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

We examined the bacterial endophytic microbiome within the root interior of rice (Oryza sativa) 55 days after growth in soil with and without urea-N fertilizer and/or biofertilization with a growth-promotive strain (Rhizobium leguminosarum bv. trifolii E11). After depletion of rhizoplane communities, washed roots were macerated and their endophyte communities were analyzed by 16S rRNA 454 gene amplicon pyroseqencing. This analysis clustered 99,990 valid sequence reads into 1,105 Operational Taxonomic Units (OTUs) with 97% sequence identity, 133 of which represented a consolidated “core” assemblage representing 12.04% of the fully detected OTU richness. Taxonomic affiliations indicated Proteobacteria as the most abundant phylum (especially α- and γ-Proteobacteria classes), followed by Firmicutes, Bacteroidetes, Verrucomicrobia, Actinobacteria, and several other phyla. Dominant genera included Rheinheimera, unclassified Rhodospirillaceae, Pseudomonas, Asticcacaulis, Sphingomonas and Rhizobium. Several OTUs had close taxonomic affiliation to genera of diazotrophic rhizobacteria, including Rhizobium, Mesorhizobium, Bradyrhizobium, Azospirillum, Azoarcus, Azonexus, Azovibrio, Azospira, Azotobacter, unclassified Rhizobiales, Devosia and cyanobacteria. The endophytic microbiome was restructured within roots receiving growth-promoting treatments. Compared to the untreated control, endophyte communities receiving urea-N and/or biofertilizer treatments were significantly reduced in OTU richness and relative read abundances. Several unique OTUs were enriched in each of the treatment communities. These alterations in community structure of root endophytes reveal dynamic interactions in the host plant microbiome, some of which may influence the well-documented positive synergistic impact of rhizobial biofertilizer inoculation plus low doses of urea N-fertilizer on growth-promotion of rice, considered by many as one of the world’s most important food crops.