Plant growth-promoting genes from metagenomic DNA of rice rhizosphere show marked diversity

This study assessed the distribution and diversity of important plant growth-promoting genes from the metagenomic DNA of rice rhizosphere soil. The multiplex polymerase chain reaction (mPCR) was employed for the simultaneous amplification of three genes from the metagenomic DNA: nifH (dinitrogenase reductase), pqqC (pyrroloquinoline quinone synthase) and accd-DR (1-aminocyclopropane-1-carboxylate deaminase). Both clone-based sequencing and next generation sequencing (NGS) of the above genes were performed, assess the diversity in this study. 96 nifH clones selected from the metagenomic DNA of rice rhizosphere showed 15 different groups, based on restriction fragment length polymorphism (RFLP). Sequencing of the representative 15 clones revealed a high similarity to uncultured bacteria. Similarly, 12 clones of pqqC were analyzed which showed alignment to both uncultured and cultured bacteria. NGS of nifH revealed the presence of fourteen genera with different numbers of operational taxonomic units (OTUs), the dominant genus being Halorhodospira . pqqC and accd-DR were represented by seven genera and contained various number of OTUs. Apart, pqqC showed the highest percentage of Pseudomonas sp. (48%) whereas accd-DR had the dominance of Acidovorax sp. (58%). Nevertheless, mPCR could be used to amplify a number of plant growth promoting genes of bacteria in one reaction from metagenomic DNA of rhizosphere soil of different crops. Findings suggest remarked diversity of nifH , pqqC and accd-DR genes occurrence in rice rhizosphere.