The Uncultured Microbial Majority

Annual Review of Microbiology

Volumn 57, Issue , 2003, Pages 369-394

  Rappé, Michael S ^a   Giovannoni, Stephen J ^a  

^a OREGON STATE UNIVERSITY   (United States)

Author keywords

16S rRNA; Candidate phylum; Microbial diversity; Molecular phylogeny

Indexed keywords

RIBOSOME DNA; RIBOSOME RNA; RNA 16S;

BACTERIAL GENETICS; BACTERIUM CULTURE; GENE CLUSTER; GENE SEQUENCE; GENETIC VARIABILITY; GEOGRAPHIC DISTRIBUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; REVIEW; UNINDEXED SEQUENCE;

DNA, BACTERIAL; EVOLUTION, MOLECULAR; GENOME, BACTERIAL; GRAM-NEGATIVE BACTERIA; GRAM-POSITIVE BACTERIA; PHYLOGENY; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SOIL MICROBIOLOGY; VARIATION (GENETICS); WATER MICROBIOLOGY;

BACTERIA (MICROORGANISMS);

EID: 0242523909     PISSN: 00664227     EISSN: None     Source Type: Book Series    
DOI: 10.1146/annurev.micro.57.030502.090759     Document Type: Review

References (120)

1. Amann RI, Ludwig W, Schleifer K-H. 1995. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59:143-69
2. Anbar AD, Knoll AH. 2002. Proterozoic ocean chemistry and evolution: a bioinorganic bridge? Science 297:1137-42
3. Bano N, Hollibaugh JT. 2002. Phylogenetic composition of bacterioplankton assemblages from the Arctic Ocean. Appl. Environ. Microbiol. 68:505-18
4. Barns SM, Takala SL, Kuske CR. 1999. Wide distribution and diversity of members of the bacterial kingdom Acidobacterium in the environment. Appl. Environ. Microbiol. 65:1731-37
5. Bauld J, Staley JT. 1976. Planctomyces maris sp. nov.: a marine isolate of the Planctomyces-Blastocaulis group of budding bacteria. J. Gen. Microbiol. 97:45-55
6. Béjà O, Koonin EV, Aravind L, Taylor LT, Seitz H, et al. 2002. Comparative genomic analysis of archaeal genotypic variants in a single population and in two different oceanic provinces. Appl. Environ. Microbiol. 68:335-45
7. Béjà O, Suzuki MT, Koonin EV, Aravind L, Hadd A, et al. 2000. Construction and analysis of bacterial artificial chromosome libraries from a marine microbial assemblage. Environ. Microbiol. 2:516-29
8. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Rapp BA, Wheeler DL. 2002. GenBank. Nucleic Acids Res. 30: 17-20
9. Boetius A, Ravenschlag K, Schubert CJ, Rickert D, Widdel F, et al. 2000. A marine microbial consortium apparently mediating anaerobic oxidation of methane. Nature 407:623-26
10. Boone DR, Castenholz RW, Garrity GM, eds. 2001. Bergey's Manual of Systematic Bacteriology, Vol. 1. New York: Springer
11. Bowman JP, McCammon SA, McCuaig RD, Gibson JAE, Nichols PD. 2002. Characterization of continental shelf sediments collected off Antarctica: microbial metabolic activity, community structure and biogeography. http://www. ncbi.nlm.nih.gov/Entrez/
12. Bowman JP, Rea SM, McCammon SA, McMeekin TA. 2000. Diversity and community structure within anoxic sediment from marine salinity meromictic lakes and a coastal meromictic marine basin, Vestfold Hills, Eastern Antarctica. Environ. Microbiol. 2:227-37
13. Buckley DH, Schmidt TM. 2002. Exploring the diversity of soil - a microbial rain forest. See Ref. 95a, pp. 183-208
14. Bult CJ, White O, Olsen GJ, Zhou L, Fleischmann RD, et al. 1996. Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii. Science 273:1058-73
15. Chandler DP, Brockman FJ, Bailey TJ, Fredrickson JK. 1998. Phylogenetic diversity of Archaea and Bacteria in a deep subsurface paleosol. Microb. Ecol. 36:37-50
16. Chin K-J, Liesack W, Janssen PH. 2001. Opitutus terrae gen. nov., sp. nov., to accommodate novel strains of the division 'Verrucomicrobia' isolated from rice paddy soil. Int. J. Syst. Evol. Microbiol. 51:1965-68
