Effect of plant host and contamination on structure of rhizosphere microbial communities

In light of environmental concerns for polycyclic aromatic compounds (PAHs) contamination in soil, promises of phytoremediation as economic and effective strategy of environmental clean-up and importance of rhizosphere bacteria in bioremediation, soil productivity and plant growth, we studied rhizosphere microbial communities structure as a function of plant type and concentration of the contaminant in two different experimental settings. In a bioremediation approach, mimicking possible field experiment, we prepared soil treatments by mixing contaminated soil with uncontaminated soil in different proportion. Bacterial 16S rDNA terminal restriction fragment polymorphism (TRFLP) profiles of three month old wheat (Triticum aestivum), lettuce (Lactuca sativa var. Tango), zucchini (Cucurbita pepo spp. pepo var. Black Beauty) and pumpkin (Cucurbita pepo spp. pepo var. Howden) were compared. Our data suggests that in highly polluted soils the rhizosphere microbial community structure is governed more by the degree of contamination than the plant host type. In another, ecological, approach we amended soils with coal tar and examined changes in bacterial community structure from zucchini and wheat rhizosphere as a function of time. Clustering and canonical correspondence analysis (CCA) of TRFLP profiles suggest that in moderately polluted soils contamination drives the structure of rhizosphere microbial communities in young plants. As the plant matures, however, it dominates in defining the structure of rhizosphere microbial communities. Phylogenetic assignment of terminal restriction fragments (TRFs) from the second experimental design using the Ribosomal Database Project (RDP) database allowed us to explore the bacterial communities species composition. The analysis of assigned fragments showed results similar to CCA, suggesting potential usability of phylogenetic fragment assignment as a complementary technique in microbial ecology that does not require an additional time and expenses for sequencing, though reliability of the phylogenetic assignments needs to be addressed.