Rice root-associated bacteria: insights into community structures across 10 cultivars

Abstract

In this study, the effects of plant genotype, soil type and nutrient use efficiency on the composition of different bacterial communities associated with rice roots were investigated. Thus, total bacteria, Alpha- and Betaproteobacteria, Pseudomonas and Actinobacteria were studied using PCR, followed by denaturing gradient gel electrophoresis (PCR-DGGE). Rice genotype determined, to a large extent, the composition of the different bacterial communities across cultivars. Several cultivars belonging to Oryza sativa ssp. indica tended to select similar bacterial communities, whereas those belonging to subspecies japonica and aromatica selected ones with divergent community structures. An effect of soil type was pronounced for the Actinobacteria communities, while a small effect of 'improved' and 'traditional' plants was noted for all communities analyzed. A few dominant bands in PCR-DGGE, affiliated with Rhizobium radiobacter, Dickeya zeae, Mycobacterium bolletii and with members of the Rhizobiales, Rhodospirillaceae and Paenibacillaceae, were spread across cultivars. In contrast, a majority of bands (e.g. affiliated with Enterobacter cloacae or Burkholderia kururiensis) was only present in particular cultivars or was erratically distributed among rice replicates. These findings suggested that both bacterial adaptation and plant genotype contribute to the shaping of the dynamic bacterial communities associated with roots of rice plants.

Fig. 1

PCR-DGGE profiles of bacterial (a), alphaproteobacterial (b) and betaproteobacterial (c) communities associated with root tissues of ten rice cultivars. Arrows indicate identified DGGE bands obtained from excised bands and co-migrated isolates, respectively, right and left ‘head’ directions. Internal arrows are cultivar-specific bands, whereas ‘edge’ arrows are generic bands.

Fig. 2

Biplot ordination generated by redundancy analysis (RDA) of the PCR-based denaturing gradient gel electrophoresis (PCR-DGGE) profiles from total bacterial (a), alphaproteobacterial (b), betaproteobacterial (c), actinobacterial (d) and pseudomonads (e) communities associated with roots of ten rice cultivars. Each symbol represents the bacterial community composition associated with roots of an individual plant. Open and close symbols represent improved and traditional cultivars, respectively. Crosses represent the centroid position of the nominal environmental variables (effects). Environmental variable with significant influence on the variation of community composition is shown with asterisks (P < 0.05). The variations of each ordination axis are presented in percentage.