1
|
Park S, Kim I, Chhetri G, Jung Y, Woo H, Seo T. Cellulomonas alba sp. nov. and Cellulomonas edaphi sp. nov., isolated from wetland soils. Int J Syst Evol Microbiol 2024; 74. [PMID: 38214698 DOI: 10.1099/ijsem.0.006235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2024] Open
Abstract
Two novel strains were isolated from wetland soils in Goyang, Republic of Korea. The two Gram-stain-positive, facultatively anaerobic, rod-shaped bacterial-type strains were designated MW4T and MW9T. Phylogenomic analysis based on whole-genome sequences suggested that both strains belonged to the genus Cellulomonas. The cells of strain MW4T were non-motile and grew at 20-40 °C (optimum, 35 °C), at pH 6.0-10.0 (optimum, pH 8.0) and in the presence of 0-1.0% NaCl (optimum, 0 %). The cells of strain MW9T were non-motile and grew at 20-40 °C (optimum, 35 °C), at pH 5.0-9.0 (optimum, pH 8.0) and in the presence of 0-1.0% NaCl (optimum, 0 %). The average nucleotide identity (77.1-88.1 %) and digital DNA-DNA hybridization values (21.0-34.8 %) between the two novel strains and with their closely related strains fell within the range for the genus Cellulomonas. The novel strains MW4T and MW9T and reference strains possessed alkane synthesis gene clusters (oleA, oleB, oleC and oleD). Phylogenomic, phylogenetic, average nucleotide identity, digital DNA-DNA hybridization, physiological and biochemical data indicated that the novel strains were distinct from other members of the family Cellulomonadaceae. We propose the names Cellulomonas alba sp. nov. (type strain MW4T=KACC 23260T=TBRC 17645T) and Cellulomons edaphi sp. nov. (type strain MW9T=KACC 23261T=TBRC 17646T) for the two strains.
Collapse
Affiliation(s)
- Sunho Park
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Inhyup Kim
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Geeta Chhetri
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Yonghee Jung
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Haejin Woo
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Taegun Seo
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| |
Collapse
|
2
|
Jiang L, Choe H, Peng Y, Jeon D, Cho D, Jiang Y, Lee JH, Kim CY, Lee J. Sphingomonas abietis sp. nov., an Endophytic Bacterium Isolated from Korean Fir. J Microbiol Biotechnol 2023; 33:1292-1298. [PMID: 37528562 PMCID: PMC10619552 DOI: 10.4014/jmb.2303.03017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 06/20/2023] [Accepted: 07/06/2023] [Indexed: 08/03/2023]
Abstract
PAMB 00755T, a bacterial strain, was isolated from Korean fir leaves. The strain exhibits yellow colonies and consists of Gram-negative, non-motile, short rods or ovoid-shaped cells. It displays optimal growth conditions at 20°C, 0% NaCl, and pH 6.0. Results of 16S rRNA gene-based phylogenetic analyses showed that strain PAMB 00755T was most closely related to Sphingomonas chungangi MAH-6T (97.7%) and Sphingomonas polyaromaticivorans B2-7T (97.4%), and ≤96.5% sequence similarity to other members of the genus Sphingomonas. The values of average nucleotide identity (79.9-81.3%), average amino acid identity (73.3-75.9%), and digital DNA-DNA hybridization (73.3-75.9%) were significantly lower than the threshold values for species boundaries; these overall genome-related indexes (OGRI) analyses indicated that the strain represents a novel species. Genomic analysis revealed that the strain has a 4.4-Mbp genome encoding 4,083 functional genes, while the DNA G+C content of the whole genome is 66.1%. The genome of strain PAMB 00755T showed a putative carotenoid biosynthetic cluster responsible for its antioxidant activity. The respiratory quinone was identified as ubiquinone 10 (Q-10), while the major fatty acids in the profile were identified as C18:1ω7c and/or C18:1ω6c (summed feature 8). The major polar lipids of strain PAMB 00755T were diphosphatidylglycerol, phosphatidylethanolamine, sphingoglycolipid, and phosphatidylcholine. Based on a comprehensive analysis of genomic, phenotypic, and chemotaxonomic characteristics, we proposed the name Sphingomonas abietis sp. nov. for this novel species, with PAMB 00755T as the type strain (= KCTC 92781T = GDMCC 1.3779T).
