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PMID: 9251225 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

PCR primers to amplify 16S rRNA genes from cyanobacteria.

Applied and environmental microbiology ·Vol. 63 ·No. 8 ·1997-08-00 ·Pages 3327-32

Nübel U, Garcia-Pichel F, Muyzer G

Abstract

We developed and tested a set of oligonucleotide primers for the specific amplification of 16S rRNA gene segments from cyanobacteria and plastids by PCR. PCR products were recovered from all cultures of cyanobacteria and diatoms that were checked but not from other bacteria and archaea. Gene segments selectively retrieved from cyanobacteria and diatoms in unialgal but nonaxenic cultures and from cyanobionts in lichens could be directly sequenced. In the context of growing sequence databases, this procedure allows rapid and phylogenetically meaningful identification without pure cultures or molecular cloning. We demonstrate the use of this specific PCR in combination with denaturing gradient gel electrophoresis to probe the diversity of oxygenic phototrophic microorganisms in cultures, lichens, and complex microbial communities.

MeSH Terms
Cyanobacteria/genetics DNA Primers/genetics Diatoms/genetics Lichens/genetics Molecular Sequence Data Oxygen/metabolism Plastids/genetics Polymerase Chain Reaction/methods RNA, Ribosomal, 16S/genetics Sensitivity and Specificity Symbiosis
Chemicals
DNA Primers RNA, Ribosomal, 16S Oxygen
Authors & Affiliations
3 authors, click to expand affiliations / ORCID
Nübel U
Max Planck Institute for Marine Microbiology, Bremen, Germany.
Garcia-Pichel F
Muyzer G
References (28)
28 references, click to expand
  1. Sequence heterogeneities of genes encoding 16S rRNAs in Paenibacillus polymyxa detected by temperature gradient gel electrophoresis.
    J Bacteriol. 1996 Oct;178(19):5636-43 PMID: 8824607
  2. Enrichment culture and microscopy conceal diverse thermophilic Synechococcus populations in a single hot spring microbial mat habitat.
    Appl Environ Microbiol. 1996 Mar;62(3):1045-50 PMID: 11536748
  3. Distribution of sulfate-reducing bacteria in a stratified fjord (Mariager Fjord, Denmark) as evaluated by most-probable-number counts and denaturing gradient gel electrophoresis of PCR-amplified ribosomal DNA fragments.
    Appl Environ Microbiol. 1996 Apr;62(4):1405-15 PMID: 8919802
  4. Cyanobacterial community structure as seen from RNA polymerase gene sequence analysis.
    Appl Environ Microbiol. 1994 Sep;60(9):3212-9 PMID: 7944363
  5. Phylogenetic relationships of Thiomicrospira species and their identification in deep-sea hydrothermal vent samples by denaturing gradient gel electrophoresis of 16S rDNA fragments.
    Arch Microbiol. 1995 Sep;164(3):165-72 PMID: 7545384
  6. How close is close: 16S rRNA sequence identity may not be sufficient to guarantee species identity.
    Int J Syst Bacteriol. 1992 Jan;42(1):166-70 PMID: 1371061
  7. Phylogenetic relationships of nonaxenic filamentous cyanobacterial strains based on 16S rRNA sequence analysis.
    J Mol Evol. 1996 Feb;42(2):194-200 PMID: 8919871
  8. Sequence-determined DNA separations.
    Annu Rev Biophys Bioeng. 1984;13:399-423 PMID: 6234857
  9. Biodiversity within hot spring microbial mat communities: molecular monitoring of enrichment cultures.
    Antonie Van Leeuwenhoek. 1997 Feb;71(1-2):143-50 PMID: 9049026
  10. The RDP (Ribosomal Database Project).
    Nucleic Acids Res. 1997 Jan 1;25(1):109-11 PMID: 9016515
  11. Identification and phylogenetic analysis of toxigenic cyanobacteria by multiplex randomly amplified polymorphic DNA PCR.
