Seasonal distributions of dominant 16S rRNA-defined populations in a hot spring microbial mat examined by denaturing gradient gel electrophoresis

Applied and Environmental Microbiology

Volumn 63, Issue 4, 1997, Pages 1375-1381

  Ferris, M J ^a   Ward, D M ^a  

^a MONTANA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIUM; CYANOBACTERIUM; DENATURING GRADIENT GEL ELECTROPHORESIS; NONHUMAN; POPULATION STRUCTURE; SEASONAL VARIATION; THERMAL SPRING;

BACTERIA (MICROORGANISMS); CYANOBACTERIA; OCTOPUS;

BACTERIA; CYANOBACTERIA; HOT SPRING; MICROBIAL MAT; SEASONALITY; SPATIAL DISTRIBUTION; THERMAL GRADIENT;

USA, WYOMING, YELLOWSTONE NATIONAL PARK, OCTOPUS SPRING;

EID: 0030613348     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/aem.63.4.1375-1381.1997     Document Type: Article

References (47)

1. Abrams, E. S., S. E. Murdaugh, and L. S. Lerman. 1990. Comprehensive detection of single hase changes in human genomic DNA using denaturing gradient gel electrophoresis and a GC clamp. Genomics 7:463-475.
2. Abrams, E. S., and V. P. Stanton. 1992. Use of denaturing gradient gel electrophoresis to study conformational transitions in nucleic acids. Methods Enzymol. 212:71-104.
3. 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.
4. Bauld, J., and T. D. Brock. 1973. Ecological studies Chloroflexus, a gliding photosynthetic bacterium. Arch. Microbiol. 92:267-284.
5. Begon, M., J. L. Harper, and C. R. Townsend. 1990. Ecology: individuals, populations, and communities, 2nd ed. Blackwell Scientific Publications, Boston, Mass.
6. Borneman, J., P. W. Skroch, 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.
7. Brock, T. D. 1967. Microorganisms adapted to high temperatures Nature 214:882-885.
8. Brock, T. D., and M. L. Brock. 1968. Relationship between environmental temperature and optimum temperature of bacteria along a hot sprine thermal gradient. J. Appl. Bacteriol. 31:54-58.
9. 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-ereen algae. Blackwell Scientific Publications Ltd., Oxford, United Kingdom.
10. Castenholz, R. W. 1981. Isolation and cultivation of thermophilic cyanobacteria, p. 236-246. In M. P. Starr, H. Stolp, H. G. Trüper, A. Balows, and H. G. Schlegel (ed.), The prokaryotes. Springer-Verlag KG, Berlin, Germany.
11. Castenholz, R. W., and J. B. Waterbury. 1989. Oxygenic photosynthetic bacteria, p. 1710-1806. In J. T. Staley, M. P. Bryant, N. Pfennig, and J. G. Holt (ed.), Bergey's manual of systematic bacteriology, vol. 3. The Williams & Wilkins Co., Baltimore, Md.
12. 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.
13. Delwart, E. L., E. G. Shpaer, and J. I. Mullins. 1995. Heteroduplex mobility assays for phylogenetic analysis, p. 154-160. In M. A. Innis, D. H. Gelfand, and J. J. Sninsky (ed.), PCR strategies. Academic Press, Inc., San Diego, Calif.
14. 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.
15. Fernandez, E., T. Bienvenu, F. D. Arramond, K. Beldjord, J. C. Kaplan, and C. Beldjord. 1993. Use of chemical clamps in denaturing gradient gel electrophoresis: application in the detection of the most frequent Mediterranean beta-thalassemic mutations. PCR Methods Applic. 3:122-124.
16. 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.
17. 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.
18. Field, K. G., D. Gordon, T. Wright, M. Rappe, 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.
19. Futuyma, D. J. 1986. Evolutionary biology, 2nd ed. Sinauer Assoc., Inc., Sunderland, Mass.
20. Lessa, E. P. 1992. Rapid surveying of DNA sequence variation in natural populations. Mol. Biol. Evol. 9:323-330.
21. 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. Bacteriol. 174:5072-5078.
22. Madigan, M. T., and T. D. Brock. 1977. Adaptation by hot spring phototrophs to reduced light intensities. Arch. Microbiol. 113:111-120.
23. Maniatis, T., E. F. Fritsch, and J. Sambrook. 1982. Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
24. Mayr, E. 1982. The growth of biological thought: diversity, evolution and inheritance. Harvard University Press, Cambridge, Mass.
25. 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.
26. 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.
27. Nubel, U., B. Engelen, A. Felske, J. Snaidr, A. Wreshuber, R. I. Amann, and W. Ludwig. 1996. Sequence heterogeneities of genes encoding 16S rRNAs in Paenibacillus polymyxa detected by temperature gradient gel electrophoresis. J. Bacteriol. 178:5636-5643.
28. Peary, J. A., and R. W. Castenholz. 1964. Temperature strains of a thermophilic blue-green alga. Nature 202:720-721.
29. Rainey, F. A., N. L. Ward-Rainey, and E. Stackebrandt. 1996. Clostridium paradoxum DSM 7308T contains multiple 16S rRNA genes with heterogeneous intervening sequences. Microbiology 142:2087-2091.
30. Ramsing, N. B. and D. M. Ward. 1996. Unpublished results.
31. Ramsing, N. B., M. J. Ferris, and D. M. Ward. Light-induced motility of thermophilic Synechococcus isolates from Octopus Spring, Yellowstone National Park. Submitted for publication.
32. 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.
33. Ruff-Roberts, A. L., G. J. 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.
34. 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.
35. Sheridan, R. P. 1976. Sun-shade ecotypes of a bluegreen alga in a hot spring. J. Phycol. 12:279-285.
36. Sheridan, R. P. 1979. Seasonal variation in sun-shade ecotypes of Plectonema notatum (cyanophyta). J. Phycol. 15:223-226.
37. 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.
38. 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.
39. 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.
40. 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.
41. Ward, D. M., M. J. Ferris, and M. M. Bateson. Organization of native populations within hot spring microbial mat communities: need for a more ecological approach. In Proceedings of the 7th Symposium of the International Society for Microbial Ecology, Santos, Brazil, September 1995, in press.
42. 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, p. 33-44. In L. J. Stal and P. Caumette (ed.), Microbial mats: structure, development and environmental significance. Springer-Verlag KG, Berlin, Germany.
43. 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 Leeuwenhoek 71:143-150.
44. Ward, D. M., R. Weller, and M. M. Bateson. 1990. 16S rRNA sequences reveal uncultured inhabitants of a well-studied thermal community. FEMS Microbiol. Rev. 75:105-116.
45. Ward, D. M., R. Weller, and M. M. Bateson. 1990. 16S rRNA sequences reveal numerous uncultured microorganisms in a natural community. Nature 345:63-65.
46. Weller, R., M. M. Bateson, B. K. Heimbuch, E. D. Kopczynski, and D. M. Ward. 1992. Uncultivated cyanobacteria. Chloroflexus-like inhabitants, and spirochete-like inhabitants of a hot spring microbial mat. Appl. Environ. Microbiol. 58:3964-3969.
47. Weller, R., J. W. Weller, and D. M. Ward. 1991. 16S rRNA sequences of uncultivated hot spring cyanohacterial mat inhabitants retrieved as randomly primed cDNA. Appl. Environ. Microbiol. 57:1146-1151.