Collapse
Affiliation(s)
- Lingmin Jiang
- Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup 56212, Republic of Korea
- Present address: National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, P.R. China
| | - Hanna Choe
- Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup 56212, Republic of Korea
| | - Yuxin Peng
- Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup 56212, Republic of Korea
| | - Doeun Jeon
- Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup 56212, Republic of Korea
| | - Donghyun Cho
- Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup 56212, Republic of Korea
| | - Yue Jiang
- Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup 56212, Republic of Korea
| | - Ju Huck Lee
- Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup 56212, Republic of Korea
- Department of Biosystem and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
| | - Cha Young Kim
- Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup 56212, Republic of Korea
| | - Jiyoung Lee
- Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup 56212, Republic of Korea
- Department of Biosystem and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
| |
Collapse
|
3
|
Park S, Kim I, Chhetri G, So Y, Jung Y, Woo H, Seo T. Roseateles albus sp. nov., Roseateles koreensis sp. nov. and Janthinobacterium fluminis sp. nov., isolated from freshwater at Jucheon River, and emended description of Roseateles aquaticus comb. nov. Int J Syst Evol Microbiol 2023; 73. [PMID: 37750754 DOI: 10.1099/ijsem.0.006043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2023] Open
Abstract
Three Gram-stain-negative, facultatively anaerobic, rod-shaped, catalase-positive, oxidase-negative bacterial strains were designated as hw1T, hw8T and hw3T. Strains hw1T, hw8T and hw3T grew at 15-28 °C (optimum, 25 °C), 15-35 °C (optimum, 30 °C) and 4-28 °C (optimum, 20 °C), respectively, and at pH 7.0-12.0 (optimum, pH 9.0), pH 6.0-11.0 (optimum, pH 9.0) and 5.0-12.0 (optimum, pH 7.0), respectively. Additionally, strains hw1T and hw8T only grew when the NaCl concentration was 0 %, while strain hw3T grew at between 0 and 0.5 % (w/v; optimum, 0 %). The average nucleotide identity (ANI) values between strains hw1T, hw8T and the Roseateles type strains ranged from 73.8 to 84.2 %, while the digital DNA-DNA hybridization (dDDH) values ranged from 19.7 to 27.5 %. The ANI values between strain hw3T and the Janthinobacterium type strains ranged from 78.7 to 80.7 %, while dDDH values ranged from 22.3 to 23.0 %. The draft genomes of strains hw1T, hw8T and hw3T consisted of 5.5, 4.4 and 5.9 Mbp, with DNA G+C contents of 61.7, 61.8 and 66.0 mol%, respectively. The results of the dDDH, ANI, phylogenetic, biochemical and physiological analyses indicated that the novel strains were distinct from other members of their genera. Thus, we proposed the names Roseateles albus sp. nov. (type strain hw1T= KACC 22887T= TBRC 16613T), Roseateles koreensis sp. nov. (type strain hw8T= KACC 22885T= TBRC 16614T) and Janthinobacterium fluminis sp. nov. (type strain hw3T= KACC 22886T= TBRC 16615T).
