Bacterial diversity of the rhizosphere of maize (Zea mays) grown in tropical soil studied by temperature gradient gel electrophoresis

The bacterial diversity and population dynamics in the rhizosphere of two maize cultivars (Nitroflint and Nitrodent) grown in tropical soils was studied, by traditional cultivation techniques and 16S rRNA gene-based molecular analysis of DNA directly extracted from soil and rhizosphere samples. Rhizosphere and soil samples were taken at three different plant growth stages. Total aerobic bacterial counts were determined. Fingerprints of the most dominant bacterial population were generated by TGGE separation of 16S rRNA gene fragments amplified from total community DNA using eubacterial specific primers. To reduce the complexity of TGGE fingerprints or to analyse less abundant populations, primers specific for different phylogenetic groups have been used. A comparison of the cfu obtained for rhizosphere of both cultivars indicated significant differences only for rhizosphere and soil samples taken 40 days after sowing. However, a comparison of TGGE patterns indicated that the composition of the bacterial community analysed at different plant growth stages for both cultivars was similar. A comparison of alpha-, beta -proteobacterial and actinomycete TGGE patterns of both cultivars confirmed this observation. The eubacterial TGGE profiles reflected strong seasonal population shifts in the bacterial rhizosphere community of both maize cultivars which could be also observed in the TGGE patterns of alpha- and beta -proteobacteria and to a lesser extent for actinomycetes. The rhizosphere effect was much more pronounced for young roots compared to samples taken from mature maize plants. The rhizosphere fingerprints showed a reduced complexity for young plants with up to five dominating bands while for mature plants patterns similar to those of soil were observed. Sequencing of dominant clones indicated that the dominant population found at all plant growth stages can be assigned to Arthrobacter populations.