Photosynthetic and Phylogenetic Primers for Detection of Anoxygenic Phototrophs in Natural Environments

Applied and Environmental Microbiology

Volumn 67, Issue 7, 2001, Pages 2922-2926

  Achenbach, Laurie A ^a   Carey, Jennifer ^a,b   Madigan, Michael T ^a  

^a SOUTHERN ILLINOIS UNIVERSITY   (United States)

^b VANDERBILT UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; BACTERIAL PROTEIN; PRIMER DNA; PUFM PROTEIN, BACTERIA; RIBOSOME DNA; RNA 16S;

ANAEROBIC GROWTH; ARTICLE; BACTERIUM; CHLOROBI; GENETICS; ISOLATION AND PURIFICATION; METHODOLOGY; PHOTOSYNTHESIS; PHYLOGENY; POLYACRYLAMIDE GEL ELECTROPHORESIS; POLYMERASE CHAIN REACTION; RNA GENE;

ANAEROBIOSIS; BACTERIA; BACTERIAL PROTEINS; CHLOROBI; DNA PRIMERS; DNA, BACTERIAL; DNA, RIBOSOMAL; ELECTROPHORESIS, POLYACRYLAMIDE GEL; GENES, RRNA; PHOTOSYNTHESIS; PHOTOSYNTHETIC REACTION CENTER COMPLEX PROTEINS; PHYLOGENY; POLYMERASE CHAIN REACTION; RNA, RIBOSOMAL, 16S;

EID: 0035403872     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.67.7.2922-2926.2001     Document Type: Article

References (37)