Collapse
Affiliation(s)
- Sunho Park
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Inhyup Kim
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Geeta Chhetri
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Yoonseop So
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Yonghee Jung
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Haejin Woo
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Taegun Seo
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| |
Collapse
|
4
|
Chhetri G, Kim I, Seo T. Devosia oryzisoli sp. nov., a novel moderately halotolerant bacterium isolated from the roots of rice plants and genome mining revealed the biosynthesis potential as plant growth promoter. Antonie Van Leeuwenhoek 2023; 116:231-242. [PMID: 36525157 DOI: 10.1007/s10482-022-01800-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022]
Abstract
A Gram-stain-negative, halotolerant bacterium designated as PTR5T was isolated from the roots of rice plants, collected in Ilsan, South Korea. Cells were, aerobic, asporogenous, motile, rod-shaped, white in color, and grew at 5-38 °C (optimum 30 °C), at pH 5.0-0-8.0 (optimum, 7.0) and tolerates up to 10% (w/v) NaCl (optimum, 0% NaCl). According to the EZbioCloud server the most closely related Devosia species to strain PTR5T based on 16 S rRNA gene sequence comparison are Devosia crocina (97.4%), followed by D. soli (97.2%), D. lucknowensis (96.9%) and D. marina (96.5%). The respiratory quinone was identified as Q-10. The major polar lipids were phosphatidylglycerol and diphosphatidylglycerol. C16:0, C18:1 ω7c 11-methyl and summed feature 8 (comprising C18:1 ω7c/C18:1 ω6c) constituted the main cellular fatty acids. The draft genome sequence of strain PTR5T was 3,689,283 bp in size. The average nucleotide identity (ANI), digital DNA-DNA hybridization (dDDH) and amino acid identity (AAI) values between strain PTR5T and its close relative were 72.8-76.8%, 19-20.7% and 70.3-75%, respectively. The G + C content was 63.7%. Strain PTR5T was able to produce siderophore and indole acetic acid (IAA) in the presence of L-tryptophan. Genes for siderophore production, auxin responsive and tryptophan biosynthesis were present in the genome of novel strain. Also, gene clusters involved in detoxification of various metal pollutants and antibiotics were also revealed in the genome of novel strain PTR5T, this suggest that novel strain can facilitate bioremediation of heavy metals and antibiotics in contaminated areas. This study aimed to determine the detailed taxonomic position of the strain PTR5T using the modern polyphasic approach. On the basis of evidence presented in this study, strain PTR5T is considered to represent a novel species of the genus Devosia, for which the name Devosia oryzisoli sp. nov. (type strain PTR5T (KCTC 82691T = TBRC 15163T) is proposed.
Collapse
Affiliation(s)
- Geeta Chhetri
- Department of Life Science, Dongguk University-Seoul, 10326, Goyang, South Korea
| | - Inhyup Kim
- Department of Life Science, Dongguk University-Seoul, 10326, Goyang, South Korea
| | - Taegun Seo
- Department of Life Science, Dongguk University-Seoul, 10326, Goyang, South Korea.
| |
Collapse
|
5
|
Kang M, Chhetri G, Kim I, So Y, Seo T. Comparative genomic analyses of four novel Ramlibacter species and the cellulose-degrading properties of Ramlibacter cellulosilyticus sp. nov. Sci Rep 2022; 12:21233. [PMID: 36482214 PMCID: PMC9731981 DOI: 10.1038/s41598-022-25718-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 12/05/2022] [Indexed: 12/13/2022] Open
Abstract
In this study, four novel bacterial strains, USB13T, AW1T, GTP1T, and HM2T, were isolated from various environments in Busan and Jeju Island, Republic of Korea. The 16S rRNA sequencing results indicated that the four novel strains belong to the genus Ramlibacter. All four strains were tested for their potential cellulolytic properties, where strain USB13T was identified as the only novel bacterium and the first within its genus to show cellulolytic activity. When tested, the highest activities of endoglucanase, exoglucanase, β-glucosidase, and filter paper cellulase (FPCase) were 1.91 IU/mL, 1.77 IU/mL, 0.76 IU/mL, and 1.12 IU/mL, respectively at pH 6.0. Comparisons of draft whole genome sequences (WGS) were also made using average nucleotide identity, digital DNA-DNA hybridization values, and average amino acid identity values, while whole genome comparison was visualized using the BLAST Ring Image Generator. The G + C contents of the strains ranged from 67.9 to 69.9%, while genome sizes ranged from 4.31 to 6.15 Mbp. Based on polyphasic evidence, the novel strains represent four new species within the genus Ramlibacter, for which the names Ramlibacter cellulosilyticus sp. nov. (type strain, USB13T = KACC 21656T = NBRC 114839T) Ramlibacter aurantiacus sp. nov. (type strain, AW1T = KACC 21544T = NBRC 114862T), Ramlibacter albus sp. nov. (type strain, GTP1T = KACC 21702T = NBRC 114488T), and Ramlibacter pallidus sp. nov. (type strain, HM2T = KCTC 82557T = NBRC 114489T) are proposed.
