Natural view of microbial biodiversity within hot spring cyanobacterial mat communities

Microbiology and Molecular Biology Reviews

Volumn 62, Issue 4, 1998, Pages 1353-1370

  Ward, David M ^a   Ferris, Michael J ^a   Nold, Stephen C ^a   Bateson, Mary M ^a  

^a MONTANA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA;

ARTICLE; BACTERIUM CONTAMINATION; BIODIVERSITY; CYANOBACTERIUM; ECOLOGY; GENE SEQUENCE; GEOGRAPHIC DISTRIBUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; RNA SEQUENCE; SPECIES DIFFERENCE; THERMAL SPRING;

BACTERIA (MICROORGANISMS); CYANOBACTERIA; NEGIBACTERIA; OCTOPUS; PROKARYOTA;

EID: 0031737291     PISSN: 10922172     EISSN: None     Source Type: Journal    
DOI: 10.1128/mmbr.62.4.1353-1370.1998     Document Type: Article

References (178)

1. Amann, R. I., W. Ludwig, and K. H. Schleifer. 1995. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59:143-169.
2. Anderson, K. L., T. A. Tayne, and D. M. Ward. 1987. Formation and fate of fermentation products in hot spring cyanobacterial mats. Appl. Environ. Microbiol. 53:2343-2352.
3. Baas Becking, L. G. M. 1934. Geobiologie of inleiding tot de milieukunde. W. P. van Stockum and Zoon N.V., The Hague, The Netherlands.
4. Barns, S. M., C. F. Delwiche, J. D. Palmer, and N. R. Pace. 1996. Perspectives on archaeal diversitv, thermophily and monophyly from environmental rRNA sequences. Proc. Natl. Acad. Sci. USA 93:9188-9193.
5. Barns, S. M., R. E. Fundyga, M. W. Jeffries, and N. R. Pace. 1994. Remarkable archaeal diversity detected in a Yellowstone National Park hot spring environment. Proc. Natl. Acad. Sci. USA 91:1609-1613.
6. Bateson, M. M., K. J. Thibault, and D. M. Ward. 1990. Comparative analysis of 16S ribosomal RNA sequences of Thermus species. Syst. Appl. Microbiol. 13:8-13.
7. Bateson, M. M., and D. M. Ward. 1988. Photoexcretion and fate of glycolate in a hot spring cyanobacterial mat. Appl. Environ. Microbiol. 54:1738-1743.
8. Bateson, M. M., J. Wiegel, and D. M. Ward. 1989. Comparative analysis of 16S ribosomal RNA sequences of thermophilic fermentative bacteria isolated from hot spring cyanobacterial mats. Syst. Appl. Microbiol. 12:1-7.
9. Bauld, J., and T. D. Brock. 1973. Ecological studies of Chloroflexis, a gliding photosynthetic bacterium. Arch. Microbiol. 92:267-284.
10. Bauld, J., and T. D. Brock. 1974. Algal excretion and bacterial assimilation in hot spring algal mats. J. Phycol. 10:101-106.
11. Begon, M., J. L. Harper, and C. R. Townsend. 1990. Ecology: individuals, populations and communities. Blackwell Scientific Publications, Cambridge, Mass.
12. Ben-Bassat, A., and J. G. Zeikus. 1981. Thermobacteroides acetoethylicus gen. nov. and spec. nov., a new chemoorganotrophic, anaerobic, thermophilic bacterium. Arch. Microbiol. 128:365-370.
13. Bintrim, S. B., T. J. Donohue, J. Handelsman, G. P. Roberts and R. M. Goodman. 1997. Molecular phylogeny of Archaea from soil. Proc. Natl. Acad. Sci. USA 94:277-282.
14. Borneman, J., P. Skrock, K. M. O'Sullivan, J. A. Palus, N. G. Rumjanek, J. L. Jansen, J. Nienhuis, and E. W. Triplett. 1996. Molecular microbial diversity of an agricultural soil in Wisconsin. Appl. Environ. Microbiol. 62:1935-1943.
15. Borneman, J., and E. W. Triplett. 1997. Molecular microbial diversity in soils from eastern Amazonia: evidence for unusual microorganisms and microbial population shifts associated with deforestation. Appl. Environ. Microbiol. 63:2647-2653.
16. Britschgi, T. B., and S. J. Giovannoni. 1991. Phylogenetic analysis of a natural marine bacterioplankton population by rRNA gene cloning and sequencing. Appl. Environ. Microbiol. 57:1707-1713.
17. Brock, T. D. 1967. Micro-organisms adapted to high temperatures. Nature 214:882-885.
18. Brock, T. D. 1978. Thermophilic microorganisms and life at high temperatures. Springer-Verlag, New York, N.Y.
19. Brock, T. D. 1987. The study of microorganisms in situ: progress and problems. Symp. Soc. Gen. Microbiol. 41:1-17.
20. Brock, T. D., and M. L. Brock. 1969. Effect of light intensity on photosynthesis by thermal algae adapted to natural and reduced sunlight. Limnol. Oceanogr. 14:334-341.
