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Appl Environ Microbiol. Nov 1997; 63(11): 4485–4493.
PMCID: PMC168767

Biodiversity of a Burkholderia cepacia population isolated from the maize rhizosphere at different plant growth stages.


A Burkholderia cepacia population naturally occurring in the rhizosphere of Zea mays was investigated in order to assess the degree of root association and microbial biodiversity at five stages of plant growth. The bacterial strains isolated on semiselective PCAT medium were mostly assigned to the species B. cepacia by an analysis of the restriction patterns produced by amplified DNA coding for 16S rRNA (16S rDNA) (ARDRA) with the enzyme AluI. Partial 16S rDNA nucleotide sequences of some randomly chosen isolates confirmed the ARDRA results. Throughout the study, B. cepacia was strictly associated with maize roots, ranging from 0.6 to 3.6% of the total cultivable microflora. Biodiversity among 83 B. cepacia isolates was analyzed by the random amplified polymorphic DNA (RAPD) technique with two 10-mer primers. An analysis of RAPD patterns by the analysis of molecular variance method revealed a high level of intraspecific genetic diversity in this B. cepacia population. Moreover, the genetic diversity was related to divergences among maize root samplings, with microbial genetic variability markedly higher in the first stages of plant growth; in other words, the biodiversity of this rhizosphere bacterial population decreased over time.

