Alterations in the Root Endophyte Microbiome of Rice Receiving Growth-Promoting Treatments of Urea-N and Rhizobium Biofertilizer

An issue of ecological importance that can ultimately impact the advancement of successful, sustainable agricultural practices for production of very important crop plants like rice is the extent to which biofertilizer inoculation with effective plant growth-promoting rhizobacteria (PGPR), application of a low dose of urea-N fertilizer, or the simultaneous combination of both treatments alters the natural endophytic bacteriome that develops within its roots. This specific topic has not been previously investigated. Here we describe studies focused on two interrelated objectives to fill that gap. The first objective was to utilize the culture-independent analysis of prokaryotic 16S rDNA gene sequences to compare the richness and distribution of abundance among the diverse taxa of bacterial endophytes representing the pooled “whole” bacteriome of all detected OTUs that colonize the interior of rice roots grown in soil with and without these treatments vs. the assemblage of the consolidated “core” endophytic community whose OTU richness is reproducibly found within the plant's roots regardless of which treatment they have received (i. e., no treatment-specific community taxa). The second objective was to examine how the community diversity of bacterial endophytes in the rice root microbiome may be restructured by inoculation with an effective rhizobacterial biofertilizer strain, application with a low dose of urea-N fertilizer, or the simultaneous combination of both treatments to optimally promote the development of the same rice variety grown in the same soil. These objectives were designed to provide insights into the biological complexity of beneficial plant-microbe interactions, rice microbiome diversity and associations with (bio)fertilizer