Determination of the endophytic microorganism profiles of the some endemic plants in the İzmir province using DGGE

This study was aimed to evaluate the bacterial and the fungal endophyte diversity of the root parts of Styrax officinalis and Dianthus erinaceus endemic plant species by culture independent DGGE method. The endophytic bacterial and fungal communitiy structures in the roots of the plants were revealed using 16S rDNA, ITS DGGE fingerprinting and phylogenetic analysis. Plant samples were collected from Kemalpaşa district of İzmir province and brought to the laboratory at the same day. The surface of the roots were subjected to sterilization and cheched for their sterility. Following the total DNA isolation from plant samples, recovery of 16S rDNA and ITS DGGE of the amplicons from the gel and sequence analysis were performed. A total of 10 bacterial and 13 fungal phylotypes were obtained from two plant samples. Phylotypes were compared with NCBI-GenBank database in terms of their similarities to the bacterial and fungal sequences. It has been determined that the majority of the dominant endophytic bacterium diversity in root parts of plant specimens is constituted by Protobacteria phylum and subfilums. The fungal diversity is constituted by Penicillium sp., Alternaria sp. and uncultured Cladosporium sp. belonging to the Ascomycota phylum. In our study, the endophytic bacterial and fungal diversity of D. erinaceus was found to be higher than S. officinalis.