Improvement of growth, yield and diversity of bacterial community of rice by the application of probiotic Paraburkholderia and Delftia

Background: Plant probiotic bacteria enhance growth and yield of crop plant when applied in appropriate time and dose. Two rice probiotic bacteria, Paraburkholderia fungorum strain BRRh-4 and Delftia sp. strain BTL-M2 promote growth and yield of plants. However, no information is available on application of these two bacteria on growth, yield, and diversity and population of bacteriome in roots and rhizosphere soils of the treated rice plants. This study aimed to assess the effects of growth, yield and bacteriome in roots and rhizosphere of rice by the application of BRRh-4 and BTL-M2 with varying doses of recommended N, P and K fertilizers. Results: : Application of BRRh-4 and BTL-M2 strains also significantly increased seed germination, growth and yield of rice compared to untreated control. Interestingly, the grain yield of rice by these bacteria with 50% reduced recommended doses of N, P, and K fertilizers were statistically similar to or better than the rice plants treated with 100% doses of these chemical fertilizers only. The metagenomics analysis by next generation sequencing revealed that the diversity in bacteriome were significantly higher (PERMANOVA, p = 0.0312) in the rice plants and rhizosphere soils that received both probiotic bacteria and chemical fertilizers compared to the rice plants treated with chemical fertilizers only. However, the diversity in bacteriome was more significant (p = 0.019, Kruskal-Wallis test) in the root bacteriome signature than in the rhizosphere soils. Out of 185 bacterial genera detected, Prevotella was found to be the predominant genus in both soil and root metagenomes. However, the relative abundance of Prevotella remained two-fold higher in the soil metagenome (52.02%) than in the root metagenome (25.04%). The other predominant bacterial genera detected in the rice root metagenome were Bacillus (11.07%), Planctomyces (4.06%), Faecalibacterium (3.91%), Deinococcus (2.97%), Bacteroides (2.61%), and Chryseobacterium (2.30%). On the other hand, rhizosphere soil metagenome had Bacteroides (12.38%), Faecalibacterium (9.50%), Vibrio (5.94%), Roseomonas (3.40%), and Delftia (3.02). Conclusions: Taken together, our results indicate that improvement of growth and yield of rice by P. fungorum strain BRRh-4 and Delftia sp. strain BTL-M2 is likely linked with modulation of diversity, structures, and signature of bacteriome in roots and rhizosphere soils. This study for the first time demonstrated that application of two plant growth promoting bacteria significantly improve growth, yield and increase the diversity of bacterial community in rice.