakes. In: Prosser JI (ed) Nitrification. IRL Press, Oxford, pp 127-156
52. Haygood MG, Distel DL (1993) Bioluminescent symbionts of flashlight fishes and deep-sea anglerfishes form unique lineages related to the genus Vibrio. Nature 363:154-156
53. Head IM, Hiorns WD, Embley TM, McCarthy AJ, Saunders JR (1993) The Phylogeny of autotrophic ammonia-oxidising bacteria as determined by analysis of 16S ribosomal RNA gene sequences. J Gen Microbiol 139:1147-1153
54. Head IM, Gray ND, Pickup RW, Jones JG (1995) The biogeochemical role of Achromatium oxaliferum. In: Grimalt JO, Dorronsoro C (eds) Organic geochemistry: developments and applications to energy, climate, environment, and human history. (Selected papers from the 17th International Meeting on Organic Geochemistry, 4-8 September 1995, Donostia-San Sebastián, The Basque Country, Spain) AIGOA, Donostia-San Sebastian, pp 895-898
55. Head IM, Gray ND, Clarke KJ, Pickup RW, Jones JG (1996) The phylogenetic position and ultrastructure of the uncultured bacterium Achromatium oxaliferum Microbiology 142: 2341-2354
56. Herring PJ (1982) Aspects of the bioluminescence of fishes. Oceanogr Marine Biol 20:415-470
57. Hicks R, Amann RI, Stahl DA (1992) Dual staining of natural bacterioplankton with 4′,6-diamidino-2-phenylindole and fluorescent oligonucleotide probes targeting kingdom level 16S rRNA sequences. Appl Environ Microbiol 58:2158-2163
58. Hiorns WD, Hastings RC, Head IM, McCarthy AJ, Saunders JR, Pickup RW, Hall GH (1995) Amplification of 16S ribosomal RNA genes of autotrophic ammonia-oxidising bacteria demonstrates the ubiquity of nitrosospiras in the environment. Microbiology 141:2793-2800
59. Holben WE, Jansson JK, Chelm BK, Tiedje JM (1988) DNA probe method for the detection of specific microorganisms in the soil community. Appl Environ Microbiol 54:703-711
60. Holmes AJ, Owens NJP, Murrell JC (1995) Detection of novel marine methanotrophs using phylogenetic and functional gene probes after methane enrichment. Microbiol 141:1947-1955
61. Hovanec TA, DeLong EF (1996) Comparative analysis of nitrifying bacteria associated with freshwater and marine aquaria. Appl Environ Microbiol 62:2888-2896
62. Jukes TH, Cantor CR (1969) Evolution of protein molecules. In: Munro HN (ed) Mammalian protein metabolism. Academic Press, New York, pp 21-132
63. Koops H-P, Harms H (1985) Deoxyribonucleic acid homology among 96 strains of ammonia-oxidizing bacteria. Arch Microbiol 141:214-218
64. Koops H-P, Möller UC (1991) The lithotrophic ammonia-oxidizing bacteria. In: Balows A, Truper HG, Dworkin M, Harder W, Schleifer KH (eds) The prokaryotes, 2nd ed. Fischer-Verlag, New York, pp 2625-2637
65. Koops H-P, Böttcher B, Möller UC, Pommerening-Roeser A, Stehr G (1991) Classification of eight new species of ammonia-oxidizing bacteria: Nitrosomonas communis sp. nov., Nitrosomonas ureae sp. nov., Nitrosomonas aestuarii sp. nov., Nitrosomonas marina sp. nov., Nitrosomonas nitrosa sp. nov., Nitrosomonas eutropha sp. nov., Nitrosomonas oligotropha sp. nov., and Nitrosomonas halophila sp. nov. J Gen Microbiol 137:1689-1700
66. Kopczynski ED, Bateson MM, Ward DM (1994) Recognition of chimeric small subunit ribosomal DNAs composed of genes from uncultivated microorganisms. Appl Environ Microbiol 60:746-748
67. La Riviere JWM, Schmidt K (1989) The genus Achromatium. In: Staley JT, Bryant MP, Pfennig N, Holt JG (eds) Bergey's manual of systematic bacteriology, vol 3. Williams and Wilkins, Baltimore, pp 2131-2133
