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

Abstract

A field experiment was conducted with cultivation of hybrid and conventional cultivars in a rice paddy from China. Rhizosphere soil was sampled and CO 2 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 CO 2 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.

Analysis of bacterial and fungal communities in continuous-cropping ramie (Boehmeria nivea L. Gaud) fields in different areas in China

“…The decrease in these species directly led to the decrease in rhizosphere microbial diversity in Jiangxi. Ascomycota, Basidiomycota, and Zygomycota were the dominant fungal phyla, which was consistent with the findings of previous studies in citrus 34 Ascomycota and Basidiomycota are important fungi in most soils 35,36 , and the species in both phyla are involved in C cycling by degrading organic substances 37,38 . We observed significant differences in the relative abundance of Ascomycota and Basidiomycota in our samples; especially in Sichuan, the abundance of Ascomycota was the highest compared with that in the other three regions.…”

Heavy metal pollution decreases microbial abundance, diversity and activity within particle-size fractions of a paddy soil

“…Hussain et al . () also reported that Ascomycota dominated the fungal community in the rhizosphere of rice plants. In the present study, Ascomycota and Basidiomycota were found to be predominant across all of the fractions, which suggested a ubiquity of these species and an important role in agroecosystems.…”

“…The majority of the band types observed in the present study (B1‐B3, B11 and B13‐B17), particularly the dominant bands, were shared by all of the fractions, indicating that the bacterial community structure was highly stable. Sequencing of these bands revealed that Acidobacteria, Betaproteobacteria , Gammaproteobacteria and Chloroflexi were the predominant groups (Table ), and these genera are commonly found in rice paddies, as reported in previous studies by our group (Hussain et al ., ; Chen et al ., ). These findings indicate that these bacteria are widely distributed and survive well across all fractions and may play an important role in the turnover and stability of SOC.…”

Screening of plant growth promoting bacteria (PGPB) from rhizosphere and bulk soil of Caragana microphylla in different habitats and their effects on the growth of Arabidopsis seedlings

“…The root system, the microorganisms and the soil form an underground micro-ecosystem in the rhizosphere [4]. The rhizosphere microbial community varies among plant species, growth stages and environmental habitats [5] and often includes plant growth-promoting bacteria (PGPB), which colonise plant roots [6]. Certain PGPR strains improve the ability of plants to adapt to a stressful environment [7], such as drought and salinity [8,9].…”