Bacterial community structure and colonization patterns of <em>Fagus sylvatica</em> L. ectomycorrhizospheres as determined by fluorescence <em>in situ</em> hybridization and confocal laser scanning microscopy.

The bacterial community structure of ecto-mycorrhizospheres on beech (Fagus sylvatica) grown in natural forest soil in southern Germany was examined by fluorescence in situ hybridization (FISH) using fluorescent oligonucleotide probes, targeting phylogenetic relevant sequences of the 16S and 23S rRNA. Lactarius subdulcis, L. vellereus, L. rubrocinctus and Laccaria amethystina were found to be the prevalent fungi forming ectomycorrhizae with F. sylvatica. For FISH studies using confocal laser scanning microscopy, oligonucleotide probes labeled with carboxymethylindocyanine-succinimidyl ester allowed detection of associated bacteria, because the autofluorescence of ectomycorrhiza samples could be overcome in the infrared. Bacteria of the alpha-, beta and gamma-subclasses of the proteobacteria were detected in high numbers on mantle surfaces, while members of other phylogenetically defined groups were found in smaller numbers. This contrasts with previous published results on the cultivation of mycorrhiza-associated bacteria. Hybridizing bacteria were also found within damaged cells of the hyphal mantle of L. rubrocinctus, as well as on emanating hyphae of L. amethystina. Using a newly developed extraction protocol for bacteria associated with ectomycorhizas, the two most common fungi on F. sylvatica, L. vellereus and L. subdulcis, were mostly associated with members of the alpha- and beta-subclasses of the proteobacteria. The proportion of hybridizing bacteria varied between the two ectomycorrhizae, which were thus host to distinct populations of bacteria

Microbial community analysis in the rhizosphere by in situ and ex situ application of molecular probing, biomarker and cultivation techniques.

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