17. Chisholm SW, Frankel SL, Goericke R, Olson RJ, Palenik B, et al. 1992. Prochlorococcus marinus nov. gen. Nov. sp.: an oxyphototrophic marine prokaryote containing divinyl chlorophyll a and b. Arch. Microbiol. 157:297-300
18. Chisholm SW, Olsen RJ, Zehler ER, Goericke R, Waterbury JB, Welschmeyer NA. 1988. A novel free-living prochlorophyte abundant in oceanic euphotic zone. Nature 334:340-43
19. Cohan FM. 2001. Bacterial species and speciation. Syst. Biol. 50:513-24
20. Coolen MJL, Cypionka H, Sass AM, Sass H, Overmann J. 2002. Ongoing modification of Mediterranean Pleistocene sapropels mediated by prokaryotes. Science 296:2407-10
21. Dalevi D, Hugenholtz P, Blackall LL. 2001. A multiple-outgroup approach to resolving division-level phylogenetic relationships using 16S rDNA data. Int. J. Syst. Evol. Microbiol. 51:385-91
22. DeLong EF. 1992. Archaea in coastal marine environments. Proc. Natl. Acad. Sci. USA 89:5685-89
23. DeLong EF, Franks DG, Alldredge AL. 1993. Phylogenetic diversity of aggregate-attached vs. free-living marine bacterial assemblages. Limnol. Oceanogr. 38:924-34
24. Derakshani M, Lukow T, Liesack W. 2001. Novel bacterial lineages at the subdivision level as detected by signature nucleotide targeted recovery of 16S rRNA genes from bulk soil and rice roots of flooded rice microcosms. Environ. Microbiol. 67:623-31
25. Dojka MA, Harris JK, Pace NR. 2000. Expanding the known diversity and environmental distribution of an uncultured phylogenetic division of bacteria. Appl. Environ. Microbiol. 66:1617-21
26. Dojka MA, Hugenholtz P, Haack SK, Pace NR. 1998. Microbial diversity in a hydrocarbon-and chlorinated-solvent-contaminated aquifer undergoing intrinsic bioremediation. Appl. Environ. Microbiol. 64:3869-77
27. Dunbar J, Barns SM, Ticknor LO, Kuske CR. 2002. Empirical and theoretical bacterial diversity in four Arizona soils. Appl. Environ. Microbiol. 68:3035-45
28. Eder W, Schmidt M, Koch M, Garbe-Schönberg D, Huber R. 2002. Prokaryotic phylogenetic diversity and corresponding geochemical data of the brine-seawater interface of the Shaban Deep, Red Sea. Environ. Microbiol. 4:758-63
29. Ehrich S, Behrens D, Lebedeva E, Ludwig W, Bock E. 1995. A new obligately chemolithoautotrophic, nitrite-oxidizing bacterium, Nitrospira moscoviensis sp. nov. and its phylogenetic relationship. Arch. Microbiol. 164:16-23
30. Field KG, Gordon D, Wright T, Rappé M, Urbach E, et al. 1997. Diversity and depth-specific distribution of SAR11 cluster rRNA genes from marine planktonic bacteria. Appl. Environ. Microbiol. 63:63-70
31. Fox GE, Stackebrandt E, Hespell RB, Gibson J, Maniloff J, et al. 1980. The phylogeny of prokaryotes. Science 209:457-63
32. Fuhrman JA, Davis AA. 1997. Widespread Archaea and novel Bacteria from the deep sea as shown by 16S rRNA gene sequences. Mar. Ecol. Prog. Ser. 150: 275-85
33. Fuhrman JA, McCallum K, Davis AA. 1992. Novel major archaebacterial group from marine plankton. Nature 356:148-49
34. Fuhrman JA, McCallum K, Davis AA. 1993. Phylogenetic diversity of subsurface marine microbial communities from the Atlantic and Pacific Oceans. Appl. Environ. Microbiol. 59:1294-302
35. Galvez A, Maqueda M, Martinez-Bueno M, Valdivia E. 1998. Publication rates reveal trends in microbiological research. ASM News 64:269-75
36. Garrity GM, Holt JG. 2001. The road map to the Manual. See Ref. 10, 1:119-66
37. Gibson J, Ludwig W, Stackebrandt E, Woese CR. 1985. The phylogeny of the green photosynthetic bacteria: absence of a close relationship between Chlorobium and Chloroflexus. Syst. Appl. Microbiol. 6:152-56
38. Giovannoni S, Rappé M. 2000. Evolution, diversity and molecular ecology of marine prokaryotes. In Microbial Ecology of the Oceans, ed. DL Kirchman, pp. 47-84. New York: Wiley