68. La Riviere JWM, Schmidt K (1991) Morphologically conspicuous sulfur-oxidizing Eubacteria. In: Balows A, Truper HG, Dworkin M, Harder W, Schleifer KH (eds) The prokaryotes, 2nd edn. Fischer-Verlag, New York, pp 3934-3947
69. Lee S, Malone C, Kemp PF (1993) Use of multiple 16S rRNA-targeted fluorescent probes to increase signal strength and measure cellular RNA from natural planktonic bacteria. Marine Ecol Prog Ser 101:193-201
70. Liesack W, Weyland H, Stackebrandt E (1991) Potential risks of gene amplification by PCR as determined by 16S rDNA analysis of a mixed culture of strict barophilic bacteria. Microb Ecol 21:191-198
71. MacNaughton SJ, O'Donnell AG, Embley TM (1994) Permeablization of mycolic acid containing actinomycetes for in situ hybridization with fluorescently labelled oligonucleotide probes. Microbiology 140:2859-2865
72. Maidak BL, Larsen N, McCaughey MJ, Overbeek R, Olsen GJ, Fogel K, Blandy J, Woese CR (1994) The ribosomal database project. Nucl Acids Res 22:3485-3487
73. Mann S, Sparks NHC, Board RG (1990) Magnetotactic bacteria: microbiology, biomineralization, paeleomagnetism, and biotechnology. Adv Microb Physiol 31:125-181
74. Manz W, Amann R, Ludwig W, Wagner M, Schleifer K-H (1992) Phylogenetic oligodeoxynucelotide probes for the major subclasses of the proteobacteria: problems and solutions. Syst Appl Microbiol 15:593-600
75. Manz W, Szewzyk U, Ericsson P, Amann R, Schleifer KH, Stenstrom TA (1993) In situ identification of bacteria in drinking water and adjoining biofilms by hyridization with 16S ribosomal RNA-directed and 23S ribosomal RNA-directed fluorescent oligonucleotide probes. Appl Environ Microbiol 59:2293-2298
76. Massol-Deya A, Weller R, Rios-Hernandez L, Zhou J-Z, Hickey RF, Tiedje JM (1997) Succession and convergence of biofilm communities in fixed-film reactors treating aromatic hydrocarbons in groundwater. Appl Environ Microbiol 63: 270-276
77. McCaig AE, Embley TM, Prosser JI (1994) Molecular analysis of enrichment cultures of marine ammonia oxidizers. FEMS Microbiol Lett 120:363-368
78. Mevarech M, Hirsch-Twizer S, Goldman S, Yakobson E, Eisenberg H, Dennis PP (1989) Isolation and characterization of the rRNA gene clusters of Halobacterium marismortui. J Bacteriol 171:3479-3485
79. Mobarry BK, Wagner M, Urbain V, Rittman BE, Stahl DA (1996) Phylogenetic probes for analysing abundance and spatial organization of nitrifying bacteria. Appl Environ Microbiol 62:2156-2162
80. Moller S, Pedersen AR, Poulsen LK, Arvin E, Molin S (1996) Activity and three-dimensional distribution of toluene-degrading Pseudomonas putida in multispecies biofilm assessed by quantitative in situ hybridization and scanning confocal laser microscopy. Appl Environ Microbiol 62:4632-4640
81. Moré M, Herrick JB, Silva MO, Ghiorse WC, Madsen EJ (1994) Quantitative cell lysis of indigenous microorganisms and rapid extraction of microbial DNA from sediment. Appl Environ Microbiol 60:1572-1580
82. Müller M (1988) Energy metabolism in protozoa without mitochondria. Ann Rev Microbiol 42:465-488
83. Muyzer G, de Waal EC, Uitterrlinden AG (1993) Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microbiol 59:695-700
84. Olsen GJ, Lane DJ, Giovannoni SJ, Pace NR (1986) Microbial ecology and evolution: a ribosomal RNA approach. Ann Rev Microbiol 40:337-365
