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

• Published in: Antonie van Leeuwenhoek Vol. 117; no. 1; p. 72
• Main Authors: Woo, Haejin, Chhetri, Geeta, Kim, Inhyup, So, Yoonseop, Park, Sunho, Jung, Yonghee, Seo, Taegun
• Format: Journal Article
• Language: English
• Published: Cham Springer International Publishing 01-12-2024; Springer Nature B.V
• Subjects: Bacterial Typing Techniques; Base Composition; Biomedical and Life Sciences; Catalase; Deoxyribonucleic acid; DNA; DNA, Bacterial - genetics; Fatty Acids - analysis; Fatty Acids - metabolism; Gene sequencing; Genomes; Hybridization; Life Sciences; Lipids; Medical Microbiology; Menaquinones; Microbiology; New species; Nucleic Acid Hybridization; Nucleotides; OriginalPaper; Pedobacter; Pedobacter - classification; Pedobacter - genetics; Pedobacter - isolation & purification; Pedobacter - physiology; pH effects; Phosphatidylethanolamine; Phospholipids - analysis; Phylogenetics; Phylogeny; Plant Sciences; Quinones; Republic of Korea; RNA, Ribosomal, 16S - genetics; rRNA 16S; Sequence Analysis, DNA; Similarity; Sodium chloride; Soil Microbiology; Soil Science & Conservation; Soils; Republic of Korea; Soil; Novel species; Sphingobacteriaceae; Pedobacter; Pedobacter rhodius; Pedobacter punctiformis
• ISSN: 0003-6072; 1572-9699; 1572-9699
• DOI: 10.1007/s10482-024-01963-z

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
16:1
ω
7
c
and/or C
16:1
ω
6
c
) 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.