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Soil bacterial communities were analyzed in different habitats (bulk soil, rhizosphere, rhizoplane) of poplar tree microcosms (Populus tremula ´ P. alba) using cultivation-independent methods. The roots of poplar trees regularly experience flooded and anoxic conditions. Therefore, we also determined the effect of flooding on microbial communities in microcosm experiments. Total community DNA was extracted and bacterial and archaeal 16S rRNA genes were amplified by PCR and analyzed by terminal restriction fragment length polymorphism (T-RFLP) analysis, cloning and sequencing. Clone libraries were created from all three habitats under both unflooded and flooded conditions resulting in a total of bacterial 281 sequences. Numbers of different sequences (<97% similarity) in the different habitats represented 16-55% of total bacterial species richness determined from the nonparametric richness estimator Chao1. According to the number of different terminal restriction fragments (T-RFs), all of the different habitats contained approximately 20 different operational taxonomic units (OTUs), except the flooded rhizoplane habitat whose community contained less OTUs. Results of cloning and T-RFLP analysis generally supported each other. Correspondence analysis of T-RFLP patterns showed that the bacterial communities were different in bulk soil, rhizosphere and rhizoplane and changed upon flooding. For example OTUs representing Bacillus sp. were highest in the unflooded bulk soil and rhizosphere. Sequences related to Aquaspirillum, on the other hand, were predominant on the poplar roots and in the rhizosphere of flooded microcosms but were rarely found in the other habitats. The archaeal community was dominated in all compartments, both flooded and unflooded, by sequences of the uncultivated Crenarchaeota lineage 1.1b (99%). This dominance indicates their importance not only in soils but also in the rhizosphere and on roots of poplar trees. Only two sequences from the rhizoplane habitat were affiliated within the Euryarchaeota. No methanogens were detected via cloning. Insights into the structure of Bacteria and Archaea, also in dependence of flooding, were first gained in this study using molecular methods. Further, abundant microorganisms could be identified.