plant surface microbiology.pdf

450
Anton Hartmann et al.
The rhizosphere is defined as the soil compartment which is greatly influenced
by plant roots (Campbell and Greaves 1990a). The rhizosphere microbial
community is shaped by the effect of root exudates (Brimecomb et al.
2001). Several methodological approaches are available to study the rhizosphere
carbon flow and the microbial population dynamics induced by rootborn
carbon sources (Morgan and Whipps 2001). In addition, multiple communicative
links exist between the rhizosphere microflora and the roots on
the basis of highly specific organic signals (Werner 2001). It is appropriate to
distinguish the root itself (with the endorhizosphere and the root surface, the
rhizoplane) from the soil compartment surrounding the root (bulk soil and
ectorhizosphere). In the following sections, two experimental approaches to
investigate root-associated bacterial communities are presented. Figure 1
provides a flow diagram of the separation of the rhizosphere compartments
and the various in situ and ex situ methods applied. On one hand, population
and functional studies can be conducted directly in the rhizoplane (in situ) by
combining specific fluorescence probing with confocal laser scanning microscopy
yielding detailed information about the localization and small scale
distribution of bacterial cells and their activities on the root surface (Sect. 2).
On the other hand, the separated rhizosphere compartments and the bacteria
extracted from these different compartments allow a variety of subsequent ex
situ-studies (Sect. 3). Studies, such as cultivation of bacteria on plates and
microscopic counting of bacteria on filters after FISH analysis provide quan-
Plants
Roots with
adhering soil
Shaking,
washing
Root free soil
(Compartment I)
Ectorhizosphere soil
(Compartment II)
Roots: Rhizoplane
and endorhizosphere
(Compartment III)
ISS ESS
Fixation Extraction
In situ-studies (ISS):
FISH, Immunolabeling, monitoring
of fluorescence tagged bacteria and
constructs
ISS ESS
Ex situ-studies (ESS):
DNA-extraction, PCR-amplification of
phylogenetic marker regions / TGGE
PLFA-biomarker,CSLP-techniques
Fig. 1. Flow diagram of separation of rhizosphere compartments and overview of in situ
and ex situ analyses using molecular probing, biomarker and cultivation techniques