85. Olsen GJ, Woese CR, Overbeek R (1994) The winds of (evolutionary) change: breathing new life into microbiology. J Bacteriol 176:1-6
86. Osborn AM, Bruce KD, Strike P, Ritchie DA (1993) Polymerase chain reaction-restriction length polymorphism analysis shows divergence among mer determinants from Gram-negative soil bacteria indistinguishable by DNA-DNA hybridisation. Appl Environ Microbiol 59:4024-4030
87. Pace NR, Stahl DA, Lane DJ, Olsen GJ (1986) The analysis of natural microbial populations by ribosomal RNA sequences. Adv Microb Ecol 9:1-55
88. Paerl HW (1993) Interaction of nitrogen and carbon cycles in the marine environment. In: Ford TE (ed) Aquatic microbiology: an ecological approach. Blackwell Scientific Publications, Boston, pp 343-381
89. Prosser JI (1989) Autotrophic nitrification in bacteria. Adv Microb Physiol 30:125-181
90. Rainey FA, Ward N, Sly LI, Stackebrandt E (1994) Dependence on the taxon composition of clone libraries for PCR-amplified, naturally occurring 16S rDNA on the primer pair and the cloning system used. Experientia 50:796-797
91. Ramsing NB, Fossing H, Ferdelman TG, Andersen F, Thamdrup B (1996) The distribution of bacterial populations in a stratified Fjord (Manager Fjord, Denmark) quantified by in situ hybridization and related to chemical gradients in the water column. Appl Environ Microbiol 62:1391-1404
92. Raskin L, Rittman BE, Stahl DA (1996) Competition and co-existence of sulfate-reducing and methanogenic populations in anaerobic biofilms. Appl Environ Microbiol 62:3847-3857
93. Reysenbach A, Giver LJ, Wickham GS, Pace NR (1992) Differential amplification of rRNA genes by polymerase chain reaction. Appi Environ Microbiol 58:3417-3418
94. Rochelle PA, Fry JC, Parkes RJ, Weightman AJ (1992) DNA extraction for 16S rRNA gene analysis to determine genetic diversity in deep sediment communities. FEMS Microbiol Lett 100:59-66
95. Roller C, Wagner M, Amann R, Ludwig W, Schleifer K-H (1994) In situ probing of Gram-positive bacteria with high DNA G+C content using 23S rRNA-targeted oligonucleotides. Microbiology 140:2849-2858
96. Schleifer K-H, Ludwig W (1994) Molecular taxonomy: classification and identification. In: Priest FG, Ramos-Cormenzana A, Tindall BJ (eds) Bacterial diversity and systematics. Plenum Press, New York, pp 1-15
97. Schramm A, Larsen LH, Revsbech NP, Ramsing NB, Amman R, Schleifer K-H (1996) Structure and function of a nitrifying biofilm as determined by in situ hybridization and the use of microelectrodes. Appl Environ Microbiol 62:4641-4647
98. Silva MC, Moré MI, Batt CA (1995) Development of a molecular detection method for naphthalene degrading pseudomonads. FEMS Microbiol Ecol 18:225-235
99. Sprent JI (1987) The ecology of the nitrogen cycle. Cambridge University Press, Cambridge
100. Spring S, Amann R, Ludwig W, Schleifer K-H, Petersen N (1992) Phylogenetic diversity and identification of nonculturable magnetotactic bacteria. Syst Appl Microbiol 15:116-122
101. Spring S, Amann R, Ludwig W, Schleifer K-H, van Gemerden H, Petersen N (1993) Dominating role of an unusual magnetotactic bacterium in the microaerophilic zone of a freshwater sediment. Appl Environ Microbiol 59:2397-2403
102. Stahl DA (1995) Application of phylogenetically based hybridization probes to microbial ecology. Molec Ecol 4:535-542
