plant surface microbiology.pdf

24 Microbial Community Analysis in the
Rhizosphere by in Situ and ex Situ Application of
Molecular Probing, Biomarker and Cultivation
Techniques
Anton Hartmann, Rüdiger Pukall, Michael Rothballer,
Stephan Gantner, Sigrun Metz, Michael Schloter
and Bernhard Mogge
1 Introduction
It is well known that the bacterial diversity in soil habitats is much greater
compared to the artificial cultivation techniques (Torsvik et al. 1996;
Chatzinotas et al. 1998). It is generally accepted that only a combination of
methods including cultivation and several cultivation-independent techniques
is able to provide a more representative picture of the microbial diversity
in environmental habitats (Wagner et al. 1993; Liesack et al. 1997). This is
also true for the plant/soil compartment, although the degree of culturability
is thought to be higher on the root surface. Supposedly, rhizosphere microbes
respond to the presence of easily consumable substrates on the root surface
with fast growth rates, which is indicative for r-strategy; successful colonization
of the rhizosphere is the final result of this behavior.
In-depth characterization of bacterial communities residing in environmental
habitats has been greatly stimulated by the application of molecular
phylogenetic tools, such as 16S ribosomal RNA-directed oligonucleotide
probes derived from extensive 16S rDNA sequence analysis. These phylogenetic
probes can be successfully applied in diverse microbial habitats using
the fluorescence in situ hybridization (FISH) technique (Giovannoni et al.
1988; Amann et al. 1995; Tas and Lindström 2001). In addition, the application
of the immunofluorescence techniques to detect specific subpopulations of
enzymes and of fluorescence marker-tagged bacteria or reporter constructs
enables a highly resolving population and functional analysis (Hartmann et
al. 1997; Unge et al. 1999). Phylogenetic in situ studies of the population structure
can thus be supplemented with functional or phenotypic in situ investigation
approaches.
Plant Surface Microbiology
A.Varma, L. Abbott, D. Werner, R. Hampp (Eds.)
© Springer-Verlag Berlin Heidelberg 2004