Collapse
Affiliation(s)
- Minchung Kang
- grid.255168.d0000 0001 0671 5021Department of Life Science, Dongguk University-Seoul, Goyang, 10326 Korea
| | - Geeta Chhetri
- grid.255168.d0000 0001 0671 5021Department of Life Science, Dongguk University-Seoul, Goyang, 10326 Korea
| | - Inhyup Kim
- grid.255168.d0000 0001 0671 5021Department of Life Science, Dongguk University-Seoul, Goyang, 10326 Korea
| | - Yoonseop So
- grid.255168.d0000 0001 0671 5021Department of Life Science, Dongguk University-Seoul, Goyang, 10326 Korea
| | - Taegun Seo
- grid.255168.d0000 0001 0671 5021Department of Life Science, Dongguk University-Seoul, Goyang, 10326 Korea
| |
Collapse
|
6
|
Jeon D, Jiang L, Peng Y, Seo J, Li Z, Park SH, Jeong RD, Park SJ, Jeong JC, Lee J. Sphingomonas cannabina sp. nov., isolated from Cannabis sativa L. 'Cheungsam'. Int J Syst Evol Microbiol 2022; 72. [PMID: 36260506 DOI: 10.1099/ijsem.0.005566] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023] Open
Abstract
A Gram-negative, aerobic, rod-shaped bacterium, designated DM2-R-LB4T was isolated from Cannabis sativa L. 'Cheungsam' in Andong, Republic of Korea. The strain DM2-R-LB4T grew at temperatures of 15-45 °C (optimum, 30-37 °C), pH of 5.5-9 (optimum, 8.0), and 0-2 % (w/v) NaCl concentration (optimum, 0%). Phylogenetic analyses based on the 16S rRNA gene sequences revealed that strain DM2-R-LB4T is related to species of the genus Sphingomonas, and shared 97.8 and 97.5% similarity to Sphingomonas kyenggiensis KCTC 42244T and Sphingomonas leidyi DSM 4733T, respectively. The DNA G+C content was 67.9 mol% and genome analysis of the strain DM2-R-LB4T revealed that the genome size was 4 386 171 bp and contained 4 009 predicted protein-coding genes. The average nucleotide identity (ANI) values between strain DM2-R-LB4T and S. kyenggiensis KCTC 42244T, and S. leidyi DSM 4733T was 76.8 and 76.7 %, respectively, while the values of digital DNA-DNA hybridization (dDDH) were 20.7 and 20.6 %, respectively. C14 : 0 2-OH, C16 : 0, and summed feature 8 (C18 : 1 ω6c and/or C18 : 1 ω7c) were the major fatty acids (>10 %) in the strain DM2-R-LB4T. The polar lipids comprised diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), phosphatidylglycerol (PG), phosphatidylcholine (PC), sphingoglycolipid (SGL), glycolipid (GL), phospholipid (PL), and two unidentified polar lipids (L1 and L2). Ubiquinone-10 (Q-10) was the only respiratory quinone. The polyamine pattern was found to contain homospermidine, putrescine, and spermidine. The results of phylogenetic anlayses, polyphasic studies, revealed that strain DM2-R-LB4T represents a novel species of the genus Sphingomonas, for which the name Sphingomonas cannabina sp. nov., is proposed. The type strain is DM2-R-LB4T (=KCTC 92075T = GDMCC 1.3018T).
