Clone-based sequencing and NGS of plant growth-promoting genes from metagenomic DNA of rice rhizosphere show marked diversity

Abstract

Abstract Backgrounds and AimsAn attempt has been made to assess the distribution and diversity of important plant growth-promoting genes from the metagenomic DNA of rice rhizosphere soil. Methods A novel multiplex polymerase chain reaction was developed for the amplification of three important genes namely nifH, pqqC and accd-DR simultaneously from the metagenomic DNA. Next generation sequencing was employed for the sequencing of above genes for the assessment of diversity. Results Ninety six nifH clones from the metagenomic DNA of rice rhizosphere were selected which belonged to 15 groups on the basis of RFLP. Sequencing of the representative 15 clones showed higher level of similarity with the uncultured bacteria. Similarly, 12 clones of pqqC were selected, majority of the clones showed similarity with both uncultured and cultured bacteria. NGS of nifH showed fourteen types of genera with varying number of OTUs, the dominant genus identified as Halorhodospira (7.38%). pqqC and accd-DRshowed seven types of genera with varying number of OTUs. The highest abundance of Pseudomonas sp. (48.73%) was noted in pqqC and accd-DR showed the abundance of Acidovorax sp. (58.28%). Conclusions Altogether, findings of this study suggest marked diversity in nifH, pqqC and accd-DRgenes in rice rhizosphere. It would be desirable to apply both clone-based sequencing and NGS for the analysis of total bacterial community and plant growth promoting genes from the metagenome of any habitat.