39. Giovannoni SJ, Britschgi TB, Moyer CL, Field KG. 1990. Genetic diversity in Sargasso Sea bacterioplankton. Nature 345: 60-63
40. Giovannoni SJ, Rappé MS, Vergin KL, Adair NL. 1996. 16S rRNA genes reveal stratified open ocean bacterioplankton populations related to the Green Non-Sulfur bacteria. Proc. Natl. Acad. Sci. USA 93:7979-84
41. 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. 62:1171-77
42. Hedlund BP, Gosink JJ, Staley JT. 1996. Phylogeny of Prosthecobacter, the fusiform caulobacters: members of a recently discovered division of the Bacteria. Int. J. Syst. Bacteriol. 46:960-66
43. Hedlund BP, Gosink JJ, Staley JT. 1997. Verrucomicrobia div. nov., a new division of the Bacteria containing three new species of Prosthecobacter. Antonie van Leeuwenhoek 72:29-38
44. Hentschel U, Hopke J, Horn M, Fredrich AB, Wagner M, et al. 2002. Molecular evidence for a uniform microbial community in sponges from different oceans. Environ. Microbiol. 68:4431-40
45. Hippe H. 2000. Leptospirillum gen. nov. (ex Markosyan 1972), nom. rev., including Leptospirillum ferrooxidans sp. nov. (ex Markosyan 1972), nom. rev. and Leptospirillum thermoferrooxidans sp. nov. (Golovacheva et al. 1992). Int. J. Syst. Evol. Microbiol. 50:501-3
46. Holmes AJ, Tujula NA, Holley M, Contos A, James JM, et al. 2001. Phylogenetic structure of unusual aquatic microbial formations in Nullarbor caves, Australia. Environ. Microbiol. 3:256-64
47. Huber R, Langworthy TA, König H, Thomm M, Woese CR, et al. 1986. Thermotoga maritima sp. nov. represents a new genus of unique extremely thermophilic eubacteria growing up to 90°C. Arch. Microbiol. 144:324-33
48. Huber R, Wilharm T, Huber D, Trincone A, Burggraf S, et al. 1992. Aquifex pyrophilus gen. nov. sp. nov., represents a novel group of marine hyperthermophilic hydrogen-oxidizing bacteria. Syst. Appl. Microbiol. 15:340-51
49. Hugenholtz P. 2002. Exploring prokaryotic diversity in the genomic era. Genome Biol. 3:reviews0003.1-03.8
50. Hugenholtz P, Goebel BM, Pace NR. 1998. Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J. Bacteriol. 180:4765-74
51. Hugenholtz P, Pitulle C, Hershberger KL, Pace NR. 1998. Novel division level bacterial diversity in a Yellowstone hot spring. J. Bacteriol. 180:366-76
52. Hugenholtz P, Tyson GW, Webb RI, Wagner AM, Blackall LL. 2001. Investigation of candidate division TM7, a recently recognized major lineage of the domain Bacteria with no known pure-culture representatives. Appl. Environ. Microbiol. 67: 411-19
53. Janssen PH, Schuhmann A, Mörschel E, Rainey FA. 1997. Novel anaerobic ultramicrobacteria belonging to the Verrucomicrobiales lineage of bacterial descent isolated by dilution culture from anoxic rice paddy soil. Appl. Environ. Microbiol. 63:1382-88
54. Jeanthon C, L'Haridon S, Cueff V, Banta A, Reysenbach AL, Prieur D. 2002. Thermodesulfobacterium hydrogeniphilum sp. nov. a thermophilic chemolithoautotrophic sulfate reducing bacterium isolated from a deep sea hydrothermal vent at Guaymas basin and emendation of the genus Thermodesulfobacterium. Int. J. Syst. Evol. Microbiol. 52:765-72
55. Lane DJ. 1991. 16S/23S rRNA sequencing. In Nucleic Acid Techniques in Bacterial Systematics, ed. E Stackebrandt, M Goodfellow, pp. 115-75. New York: Wiley
56. Layton AC, Karanth PN, Lajoie CA, Meyers AJ, Gregory IR, et al. 2000. Quantification of Hyphomicrobium populations in activated sludge from an industrial wastewater treatment system as determined by 16S rRNA analysis. Appl. Environ. Microbiol. 66:1167-74