Collapse
Affiliation(s)
- Doeun Jeon
- Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup 56212, Republic of Korea
- Department of Applied Biology, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Lingmin Jiang
- Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup 56212, Republic of Korea
| | - Yuxin Peng
- Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup 56212, Republic of Korea
| | - Jiyoon Seo
- Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup 56212, Republic of Korea
| | - Zhun Li
- Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup 56212, Republic of Korea
| | - Seung-Hwan Park
- Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup 56212, Republic of Korea
| | - Rae-Dong Jeong
- Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup 56212, Republic of Korea
| | - Soon Ju Park
- Division of Biological Science, Wonkwang University, Iksan 54538, Republic of Korea
| | - Jae Cheol Jeong
- Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup 56212, Republic of Korea
| | - Jiyoung Lee
- Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup 56212, Republic of Korea
| |
Collapse
|
7
|
Luo Y, Zhou M, Wang F, Sheng H. Sphingomonas psychrotolerans sp. nov., isolated from root surface of Leontopodium leontopodioides in the Tianshan Mountains, Xinjiang, China. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005396] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel rod-shaped, Gram-stain-negative, aerobic bacterial strain, designated Cra20T, was isolated from the root surface of Leontopodium leontopodioides collected in the Tianshan Mountains, Xinjiang, PR China. Phylogenetic analysis based on 16S rRNA gene sequences, indicated that strain Cra20T was affiliated with the genus
Sphingomonas
, and was most closely related to
Sphingomonas gei
ZFGT-11T (99.0 %),
Sphingomonas naasensis
KIS18-15T (97.8%) and
Sphingomonas kyeonggiensis
THG-DT81T (97.2 %). The average nucleotide identity values between strain Cra20T,
S. gei
ZFGT-11T,
S. naasensis
KIS18-15T and
S. kyeonggiensis
THG-DT81T were 86.2, 84.2 and 78.2 %, respectively. The genomic DNA G+C content of strain Cra20T was 65.6 mol% (whole genome sequence), and Q-10 was the predominant ubiquinone. The major cellular fatty acids of strain Cra20T were summed feature 8 (comprising C18 : 1
ω6c and/or C18 : 1
ω7c, 67.3 %) and C14 : 0 2-OH (6.4 %). On the basis of genotypic, phenotypic and biochemical data, strain Cra20T is considered to represent a novel species of the genus
Sphingomonas
, for which the name Sphingomonas psychrotolerans sp. nov. is proposed. The type strain is Cra20T (=CGMCC 1.15510T=NBRC 112697T).
Collapse
Affiliation(s)
- Yang Luo
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, PR China
- School of Life Sciences, Shangrao Normal University, Shangrao Agricultural Technology Innovation Research Institute, Shangrao 334000, PR China
| | - Meng Zhou
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, PR China
- School of Life Sciences, Shangrao Normal University, Shangrao Agricultural Technology Innovation Research Institute, Shangrao 334000, PR China
| | - Fang Wang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, PR China
| | - Hongmei Sheng
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, PR China
| |
Collapse
|
8
|
Kang M, Chhetri G, Kim J, Kim I, So Y, Seo T. Tumebacillus amylolyticus sp. nov., isolated from garden soil in Korea. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005376] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A starch-degrading novel strain, designated as strain ITR2T, was isolated from a soil sample collected from a garden near Dongguk University located in Goyang, Republic of Korea. The strain was identified as Gram-stain-positive, rod-shaped, and motile by means of peritrichous flagella. Moreover, 16S rRNA gene analysis revealed the novel strain to form a separate clade with
Tumebacillus permanentifrigoris
Eur1 9.5T (98.3 %) while also clustering with
Tumebacillus flagellatus
GST4T (97.9 %). Strain ITR2T grew optimally at temperatures of 20–30 °C, at pH 6.0–7.0 and at NaCl concentrations of 0–1 %. The sole quinone was menaquinone-7 and the cell-wall peptidoglycan comprised alanine, aspartic acid, glutamic acid, lysine and meso-diaminopimelic acid (type-A1γ peptidoglycan). The major fatty acids (>10%) of the novel strain were C16 : 0, iso-C14 : 0, iso-C15 : 0 and anteiso-C15 : 0, while the major polar lipids were phosphatidylmonomethylethanolamine, phosphatidylethanolamine, phosphatidylglycerol and one unidentified phospholipid. Other polar lipids of the novel strain included, two unidentified glycolipids, three unidentified phospholipids and one unidentified lipid. The in silico DNA–DNA hybridization values between strain ITR2T and its reference strains (
T. permanentifrigoris
DSM 18773T and
T. flagellatus
GST4T) were 21.3 and 23.9 %, respectively, while the average nucleotide identity values were 78.5 and 81.2 %, respectively. The genomic DNA G+C content was 54.9 mol%. Based on the phylogenetic, chemotaxonomic and genomic data obtained in the present study, we propose Tumebacillus amylolyticus sp. nov. to be a novel species within the genus
Tumebacillus
. The type strain is ITR2T (=KCTC 43280T=NBRC 114753T).
