Phylogenetic study of endophytic bacterial strains using gyrB, rpoD, FEN and nifH genes

Tomato is one of the most important commercial crops in the world especially Iran. The use of entophytic bacteria is one of the new ways to manage this disease. In this study, eight tomato endophytic bacteria namely Pseudomonas fluorescens NZ105, Bacillus pumilus strains NZ103 and 106, Bacillus subtilis NZ104, Bacillus safensis NZ107, Enterobacter ludwigii NZ108, Serratia marcescens NZ102 and Pseudomonas baetica NZ101were identified based on 16S rRNA gene sequence analysis. These were further examined for conserved genes of gyrB and rpoD, two functional antibiotic-producing FEN and nitrogen-stabilizing nifH genes. Among these, only P. fluorescens NZ105 have gyrB and rpoD genes and B. safensis and S. marcescens have antibiotic-producing FEN gene. None of the eight isolates harbouring nitrogen-fixing nifH gene compared to the positive control Azotobacter chroococum. The phylogeny of eight endophytic bacteria formed tight monophyletic branches supported by high bootstrap probabilities. The high sequence similarity revealed a close phylogenetic relationship between B. safensis and B. albus.