57. L'Haridon S, Cilia V, Messner P, Raguenes G, Gambacorta A, et al. 1998. Desulfurobacterium thermolithotophum gen. nov. sp. nov. a novel autotrophic, sulphur-reducing bacterium isolated from a deep sea hydrothermal vent. Int. J. Syst. Bacteriol. 48:701-11
58. Li L, Kato C, Horikoshi K. 1999. Microbial diversity in sediments collected from the deepest cold-sea area, the Japan Trench. Mar. Biotechnol. 1:391-400
59. Liesack W, Stackebrandt E. 1992. Occurrence of novel groups of the domain Bacteria as revealed by analysis of genetic material isolated from an Australian terrestrial environment. J. Bacteriol. 174:5072-78
60. Lindsay MR, Webb RI, Strous M, Jetten MSM, Butler MK, et al. 2001. Cell compartmentalisation in planctomycetes: novel types of structural organisation for the bacterial cell. Arch. Microbiol. 175: 413-29
61. Lockhart PJ, Howe CJ, Bryant DA, Beanland TJ, Larkum AWD. 1992. Substitutional bias confounds inference of cyanelle origins from sequence data. J. Mol. Evol. 34:153-62
62. López-García P, López-López A, Moreira D, Rodríguez-Valera F. 2001. Diversity of free-living prokaryotes from a deep-sea site at the Antarctic Polar Front. FEMS Microbiol. Ecol. 36:193-202
63. Ludwig W, Bauer SH, Bauer M, Held I, Kirchhof G, et al. 1997. Detection and in situ identification of representatives of a widely distributed new bacterial phylum. FEMS Microbiol. Lett. 153:181-90
64. Ludwig W, Klenk H-P. 2001. Overview: a phylogenetic backbone and taxonomic framework for prokaryotic systematics. See Ref. 10, 1:49-65
65. Ludwig W, Strunk O, Klugbauer S, Klugbauer N, Weizenegger M, et al. 1998. Bacterial phylogeny based on comparative sequence analysis. Electrophoresis 19:554-68
66. Madrid VM, Aller JY, Aller RC, Christoserdov AY. 2001. High prokaryote diversity and analysis of community structure in mobile mud deposits off French Guiana identification of two new bacterial candidate divisions. Environ. Microbiol. 37:197-209
67. Madrid VM, Taylor GT, Scranton MI, Christoserdov AY. 2001. Phylogenetic diversity of bacterial and archaeal communities in the anoxic zone of the Cariaco Basin. Appl. Environ. Microbiol. 67:1663-74
68. Maidak BL, Cole JR, Lilburn TG, Parker CT Jr, Saxman PR, et al. 2001. The RDP-II (Ribosomal Database Project). Nucleic Acids Res. 29:173-74
69. Markosyan GE. 1972. A new iron-oxidizing bacterium, Leptospirillum ferrooxidans gen. et sp. nov. Biol. Zh. Armen. 25:26
70. Maymó-Gatell X, Chien Y-t, Gossett JM, Zinder SH. 1997. Isolation of a bacterium that reductively dechlorinates tetrachloroethene to ethene. Science 276:1568-71
71. Miroshnichenko ML, Kostrikina NA, Chernyh NA, Pemenov NY, Tourova TP, et al. 2003. Caldithrix abyssi gen. nov., sp. nov., a nitrate-reducing, thermophilic, anaerobic bacterium isolated from a Mid-Atlantic Ridge hydrothermal vent, represents a novel bacterial lineage. Int. J. Syst. Evol. Microbiol. 53:323-29
72. Moore LR, Post AF, Rocap G, Chisholm SW. 2002. Utilization of different nitrogen sources by the marine cyanobacteria Prochlorococcus and Synechococcus. Limnol. Oceanogr. 47:989-96
73. Moran NA, Munson MA, Baumann P, Ishikawa H. 1993. A molecular clock in endosymbiotic bacteria is calibrated using the insect hosts. Proc. R. Soc. London Ser. B 253:167-71
74. Nelson KE, Clayton RA, Gill SR, Gwinn ML, Dodson RJ, et al. 1999. Evidence for lateral gene transfer between Archaea and Bacteria from genome sequence of Thermotoga maritima. Nature 399:323-29
75. Ohkuma M, Kudo T. 1996. Phylogenetic diversity of the intestinal bacterial community in the termite Reticulitermes speratus. Appl. Environ. Microbiol. 62:461-68
76. Olsen GJ, Lane DL, Giovannoni SJ, Pace NR, 1986. Microbial ecology and evolution: a ribosomal RNA approach. Annu. Rev. Microbiol. 40:337-65
