Abstract
A flagellate, rod–shaped bacterium designated strain M15T 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 Rhizobium, with the highest 16S rRNA similarity to Rhizobium radiobacter LMG140T (99.64%) and Rhizobium pusense NRCPB10T (99.36%), respectively. The complete genome of the strain M15T has a 59.28% G+C content, and the highest average nucleotide identity (ANI) and DNA-DNA relatedness (DDH) values were obtained with R. radiobacter LMG140T (88.11%, 54.80%), R. pusense NRCPB10T (86.00%, 53.00%) and R. nepotum 39/7T (88.80%, 49.80%), respectively. Plant growth-promoting characteristics tests showed that the strain M15T 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 M15T represented a novel species of the genus Rhizobium, named Rhizobium oryzihabitans sp. nov. The type strain is M15T (=JCM 32903T = ACCC 60121T), and the strain M15T can be a novel biofertilizer Rhizobium to reduce the use of synthetic fertilizers for plant growth promotion.
Highlights
The genus Rhizobium, belonging to the family Rhizobiaceae within the order Rhizobiales of the class Alphaproteobacteria, was first described by Frank as root and/or stem nodulating bacteria [1]
Growth occurred at 15–50 ◦C.The pH range for growth was 5.0–12.0 and the tolerance of NaCl was up to 7.0% (w/v), which indicated that strain M15T endowed with inherent capability to cope with high concentration of salt or overly alkaline in soil
Strain M15T could be distinguished from R. radiobacter LMG140T in utilization of D-psicose, methyl pyruvate, mono–methyl–succinate, β–hydroxy butyric acid and growth at NaCl (7.0%) and pH11.0
Summary
The genus Rhizobium, belonging to the family Rhizobiaceae within the order Rhizobiales of the class Alphaproteobacteria, was first described by Frank as root and/or stem nodulating bacteria [1]. Several Rhizobium species have been described on the basis of non-symbiotic strains isolated from rice recently, such as Rhizobium oryziradicis, Rhizobium rhizospherae, Rhizobium pseudoryzae, Rhizobium rhizoryzae, and Rhizobium oryzicola [9,10,11,12]. Rhizobium is a well–known plant microbiota for nitrogen fixation traits with legume host and non-legume plant growth promoters [14,15,16]. Such as, Rhizobium leguminosarum trifolii E11 is able to promote rice plant growth by phosphate solubilization and IAA production; Bradyrhizobium japonicum can promote the growth of radishes by siderophore production [16], and so on. The mechanisms have been studied thoroughly and used widely in agricultural applications
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