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 SJ11^T and HCMS5-2 ^T, were isolated from soil in South Korea. The growth of strain SJ11^T 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 SJ11^T had the highest 16S rRNA similarities with Pedobacter jejuensis THG-DR3^T (98.5%) and strain HCMS5-2 ^T had the highest similarities with Pedobacter nototheniae 36B243^T (98.7%). The digital DNA-DNA hybridization value of strain SJ11^T with Pedobacter jejuensis THG-DR3^T was 23.6%, with an average nucleotide identity value of 79.6%, and that of strain HCMS5-2 ^T with Pedobacter nototheniae 36B243^T was 26.4%, with an average nucleotide identity value of 83.1%. The predominant cellular fatty acids (> 10%) of SJ11^T and HCMS5-2 ^T were iso-C_15:0, summed feature 3 (comprising C_16:1ω7c and/or C_16:1ω6c) and iso-C_17:0 3-OH. The genome size of strain SJ11^T 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 SJ11^T and HCMS5-2 ^T were phosphatidylethanolamine and menaquinone NK-7, respectively. Results of this study showed that strains SJ11^T and HCMS5-2 ^T belonged to the genus Pedobacter as novel species, of which the name Pedobacter rhodius sp. nov., with the type strain SJ11^T (= 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.