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CABI Book Chapter

Molecular approaches to soil, rhizosphere and plant microorganism analysis.

Book cover for Molecular approaches to soil, rhizosphere and plant microorganism analysis.


This book comprises a comprehensive collection of molecular methods for studying microorganisms that occur in the soil or that are associated with plants, at the community, population, taxonomic and functional group levels. It contains 16 chapters encompassing most techniques that are currently available for these purposes, and offers analyses of their respective strengths and limitations. In doin...

Chapter 12 (Page no: 198)

Molecular ecology of arbuscular mycorrhizal fungi: a review of PCR-based techniques.

Some methodological approaches used in the molecular identification of arbuscular mycorrhizal (AM) fungi are reviewed and discussed. Focus is given on the polymerase chain reaction-based nucleic acid methods. The genes used for AM fungi communities, sequence heterogeneity within spores and species and the community fingerprinting approaches are discussed. Also provided are the key questions addressed for the ecology and population biology of AM fungi. Finally, a practical example of AM fungi identification and phylogenetic analysis is given.

Other chapters from this book

Chapter: 1 (Page no: 1) Genomic analyses of microbial processes in biogeochemical cycles. Author(s): Shilpi Sharma Karl, H. Schloter, M.
Chapter: 2 (Page no: 18) Applications of nucleic acid microarrays in soil microbial ecology. Author(s): Loy, A. Taylor, M. W. Bodrossy, L. Wagner, M.
Chapter: 3 (Page no: 42) Metagenomics for the study of soil microbial communities. Author(s): Steele, H. L. Streit, W. R.
Chapter: 4 (Page no: 55) In vivo expression technology (IVET) for studying niche-specific gene expression by plant- and soil-colonizing bacteria. Author(s): Rediers, H. Mot, R. de
Chapter: 5 (Page no: 84) Analysing microbial community structure by means of terminal restriction fragment length polymorphism (T-RFLP). Author(s): Blackwood, C. B.
Chapter: 6 (Page no: 99) Characterization of phylloplane and rhizosphere microbial populations using PCR and denaturing gradient gel electrophoresis (DGGE). Author(s): O'Callaghan, M. Lorenz, N. Gerard, E. M.
Chapter: 7 (Page no: 116) Molecular tools for studying plant growth-promoting rhizobacteria (PGPR). Author(s): Franks, A. Ryan, R. P. Abbas, A. Mark, G. L. O'Gara, F.
Chapter: 8 (Page no: 132) Detection of autotrophic sulphur- and iron-oxidizing bacteria using labelled fatty acid methyl esters (FAMEs). Author(s): Lipski, A.
Chapter: 9 (Page no: 146) Molecular analyses of soil denitrifying bacteria. Author(s): Philippot, L. Hallin, S.
Chapter: 10 (Page no: 166) Ecology of Streptomyces in soil and rhizosphere. Author(s): Strap, J. L. Crawford, D. L.
Chapter: 11 (Page no: 183) Molecular ecology of ectomycorrhizal fungal communities: new frontiers. Author(s): Anderson, I. C.
Chapter: 13 (Page no: 213) Transcriptomics for determining gene expression in symbiotic root-fungus interactions. Author(s): Franken, P. Krajinski, F.
Chapter: 14 (Page no: 236) Differentiation of nitrogen-fixing legume root nodule bacteria (rhizobia). Author(s): Lindström, K. Kokko-Gonzales, P. Terefework, Z. Räsänen, L. A.
Chapter: 15 (Page no: 259) Molecular markers for studying the ecology of rhizobia. Author(s): Sessitsch, A.
Chapter: 16 (Page no: 272) Molecular characterization of bacterial plant pathogens. Author(s): Godfrey, S. A. Jackson, R. W.