Collapse
Affiliation(s)
- Minchung Kang
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, South Korea
| | - Geeta Chhetri
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, South Korea
| | - Jiyoun Kim
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, South Korea
| | - Inhyup Kim
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, South Korea
| | - Yoonseop So
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, South Korea
| | - Taegun Seo
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, South Korea
| |
Collapse
|
9
|
Kang M, Seo T. Rhizobium setariae sp. nov., an Indole-3-Acetic Acid-Producing Bacterium Isolated from Green Foxtail, Setaria viridis. Curr Microbiol 2022; 79:162. [PMID: 35435479 DOI: 10.1007/s00284-022-02860-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Accepted: 03/30/2022] [Indexed: 11/30/2022]
Abstract
A Gram-negative, indole-3-acetic acid-producing, aerobic, motile strain, designated as KVB221T, was isolated from a green foxtail plant, Setaria viridis, from a park near the coast of Haeundae Beach, Busan, Republic of Korea. The 16S rRNA gene analysis revealed strain KVB221T to be a member of the genus Rhizobium, from which Rhizobium alvei TNR-22T (97.2%), Rhizobium daejeonense L61T (96.9%), and Rhizobium ipomoeae shin9-1T (95.7%) were selected for comparative analysis. Growth of the strain was observed at 10-50 °C (optimum 25-30 °C), at pH 5-10 (optimum pH 7), and in the presence of 0-8% NaCl (optimum 0%). The strain was observed to produce 36.3 ± 0.8 μg/ml of indole following 5 days of incubation. The major fatty acids are comprised of C16:0, C19:0 cyclo ω8c, C18:1 ω7c, and the unresolved group summed feature 8 (C18:1 ω7c and/or C18:1 ω6c), while major polar lipids are identified as phosphatidylcholine (PC), phosphatidylethanolamine (PE), phosphatidylglycerol (PG), and phosphatidylmonomethylethanolamine (PME). The predominant quinone is Q-10 and the DNA G+C content of the strain is 59.3%. Based on publicly available genome data between strain KVB221T and its closely related strains, the average nucleotide identity and in silico DNA-DNA hybridization values ranged from 72.7 to 73.1 and 19.7 to 20.4%, respectively. Based on the chemotaxonomic, phenotypic, and genomic comparisons reported here, we propose Rhizobium setariae sp. nov. as a novel species belonging to the genus Rhizobium. The type strain is KVB221T (= KACC 21713T = NBRC 114644T).
