Abstract:
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.