77. Oyaizu H, Debrunner-Vossbrinck B, Mandelco L, Studier JA, Woese CR. 1987. The Green Non-Sulfur Bacteria: a deep branching in the eubacterial line of descent. System. Appl. Microbiol. 9:47-53
78. Pace NR. 1997. A molecular view of microbial diversity and the biosphere. Science 276:734-40
79. 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
80. Parpais J, Marie D, Partensky F, Morin P, Vaulot D. 1996. Effect of phosphorus starvation on the cell cycle of the photosynthetic prokaryote Prochlorococcus spp. Mar. Ecol. Prog. Ser. 132:265-74
81. Partensky F, Hess WR, Vaulot D. 1999. Prochlorococcus, a marine photosynthetic prokaryote of global significance. Microbiol. Mol. Biol. Rev. 63:106-27
82. Paster BJ, Ludwig W, Weisburg WG, Stackebrandt E, Hespell RB, et al. 1985. A phylogenetic grouping of the Bacteroides, Cytophagas, and certain Flavobacteria. Syst. Appl. Microbiol. 6:34-42
83. Philippe H, Laurent J. 1998. How good are deep phylogenetic trees? Curr. Opin. Genet. Dev. 8:616-23
84. Rappé MS, Connon SA, Vergin KL, Giovannoni SJ. 2002. Cultivation of the ubiquitous SAR11 marine bacterioplankton clade. Nature 418:630-33
85. Rappé MS, Vergin K, Giovannoni SJ. 2000. Phylogenetic comparisons of a coastal bacterioplankton community with its counterparts in open ocean and freshwater systems. FEMS Microbiol. Ecol. 33:219-32
86. Reysenbach A-L, Longnecker K, 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. 66:3798-806
87. Schlesner H, Stackebrandt E. 1986. Assignment of the genera Planctomyces and Pirella to a new family Planctomycetaceae fam. nov. and description of the order Planctomycetales ord. nov. Syst. Appl. Microbiol. 8:174-76
88. Schmidt JM. 1978. Isolation and ultrastructure of freshwater strains of Planctomyces. Curr. Microbiol. 1:65-71
89. Sekiguchi Y, Takahashi H, Kamagata Y, Ohashi A, Harada H. 2001. In situ detection, isolation, and physiological properties of a thin filamentous microorganism abundant in methanogenic granular sludges: a novel isolate affiliated with a clone cluster, the green non-sulfur bacteria subdivision I. Appl. Environ. Microbiol. 67:5740-49
90. Snel B, Bork P, Huynen MA. 1999. Genome phylogeny based on gene content. Nat. Genet. 21:108-10
91. Stackebrandt E, Liesack W, Göebel BM. 1993. Bacterial diversity in a soil sample from a subtropical Australian environment as determined by 16S rRNA analysis. FASEB J. 7:232-36
92. Stackebrandt E, Murray RGE, Truper HG. 1988. Proteobacteria classis nov., a name for the phylogenetic taxon that includes the purple bacteria and their relatives. Int. J. Syst. Bacteriol. 38:321-25
93. Stackebrandt E, Rainey FA, Ward-Rainey NL. 1997. Proposal for a new hierarchic classification system, Actinobacteria classis nov. Int. J. Syst. Bacteriol. 47:479-91
94. Stackebrandt E, Woese CR. 1981. The evolution of prokaryotes. In Molecular and Cellular Aspects of Microbial Evolution, ed. MJ Carlile, JR Collins, BEB Mosely, 32:1-31. Cambridge: Cambridge Univ. Press
95. Staley JT. 1973. Budding bacteria of the Pasteuria-Blastobacter group. Can. J. Microbiol. 19:609-14
96. 95a. Staley JT, Reysenbach A-L, eds. 2002. Biodiversity of Microbial Life: Foundations of Earth's Biosphere. New York: Wiley-Liss
97. Strous M, Fuerst JA, Kramer EHM, Logemann S, Muyzer G, et al. 1999. Missing lithotroph identified as new planctomycete. Nature 400:446-49
98. Suzuki MT, Béjà O, Taylor LT, DeLong EF. 2001. Phylogenetic analysis of ribosomal RNA operons from uncultivated coastal marine bacterioplankton. Environ. Microbiol. 3:323-31
99. Swofford D. 2000. PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). Sunderland, MA: Sinauer
100. Tatusov RL, Koonin EV, Lipman DJ. 1997. A genomic perspective on protein families. Science 278:631-37