1. Amann, R. I., W. Ludwig, and K. Schileifer. 1995. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59:143-169.
2. Benson, D. A., I. Karsch-Mizrachi, D. J. Lipman, J. Ostell, B. A. Rapp, and D. L. Wheeler. 2000. GenBank. Nucleic Acids Res. 28:8-15.
3. Bryantseva, I. A., V. M. Gorlenko, E. I. Kompantseva, L. A. Achenbach, and M. T. Madigan. 1999. Heliorestis daurensis gen. nov. sp. nov., an alkaliphilic coiled to rod-shaped phototrophic heliobacterium from an alkaline Siberian soda lake. Arch. Microbiol. 172:167-174.
4. Cahill, A. D., and J. F. Stolz. 1995. Polyclonal antibodies to chlorosome proteins as probes for green sulfur bacteria. Appl. Environ. Microbiol. 61: 784-787.
5. Casamayor, E. O., J. I. Calderén-Paz, J. Mas, and C. Pedrós-Alió. 1998. Identification of phototrophic sulfur bacteria through the analysis of 1mwRNA band patterns. Arch. Microbiol. 170:269-278.
6. Casamayor, E. O., H. Schäfer, L. Bañeras, C. Pedrós-Alió, and G. Muyzer. 2000. Identification of and spatio-temporal differences between microbial assemblages from two neighboring sulfurons lakes: comparison by microscopy and denaturing gradient gel electrophoresis. Appl. Environ. Microbiol. 66:499-508.
7. 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.
8. Coolen, M. J. L., and J. Overmann. 1998. Analysis of subfossil molecular remains of purple sulfur bacteria in a lake sediment. Appl. Environ. Microbiol. 64:4513-4521.
9. Corson, G. E., K. V. P. Nagashima, K. Matsuura, Y. Sakuragi, R. Wettasinghe, H. Qin, R. Allen, and D. B. Knaff. 1999. Genes encoding light-harvesting and reaction center proteins from Chromatium vinosum. Photosyn. Res. 59:39-52.
10. Fröstl, J. M., and J. Overmann. 2000. Phylogenetic affiliation of the bacteria that constitute phototrophic consortia. Arch. Microbiol. 174:50-58.
11. Gilbert, D. G. 1993. SeqApp, 1.9a157 ed. Biocomputing Office, Biology Dept., Indiana University, Bloomington.
12. 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.
13. Gordon, D. A., J. Priscu, and S. Giovannoni. 2000. Origin and phylogeny of microbes living in permanent Antarctic lake ice. Microb. Ecol. 39:197-202.
14. Imhoff, J. F. 1995. Taxonomy and physiology of phototrophic purple bacteria and green sulfur bacteria, p. 1-15. In R. E. Blakenship, M. T. Madigan, and C. E. Bauer (ed.), Anoxygenic photosynthetic bacteria. Kluwer Academic Publishers, Dordrecht, The Netherlands.
15. 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.
16. Madigan, M. T. 1988. Microbiology, physiology, and ecology of phototrophic bacteria, p. 39-111. In A. J. B. Zehner (ed.), Biology of anaerobic microorganisms. John Wiley & Sons, New York, N.Y.
17. Madigan, M. T. 1995. Microbiology of nitrogen fixation in photosynthetic bacteria, p. 915-928. In R. E. Blankenship, M. T. Madigan, and C. E. Bauer (ed.), Anoxygenic photosynthetic bacteria. Kluwer Academic Publishers, Dordrecht, The Netherlands.
18. Madigan, M. T. 2000. The family Heliobacteriaceae, p. 615-620. In G. Garrity (ed.), Bergey's manual of systematic bacteriology, vol. 1. Springer, New York, N.Y.
19. Madigan, M. T., and J. G. Ormerod. 1995. Taxonomy, physiology and ecology of heliobacteria, p. 17-30. In R. E. Blankenship, M. T. Madigan, and C. E. Bauer (ed.), Anoxygenic photosynthetic bacteria. Kluwer Academic Publishers, Dordrecht, The Netherlands.
20. Maidak, B. L., J. R. Cole, C. T. Parker, G. M. Garrity, N. Larsen, B. Li, T. G. Lilburn, M. J. McCaughey, G. J. Olsen, R. Overbeek, S. Pramanik, T. M. Schmidt, J. M. Tiedje, and C. R. Woese. 1999. A new version of the RDP (Ribosomal Database Project). Nucleic Acids Res. 27:171-173.
21. Muyzer, G., E. C. der 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.
22. Myers, R. M., T. Maniatis, and L. S. Lerman. 1987. Detection and localization of single base changes by denaturing gradient gel electrophoresis. Methods Enzymol. 155:501-527.
23. Nagashima, K. V. P., A. Hiraishi, K. Shimada, and K. Matsuura. 1997. Horizontal transfer of genes coding for the photosynthetic reaction centers of purple bacteria. J. Mol. Evol. 45:131-136.
24. Overmann, J., M. J. L. Coolen, and C. Tuschak. 1999. Specific detection of different phylogenetic groups of chemocline bacteria based on PCR and denaturing gradient gel electrophoresis of 16S rRNA gene fragments. Arch. Microbiol. 172:83-94.
25. Overmann, J., and C. Tuschak. 1997. Phylogeny and molecular fingerprinting of green sulfur bacteria. Arch. Microbiol. 167:302-309.
26. Øvreås, L., L. Forney, F. L. Daae, and V. Torsvik. 1997. Distribution of bacterioplankton in meromictic Lake Sælenvannet, as determined by denaturing gradient gel electrophoresis of PCR-amplified gene fragments coding for 16S rRNA. Appl. Environ. Microbiol. 63:3367-3373.
27. Pfennig, N. 1989. Ecology of phototrophic purple and green sulfur bacteria, p. 81-96. In H. G. Schlegel and B. Bowien (ed.). Autotrophic bacteria. Springer-Verlag, New York, N.Y.
28. Pierson, B. K., and R. W. Castenholz. 1995. Taxonomy and physiology of filamentous anoxygenic phototrophs, p. 31-47. In R. E. Blakenship, M. T. Madigan, and C. E. Bauer (ed.), Anoxygenic photosynthetic bacteria. Kluwer Academic Publishers, Dordrecht, The Netherlands.
29. Pierson, B. K., and J. M. Olson. 1987. Photosynthetic bacteria, p. 21-42. In J. Amesz (ed.), Photosynthesis. Elsevier Science Publishers, B.V. Amsterdam, The Netherlands.
30. Skirnisdottir, S., G. O. Hreggvidsson, S. Hjorleifsdottir, V. T. Marteinsson, S. K. Petursdottir, O. Holst, and J. K. Kristjansson. 2000. Influence of sulfide and temperature on species composition and community structure of hot spring microbial mats. Appl. Environ. Microbiol. 66:2835-2841.
31. Trüper, H. G., and N. Pfennig. 1981. Characterization and identification of the anoxygenic phototrophic bacteria, p. 299-312. In M. P. Starr, H. Stolp, H. G. Trüper, A. Balows, and H. G. Schlegel (ed.), The prokaryotes. Springer-Verlag, New York, N.Y.
32. Tuschak, C., J. Glaeser, and J. Overmann. 1999. Specific detection of green sulfur bacteria by in situ hybridization with a fluorescently labeled oligonucleotide probe. Arch. Microbiol. 171:265-272.
33. Van Gemerden, H., and H. H. Beeftink. 1983. Ecology of phototrophic bacteria, p. 146-185. In J. G. Ormerod (ed.), The phototrophic bacteria. University of California Press, Berkeley.
34. Wahlund, T., R. W. Castenholz, C. R. Woese, and M. T. Madigan. 1991. A thermophilic green sulfur bacterium from New Zealand hot springs. Chlorobium tepidum, nov. sp. Arch. Microbiol. 156:81-91.
35. Watanabe, Y., R. G. Feick, and J. A. Shiozawa. 1995. Cloning and sequencing of the genes encoding the light-harvesting B806-866 polypeptides and initial studies on the transcriptional organization of puf2B, puf2A and puf2C in Chloroflexus aurantiacus. Arch. Microbiol. 163:124-130.
36. Woese, C. R. 1992. Prokaryote systematics: the evolution of a science, p. 3-18. In A. Balows, H. G. Trüper. M. Dworkin, W. Harder, and K.-H. Schleifer (ed.), The prokaryotes, 2nd ed. Springer-Verlag, New York, N.Y.
37. Woese, C. R., L. Mandelco, D. Yang, R. Gherna, and M. T. Madigan. 1990. The case for relationship of the flavobacteria and their relatives to the green sulfur bacteria. Syst. Appl. Microbiol. 13:258-262.