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PMID: 12089000 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

Analysis of bacterial community composition by oligonucleotide fingerprinting of rRNA genes.

Applied and environmental microbiology ·Vol. 68 ·No. 7 ·2002-07-00 ·Pages 3243-50

Valinsky L, Della Vedova G, Scupham AJ, Alvey S, Figueroa A, Yin B, Hartin RJ, Chrobak M, Crowley DE, Jiang T, Borneman J

Abstract

One of the first steps in characterizing an ecosystem is to describe the organisms inhabiting it. For microbial studies, experimental limitations have hindered the ability to depict diverse communities. Here we describe oligonucleotide fingerprinting of rRNA genes (OFRG), a method that permits identification of arrayed rRNA genes (rDNA) through a series of hybridization experiments using small DNA probes. To demonstrate this strategy, we examined the bacteria inhabiting two different soils. Analysis of 1,536 rDNA clones revealed 766 clusters grouped into five major taxa: Bacillus, Actinobacteria, Proteobacteria, and two undefined assemblages. Soil-specific taxa were identified and then independently confirmed through cluster-specific PCR of the original soil DNA. Near-species-level resolution was obtained by this analysis as clones with average sequence identities of 97% were grouped in the same cluster. A comparison of these OFRG results with the results obtained in a denaturing gradient gel electrophoresis analysis of the same two soils demonstrated the significance of this methodological advance. OFRG provides a cost-effective means to extensively analyze microbial communities and should have applications in medicine, biotechnology, and ecosystem studies.

MeSH Terms
Bacteria/classification,genetics DNA Fingerprinting DNA, Bacterial/analysis Molecular Sequence Data Phylogeny RNA, Ribosomal/genetics
Chemicals
DNA, Bacterial RNA, Ribosomal
Authors & Affiliations
11 authors, click to expand affiliations / ORCID
Valinsky Lea
Department of Plant Pathology. Department of Environmental Sciences, University of California, Riverside, CA 92521, USA.
Della Vedova Gianluca
Scupham Alexandra J
Alvey Sam
Figueroa Andres
Yin Bei
Hartin R Jack
Chrobak Marek
Crowley David E
Jiang Tao
Borneman James
References (26)
26 references, click to expand
  1. Molecular microbial diversity of an agricultural soil in Wisconsin.
    Appl Environ Microbiol. 1996 Jun;62(6):1935-43 PMID: 8787391
  2. A nested array of rRNA targeted probes for the detection and identification of enterococci by reverse hybridization.
    Syst Appl Microbiol. 2000 Dec;23(4):563-72 PMID: 11249027
  3. High diversity in DNA of soil bacteria.
    Appl Environ Microbiol. 1990 Mar;56(3):782-7 PMID: 2317046
  4. Probe selection algorithms with applications in the analysis of microbial communities.
    Bioinformatics. 2001;17 Suppl 1:S39-48 PMID: 11472991
  5. Gene-representing cDNA clusters defined by hybridization of 57,419 clones from infant brain libraries with short oligonucleotide probes.
    Genomics. 1996 Oct 1;37(1):29-40 PMID: 8921367
  6. Genetic diversity in Sargasso Sea bacterioplankton.
    Nature. 1990 May 3;345(6270):60-3 PMID: 2330053
  7. Phylogenetic structure of the prokaryotic domain: the primary kingdoms.
    Proc Natl Acad Sci U S A. 1977 Nov;74(11):5088-90 PMID: 270744
  8. Remarkable archaeal diversity detected in a Yellowstone National Park hot spring environment.
    Proc Natl Acad Sci U S A. 1994 Mar 1;91(5):1609-13 PMID: 7510403
  9. Biological Suppression and Natural Population Decline of Heterodera schachtii in a California Field.
    Phytopathology. 1999 May;89(5):434-40 PMID: 18944757
  10. Phylogenetic identification and in situ detection of individual microbial cells without cultivation.
    Microbiol Rev. 1995 Mar;59(1):143-69 PMID: 7535888
  11. Oligonucleotide microchips as genosensors for determinative and environmental studies in microbiology.
    Appl Environ Microbiol. 1997 Jun;63(6):2397-402 PMID: 9172361
  12. Reliable hybridization of oligonucleotides as short as six nucleotides.
    DNA Cell Biol. 1990 Sep;9(7):527-34 PMID: 2222813
  13. Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA.
    Appl Environ Microbiol. 1997 Nov;63(11):4516-22 PMID: 9361437
  14. A molecular view of microbial diversity and the biosphere.
    Science. 1997 May 2;276(5313):734-40 PMID: 9115194
  15. Optimization by simulated annealing.
    Science. 1983 May 13;220(4598):671-80 PMID: 17813860
  16. Rhizosphere microbial community structure in relation to root location and plant iron nutritional status.
    Appl Environ Microbiol. 2000 Jan;66(1):345-51 PMID: 10618246
  17. Molecular microbial diversity in soils from eastern Amazonia: evidence for unusual microorganisms and microbial population shifts associated with deforestation.
    Appl Environ Microbiol. 1997 Jul;63(7):2647-53 PMID: 9212415
  18. Direct detection of 16S rRNA in soil extracts by using oligonucleotide microarrays.
    Appl Environ Microbiol. 2001 Oct;67(10):4708-16 PMID: 11571176
  19. Single-base-pair discrimination of terminal mismatches by using oligonucleotide microarrays and neural network analyses.
    Appl Environ Microbiol. 2002 Jan;68(1):235-44 PMID: 11772632
  20. cDNA screening by array hybridization.
    Methods Enzymol. 1999;303:165-78 PMID: 10349645
  21. Application of sequence-specific labeled 16S rRNA gene oligonucleotide probes for genetic profiling of cyanobacterial abundance and diversity by array hybridization.
    Appl Environ Microbiol. 2000 Sep;66(9):4004-11 PMID: 10966421
  22. Conservation of primary structure in 16S ribosomal RNA.
    Nature. 1975 Mar 6;254(5495):83-6 PMID: 1089909
  23. Hybridization analyses of arrayed cDNA libraries.
    Trends Genet. 1991 Oct;7(10):314-7 PMID: 1781028
  24. Phylogenetic measurement in procaryotes by primary structural characterization.
    J Mol Evol. 1972 Jun;1(2):173-84 PMID: 24173440
  25. 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
  26. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya.
    Proc Natl Acad Sci U S A. 1990 Jun;87(12):4576-9 PMID: 2112744
Article Info
Journal
Applied and environmental microbiology
Abbr.
Appl Environ Microbiol
ISSN
0099-2240
DOI
10.1128/AEM.68.7.3243-3250.2002
Published
2002-07-00
Pages
3243-50
Language
English
Region
United States
NLM ID
7605801
PMCID
PMC126790
Subset
IM
Databases
GENBANK
AF423203, AF423204, AF423205, AF423209, AF423216, AF423219, AF423220, AF423222, AF423223, AF423226, AF423227, AF423230, AF423232, AF423233, AF423237, AF423238, AF423240, AF423244, AF423246, AF423249, AF423250, AF423251, AF423253, AF423256, AF423258, AF423259, AF423260, AF423262, AF423270, AF423272, AF423277, AF423278, AF423281, AF423283, AF423284, AF423285, AF423288, AF423289, AF423290, AF423291, AF423295, AF423296, AF423298, AF423299, AF423304, AF423305, AF497759
External Links
PubMed source DOI: 10.1128/AEM.68.7.3243-3250.2002 PMC Full Text View journal details
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