Polyphasic analysis of the bacterial community in the rhizosphere and roots of Cyperus rotundus L. grown in a petroleum-contaminated soil.

Cyperus rotundus L. is a perennial herb which was found prevailing in an area in the northeast of Brazil previously contaminated with petroleum. In order to enlarge the knowledge of microorganism-plant interaction in phytoremediation, the bacterial community present in the rhizosphere and roots of C. rotundus was evaluated by culture-dependent and molecular approaches. PCR-DGGE analyses based on the 16S rRNA gene showed that the profiles of bulk soil, rhizosphere and root samples had a high degree of similarity. A complex community of alkane utilizing-bacteria and a variable nitrogen-fixing community were observed when the PCR-DGGE analyses were based on the genes alkB and nifH, respectively. In addition, two clone libraries were generated from the alkB fragments of bulk and rhizosphere soils. Statistical analyses showed that the libraries were different concerning the alkB population composition. Using culture-dependent techniques, 209 bacterial strains were isolated from the rhizosphere and rhizoplane/roots of C. rotundus. Dot blotting analysis showed that the DNA from 17 strains hybridized, simultaneously, with the alkB and nifH probes. After partial 16S rRNA gene sequencing, these strains were affiliated with the genera Bosea, Cupriavidus, Enterobacter, Gordonia, Mycoplana, Pandoraea, Pseudomonas, Rhizobium and Rhodococcus. They can be considered of great potential for phytoremediation in this tropical soil area.