Skip to main content
PMC home page
Applied and Environmental Microbiology logoLink to Applied and Environmental Microbiology
. 1991 Apr;57(4):1146–1151. doi: 10.1128/aem.57.4.1146-1151.1991

16S rRNA sequences of uncultivated hot spring cyanobacterial mat inhabitants retrieved as randomly primed cDNA.

R Weller 1, J W Weller 1, D M Ward 1
PMCID: PMC182859  PMID: 1711832

Abstract

Cloning and analysis of cDNAs synthesized from rRNAs is one approach to assess the species composition of natural microbial communities. In some earlier attempts to synthesize cDNA from 16S rRNA (16S rcDNA) from the Octopus Spring cyanobacterial mat, a dominance of short 16S rcDNAs was observed, which appear to have originated only from certain organisms. Priming of cDNA synthesis from small ribosomal subunit RNA with random deoxyhexanucleotides can retrieve longer sequences, more suitable for phylogenetic analysis. Here we report the retrieval of 16S rRNA sequences from three formerly uncultured community members. One sequence type, which was retrieved three times from a total of five sequences analyzed, can be placed in the cyanobacterial phylum. A second sequence type is related to 16S rRNAs from green nonsulfur bacteria. The third sequence type may represent a novel phylogenetic type.

Full text

PDF
1146

Images in this article

1147Image
on p.1147
1148Image
on p.1148

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Achenbach-Richter L., Gupta R., Stetter K. O., Woese C. R. Were the original eubacteria thermophiles? Syst Appl Microbiol. 1987;9:34–39. doi: 10.1016/s0723-2020(87)80053-x. [DOI] [PubMed] [Google Scholar]
  2. Brosius J., Palmer M. L., Kennedy P. J., Noller H. F. Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia coli. Proc Natl Acad Sci U S A. 1978 Oct;75(10):4801–4805. doi: 10.1073/pnas.75.10.4801. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. DeLong E. F., Wickham G. S., Pace N. R. Phylogenetic stains: ribosomal RNA-based probes for the identification of single cells. Science. 1989 Mar 10;243(4896):1360–1363. doi: 10.1126/science.2466341. [DOI] [PubMed] [Google Scholar]
  4. Doemel W. N., Brock T. D. Structure, growth, and decomposition of laminated algal-bacterial mats in alkaline hot springs. Appl Environ Microbiol. 1977 Oct;34(4):433–452. doi: 10.1128/aem.34.4.433-452.1977. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Doolittle W. F. Postmaturational cleavage of 23s ribosomal ribonucleic acid and its metabolic control in the blue-green alga Anacystis nidulans. J Bacteriol. 1973 Mar;113(3):1256–1263. doi: 10.1128/jb.113.3.1256-1263.1973. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Embley T. M., Smida J., Stackebrandt E. Reverse transcriptase sequencing of 16S ribosomal RNA from Faenia rectivirgula, Pseudonocardia thermophila and Saccharopolyspora hirsuta, three wall type IV actinomycetes which lack mycolic acids. J Gen Microbiol. 1988 Apr;134(4):961–966. doi: 10.1099/00221287-134-4-961. [DOI] [PubMed] [Google Scholar]
  7. Giovannoni S. J., Britschgi T. B., Moyer C. L., Field K. G. Genetic diversity in Sargasso Sea bacterioplankton. Nature. 1990 May 3;345(6270):60–63. doi: 10.1038/345060a0. [DOI] [PubMed] [Google Scholar]
  8. Green C. J., Stewart G. C., Hollis M. A., Vold B. S., Bott K. F. Nucleotide sequence of the Bacillus subtilis ribosomal RNA operon, rrnB. Gene. 1985;37(1-3):261–266. doi: 10.1016/0378-1119(85)90281-1. [DOI] [PubMed] [Google Scholar]
  9. Gutell R. R., Weiser B., Woese C. R., Noller H. F. Comparative anatomy of 16-S-like ribosomal RNA. Prog Nucleic Acid Res Mol Biol. 1985;32:155–216. doi: 10.1016/s0079-6603(08)60348-7. [DOI] [PubMed] [Google Scholar]
  10. Lane D. J., Pace B., Olsen G. J., Stahl D. A., Sogin M. L., Pace N. R. Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. Proc Natl Acad Sci U S A. 1985 Oct;82(20):6955–6959. doi: 10.1073/pnas.82.20.6955. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Marrs B., Kaplan S. 23 s precursor ribosomal RNA of Rhodopseudomonas spheroides. J Mol Biol. 1970 Apr 28;49(2):297–317. doi: 10.1016/0022-2836(70)90247-0. [DOI] [PubMed] [Google Scholar]