103. Stahl DA, Amann RI (1991) Development and application of nucleic acid probes in bacterial systematics. In: Stackebrandt E, Goodfellow M (eds) Nucleic acid techniques in bacterial systematics. John Wiley & Sons, Chichester, England, pp 205-248
104. Stahl DA, Lane DJ, Olsen GJ, Pace NR (1984) Analysis of hydrothermal vent-associated symbionts by ribosomal RNA sequences. Science 224:409-411
105. Stahl DA, Lane DJ, Olsen GJ, Pace NR (1985) Characterization of a Yellowstone hot spring microbial community by 5S ribosomal RNA sequences Appl Environ Microbiol 49:1379-1384
106. Stahl DA, Lane DJ, Olsen GJ, Heller DJ, Schmidt TM, Pace NR (1987) Phylogentic analysis of certain sulfide-oxidizing and related morphologically conspicuous bacteria by 5S ribonucleic acid sequences. Int J Syst Bacteriol 37:116-122
107. Stein JL, Marsh TL, Wu KY, Shizuya H, DeLong EF (1996) Characterization of uncultivated prokaryotes - isolation and analysis of a 40-kilobase-pair genome fragment from a planktonic marine Archaeon. J Bacteriol 178:591-599
108. Suzuki MT, Giovannoni SJ (1996) Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl Environ Microbiol 62:625-630
109. Swofford DL, Olsen GJ (1990) Phylogeny reconstruction. In: Hillis DM, Moritz C (eds) Molecular systematics. Sinauer Associates, Sunderland, Mass., pp 411-501
110. Teske A, Alm E, Regan JM, Rittman BE, Stahl DA (1994) Evolutionary relationships among ammonia-and nitrite-oxidizing bacteria. J Bacteriol 176:6623-6630
111. Teske A, Wawer C, Muyzer G, Ramsing NB (1996) Distribution of sulfate-reducing bacteria in a stratified fjord (Mariager Fjord, Denmark) as evaluated by most-probable-number counts and denaturing gradient gel electrophoresis of PCR-amplified ribosomal DNA fragments. Appl Environ Microbiol 62:1405-1415
112. Thomas EJG, King RK, Burchack J, Gannon VPJ (1991) Sensitive and specific detection of Listeria monocytogenes in milk and ground beef with the polymerase chain reaction. Appl Environ Microbiol 57:2576-2580
113. Trebesius KR, Amann R, Ludwig W, Mühlegger K, Schleifer K-H (1994) Identification of whole fixed bacterial cells with non-radioactive rRNA-targeted transcript probes. Appl Environ Microbiol 60:3228-3235
114. Tsai Y-L, Olson BH (1991) Rapid method for direct extraction of DNA from soil and sediments. Appl Environ Microbiol 57:1070-1074
115. Tsai Y-L, Olson BH (1992) Detection of low numbers of bacterial cells in soils and sediments by polymerase chain reaction. Appl Environ Microbiol 58:754-757
116. Utaker JB, Bakken L, Jiang QQ, Nes IF (1996) Phylogenetic analysis of 7 new isolates of ammonia-oxidizing bacteria based on 16s ribosomal RNA gene sequences. Syst Appl Microbiol 18:549-559
117. Van de Peer Y, Chapelle S, De Wachter R (1996) A quantitative map of nucleotide substitution rates in bacterial rRNA. Nucl Acids Res 24:3381-3391
118. Voytek MA, Ward BB (1995) Detection of ammonium-oxidizing bacteria in the beta-subclass of the class proteobacteria in aquatic samples with the PCR. Appl and Environ Microbiol 61:1444-1450
119. Wagner M, Amann R, Lemmer H, Schleifer K-H (1993) Probing activated sludge with oligonucleotides specific for proteo-bacteria: inadequacy of culture-dependent methods for describing microbial community structure. Appl Environ Microbiol 59:1520-1525
120. Wagner M, Amann R, Kämpfer P, Assmus B, Hartmann A, Hutzler P, Springer N, Schleifer KH (1994) Identification and in situ detection of Gram-negative filamentous bacteria in activated sludge. Syst Appl Microbiol 17:405-417
