Microbial community structure and function in common bean phytosphere

Abstract

The spatial, temporal, nutritional, and microbe inoculational effects on microbial community structure and function in the symbiotic association with common bean (Phaseolus vulgaris var. vulgaris) were investigated at phenotypic and genotypic levels. A culture-independent DGGE analysis of PCR amplified 16S rRNA, nifH, or nodA gene fragments in extracted DNA from soil and plant showed the bacterial community structure and dynamics depended on habitats (rhizosphereㆍrhizoplane, endorhizosphere, bulk soil, unplanted soil, and phyllosphereㆍphylloplane), plant age (3 and 6 weeks), nutritional status (carbon and/or nitrogen source supply), microbe inoculation (legume-planted soil adding as microbial source) conditions. And these were considered relating to their functions in the ecosystem by the characterization of physicochemical properties of soil and plant; the measurement of acetylene reduction (nitrogen fixation) and root nodulation activity; the cultivation of nitrogen fixing and root nodulationg bacteria; and the observation of microbes near the plant using SEM and fluorescence microscope. The cluster analysis of DGGE band profiles revealed that the rhizosphere effect became weak whereas overall plant effect became strong as plant grew, and, in temporal dynamics, the spatial specificity was increased whereas whole bacterial community size was not changed. And endophytes in root and leaf were limited and similar. Sequence analysis of selected DGGE bands and cellulose-degrading isolates revealed rhizosphereㆍrhizoplane were dominated by sphingobacteria (Flexibacter group), while endorhizosphere and phyllosphereㆍendophyllosphere were dominated by actinomycetales in common. External nitrogen source affected the nifH gene diversity, and external carbon source made the plant-microbe interaction weak by substituting for the plant role. Generally, the effect of external carbon source was stronger, and functional gene diversity was more specific. Nitrogen fixing bacteria...