21. Brock, T. D., and M. L. Brock. 1969. Recovery of a hot spring community from a catastrophe. J. Phycol. 5:75-77.
22. Brock, T. D., and H. Freeze. 1969. Thermus aquaticus gen. n. and sp. n., a nonsporulating extreme thermophile. J. Bacteriol. 98:289-297.
23. Castenholz, R. W. 1973. Ecology of blue-green algae in hot springs, p. 379-414. In N. G. Carr and B. A. Whitton (ed.), The biology of blue-green algae. University of California Press, Los Angeles, Calif.
24. Castenholz, R. W. 1978. The biogeography of hot spring algae through enrichment cultures. Mitt. Int. Ver. Limnol. 21:296-315.
25. Castenholz, R. W. 1981. Isolation and cultivation of thermophilic cyanobacteria, p. 236-246. In M. P. Starr, H. Stolp, H. G. Truper, A. Balows, and H. G. Schlegel (ed.), The prokaryotes: a handbook in habitats, isolation, and identification of bacteria. Springer-Verlag, Berlin, Germany.
26. Castenholz, R. W. 1992. Species usage, concept, and evolution in the cyanobacteria (blue-green algae). J. Phycol. 28:737-745.
27. Castenholz, R. W. 1996. Endemism and biodiversity of thermophilic cyanobacteria. Nova Hedwigia 112:33-47.
28. Castenholz, R. W., J. Bauld, and B. B. Jørgensen. 1990. Anoxygenic microbial mats of hot springs: thermophilic Chlorobium sp. FEMS Microbiol. Ecol. 74:325-336.
29. Castenholz, R. W., and F. Garcia-Pichel. Cyanobacterial responses to UV radiation. In M. Potts and B. Whitton (ed.), Ecology of cyanobacteria, in press. Kluwer, Dordrecht, The Netherlands.
30. Choi, B. K., B. J. Paster, F. E. Dewhirst, and U. B. Gobel. 1994. Diversity of cultivable and uncultivable oral spirochetes from a patient with severe destructive periodontitis. Infect. Immun. 62:1889-1895.
31. Collins, M. D., P. A. Lawson, A. Willems, J. J. Cordoba, J. Fernandez-Garayzabal, P. Garcia, J. Cai, H. Hippe, and J. A. E. Farrow. 1994. The phylogeny of the genus Clostridium: proposal of five new genera and eleven new species combinations. Int. J. Syst. Bacteriol. 44:812-826.
32. Dobson, G., D. M. Ward, N. Robinson, and G. Eglinton. 1988. Biogeochemistry of hot spring environments: extractable lipids of a cyanobacterial mat. Chem. Geol. 68:155-179.
33. Doemel, W. N., and T. D. Brock. 1977. Structure, growth, and decomposition of laminated algal-bacterial mats in alkaline hot springs. Appl. Environ. Microbiol. 34:433-452.
34. Embley, T. M., and E. Stackebrandt. 1997. Species in practice: exploring uncultured prokaryote diversity in natural samples, p. 61-81. In M. F. Claridge, H. A. Dawah, and M. R. Wilson (ed.), Species: the units of biodiversity. Chapman & Hall, London, England.
35. Farrelly, V., F. A. Rainey, and E. Stackebrandt. 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.
36. Ferris, M. J., G. Muyzer, and D. M. Ward. 1996. Denaturing gradient gel electrophoresis profiles of 16S rRNA-defined populations inhabiting a hot spring microbial mat community. Appl. Environ. Microbiol. 62:340-346.
37. Ferris, M. J., S. C. Nold, N. P. Revsbech, and D. M. Ward. 1997. Population structure and physiological changes within a hot spring microbial mat community following disturbance. Appl. Environ. Microbiol. 63:1367-1374.
38. Ferris, M. J., S. C. Nold, C. M. Santegoeds, and D. M. Ward. Examining bacterial population diversity within the Octopus Spring microbial mat community. In A.-L. Reysenbach (ed.), Thermophiles, in press. Plenum Publishing Corp., New York, N.Y.
39. Ferris, M. J., and B. P. Palenik. Cyanobacterial community structure changes with depth in an oligotrophic ocean environment. Nature, in press.
40. Ferris, M. J., A. L. Ruff-Roberts, E. D. Kopczynski, M. M. Bateson, and D. M. Ward. 1996. Enrichment culture and microscopy conceal diverse thermophilic Synechococcus populations in a single hot spring microbial mat habitat. Appl. Environ. Microbiol. 62:1045-1050.
41. Ferris, M. J., and D. M. Ward. 1997. Seasonal distributions of dominant 16S rRNA-defined populations in a hot spring microbial mat examined by denaturing gradient gel electrophoresis. Appl. Environ. Microbiol. 63:1375-1381.
42. Field, K. G., D. Gordon, T. Wright, M. Rappé, E. Urbach, K. Vergin, and S. J. Giovannoni. 1997. Diversity and depth-specific distribution of SAR11 cluster rRNA genes from marine planktonic bacteria. Appl. Environ. Microbiol. 63:63-70.
43. Figueras, J. B., L. J. Garcia-Gil, and C. A. Abella. 1997. Phylogeny of the genus Chlorobium based on 16S rDNA sequence. FEMS Microbiol. Lett. 152:31-36.