121. Wagner M, Erhart D, Manz W, Amann R, Lemmer N, Wedi D, Schleifer K-H (1994) Development of an rRNA-targeted oligonucleotide probe specific for the genus Acinetobacter, and its application for in situ monitoring in activated sludge. Appl Environ Microbiol 60:792-800
122. Wagner M, Rath G, Amann R, Koops H-P, Schleifer K-H (1995) In situ identification of ammonia-oxidizing bacteria. Syst Appl Microbiol 18:251-264
123. Wallner G, Amann R, Beisker W (1993) Optimizing fluorescent in situ hybridization of suspended cells with rRNA-targeted oligonucleotide probes for flow cytometric identification of microorganisms. Cytometry 14:136-143
124. Wang GC-Y, Wang Y (1996) The frequency of chimeric molecules as a consequence of PCR co-amplification of 16S rRNA genes from different bacterial species. Microbiology 142:1107-1114
125. Ward DM, Weller R, Bateson MM (1990) 16S rRNA sequences reveal numerous uncultured microorganisms in a natural community. Nature 345:63-65
126. Ward DM, Weller R, Bateson MM (1990) 16S rRNA sequences reveal uncultured inhabitants of a well-studied thermal community. FEMS Microbiol Rev 75:105-116
127. Ward DM, Bateson MM, Weller R, Ruff-Roberts AL (1992) Ribosomal RNA analysis of microorganisms as they occur in nature. Adv Microb Ecol 12:219-286
128. Watson SW, Bock E, Harms H, Koops H-P, Hooper AB (1989) Nitrifying bacteria. In: Staly JT, Bryant MP, Pfennig N, Holt JG (eds) Bergey's manual of systematic bacteriology, vol 3. Williams and Wilkins, Baltimore, pp 1808-1834
129. Weller R, Ward DM (1989) Selective recovery of 16S rRNA sequences from natural microbial communities in the form of cDNA. Appl Environ Microbiol 55:1818-1822
130. Wilson KH (1994) Detection of culture-resistant bacterial pathogens by amplification and sequencing of ribosomal DNA. Clin Infect Dis 18:958-962
131. Winogradsky S (1949) Microbiologie du sol, problemes et methodes. Barneoud Freres, France
132. Woese CR (1987) Bacterial evolution. Microbiol Rev 51:221-271
133. Woese CR (1994) There must be a prokaryote somewhere: Microbiology's search for itself. Microbiol Rev 58:1-9
134. Woese CR, Fox GE (1977) Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc Natl Acad Sci USA 74:5088-5090
135. Woese CR, Weisburg WG, Paster BJ, Hahn CM, Tanner RS, Krieg NR, Koops H-P, Harms H, Stackebrandt E (1984) The phylogeny of purple bacteria: the beta subdivision. Syst Appl Microbiol 5:327-336
136. Woese CR, Wcisburg WG, Hahn CM, Paster BJ, Zablen LB, Lewis BJ, Macke TJ, Ludwig W, Stackebrandt E (1985) The phylogeny of purple bacteria: the gamma subdivision. Syst Appl Microbiol 6:25-33
137. Woese CR, Kandler O, Wheelis ML (1990) Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci USA 87:4576-4579
138. Wood AP, Kelly DP (1989) Isolation and characterization of Thiobacillus thyasiris sp. nov., a novel marine facultative autotroph and the putative symbiont of Thyasira flexuosa. Arch Microbiol 152:160-166
139. Young M, Cole ST (1993) Clostridium. In: Sonenshein AL, Hoch JA, Losick R (eds) Bacillus subtilis and other Gram-positive organisms. American Society for Microbiology, Washington, DC, pp 35-52
140. Zarda B, Amann R, Wallner G, Schleifer K-H (1991) Identification of single cells using digoxigenin-labelled rRNA-targeted oligonucleotides. J Gen Microbiol 137:2823-2830
141. Zuckerkandl E, Pauling L (1965) Molecules as documents of evolutionary history. J Theor Biol 8:357-366