Isolation, Identification and Characterization of Endophytic Bacterium <i>Rhizobium oryzihabitans</i> sp. nov., from Rice Root with Biotechnological Potential in Agriculture

• Main Authors: Juanjuan Zhao, Xia Zhao, Junru Wang, Qi Gong, Xiaoxia Zhang, Guishan Zhang
• Format: Article
• Language: English
• Published: MDPI AG 2020-04-01
• Series: Microorganisms
• Subjects: Plant-promoting endophytic bacteria; <i>Rhizobium oryzihabitans</i> sp. nov.; Comparative genome analysis
• Online Access: https://www.mdpi.com/2076-2607/8/4/608

A flagellate, rod–shaped bacterium designated strain M15^T was isolated from rice roots. Phylogenetic analysis based on the sequences of the 16S rRNA, housekeeping genes and genomes showed that the isolate belonged to the genus <i>Rhizobium</i>, with the highest 16S rRNA similarity to <i>Rhizobium radiobacter</i> LMG140^T (99.64%) and <i>Rhizobium pusense</i> NRCPB10^T (99.36%), respectively. The complete genome of the strain M15^T has a 59.28% G+C content, and the highest average nucleotide identity (ANI) and DNA-DNA relatedness (DDH) values were obtained with <i>R. radiobacter</i> LMG140^T (88.11%, 54.80%), <i>R. pusense</i> NRCPB10^T (86.00%, 53.00%) and <i>R. nepotum</i> 39/7^T (88.80%, 49.80%), respectively. Plant growth-promoting characteristics tests showed that the strain M15^T produced siderophore, 1–aminocyclopropane–1–carboxylate (ACC) deaminase and indole-3-acetic acid (IAA) and also produced some secondary metabolites according to the analysis of the comparative genomes. Based on the data mentioned above, we proposed that the strain M15^T represented a novel species of the genus <i>Rhizobium</i>, named <i>Rhizobium oryzihabitans</i> sp. nov. The type strain is M15^T (=JCM 32903^T  = ACCC 60121^T), and the strain M15^T can be a novel biofertilizer <i>Rhizobium</i> to reduce the use of synthetic fertilizers for plant growth promotion.