Molecular methods for biodiversity analysis of phosphate solubilizing microorganisms (PSM)

  • A. Peix
  • E. Velázquez
  • E. Martínez-Molina
Conference paper
Part of the Developments in Plant and Soil Sciences book series (DPSS, volume 102)


Although the phosphate solubilizing potential is not a very common characteristic among microorganisms, phosphate solubilizers belonging to diverse groups of microorganisms, especially bacteria, are known. The ecological role of these microorganisms in soil is very important, as they take part in the biogeochemical cycles of the main nutrient elements in the ecosystems. Thus, it is necessary to study the composition and dynamics of these microbial populations to reach a better understanding of soil microbial diversity and nutrient uptake by plants. The study of populations of microorganisms, which share the common characteristic of phosphate solubilization has great complexity, because they belong to very diverse groups sometimes not closely related under a phylogenetic point of view. Therefore good techniques are needed to perform the analysis and identification of PSM populations. The molecular techniques based on nucleic acid composition are excellent tools for this purpose, as they are precise, reproducible and not dependent on culture media composition or growth phase of microorganisms. In this paper main molecular methods based on electrophoresis of nucleic acids as LMW RNA profiling and PCR-based techniques specially DNA involving approaches are reviewed and discussed, highlighting the main advantages and drawbacks of the different methods.

Key words

biodiversity analysis DNA fingerprint phosphate solubilizing microorganisms RNA 


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  1. Cruz-Sánchez J M, Velázquez E, Mateos P and Martínez-Molina E 1997 Enhancement of resolution of low molecular weight RNA profiles by staircase electrophoresis. Electrophoresis 18, 1909–1911.PubMedCrossRefGoogle Scholar
  2. Di Cello F, Bevivino A, Chiarini L, Fani R, Paffetti D, Tabacchioni S and Dalmastri C 1997 Biodiversity of a Burkholderia cepacia population isolated from the maize rhizosphere at different plant growth stages. Appl. Environ. Microbiol. 63, 4485–4493.PubMedGoogle Scholar
  3. Hartmann A and Amarger N 1991 Genotypic diversity of an indigenous Rhizobium meliloti field population assessed by plasmid profiles, DNA fingerprinting, and insertion sequence typing. Can. J. Microbiol. 37, 600–608.CrossRefGoogle Scholar
  4. Heyndrickx M, Vauterin L, Vandamme P, Kersters K and de Vos P 1996 Applicability of combined amplified ribosomal DNA restriction analysis (ARDRA) patterns in bacterial phylogeny and taxonomy. J. Microbiol. Meth. 26, 247–259.CrossRefGoogle Scholar
  5. Höfle M G 1988 Identification of bacteria by low molecular weight RNA profiles: a new chemotaxonomic approach. J. Microbiol. Meth. 8, 235–248.CrossRefGoogle Scholar
  6. Hulton C S J, Higgins C P and Sharp P M 1991 ERIC sequences: a novel family of repetitive elements in the genomes of Escherichia coli, Salmonella typhimurium and other enterobacteria. Mol. Microbiol. 5, 825–834.PubMedCrossRefGoogle Scholar
  7. Lowry O H, Rosenbrough N J, Farr A L and Randal R J 1951 Protein measurement with Folin phenol reagent. J. Biol. Chem. 193, 265–275.PubMedGoogle Scholar
  8. Marsh T L 1999 Terminal restriction fragment length polymorphism (T-RFLP): an emerging method for characterizing diversity among homologous populations of amplification products. Curr. Opin. Microbiol. 2, 323–327.PubMedCrossRefGoogle Scholar
  9. Muyzer G 1999 DGGE/TGGE a method for identifying genes from natural ecosystems. Curr. Opin. Microbiol. 2, 317–322.PubMedCrossRefGoogle Scholar
  10. Nagpal M L, Fox K F and Fox A 1998 Utility of 16S-23S rRNA spacer region methodology: how similar are interspace regions within a genome and between strains for closely related organisms?. J. Microbiol. Meth. 33, 211–219.CrossRefGoogle Scholar
  11. Osborn A M, Moore E R B and Timmis K N 2000 An evaluation of terminal-restriction fragment length polymorphism (T-RFLP) analysis for the study of microbial community structure and dynamics. Environ. Microbiol. 2, 39–50.PubMedCrossRefGoogle Scholar
  12. Rivas R, Velázquez E, Valverde A, Mateos P F and Martínez-Molina E 2001 A two primers random amplified polymorphic DNA procedure to obtain polymerase chain reaction fingerprints of bacterial species. Electrophoresis 22, 1086–1089.PubMedCrossRefGoogle Scholar
  13. Tsai C M and Frasch C E 1982 A sensitive silver stain for detecting lipopolysaccharides in polyacrylamide gels. Anal. Biochem. 119, 115–119.PubMedCrossRefGoogle Scholar
  14. Velázquez E, Igual J M, Willems A, Fernández M P, Muñoz E, Mateos P F, Abril A, Toro N, Normand P, Cervantes E, Gillis M and Martínez-Molina E 2001a Description of Mesorhizobium chacoense sp. nov. that nodulates Prosopis alba in the Chaco Arido region (Argentina). Int. J. Syst. Evol. Microbiol. 51, 1011–1021.PubMedGoogle Scholar
  15. Velázquez E, Trujillo M E, Peix A, Palomo J L, García-Benavides P, Mateos P F, Ventosa A and Martínez-Molina E 2001b Stable low molecular weight RNA analyzed by staircase electrophoresis, a molecular signature for both prokaryotic and eukaryotic microorganisms. Syst. Appl. Microbiol. 24, 490–499.PubMedCrossRefGoogle Scholar
  16. Versalovic J, Schneider M, De Bruijn F J and Lupski J R 1994 Genomic fingerprinting of bacteria using repetitive sequence-based polymerase chain reaction. Methods Mol. Cell. Biol. 5, 25–40.Google Scholar

Copyright information

© Springer 2007

Authors and Affiliations

  • A. Peix
    • 1
  • E. Velázquez
    • 2
  • E. Martínez-Molina
    • 2
  1. 1.Departamento de Producción VegetalSalamancaSpain
  2. 2.Departamento de Microbiología y Genética, Edificio Departamental de BiologíaUniversidad de SalamancaSalamancaSpain

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