44. Forterre, P. 1997. Protein versus rRNA: problems in rooting the universal tree of life. ASM News 63:89-95.
45. Fox, G. E., J. D. Wisotzkey, and P. Jurtshuk, Jr. 1992. How close is close: 16S rRNA sequence identity may not be sufficient to guarantee species identity. Int. J. Syst. Bacteriol. 42:166-170.
46. Friedrich, M., R. J. Grosser, E. A. Kern, W. P. Inskeep, and D. M. Ward. Characterization of 16S rRNA-defined phenanthrene-degrading microorganisms enriched in the presence of model organic phases by denaturing gradient gel electrophoresis. Unpublished data.
47. Fuhrman, J. A., K. McCallum, and A. A. Davis. 1993. Phylogenetic diversity of subsurface marine microbial communities from the Atlantic and Pacific Oceans. Appl. Environ. Microbiol. 59:1294-1302.
48. Futuyma, D. J. 1986. Evolutionary biology. Sinauer Associates, Sunderland, Mass.
49. Garcia-Pichel, F., and R. W. Castenholz. 1994. On the significance of solar ultraviolet radiation for the ecology of microbial mats. p. 77-84. In L. Stal and P. Caumette (ed.), Microbial mats. Springer-Verlag, Heidelberg, Germany.
50. Giovannoni, S. J., T. B. Britschgi, C. L. Moyer, and K. G. Field. 1990. Genetic diversity in Sargasso Sea bacterioplankton. Nature 344:60-63.
51. Giovannoni, S. J., M. S. Rappe, K. L. Vergin, and N. L. Adair. 1996. 16S rRNA genes reveal stratified open ocean bacterioplankton populations related to the green non-sulfur bacteria. Proc. Natl. Acad. Sci. USA 93:7979-7984.
52. Giovannoni, S. J., E. Schabtach, and R. W. Castenholz. 1987. Isosphaera pallida, gen. and comb. nov., a gliding, budding eubacterium from hot springs. Arch. Microbiol. 147:276-284.
53. Giovannoni, S. J., S. Turner, G. J. Olsen, S. Barns, D. J. Lane, and N. R. Pace. 1988. Evolutionary relationships among cyanobacteria and green chloroplasts. J. Bacteriol. 170:3584-3592.
54. Gonzalez, I. L., J. E. Sylvester, T. F. Smith, D. Stambolian, and R. D. Schmickel. 1990. Ribosomal RNA gene sequences and hominoid phylogeny. Mol. Biol. Evol. 7:203-219.
55. Gordon, D. A., and S. J. Giovannoni. 1996. Detection of stratified microbial populations related to Chlorobium and Fibrobacter species in the Atlantic and Pacific Oceans. Appl. Environ. Microbiol. 62:1171-1177.
56. Gray, J. P., and R. P. Herwig. 1996. Phylogenetic analysis of the bacterial communities in marine sediments. Appl. Environ. Microbiol. 62:4049-4059.
57. Gunderson, J. H., M. L. Sogin, G. Wollett, M. Hollingdale, V. F. de la Cruz, A. P. Waters, and T. F. McCutchan. 1987. Structurally distinct, stage-specific ribosomes occur in Plasmodium. Science 238:933-937.
58. Huber, R., S. Burggraf, T. Mayer, S. M. Barns, P. Rossnagel, and K. O. Stetter. 1995. Isolation of a hyperthermophilic archaeum predicted by in situ RNA analysis. Nature 376:57-58.
59. Huber, R., W. Eder, S. Heldwein, G. Wanner, H. Huber, R. Rachel, and K. O. Stetter. 1998. Thermocrinis ruber gen. nov., sp. nov., a pink-filament-forming hyperthermophilic bacterium isolated from Yellowstone National Park. Appl. Environ. Microbiol. 64:3576-3583.
60. Jackson, T. J., R. F. Ramaley, and W. G. Meinschein. 1973. Thermomicrobium, a new genus of extremely thermophilic bacteria. Int. J. Syst. Bacteriol. 23:28-36.
61. Kallas, T., and R. W. Castenholz. 1982. Internal pH and ATP-ADP pools in the cyanobacterium Synechococcus sp. during exposure to growth-inhibiting low pH. J. Bacteriol. 149:229-236.
62. Kallas, T., and R. W. Castenholz. 1982. Rapid transient growth at low pH in the cyanobacterium Synechococcus sp. J. Bacteriol. 149:237-246.
63. Kimble, L. K., L. Mandelco, C. R. Woese, and M. T. Madigan. 1995. Heliobacterium modesticaldum, sp. nov., a thermophilic heliobacterium of hot springs and volcanic soils. Arch. Microbiol. 163:259-267.
64. Komatsoulis, G. A., and M. S. Waterman. 1997. A new computational method for detection of chimeric 16S rRNA artifacts generated by PCR amplification from mixed bacterial populations. Appl. Environ. Microbiol. 63:2338-2346.
65. Kopczynski, E. D., M. M. Bateson, and D. M. Ward. 1994. Recognition of chimeric small-subunit ribosomal DNAs composed of genes from uncultivated microorganisms. Appl. Environ. Microbiol. 60:746-748.