    Appl Environ Microbiol. 1995 Jun;61(6):2286-91 PMID: 16535049
  12. GenBank.
    Nucleic Acids Res. 1997 Jan 1;25(1):1-6 PMID: 9016491
  13. An early origin of plastids within the cyanobacterial divergence is suggested by evolutionary trees based on complete 16S rRNA sequences.
    Mol Biol Evol. 1995 Nov;12(6):1166-73 PMID: 8524048
  14. Gene organization and primary structure of a ribosomal RNA operon from Escherichia coli.
    J Mol Biol. 1981 May 15;148(2):107-27 PMID: 7028991
  15. Denaturing gradient gel electrophoresis profiles of 16S rRNA-defined populations inhabiting a hot spring microbial mat community.
    Appl Environ Microbiol. 1996 Feb;62(2):340-6 PMID: 8593039
  16. Genetic diversity and phylogeny of toxic cyanobacteria determined by DNA polymorphisms within the phycocyanin locus.
    Appl Environ Microbiol. 1995 Nov;61(11):3875-83 PMID: 8526499
  17. Basic local alignment search tool.
    J Mol Biol. 1990 Oct 5;215(3):403-10 PMID: 2231712
  18. Phenotypic and phylogenetic analyses show Microcoleus chthonoplastes to be a cosmopolitan cyanobacterium.
    Appl Environ Microbiol. 1996 Sep;62(9):3284-91 PMID: 8795218
  19. Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR.
    Appl Environ Microbiol. 1996 Feb;62(2):625-30 PMID: 8593063
  20. Differential amplification of rRNA genes by polymerase chain reaction.
    Appl Environ Microbiol. 1992 Oct;58(10):3417-8 PMID: 1280061
  21. Evolutionary relationships among eubacteria, cyanobacteria, and chloroplasts: evidence from the rpoC1 gene of Anabaena sp. strain PCC 7120.
    J Bacteriol. 1991 Jun;173(11):3446-55 PMID: 1904436
  22. A quantitative map of nucleotide substitution rates in bacterial rRNA.
    Nucleic Acids Res. 1996 Sep 1;24(17):3381-91 PMID: 8811093
  23. Use of polymerase chain reaction and electroporation of Escherichia coli to monitor the persistence of extracellular plasmid DNA introduced into natural soils.
    Appl Environ Microbiol. 1993 Oct;59(10):3438-46 PMID: 8250566
  24. Detection and characterization of cyanobacterial nifH genes.
    Appl Environ Microbiol. 1994 Mar;60(3):880-7 PMID: 8161180
  25. Attachment of a 40-base-pair G + C-rich sequence (GC-clamp) to genomic DNA fragments by the polymerase chain reaction results in improved detection of single-base changes.
    Proc Natl Acad Sci U S A. 1989 Jan;86(1):232-6 PMID: 2643100
  26. 16S rRNA sequences of uncultivated hot spring cyanobacterial mat inhabitants retrieved as randomly primed cDNA.
    Appl Environ Microbiol. 1991 Apr;57(4):1146-51 PMID: 1711832
  27. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA.
    Appl Environ Microbiol. 1993 Mar;59(3):695-700 PMID: 7683183
  28. Characterization of toxin-producing cyanobacteria by using an oligonucleotide probe containing a tandemly repeated heptamer.
    J Bacteriol. 1995 Oct;177(20):6021-6 PMID: 7592362
Article Info
Journal
Applied and environmental microbiology
Abbr.
Appl Environ Microbiol
ISSN
0099-2240
DOI
10.1128/aem.63.8.3327-3332.1997
Published
1997-08-00
Pages
3327-32
Language
English
Region
United States
NLM ID
7605801
PMCID
PMC168636
Subset
IM
Databases
GENBANK
AJ000708, AJ000709, AJ000710, AJ000711, AJ000712, AJ000713, AJ000714, AJ000715, AJ000716, AJ000717, AJ000718, AJ000719, AJ000720, AJ000721, AJ000722, AJ000723, AJ000724, U96442, U96443, U96444, U96445, U96446
External Links
PubMed source DOI: 10.1128/aem.63.8.3327-3332.1997 PMC Full Text View journal details
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