Pedobacter rhodius sp. nov. and Pedobacter punctiformis sp. nov., isolated from soil

Abstract

Two Gram-staining negative, catalase- and oxidase-positive, pinkish-colored and rod-shaped strains, designated SJ11T and HCMS5-2 T, were isolated from soil in South Korea. The growth of strain SJ11T was observed from 15℃ to 35℃ (optimum, 30℃), from pH 6.0 to 11.0 (optimum, pH 6.0–7.0) and with NaCl 0–1% (w/v) (optimum, 0%) and that of strain HCMS5-2 T was observed from 4℃ to 40℃ (optimum, 25℃), from pH 6.0 to pH 8.0 (optimum, pH 7.0) and with NaCl 0–5% (w/v) (optimum, 0–1%). Phylogenetic analysis based on 16S rRNA gene sequences showed that both strains belonged to the genus Pedobacter. Strain SJ11T had the highest 16S rRNA similarities with Pedobacter jejuensis THG-DR3T (98.5%) and strain HCMS5-2 T had the highest similarities with Pedobacter nototheniae 36B243T (98.7%). The digital DNA-DNA hybridization value of strain SJ11T with Pedobacter jejuensis THG-DR3T was 23.6%, with an average nucleotide identity value of 79.6%, and that of strain HCMS5-2 T with Pedobacter nototheniae 36B243T was 26.4%, with an average nucleotide identity value of 83.1%. The predominant cellular fatty acids (> 10%) of SJ11T and HCMS5-2 T were iso-C15:0, summed feature 3 (comprising C16:1ω7c and/or C16:1ω6c) and iso-C17:0 3-OH. The genome size of strain SJ11T was approximately 4.7 Mb with a G + C content of 37.7% and that of strain HCMS5-2 T was approximately 4.1 Mb with a G + C content of 36.4%. The major polar lipid and respiratory quinone of SJ11T and HCMS5-2 T were phosphatidylethanolamine and menaquinone NK-7, respectively. Results of this study showed that strains SJ11T and HCMS5-2 T belonged to the genus Pedobacter as novel species, of which the name Pedobacter rhodius sp. nov., with the type strain SJ11T (= KACC 22884 T = TBRC 16597 T) and Pedobacter punctiformis sp. nov., with the type strain HCMS5-2 T (= KACC 22863 T = TBRC 16598 T) were respectively proposed. © The Author(s), under exclusive licence to Springer Nature Switzerland AG 2024.