66. Kowalchuk, G. A., J. R. Stephen, W. De Boer, J. I. Presser, T. M. Embley, and J. W. Woldendorp. 1997. Analysis of ammonia-oxidizing bacteria of the beta subdivision of the class Proteobacteria in coastal sand dunes by denaturing gradient gel electrophoresis and sequencing of PCR-amplified 16S ribosomal DNA fragments. Appl. Environ. Microbiol. 63:1489-1497.
67. Kristjansson, J. K., G. O. Hreggvidsson, S. K. Petursdottir, M. Konradsdottir, E. Helgason, J. Gislason, and E. J. Mathur. 1996. Population structure of aerobic, nonsporeforming, thermophilic eubacteria, p. 8. In Thermophiles '96 International Conference on "The Biology, Ecology, and Biotechnology of Thermophilic Microorganisms" abstracts.
68. Kühl, M., F. Garcia-Pichel, and R. W. Castenholz. Different temperature adaptation of photosynthetic populations within a single hot spring microbial mat habitat as measured with oxygen microelectrodes. Unpublished data.
69. Lawton, J. H. 1996. Patterns in ecology. Oikos 75:145-147.
70. Lee, Y., M. K. Jain, C. Lee, C. E. Lowe, and J. G. Zeikus. 1993. Taxonomic distinction of saccharolytic thermophilic anaerobes: description of Thermoanaerobacterium xylanolyticum gen. nov., sp. nov., and Thermoanaerobacterium saccharolyticum gen. nov., sp. nov.; reclassification of Thermoanaerobium brockii, Clostridium thermosulfurogenes, and C. thermohydrosulfuricum E11-69 as Thermoanaerobacter brockii comb. nov., Thermoanaerobacterium thermosulfurigenes comb. nov., and Thermoanaerobacter thermohydrosulfuricus comb. nov., respectively; and transfer of Clostridium thermohydrosulfuricum 39E to Thermoanaerobacter ethanolicus. Int. J. Syst. Bacteriol. 43:41-51.
71. Liesack, W., and E. Stackebrandt. 1992. Occurrence of novel groups of the domain Bacteria as revealed by analysis of genetic material isolated from an Australian terrestrial environment. J. Baeteriol. 174:5072-5078.
72. Liesack, W., H. Weyland, and E. Stackebrandt. 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.
73. MacArthur, R. H., and E. O. Wilson. 1967. The theory of island biogeography. Princeton University Press, Princeton, N.J.
74. Madigan, M. T., and T. D. Brock. 1977. Adaptation by hot spring phototrophs to reduced light intensities. Arch. Microbiol. 113:111-120.
75. Maidak, B. L., G. J. Olsen, N. Larsen, R. Overbeek, M. J. McCaughey, and C. R. Woese. 1997. The RDP (Ribosomal Database Project). Nucleic Acids Res. 25:109-110.
76. Maynard-Smith, J. 1995. Do bacteria have population genetics? Symp. Soc. Gen. Microbiol. 52:1-12.
77. Mayr, E. 1982. The growth of biological thought: diversity, evolution, and inheritance. Harvard University Press, Cambridge, Mass.
78. McCutchan, T. F., V. F. de la Cruz, A. A. Lal, J. H. Gunderson, H. J. Elwood, and M. L. Sogin. 1988. Primary sequences of two small subunit ribosomal RNA genes from Plasmodium falciparum. Mol. Biochem. Parasitol. 28:63-68.
79. Miller, S. L., and A. Lazcano. 1995. The origin of life: did it occur at high temperatures? J. Mol. Evol. 41:689-692.
80. Miller, S. R., C. E. Wingard, and R. W. Castenholz. 1998. Effects of visible light and UV radiation on photosynthesis in a population of a hot spring cyanobacterium, a Synechococcus sp., subjected to high-temperature stress. Appl. Environ. Microbiol. 64:3893-3899.
81. Moore, L. R., G. Rocap, and S. W. Chisholm. 1998. Physiology and molecular phylogeny of coexisting Prochlorococcus ecotypes. Nature 393:464-467.
82. Mullins, T. D., T. B. Britschgi, R. L. Krest, and S. J. Giovannoni. 1995. Genetic comparisons reveal the same unknown bacterial lineages in Atlantic and Pacific bacterioplankton communities. Limnol. Oceanogr. 40:148-158.
83. Murray, A. E., J. T. Hollibaugh, and C. Orrego. 1996. Phylogenetic compositions of bacterioplankton from two California estuaries compared by denaturing gradient gel electrophoresis of 16S rDNA fragments. Appl. Environ. Microbiol. 62:2676-2680.
84. Muyzer, G., E. C. De Waal, and A. G. Uitterlinden. 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.
85. Mylvaganam, S., and P. P. Dennis. 1992. Sequence heterogeneity between the two genes encoding 16S rRNA from the halophilic archaebacterium Haloarcula marismortui. Genetics 130:399-410.
86. Nold, S. C., E. D. Kopczynski, and D. M. Ward. 1996. Cultivation of aerobic chemoorganotrophic proteobacteria and gram-positive bacteria from a hot spring microbial mat. Appl. Environ. Microbiol. 62:3917-3921.
