Bulk and rhizosphere soil bacterial communities studied by denaturing gradient gel electrophoresis: Plant-dependent enrichment and seasonal shifts revealed

The bacterial rhizosphere communities of three host plants of the pathogeni c fungus Verticillium dahliae, field-grown strawberry (Fragaria ananassa Du ch.), oilseed rape (Brassica napus L.), and potato (Solanum tuberosum L.), were analyzed. We aimed to determine the degree to which the rhizosphere ef fect is plant dependent and whether this effect would be increased by growi ng the same crops in two consecutive years. Rhizosphere or soil samples wer e taken five times over the vegetation periods. To allow a cultivation-inde pendent analysis, total community DNA was extracted from the microbial pell et recovered from root or soil samples. 16S rDNA fragments amplified by PCR from soil or rhizosphere bacterium DNA were analyzed by denaturing gradien t gel electrophoresis (DGGE). The DGGE fingerprints showed plant-dependent shifts in the relative abundance of bacterial populations in the rhizospher e which became more pronounced in the second year. DGGE patterns of oilseed rape and potato rhizosphere communities were more similar to each other th an to the strawberry patterns. In both years seasonal shifts in the abundan ce and composition of the bacterial rhizosphere populations were observed. Independent of the plant species, the patterns of the first sampling times for both years were characterized by the absence of some of the bands which became dominant at the following sampling times. Bacillus megaterium and A rthrobacter sp. were found as predominant populations in bulk soils. Sequen cing of dominant bands excised from the rhizosphere patterns revealed that 6 out of 10 bands resembled grain-positive bacteria. Nocardia populations w ere identified as strawberry-specific bands.