Gimibacter soli gen. nov. sp. nov., isolated from mangrove soil and insight into its ecological distribution and metabolic potential

Abstract

A Gram-stain-negative, facultatively anaerobic, motile and rod-shaped bacterium, designated as 6D33T, was isolated from mangrove soil. Growth was found to occur at 15–32 °C (optimum, 28 °C), at pH 6–9 (optimum, pH 7) and in 0–3 % NaCl (optimum, 1 %, w/v). The results of 16S rRNA gene-based analysis showed that strain 6D33T belonged to the family Temperatibacteraceae , sharing 93.1–94.4 % identity with its close neighbours within the genus Kordiimonas . The phylogenomic results indicated that strain 6D33T formed an independent branch distinct from type strains of the genus Kordiimonas . The overall genome relatedness indices of digital DNA–DNA hybridization, average nucleotide identity and amino acid identity values showed that strain 6D33T represents a novel species of a novel genus. The results of chemotaxonomic characterization indicated that the major cellular fatty acids of strain 6D33T were summed feature 9 (C16 : 0 10-methyl and/or iso-C17 : 1  ω9c), summed feature 3 (C16 : 1  ω6c and/or C16 : 1  ω7c) and iso-C15 : 0; the polar lipids comprised diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, an unidentified aminolipid and three unidentified lipids; the only respiratory quinone was ubiquinone-10. The genomic size and DNA G+C contents were 3.59 Mbp and 60.84 mol%, respectively. The 16S rRNA gene sequence reads abundance profiles revealed that the rare taxon is prevalent in marine environments, especially in sediments. Genome-scale metabolic reconstruction of strain 6D33T revealed a heterotrophic lifestyle and many pathways responsible for the degradation of aromatic compounds, suggesting application potential in aromatic hydrocarbon removal. Based on its genotypic and phenotypic characteristics, strain 6D33T is concluded to represent a novel species of the novel genus in the family Temperatibacteraceae , for which the name Gimibacter soli gen. nov. sp. nov. is proposed. The type strain of the type species is 6D33T (=GDMCC 1.1959T=KCTC 82335T).