87. Nold, S. C., and D. M. Ward. 1995. Diverse Thermus species inhabit a single hot spring microbial mat. Syst. Appl. Microbiol. 18:274-278.
88. Nold, S. C., and D. M. Ward. 1996. Photosynthate partitioning and fermentation in hot spring microbial mat communities. Appl. Environ. Microbiol. 62:4598-4607.
89. Nölling, J., D. Hahn, W. Ludwig, and W. M. De Vos. 1993. Phylogenetic analysis of thermophilic Methanobacterium sp.: evidence for a formate-utilizing ancestor. Syst. Appl. Microbiol. 16:208-215.
90. Nübel, U., B. Engelen, A. Felske, J. Snaidr, A. Wieshuber, R. I. Amann, W. Ludwig, and H. Backhaus. 1996. Sequence heterogeneities of genes encoding 16S rRNAs in Paenibacillus polymyxa detected by temperature gradient gel electrophoresis. J. Bacteriol. 178:5636-5643.
91. Ohkuma, M., and T. Kudo. 1996. Phylogenetic diversity of the intestinal bacterial community in the termite Reticulitermes speratus. Appl. Environ. Microbiol. 62:461-468.
92. Olsen, G. J., D. J. Lane, S. J. Giovannoni, and N. R. Pace. 1986. Microbial ecology and evolution: a ribosomal RNA approach. Annu. Rev. Microbiol. 40:337-365.
93. Olsen, G. J., C. R. Woese, and R. Overbeek. 1994. The winds of (evolutionary) change: breathing new life into microbiology. J. Bacteriol. 176:1-6.
94. Overmann, J., and C. Tuschak. 1997. Phylogeny and molecular fingerprinting of green sulfur bacteria. Arch. Microbiol. 167:302-309.
95. Oyaizu, H., B. Debrunner-Vossbrinck, L. Mandelco, J. A. Studier, and C. R. Woese. 1987. The green non-sulfur bacteria: a deep branching in the eubacterial line of descent. Syst. Appl. Microbiol. 9:47-53.
96. Pace, N. R. 1991. Origin of life - facing up to the physical setting. Cell 65:531-533.
97. Pace, N. R. 1996. New perspective on the natural microbial world: molecular microbial ecology. ASM News 62:463-470.
98. Pace, N. R. 1997. A molecular view of microbial diversity and the biosphere. Science 276:734-740.
99. Pace, N. R., D. A. Stahl, D. J. Lane, and G. J. Olsen. 1986. The analysis of natural microbial populations by ribosomal RNA sequences. Adv. Microb. Ecol. 9:1-55.
100. Palenik, B. 1994. Cyanobacterial community structure as seen from RNA polymerase gene sequence analysis. Appl. Environ. Microbiol. 60:3212-3219.
101. Palys, T., L. K. Nakamura, and F. M. Cohan. 1997. Discovery and classification of ecological diversity in the bacterial world: the role of DNA sequence data. Int. J. Syst. Bacteriol. 47:1145-1156.
102. Papke, R. T., N. B. Ramsing, and D. M. Ward. Unpublished data.
103. Paster, B. J., F. E. Dewhirst, W. G. Weisburg, L. A. Tordoff, G. J. Fraser, R. B. Hespell, T. B. Stanton, L, Zablen, L. Mandelco, and C. R. Woese. 1991. Phylogenetic analysis of the spirochetes. J. Bacteriol. 173:6101-6109.
104. Patel, B. K. C., H. W. Morgan, and R. M. Daniel. 1985. Thermophilic anaerobic spirochetes in New Zealand hot springs. FEMS Microbiol. Lett. 26:101-106.
105. Peary, J. A., and R. W. Castenholz. 1964. Temperature strains of a thermophilic blue-green alga. Nature 202:720-721.
106. Pierson, B. K., and R. W. Castenholz. 1974. A phototrophic gliding filamentous bacterium of hot springs. Chloroflexus auranticus, gen. and sp. nov. Arch. Microbiol. 100:5-24.
107. T contains multiple 16S rRNA genes with heterogeneous intervening sequences. Microbiology 142: 2087-2095.
108. Rainey, F. A., N. Ward, L. I. Sly, and E. Stackebrandt. 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.
109. Rainey, F. A., N. L. Ward, H. W. Morgan, R. Toalster, and E. Stackebrandt. 1993. Phylogenetic analysis of anaerobic thermophilic bacteria: aid for their reclassification. J. Bacteriol. 175:4772-4779.
110. Ramsing, N. B., M. J. Ferris, and D. M. Ward. 1997. Light-induced motility of thermophilic Synechococcus isolates from Octopus Spring, Yellowstone National Park. Appl. Environ. Microbiol. 63:2347-2354.
111. Ramsing, N. B., M. J. Ferris, and D. M. Ward. Highly ordered vertical structure of Synechococcus populations within the one-millimeter thick photic zone of a hot spring cyanobacterial mat. Unpublished data.
