Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea.
Antonie Van Leeuwenhoek. 2024 Apr 26;117(1):72. doi: 10.1007/s10482-024-01963-z.
Two Gram-staining negative, catalase- and oxidase-positive, pinkish-colored and rod-shaped strains, designated SJ11 and HCMS5-2, were isolated from soil in South Korea. The growth of strain SJ11 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 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 had the highest 16S rRNA similarities with Pedobacter jejuensis THG-DR3 (98.5%) and strain HCMS5-2 had the highest similarities with Pedobacter nototheniae 36B243 (98.7%). The digital DNA-DNA hybridization value of strain SJ11 with Pedobacter jejuensis THG-DR3 was 23.6%, with an average nucleotide identity value of 79.6%, and that of strain HCMS5-2 with Pedobacter nototheniae 36B243 was 26.4%, with an average nucleotide identity value of 83.1%. The predominant cellular fatty acids (> 10%) of SJ11 and HCMS5-2 were iso-C, summed feature 3 (comprising Cω7c and/or Cω6c) and iso-C 3-OH. The genome size of strain SJ11 was approximately 4.7 Mb with a G + C content of 37.7% and that of strain HCMS5-2 was approximately 4.1 Mb with a G + C content of 36.4%. The major polar lipid and respiratory quinone of SJ11 and HCMS5-2 were phosphatidylethanolamine and menaquinone NK-7, respectively. Results of this study showed that strains SJ11 and HCMS5-2 belonged to the genus Pedobacter as novel species, of which the name Pedobacter rhodius sp. nov., with the type strain SJ11 (= KACC 22884 = TBRC 16597) and Pedobacter punctiformis sp. nov., with the type strain HCMS5-2 (= KACC 22863 = TBRC 16598) were respectively proposed.
两株革兰氏染色阴性、触酶和氧化酶阳性、粉红色、杆状的菌株 SJ11 和 HCMS5-2 从韩国土壤中分离得到。SJ11 株的生长温度为 15℃至 35℃（最佳温度为 30℃），pH 值为 6.0 至 11.0（最佳 pH 值为 6.0-7.0），NaCl 浓度为 0-1%（w/v）（最佳为 0%），HCMS5-2 株的生长温度为 4℃至 40℃（最佳温度为 25℃），pH 值为 6.0 至 pH 8.0（最佳 pH 值为 7.0），NaCl 浓度为 0-5%（w/v）（最佳为 0-1%）。基于 16S rRNA 基因序列的系统发育分析表明，两株菌均属于 Pedobacter 属。SJ11 株与 Pedobacter jejuensis THG-DR3 的 16S rRNA 相似性最高（98.5%），HCMS5-2 株与 Pedobacter nototheniae 36B243 的相似性最高（98.7%）。SJ11 株与 Pedobacter jejuensis THG-DR3 的数字 DNA-DNA 杂交值为 23.6%，平均核苷酸同一性值为 79.6%，HCMS5-2 株与 Pedobacter nototheniae 36B243 的数字 DNA-DNA 杂交值为 26.4%，平均核苷酸同一性值为 83.1%。SJ11 和 HCMS5-2 的主要细胞脂肪酸（>10%）为 iso-C、summed feature 3（包含 Cω7c 和/或 Cω6c）和 iso-C 3-OH。SJ11 株的基因组大小约为 4.7 Mb，GC 含量为 37.7%，HCMS5-2 株的基因组大小约为 4.1 Mb，GC 含量为 36.4%。SJ11 和 HCMS5-2 的主要极性脂和呼吸醌分别为磷脂酰乙醇胺和menaquinone NK-7。研究结果表明，SJ11 和 HCMS5-2 株属于 Pedobacter 属的新种，分别命名为 Pedobacter rhodius sp. nov.，其模式株为 SJ11（=KACC 22884=TBRC 16597）和 Pedobacter punctiformis sp. nov.，其模式株为 HCMS5-2（=KACC 22863=TBRC 16598）。
