Phyllobacterium humicola sp. nov., Isolated from Leaf Soil

A novel bacterial strain, designated NSA23^T, was isolated from leaf soil collected in Japan. This strain was an aerobic, Gram-stain-negative, non-sporulating, motile, rod-shaped bacterium. Growth temperature and pH ranged from 25 °C to 40 °C (optimum 35 °C) and pH 5.0 to 9.5 (optimum pH 8.0). The dominant cellular fatty acid was summed feature 8, and ubiquinone 10 constituted the principal respiratory quinone. Comparative analysis of 16S rRNA gene sequences positioned strain NSA23^T within the genus Phyllobacterium, thereby classifying it as Phyllobacterium sp. NSA23^T. The draft genome of Phyllobacterium sp. NSA23^T consisted of 5,008,001 bp with a G + C content of 61.8%, and encoded 4,731 predicted coding sequences. Multilocus sequence analysis employing partial sequences of four conserved housekeeping genes further confirmed that Phyllobacterium sp. NSA23^T occupied a distinct phylogenetic position relative to its closest Phyllobacterium type strain relatives. Genome-based species delineation metrics, including average nucleotide identity, digital DNA-DNA hybridization, and average amino acid identity, all fell below the established thresholds for prokaryotic species circumscription. Genomic interrogation revealed conservation of energy metabolism pathways typical of rhizobia; however, comparative genomic analyses revealed that genes associated with both nitrogen fixation and denitrification are uniquely conserved in the genome of Phyllobacterium sp. NSA23^T among the examined strains. Based on its phenotypic, chemotaxonomic, and phylogenetic features, strain NSA23^T (= HUT-8149^T = KCTC 82064^T) can be considered as a novel species within the genus Phyllobacterium, for which the name Phyllobacterium humicola sp. nov. is proposed.