112. Relman, D. A., J. S. Loutit, T. M. Schmidt, S. Falkow, and L. S. Tompkins. 1990. The agent of bacillary angiomatosis: an approach to the identification of uncultured pathogens. N. Engl. J. Med. 323:1573-1580.
113. Revsbech, N. P., and D. M. Ward. 1984. Microelectrode studies of interstitial water chemistry and photosynthetic activity in a hot spring microbial mat. Appl. Environ. Microbiol. 48:270-275.
114. Reysenbach, A.-L., L. J. Giver, G. S. Wickham, and N. R. Pace. 1992. Differential amplification of rRNA genes by polymerase chain reaction. Appl. Environ. Microbiol. 58:3417-3418.
115. Reysenbach, A.-L., G. S. Wickham, and N. R. Pace. 1994. Phylogenetic analysis of the hyperthermophilic pink filament community in Octopus Spring, Yellowstone National Park. Appl. Environ. Microbiol. 60:2113-2119.
116. Robison-Cox, J. F., M. M. Bateson, and D. M. Ward. 1995. Evaluation of nearest-neighbor methods for detection of chimeric small-subunit rRNA sequences. Appl. Environ. Microbiol. 61:1240-1245.
117. Rosenzweig, M. L. 1995. Species diversity in space and time. University Press, Cambridge, England.
118. Ruff-Roberts, A. L., J. G. Kuenen, and D. M. Ward. 1994. Distribution of cultivated and uncultivated cyanobacteria and Chloroflexus-like bacteria in hot spring microbial mats. Appl. Environ. Microbiol. 60:697-704.
119. Sandbeck, K. A., and D. M. Ward. 1981. Fate of immediate methane precursors in low-sulfate, hot-spring algal-bacterial mats. Appl. Environ. Microbiol. 41:775-782.
120. Sandbeck, K. A., and D. M. Ward. 1982. Temperature adaptations in the terminal processes of anaerobic decomposition of Yellowstone National Park and Icelandic hot spring microbial mats. Appl. Environ. Microbiol. 44:844-851.
121. Santegoeds, C. M., S. C. Nold, and D. M. Ward. 1996. Denaturing gradient gel electrophoresis used to monitor the enrichment culture of aerobic chemoorganotrophic bacteria from a hot spring cyanobacterial mat. Appl. Environ. Microbiol. 62:3922-3928.
122. Schink, B., and J. G. Zeikus. 1983. Clostridium thermosulfurogenes sp. nov., a new thermophile that produces elemental sulfur from thiosulphate. J. Gen. Microbiol. 129:1149-1158.
123. Schmidt, T. M., E. F. DeLong, and N. R. Pace. 1991. Analysis of a marine picoplankton community using 16S rRNA gene cloning and sequencing. J. Bacteriol. 173:4371-4378.
124. Sheridan, R. P. 1976. Sun-shade ecotypes of a bluegreen alga in a hot spring. J. Phycol. 12:279-285.
125. Sheridan, R. P. 1979. Seasonal variation in sun-shade ecotypes of Plectonema notatum (cyanophyta). J. Phycol. 15:223-226.
126. Shiea, J., S. C. Brassell, and D. M. Ward. 1990. Mid-chain branched mono- and dimethyl alkanes in hot spring cyanobacterial mats: a direct biogenic source for branched alkanes in ancient sediments? Org. Geochem. 15:223-231.
127. Shiea, J., S. C. Brassell, and D. M. Ward. 1991. Comparative analysis of extractable lipids in hot spring microbial mats and their component photosynthetic bacteria. Org. Geochem. 17:309-319.
128. Sibley, C. G., and J. E. Ahlquist. 1987. DNA hybridization evidence of hominoid phylogeny: results from an expanded data set. J. Mol. Evol. 26:99-121.
129. Sibley, C. G., J. A. Comstock, and J. E. Ahlquist. 1990. DNA hybridization evidence of hominoid phylogeny: a reanalysis of the data. J. Mol. Evol. 30:202-236.
130. Simpson, G. G. 1961. Principles of animal taxonomy. Columbia University Press, New York, N.Y.
131. Stackebrandt, E., and B. M. Goebel. 1994. Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int. J. Syst. Bacteriol. 44:846-849.
132. Stackebrandt, E., W. Liesack, and B. M. Goebel. 1993. Bacterial diversity in a soil sample from a subtropical Australian environment as determined by 16S rDNA analysis. FASEB J. 7:232-236.
133. Stahl, D. A., and R. Amann. 1991. Development and application of nucleic acid probes, p. 205-248. In E. Stackebrandt and M. Goodfellow (ed.), Nucleic acid techniques in bacterial systematic. John Wiley & Sons, Ltd., Chichester, England.
134. Suhl, D. A., D. J. Lane, G. J. Olsen, and N. R. Pace. 1985. Characterization of a Yellowstone hot spring microbial community by 5S rRNA sequences. Appl. Environ. Microbiol. 49:1379-1384.
135. Staley, J. T. 1997. Biodiversity: are microbial species threatened? Curr. Opin. Biotechnol. 8:340-345.
136. Stetter, K. O. 1996. Hyperthermophilic procaryotes. FEMS Microbiol. Rev. 18:149-158.
137. Stetter, K. O., G. Fiala, G. Huber, R. Huber, and A. Segerer. 1990. Hyperthermophilic microorganisms. FEMS Microbiol. Rev. 75:117-124.
