Variation of bacterial and fungal community structures in the rhizosphere of hybrid and standard rice cultivars and linkage to CO2 flux

A field experiment was conducted with cultivation of hybrid and conventional cultivars in a rice paddy from China. Rhizosphere soil was sampled and CO2 flux was measured at tillering (S1), grain filling (S2) and ripening (S3) across the growth stages. Microbial community structure, abundance and activity were analyzed using a combination of functional (enzymes) and denaturing gradient gel electrophoresis (DGGE) and real-time PCR molecular approaches. Invertase and urease activities, total microbial biomass carbon, bacterial 16S rRNA and fungal internal transcribed spacer rRNA gene copies were found to be the highest at S2 under both cultivars, being greater under the hybrid cultivar than under the conventional cultivar across the stages. Moreover, the CO2 flux was 11%, 16% and 25% higher under the hybrid cultivar than under the conventional cultivar at S1, S2 and S3, respectively. Principal component analyses of the PCR-DGGE profile revealed a significant difference between conventional and hybrid cultivars across growth stages. Sequencing DGGE bands of the bacterial 16S rRNA gene showed that a particular bacterial group of Alphaproteobacteria was enhanced and several distinct operational taxonomic units markedly resembled Ascomycota under the hybrid cultivar. These illustrate a significant selection of a particular group of bacteria and fungi of the hybrid cultivar. However, the potential impacts of these cultivar effects in soil C and N cycling deserve further field studies.