101. Teske A, Hinrichs KU, Edgcomb V, Gomez AdV, Sylva SP, et al. 2002. Microbial diversity of hydrothermal sediments in the Guaymas Basin: evidence for anaerobic methanotropic communities. Appl. Environ. Microbiol. 68:1994-2007
102. Ting CS, Rocap G, King J, Chisholm SW. 2002. Cyanobacterial photosynthesis in the oceans: the origins and significance of divergent light-harvesting strategies. Trends Microbiol. 10:134-41
103. Todorov JR, Chistoserdov AY, Aller JY. 2000. Molecular analysis of microbial communities in mobile deltaic muds of Southeastern Papua New Guinea. FEMS Microbiol. Ecol. 33:147-55
104. Urbach E, Scanlan DJ, Distel DL, Waterbury JB, Chisholm SW. 1998. Rapid diversification of marine picophytoplankton with dissimilar light-harvesting structures inferred from sequences of Prochlorococcus and Synechococcus (Cyanobacteria). J. Mol. Evol. 46:188-201
105. Urbach E, Vergin KL, Young L, Morse A, Giovannoni SJ. 2001. Unusual bacterioplankton community structure in ultra-oligotrophic Crater Lake. Limnol. Oceanogr. 46:557-72
106. Wang GC-Y, Wang Y. 1997. Frequency of formation of chimeric molecules as a consequence of PCR coamplification of 16S rRNA genes from mixed bacterial genomes. Appl. Environ. Microbiol. 63:4645-50
107. Ward DM. 1998. A natural species concept for prokaryotes. Curr. Opin. Microbiol. 1:271-77
108. Ward DM, Bateson MM, Weller R, Ruff-Roberts AL. 1992. Ribosomal RNA analysis of microorganisms as they occur in nature. Adv. Microb. Ecol. 12:219-86
109. Ward DM, Papke T, Nübel U, McKitrick MC. 2002. Natural history of microorganisms inhabiting hot spring microbial mat communities: clues to the origin of microbial diversity and implications for microbiology and macrobiology. See Ref. 95a, pp. 25-48
110. Ward-Rainey N, Rainey FA, Schlesner H, Stackebrandt E. 1995. Assignment of hitherto unidentified 16S rDNA species to a main line of descent within the domain Bacteria. Microbiology 141:3247-50
111. Weller R, Bateson MM, Heimbuch BK, Kopczynski ED, Ward DM. 1992. Uncultivated cyanobacteria, Chloroflexus-like inhabitants, and spirochete-like inhabitants of a hot spring microbial mat. Appl. Environ. Microbiol. 58:3964-69
112. Whitman WB, Coleman DC, Wiebe WJ. 1998. Prokaryotes: the unseen majority. Proc. Natl. Acad. Sci. USA 95:6578-83
113. Woese CR. 1987. Bacterial evolution. Microbiol. Rev. 51:221-71
114. 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 87:4576-79
115. Woese CR, Stackebrandt E, Macke TJ, Fox GE. 1985. A phylogenetic definition of the major eubacterial taxa. Syst. Appl. Microbiol. 6:143-51
116. Wolf YI, Rogozin IB, Grishin NV, Tatusov RL, Koonin EV. 2001. Genome trees constructed using five different approaches suggest new major bacterial clades. BMC Evol. Biol. 1:8
117. Yap WH, Zhang Z, Wang Y. 1999. Distinct types of rRNA operons exist in the genome of the actinomycete Thermomonospora chomogena and evidence for horizontal transfer of an entire rRNA operon. J. Bacteriol. 181:5201-9
118. Zengler K, Toledo G, Rappé M, Elkins J, Mathur EJ, et al. 2002. Cultivating the uncultured. Proc. Natl. Acad. Sci. USA 99:15681-86
119. Zhang H, Sekiguchi Y, Hanada S, Hugenholtz P, Kim H, et al. 2003. Gemmatimonas aurantiaca gen. nov., sp. nov., a Gram-negative aerobic polyphosphate-accumulating microorganism, the first cultured representative of the new bacterial phylum Gemmatimonadetes phy. nov. Int. J. Syst. Evol. Microbiol. In press
120. Zwart G, Crump BC, Kamst-van Agterveld MP, Hagen F, Han S-K. 2002. Typical freshwater bacteria: an analysis of available 16S rRNA gene sequences from plankton of lakes and rivers. Aquat. Microb. Ecol. 28:141-55