Analysis of the dynamics of bacterial communities in the rhizosphere of the chrysanthemum via denaturing gradient gel electrophoresis and substrate utilization patterns

In order to gain a better understanding of the spatial and temporal dynamic s of bacterial communities of the rhizosphere of the chrysanthemum, two com plementary methods were used: a molecular bacterial community profiling met hod, i.e., 16S rRNA gene-based PCR followed by denaturing gradient gel elec trophoresis (DGGE), and an agar plate method in which 11 sole-carbon-source utilization tests were used. The DGGE patterns showed that the bacterial c ommunities as determined from direct rhizosphere DNA extracts were largely stable along developing roots of the chrysanthemum, with very little change over time or between root parts of different ages, The patterns were also similar to those produced with DNA extracts obtained from bulk soil samples . The DGGE patterns obtained by using microbial colonies from dilution plat es as the source of target DNA were different from those found with the dir ect DNA extracts. Moreover, these patterns showed differences among plant r eplicates but also among replicate plates, Results obtained with the sole-c arbon-source utilization tests indicated that the metabolic profile of the bacterial communities in the rhizosphere of the root tip did not change sub stantially during plant growth, This suggests selective development of spec ific bacterial populations by the presence of a root tip, On the other hand , the metabolic profile of bacterial communities in the rhizosphere of the root base changed during plant growth, With eight sole-carbon-source utiliz ation tests, a significant effect of the development stage of the plant on the number of bacteria which were able to grow on these carbon sources was observed.