Genome Insight and Description of Previously Uncultured N2-Fixing Bacterium Rhizobium terricola sp. nov., Isolated from Forest Rhizospheric Soil by Using Modified Culture Method

Abstract

A bacterial strain S-51T was isolated from rhizospheric forest soil at Kyonggi University during the study of previously uncultured bacterium. The phylogenetic analysis was based on 16S rRNA gene sequences that indicated that strain S-51T belonged to the genus Rhizobium within the family Rhizobiaceae. The closest members of strain S-51T were Rhizobium naphthalenivorans TSY03bT (98.2% sequence similarity) and Rhizobium selenitireducens ATCC BAA-1503T (98.1%). The sequence similarities of other members were <97.7%. The sole respiratory quinone was Q-10 and the major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylcholine, and unidentified glycolipid. The principal fatty acids were summed feature 8 (C18:1ω7c and/or C18:1ω6c), cyclo-C19:0ω8c, and C18:0. The DNA G+C content was 63.1 mol%. The genome was 4930044 bp long and contained N2-fixing genes, such as fixF, ntrC, and ptsN, in addition to respiratory nitrate reductase genes, such as narC, narG, narH, narI, and narJ. The average nucleotide identity (ANIu), average amino acid identity (AAI), and digital DNA-DNA hybridization (dDDH) relatedness between strain S-51T and phylogenetically related species were ≤82.6, ≤83.6 and ≤25.3%, respectively, much lower than the species delineation thresholds. Based on the polyphasic taxonomic study, strain S-51T represents a new species in the genus Rhizobium, for which the name Rhizobium terricola is proposed. The type strain is S-51T (=KACC 19117T = KEMB 9005-539T = NBRC 112711T).