  12. Olsen G. J. Earliest phylogenetic branchings: comparing rRNA-based evolutionary trees inferred with various techniques. Cold Spring Harb Symp Quant Biol. 1987;52:825–837. doi: 10.1101/sqb.1987.052.01.090. [DOI] [PubMed] [Google Scholar]
  13. Olsen G. J. Phylogenetic analysis using ribosomal RNA. Methods Enzymol. 1988;164:793–812. doi: 10.1016/s0076-6879(88)64084-5. [DOI] [PubMed] [Google Scholar]
  14. Oyaizu H., Debrunner-Vossbrinck B., Mandelco L., Studier J. A., Woese C. R. The green non-sulfur bacteria: a deep branching in the eubacterial line of descent. Syst Appl Microbiol. 1987;9:47–53. doi: 10.1016/s0723-2020(87)80055-3. [DOI] [PubMed] [Google Scholar]
  15. Tapprich W. E., Hill W. E. Involvement of bases 787-795 of Escherichia coli 16S ribosomal RNA in ribosomal subunit association. Proc Natl Acad Sci U S A. 1986 Feb;83(3):556–560. doi: 10.1073/pnas.83.3.556. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Tomioka N., Sugiura M. The complete nucleotide sequence of a 16S ribosomal RNA gene from a blue-green alga, Anacystis nidulans. Mol Gen Genet. 1983;191(1):46–50. doi: 10.1007/BF00330888. [DOI] [PubMed] [Google Scholar]
  17. Ward D. M., Weller R., Bateson M. M. 16S rRNA sequences reveal numerous uncultured microorganisms in a natural community. Nature. 1990 May 3;345(6270):63–65. doi: 10.1038/345063a0. [DOI] [PubMed] [Google Scholar]
  18. Ward D. M., Weller R., Bateson M. M. 16S rRNA sequences reveal uncultured inhabitants of a well-studied thermal community. FEMS Microbiol Rev. 1990 Jun;6(2-3):105–115. doi: 10.1111/j.1574-6968.1990.tb04088.x. [DOI] [PubMed] [Google Scholar]
  19. Weisburg W. G., Giovannoni S. J., Woese C. R. The Deinococcus-Thermus phylum and the effect of rRNA composition on phylogenetic tree construction. Syst Appl Microbiol. 1989;11:128–134. doi: 10.1016/s0723-2020(89)80051-7. [DOI] [PubMed] [Google Scholar]
  20. Weisburg W. G., Oyaizu Y., Oyaizu H., Woese C. R. Natural relationship between bacteroides and flavobacteria. J Bacteriol. 1985 Oct;164(1):230–236. doi: 10.1128/jb.164.1.230-236.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Weller R., Ward D. M. Selective Recovery of 16S rRNA Sequences from Natural Microbial Communities in the Form of cDNA. Appl Environ Microbiol. 1989 Jul;55(7):1818–1822. doi: 10.1128/aem.55.7.1818-1822.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Woese C. R. Bacterial evolution. Microbiol Rev. 1987 Jun;51(2):221–271. doi: 10.1128/mr.51.2.221-271.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Woese C. R., Stackebrandt E., Macke T. J., Fox G. E. A phylogenetic definition of the major eubacterial taxa. Syst Appl Microbiol. 1985;6:143–151. doi: 10.1016/s0723-2020(85)80047-3. [DOI] [PubMed] [Google Scholar]
  24. Yang D., Oyaizu Y., Oyaizu H., Olsen G. J., Woese C. R. Mitochondrial origins. Proc Natl Acad Sci U S A. 1985 Jul;82(13):4443–4447. doi: 10.1073/pnas.82.13.4443. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. de la Cruz V. F., Lake J. A., Simpson A. M., Simpson L. A minimal ribosomal RNA: sequence and secondary structure of the 9S kinetoplast ribosomal RNA from Leishmania tarentolae. Proc Natl Acad Sci U S A. 1985 Mar;82(5):1401–1405. doi: 10.1073/pnas.82.5.1401. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Applied and Environmental Microbiology are provided here courtesy of American Society for Microbiology (ASM)

RESOURCES

pFad - Phonifier reborn

Pfad - The Proxy pFad of © 2024 Garber Painting. All rights reserved.

Note: This service is not intended for secure transactions such as banking, social media, email, or purchasing. Use at your own risk. We assume no liability whatsoever for broken pages.


Alternative Proxies:

Alternative Proxy

pFad Proxy

pFad v3 Proxy

pFad v4 Proxy