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  • Bevivino A, Tabacchioni S, Chiarini L, Carusi MV, Del Gallo M, Visca P. Phenotypic comparison between rhizosphere and clinical isolates of Burkholderia cepacia. Microbiology. 1994 May;140(Pt 5):1069–1077. [PubMed]
  • Caugant DA, Levin BR, Selander RK. Genetic diversity and temporal variation in the E. coli population of a human host. Genetics. 1981 Jul;98(3):467–490. [PMC free article] [PubMed]
  • de Bruijn FJ. Use of repetitive (repetitive extragenic palindromic and enterobacterial repetitive intergeneric consensus) sequences and the polymerase chain reaction to fingerprint the genomes of Rhizobium meliloti isolates and other soil bacteria. Appl Environ Microbiol. 1992 Jul;58(7):2180–2187. [PMC free article] [PubMed]
  • Canfield AE, Sutton AB, Hiscock DR, Gallagher JT, Schor AM. Alpha- and beta-xylosides modulate the synthesis of fibronectin and thrombospondin-1 by endothelial cells. Biochim Biophys Acta. 1994 Aug 18;1200(3):249–258. [PubMed]
  • De Leij F, Sutton EJ, Whipps JM, Fenlon JS, Lynch JM. Impact of Field Release of Genetically Modified Pseudomonas fluorescens on Indigenous Microbial Populations of Wheat. Appl Environ Microbiol. 1995 Sep;61(9):3443–3453. [PMC free article] [PubMed]
  • Deng S, Hiruki C, Robertson JA, Stemke GW. Detection by PCR and differentiation by restriction fragment length polymorphism of Acholeplasma, Spiroplasma, Mycoplasma, and Ureaplasma, based upon 16S rRNA genes. PCR Methods Appl. 1992 Feb;1(3):202–204. [PubMed]
  • Excoffier L, Smouse PE, Quattro JM. Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics. 1992 Jun;131(2):479–491. [PMC free article] [PubMed]
  • Fani R, Bandi C, Bardin MG, Comincini S, Damiani G, Grifoni A, Bazzicalupo M. RAPD fingerprinting is useful for identification of Azospirillum strains. Microb Releases. 1993 Mar;1(4):217–221. [PubMed]
  • Franklin FC, Williams PA. Construction of a partial diploid for the degradative pathway encoded by the TOL plasmid (pWWO) from Pseudomonas putida mt-2: evidence for the positive nature of the regulation by the xyIR gene. Mol Gen Genet. 1980 Jan;177(2):321–328. [PubMed]
  • Grifoni A, Bazzicalupo M, Di Serio C, Fancelli S, Fani R. Identification of Azospirillum strains by restriction fragment length polymorphism of the 16S rDNA and of the histidine operon. FEMS Microbiol Lett. 1995 Mar 15;127(1-2):85–91. [PubMed]
  • Gurtler V, Wilson VA, Mayall BC. Classification of medically important clostridia using restriction endonuclease site differences of PCR-amplified 16S rDNA. J Gen Microbiol. 1991 Nov;137(11):2673–2679. [PubMed]
  • Hadrys H, Balick M, Schierwater B. Applications of random amplified polymorphic DNA (RAPD) in molecular ecology. Mol Ecol. 1992 May;1(1):55–63. [PubMed]
  • Istock CA, Duncan KE, Ferguson N, Zhou X. Sexuality in a natural population of bacteria--Bacillus subtilis challenges the clonal paradigm. Mol Ecol. 1992 Aug;1(2):95–103. [PubMed]
  • Jayarao BM, Doré JJ, Jr, Oliver SP. Restriction fragment length polymorphism analysis of 16S ribosomal DNA of Streptococcus and Enterococcus species of bovine origin. J Clin Microbiol. 1992 Sep;30(9):2235–2240. [PMC free article] [PubMed]
  • Klingler JM, Stowe RP, Obenhuber DC, Groves TO, Mishra SK, Pierson DL. Evaluation of the Biolog automated microbial identification system. Appl Environ Microbiol. 1992 Jun;58(6):2089–2092. [PMC free article] [PubMed]
  • Kostman JR, Edlind TD, LiPuma JJ, Stull TL. Molecular epidemiology of Pseudomonas cepacia determined by polymerase chain reaction ribotyping. J Clin Microbiol. 1992 Aug;30(8):2084–2087. [PMC free article] [PubMed]
  • Lessie TG, Hendrickson W, Manning BD, Devereux R. Genomic complexity and plasticity of Burkholderia cepacia. FEMS Microbiol Lett. 1996 Nov 1;144(2-3):117–128. [PubMed]
  • Maidak BL, Olsen GJ, Larsen N, Overbeek R, McCaughey MJ, Woese CR. The RDP (Ribosomal Database Project). Nucleic Acids Res. 1997 Jan 1;25(1):109–111. [PMC free article] [PubMed]
  • Smith JM, Smith NH, O'Rourke M, Spratt BG. How clonal are bacteria? Proc Natl Acad Sci U S A. 1993 May 15;90(10):4384–4388. [PMC free article] [PubMed]
  • McArthur JV, Kovacic DA, Smith MH. Genetic diversity in natural populations of a soil bacterium across a landscape gradient. Proc Natl Acad Sci U S A. 1988 Dec;85(24):9621–9624. [PMC free article] [PubMed]
  • Paffetti D, Scotti C, Gnocchi S, Fancelli S, Bazzicalupo M. Genetic diversity of an Italian Rhizobium meliloti population from different Medicago sativa varieties. Appl Environ Microbiol. 1996 Jul;62(7):2279–2285. [PMC free article] [PubMed]
  • Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 1987 Jul;4(4):406–425. [PubMed]
  • Sanger F, Nicklen S, Coulson AR. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463–5467. [PMC free article] [PubMed]
  • Smith JJ, Offord LC, Holderness M, Saddler GS. Genetic diversity of Burkholderia solanacearum (synonym Pseudomonas solanacearum) race 3 in Kenya. Appl Environ Microbiol. 1995 Dec;61(12):4263–4268. [PMC free article] [PubMed]
  • Souza V, Eguiarte L, Avila G, Cappello R, Gallardo C, Montoya J, Piñero D. Genetic Structure of Rhizobium etli biovar phaseoli Associated with Wild and Cultivated Bean Plants (Phaseolus vulgaris and Phaseolus coccineus) in Morelos, Mexico. Appl Environ Microbiol. 1994 Apr;60(4):1260–1268. [PMC free article] [PubMed]
  • Tabacchioni S, Visca P, Chiarini L, Bevivino A, Di Serio C, Fancelli S, Fani R. Molecular characterization of rhizosphere and clinical isolates of Burkholderia cepacia. Res Microbiol. 1995 Sep;146(7):531–542. [PubMed]
  • Vaneechoutte M, Rossau R, De Vos P, Gillis M, Janssens D, Paepe N, De Rouck A, Fiers T, Claeys G, Kersters K. Rapid identification of bacteria of the Comamonadaceae with amplified ribosomal DNA-restriction analysis (ARDRA). FEMS Microbiol Lett. 1992 Jun 15;72(3):227–233. [PubMed]
  • Vaneechoutte M, De Beenhouwer H, Claeys G, Verschraegen G, De Rouck A, Paepe N, Elaichouni A, Portaels F. Identification of Mycobacterium species by using amplified ribosomal DNA restriction analysis. J Clin Microbiol. 1993 Aug;31(8):2061–2065. [PMC free article] [PubMed]
  • Vaneechoutte M, Dijkshoorn L, Tjernberg I, Elaichouni A, de Vos P, Claeys G, Verschraegen G. Identification of Acinetobacter genomic species by amplified ribosomal DNA restriction analysis. J Clin Microbiol. 1995 Jan;33(1):11–15. [PMC free article] [PubMed]
  • Welsh J, McClelland M. Fingerprinting genomes using PCR with arbitrary primers. Nucleic Acids Res. 1990 Dec 25;18(24):7213–7218. [PMC free article] [PubMed]
  • Whittam TS, Ochman H, Selander RK. Multilocus genetic structure in natural populations of Escherichia coli. Proc Natl Acad Sci U S A. 1983 Mar;80(6):1751–1755. [PMC free article] [PubMed]
  • Whittam TS. Sex in the soil. Curr Biol. 1992 Dec;2(12):676–678. [PubMed]
  • Williams JG, Kubelik AR, Livak KJ, Rafalski JA, Tingey SV. DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res. 1990 Nov 25;18(22):6531–6535. [PMC free article] [PubMed]
  • Wise MG, McArthur JV, Wheat C, Shimkets LJ. Temporal Variation in Genetic Diversity and Structure of a Lotic Population of Burkholderia (Pseudomonas) cepacia. Appl Environ Microbiol. 1996 May;62(5):1558–1562. [PMC free article] [PubMed]

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