138. Stevenson, A. K., L. K. Kimble, C. R. Woese, and M. T. Madigan. 1997. Characterization of new heliobacteria and their habitats. Photosynth. Res. 53:1-12.
139. Suzuki, M. T., and S. J. Giovannoni. 1996. Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl. Environ. Microbiol. 62:625-630.
140. Tiedje, J. M., J.-Z. Zhou, K. Nüsslein, C. L. Moyer, and R. R. Fulthorpe. 1997. Extent and patterns of soil microbial diversity, p. 35-41. In M. T. Martins, M. I. Z. Sato, J. M. Tiedje, L. C. N. Hagler, J. Dobereiner, and P. S. Sanchez (ed.), Progress in microbial ecology. Proceedings of the Seventh International Symposium on Microbial Ecology. Brazilian Society for Microbiology/International Committee on Microbial Ecology, Sao Paulo, Brazil.
141. Tipper, J. C. 1979. Rarefaction and rarefiction - the use and abuse of a method in paleoecology. Paleobiology 5:423-434.
142. Ueda, T., Y. Suga, and T. Matsuguchi. 1995. Molecular phylogenetic analysis of a soil microbial community in a soybean field. Eur. J. Soil Sci. 46:415-421.
143. Van Regenmortel, M. H. V. 1997. Viral species, p. 17-24. In M. F. Claridge, H. A. Dawah, and M. R. Wilson (ed.), Species: the units of biodiversity. Chapman & Hall, London, England.
144. Wahlund, T. M., C. R. Woese, R. W. Castenholz, and M. T. Madigan. 1991. A thermophilic green sulfur bacterium from New Zealand hot springs, Chlorobium tepidum sp. nov. Arch. Microbiol. 156:81-90.
145. Ward, D. M. 1989. Molecular probes for analysis of microbial communities, p. 145-163. In W. G. Characklis and P. A. Wilderer (ed.), Structure and function of biofilms. John Wiley & Sons, Ltd., Chichester, England.
146. Ward, D. M. Unpublished observations.
147. Ward, D. M. 1998. A natural species concept for prokaryotes. Curr. Opin. Microbiol. 1:271-277.
148. Ward, D. M., M. M. Bateson, R. Weller, and A. L. Ruff-Roberts. 1992. Ribosomal RNA analysis of microorganisms as they occur in nature. Adv. Microb. Ecol. 12:219-286.
149. Ward, D. M., J. Bauld, R. W. Castenholz, and B. K. Pierson. 1992. Modern phototrophic microbial mats: anoxygenic, intermittently oxygenic/anoxygenic, thermal, eukaryotic, and terrestrial, p. 309-324. In J. W. Schopf and C. Klein (ed.), The proterozoic biosphere - a multidisciplinary study. Cambridge University Press, Cambridge, England.
150. Ward, D. M., E. Beck, N. P. Revsbech, K. A. Sandbeck, and M. R. Winfrey. 1984. Decomposition of hot spring microbial mats, p. 191-214. In Y. Cohen, R. W. Castenholz, and H. O. Halvorson (ed.), Microbial mats: stromatolites. Alan R. Liss, New York, N.Y.
151. Ward, D. M., S. C. Brassell, and G. Eglinton. 1985. Archaebacterial lipids in hot-spring microbial mats. Nature 318:656-659.
152. Ward, D. M., and R. W. Castenholz. Cyanobacteria in geothermal habitats. In M. Potts and B. Whitton (ed.), Ecology of cyanobacteria, in press. Kluwer, Dordrecht, The Netherlands.
153. Ward, D. M., M. J. Ferris, and M. M. Bateson. 1997. Organization of native populations within hot spring microbial mat communities: need for a more ecological approach, p. 147-153. In M. T. Martins, M. I. Z. Sato, J. M. Tiedje, L. C. N. Hagler, J. Dobereiner, and P. S. Sanchez (ed.), Progress in microbial ecology. Proceedings of the Seventh International Symposium on Microbial Ecology. Brazilian Society for Microbiology/International Committee on Microbial Ecology, Sao Paulo, Brazil.
154. Ward, D. M., M. J. Ferris, S. C. Nold, M. M. Bateson, E. D. Kopczynski, and A. L. Ruff-Roberts. 1994. Species diversity in hot spring microbial mats as revealed by both molecular and enrichment culture approaches-relationship between biodiversity and community structure. NATO ASI Ser. G35:33-44.
155. Ward, D. M., S. Panke, K.-D. Klöppel, R. Christ, and H. Fredrickson. 1994. Complex polar lipids of a hot spring cyanobacterial mat and its cultivated inhabitants. Appl. Environ. Microbiol. 60:3358-3367.
156. Ward, D. M., C. M. Santegoeds, S. C. Nold, N. B. Ramsing, M. J. Ferris, and M. M. Bateson. 1997. Biodiversity within hot spring microbial mat communities: molecular monitoring of enrichment cultures. Antonie Leeu-wenhoek 71:143-150.
