Rhizosphere Microbial Community Changes With Rice Cultivars And The Significance In Greenhouse Gases Evolution From Rice Paddy Field

It is well documented that root-derived carbon and oxygen in the rhizosphere are largely controlled by rice cultivars and growth stage. We hypothesized whether that rice cultivars trait extends to greater microbial biomass and altered the role of rhizosphere microorganisms in controlling the dynamics of soil CO2, CH4 and N2O fluxes. In the current global change scenario, the evaluation of the microbial mechanism for rice cultivars control on CO2, N2O and CH4 fluxes in rice field soil is extremely important to improve our understanding of the factors controlling the greenhouse gases emissions in similar ecosystems.One month old rice (Oriza sativa) seedlings of hybrid (Kyou 818) and conventional (Wugeng 13) rice cultivars were transplanted in randomly selected plots. Rhizosphere and bulk soil samples were collected at selected growth stages for each rice cultivar:45 days after planting (tillering stage-S1),81 days after planting (grain filling stage-S2) and 107 days after planting (ripening stage-S3). Soil samples (unplanted soil-SO) were also collected just before transplanting of seedlings to investigate the effect of the plant rhizosphere on the microbial communities.We determined general microbial activity (function) by enzyme assays (invertase and urease activities) while total bacterial, total fungal, denitrifier (nirK), ammonia oxidizing bacterial (amoA) and archaeal (amoA) communities structures and abundances were assessed by culture-independent molecular techniques including polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and quantitative real-time PCR (qPCR), respectively. Moreover, important band retrieved from DGGE gel were analyzed using sequencing and phylogenetic analysis. The main findings are given below. 1) Hybrid rice emitted 11%,16% and 25% higher CO2 than conventional rice cultivar at tillering (S1), grain filling (S2) and ripening (S3) stage, respectively. Moreover, the hybrid rice cultivar promoted greater enzyme activities, total microbial biomass, bacterial 16S rRNA gene copy numbers, fungal ITS rRNA gene copy numbers and relative fungal:bacterial ratios in the rhizosphere soil relative to conventional cultivar. Comparison of bacterial and fungal community structure by principal component analyses (PCA) of PCR-DGGE profile revealed significant difference between conventional and hybrid cultivars across growth stages. Sequence analysis of DGGE bands of bacterial 16S rRNA indicated that hybrid rice stimulated the particular bacterial group of a-Proteobacteria, whereas fungal 18S rRNA analysis revealed several distinct operational taxonomic units markedly resemble to Ascomycota (Sordariomycetes, Pezizomycetes and Leotiomycetes) in the rhizosphere of hybrid cultivar compared to conventional cultivar.2) Rice growing stages significantly affected the structures and abundances of AOB and denitrifier (nirK) communities in the rhizosphere, whereas no effect was observed on the community structure and abundance of AOA in the rhizosphere. Moreover, the amoA gene copy numbers of AOA were more than those of AOB in all soil samples. However, denitrifier (nirK) generally dominated the ammonia oxidizer (amoA) in the rhizosphere during all growth stages, suggesting better adaptability of denitrifier in the rice rhizosphere environment.3) Hybrid rice reduced the N2O emission relative to conventional cultivar. Moreover, hybrid rice stimulated higher bacterial-amoA (AOB) gene copies g-1 dry soil and lower nirK (denitrifiers) gene copies g-1 dry soil in the rhizosphere than the conventional cultivar. Comparison of AOB and denitrifying community structures by principal component analyses (PCA) of PCR-DGGE profile also revealed significant differences between conventional and hybrid cultivars at all growth stages. However, rice cultivars and growth stages did not significantly influence the structure and abundance of archaeal-amoA (AOA) in rhizosphere showing the higher stability of AOA communities. AOA and denitrifiers (nirK) diversity was limited to uncultured Crenarchaeote and Rhizobiales (Bradyrhizobiaceae and Rhizobiaceae) groups, respectively. Whereas AOB analyses revealed several distinct operational taxonomic units markedly resemble to Nitrosospira sp. in the rhizosphere of hybrid cultivar compared to conventional cultivar. Hybrid rice can select for particular group of AOB in the rhizosphere relative to AOA throughout growth periods. These results suggest that increased NO3- uptake and less adaptability of denitrifying (nirK) bacteria in the rhizosphere of hybrid cultivar may be contributing factor for less N2O emission relative to conventional cultivar.4) Compared to conventional cultivar, hybrid rice resulted in reduced CH4 emission by 31%,48% and 56% at tillering, grain filling and ripening stages, respectively. The increased abundance of total methanotrophs and decreased abundance of total methanogens were observed in the later stage of both cultivars. Rice cultivars did not significantly influence the structure of methanogenic archaea; however community structure of methanotroph was distinct between two rice cultivars. Moreover, the total copy number of pmoA genes in the rhizosphere of hybrid rice was 4.9%,5.1% and 6.2% greater than the conventional cultivar at tillering (S1), grain filling (S2) and ripening (S3) stages, respectively. However, total copy number of mcrA genes was stable between two cultivars across all growing stages except last stage (ripening-S3). A significant positive correlation (P<0.01, R2=0.87) was observed between difference in mcrA and pmoA gene abundance and CH4 flux for both cultivars across all sampling time points.