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

We examined the bacterial endophyte–enriched root-associated microbiome within rice ( Oryza sativa ) 55 days after growth in soil with and without urea fertilizer and/or biofertilization with a growth-promotive bacterial strain ( Rhizobium leguminosarum bv. trifolii E11). After treatment to deplete rhizosphere/rhizoplane communities, washed roots were macerated and their endophyte-enriched communities were analyzed by 16S ribosomal DNA 454 amplicon pyrosequencing. This analysis clustered 99,990 valid sequence reads into 1105 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 , unclassified Rhizobiales , Azospirillum , Azoarcus , unclassified Rhizobiaceae , Bradyrhizobium , Azonexus , Mesorhizobium , Devosia , Azovibrio , Azospira , Azomonas , and Azotobacter . The endophyte-enriched microbiome was restructured within roots receiving growth-promoting treatments. Compared to the untreated control, endophyte-enriched communities receiving urea 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 structure of root-associated communities suggest 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 as one of the world’s most important food crops.