157. Ward, D. M., J. Shiea, Y. B. Zeng, G. Dobson, S. Brassell, and G. Eglinton. 1989. Lipid biochemical markers and the composition of microbial mats, p. 439-454. in Y. Cohen and E. Rosenberg (ed.), Microbial mats - physiological ecology of benthic microbial communities. American Society for Microbiology, Washington, D.C.
158. Ward, D. M., T. A. Tayne, K. L. Anderson, and M. M. Bateson. 1987. Community structure and interactions among community members in hot spring cyanobacterial mats. Symp. Soc. Gen. Microbiol. 41:179-210.
159. Ward, D. M., D. Weller, and M. M. Bateson. 1990. 16S rRNA sequences reveal uncultured inhabitants of a well-studied thermal community. FEMS Microbiol. Rev. 75:105-116.
160. Ward, D. M., R. Weller, and M. M. Bateson. 1990. 16S rRNA sequences reveal numerous uncultured microorganisms in a natural community. Nature 344:63-65.
161. Ward, D. M., R. Weller, J. Shiea, R. W. Castenholz, and Y. Cohen. 1989. Hot spring microbial mats: anoxygenic and oxygenic mats of possible evolutionary significance, p. 3-15. In Y. Cohen and E. Rosenberg (ed.), Microbial mats - physiological ecology of benthic microbial communities. American Society for Microbiology, Washington, D.C.
162. Wayne, L. G., D. J. Brenner, R. R. Colwell, P. A. D. Grimont, O. Kandler, M. I. Krichevsky, L. H. Moore, W. E. C. Moore, R. G. E. Murray, E. Stackebrandt, M. P. Starr, and H. G. Trüper. 1987. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int. J. Syst. Bacteriol. 37:463-464.
163. Weller, R., M. M. Bateson, B. K. Heimbuch, E. D. Kopczynski, and D. M. Ward. 1992. Uncultivated cyanobacteria, Chloroflexus-like and spirochete-like inhabitants of a hot spring microbial mat. Appl. Environ. Microbiol. 58:3964-3969.
164. Weller, R., and D. M. Ward. 1989. Selective recovery of 16S rRNA sequences from natural microbial communities in the form of cDNA. Appl. Environ. Microbiol. 55:1818-1822.
165. Weller, R., J. W. Weller, and D. M. Ward. 1991. 16S rRNA sequences of uncultivated hot spring cyanobacterial mat inhabitants retrieved as randomly primed cDNA. Appl. Environ. Microbiol. 57:1146-1151.
166. Wiegel, J., M. Braun, and G. Gottschalk. 1981. Clostridium thermoautotrophicum species novum, a thermophile producing acetate from molecular hydrogen and carbon dioxide. Curr. Microbiol. 5:255-260.
167. Wiegel, J., and L. G. Ljungdahl. 1981. Thermoanaerobacter ethanolicus gen. nov., spec. nov., a new, extreme thermophilic, anaerobic bacterium. Arch. Microbiol. 128:343-348.
168. Wiegel, J., L. G. Ljungdahl, and J. R. Rawson. 1979. Isolation from soil and properties of the extreme thermophile Clostridium thermohydrosulfuricum. J. Bacteriol. 139:800-810.
169. Wilmotte, A. 1994. Molecular evolution and taxonomy of the cyanobacteria, p. 1-25. In D. A. Bryant (ed.), The molecular biology of cyanobacteria. Kluwer Academic Publishers, Dordrecht, The Netherlands.
170. Wilson, E. O. 1994. Naturalist. Warner Books, New York, N.Y.
171. Winogradsky, S. 1949. Microbiologie du sol, problèmes et méthodes. Masson et Cie, Paris, France.
172. Woese, C. R. 1987. Bacterial evolution. Microbiol. Rev. 51:221-271.
173. Woese, C. R. 1994. There must be a prokaryote somewhere: microbiology's search for itself. Microbiol. Rev. 58:1-9.
174. Zeikus, J. G., A. Ben-Bassat, and P. W. Hegge. 1980. Microbiology of methanogenesis in thermal, volcanic environments. J. Bacteriol. 143:432-440.
175. Zeikus, J. G., M. A. Dawson, T. E. Thompson, K. Ingvorsen, and E. C. Hatchikian. 1983. Microbial ecology of volcanic sulphidogenesis: isolation and characterization of Thermodesulfobacterium commune gen. nov. and sp. nov. J. Gen. Microbiol. 129:1159-1169.
176. Zeikus, J. G., P. W. Hegge, and M. A. Anderson. 1979. Thermoanaerobium brockii gen. nov. and sp. nov., a new chemoorganotrophic, caldoactive, anaerobic bacterium. Arch. Microbiol. 122:41-48.
177. Zeng, Y. B., D. M. Ward, S. C. Brassell, and G. Eglinton. 1992. Biogeochemistry of hot spring environments. 2. Lipid compositions of Yellowstone (Wyoming, U.S.A.) cyanobacterial and Chloroflexus mats. Chem. Geol. 95:327-345.
178. Zeng, Y. B., D. M. Ward, S. C. Brassell, and G. Eglinton. 1992. Biogechemistry of hot spring environments. 3. Apolar and polar lipids in the