Comparative evaluation of rhizospheric and rhizoplanic bacterial communities of six spontaneous plant species sharing the same vegetation unit

The microbiology of natural environments is still a relatively unexplored world; many hindrances prevent the knowledge of their actual biological diversity at bacterial level; among which the difficulty in culturing on plate media the vast majority of prokaryotic species. We sought to devise a polyphasic approach, comparing direct and culture-dependent methods, aimed at characterizing the bacterial communities rhizosphere and rhizoplane of herbaceous plants. The following tasks were pursued: 1) to define a procedure for the reliable and reproducible isolation of bacteria from the rhizospheric soil and from the rhizoplane of plants; 2) To compare the microbial communities of six spontaneous herbaceous plant species sharing the same natural habitat consisting in a ruderal vegetation site five years post-disturbance; the chosen plants are: Papaver rhoeas (Papaveraceae); Plantago lanceolata (Plantaginaceae) Daucus carota (Umbelliferae); Lotus corniculatus (Leguminosae); Taraxacum officinale (Compositae); and Lolium multiflorum (Graminaceae); 3) To analyze and count bacteria displaced from roots, using light and fluorescence microscopy visualizing: total cell counts (DAPI), live to dead cell ratio (Bac Light), and metabolically active cells (CTC+); 4) to count plate-culturable fractions of bacteria from rhizosphere and rhizoplane and assess percent culturability over the total cell counts obtained by microscopy; 5) to perform culture-independent DNA-based analyses by extracting total community DNA and PCR-amplifying 16S rDNA regions for ARDRA and DGGE comparisons. The results, comparing the outputs of: (1) computer assisted electrophoretic ARDRA fingerprinting, (2) community analysis by sequencing of 16S rDNA clone banks, (3) microscopical assessment of communities physiological status, will be discussed.