Collapse
Affiliation(s)
- Minchung Kang
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Taegun Seo
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea.
| |
Collapse
|
10
|
So Y, Chhetri G, Kim I, Kang M, Kim J, Lee B, Jang W, Seo T. Halomonas antri sp. nov., a carotenoid-producing bacterium isolated from surface seawater. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005272] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-negative, moderately halophilic bacterium, designated as strain Y3S6T, was isolated from a surface seawater sample collected from Dongangyoeng cave, Udo-myeon, Jeju-si, Jeju-do, Repulic of Korea. Cells of strain Y3S6T were aerobic, rod-shaped, non-sporulated, yellow, catalase- negative, oxidase-negative and motile with one polar flagellum. Growth of strain Y3S6T occurred at 15–40 °C (optimum: 25–30 °C), at pH 6.0–9.0 (optimum: pH 7.0) and in the presence of 0–13% NaCl (optimum: 1–6 %, w/v). The novel strain was able to produce carotenoids. Its chemotaxonomic and morphological characteristics were consistent with those of members of the genus
Halomonas
. Phylogenetic analysis of the 16S rRNA gene sequence revealed that strain Y3S6T formed a clade with
Halomonas pellis
L5T (98.97 %) and
Halomonas saliphila
LCB169T(98.90%). The average nucleotide identity and digital DNA–DNA hybridization values of strain Y3S6T with the most closely related strains for which whole genomes are publicly available were 82.3–85.2% and 62.8–66.1 %, respectively. The major fatty acids in strain Y3S6T were C16 : 0, C19 : 0 cyclo ω8c and summed feature 8 (composed of C18 : 1 ω7c and/or C18 : 1 ω6c), and the predominant quinone was Q-9. Its polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, two unidentified phosphoglycolipid, one unidentified phosphoaminoglycolipid and one unidentified phospholipid. The genomic DNA G+C content based on the draft genome sequence was 64.2 mol%. The results of physiological and biochemical tests and 16S rRNA sequence analysis clearly revealed that strain Y3S6T represents a novel species in the genus
Halomonas
, for which the name Halomonas antri sp. nov. has been proposed. The type strain is Y3S6T (=KACC 21536T=NBRC 114315=TBRC 15164T).
Collapse
Affiliation(s)
- Yoonseop So
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Geeta Chhetri
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Inhyup Kim
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Minchung Kang
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Jiyoun Kim
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Byungjo Lee
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Wonhee Jang
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Taegun Seo
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| |
Collapse
|
11
|
Dong L, Li S, Lian WH, Wei QC, Mohamad OAA, Hozzein WN, Ahmed I, Li WJ. Sphingomonas arenae sp. nov., isolated from desert soil. Int J Syst Evol Microbiol 2022; 72. [PMID: 35060847 DOI: 10.1099/ijsem.0.005195] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024] Open
Abstract
Two bacterial strains, designated as SYSU D00720T and SYSU D00722, were isolated from a desert sandy soil sample collected from Gurbantunggut Desert in Xinjiang, north-west China. Cells were Gram-stain-negative, aerobic, non-motile, rod-shaped, oxidase-positive and catalase-negative. Colonies were circular, opaque, convex, smooth, orange on Reasoner's 2A (R2A) agar. The isolates were found to grow at 4-45 °C (optimum, 28-30 °C), at pH 6.0-7.0 (optimum, 7.0) and with 0-1.5 % (w/v) NaCl (optimum, 0%). Growth was observed on R2A agar, Luria-Bertani agar and nutrient agar, but not on trypticase soy agar. The polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, sphingoglycolipid, two unidentified aminolipids, one unidentified glycolipid, one unidentified aminoglycolipid, one unidentified aminophospholipid, one unidentified phospholipid and two unidentified lipids. The main fatty acids (>10%) were C17 : 1 ω6c, summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c) and C16 : 0. The major respiratory quinone was ubiquinone-10 and the major polyamine was sym-homospermidine. The genomic DNA G+C content was 66.0 mol%. Strains SYSU D00720T and SYSU D00722 were nearly identical with a 16S rRNA gene sequence similarity of 99.6 %, and 100.0 % average nucleotide identity (ANI), average amino acid identity (AAI) and digital DNA-DNA hybridization (dDDH) values. Phylogenetic analyses clearly demonstrated that these two strains belonged to the same species of the genus Sphingomonas, and had highest sequence similarity to Sphingomonas lutea KCTC 23642T (97.3 %). The ANI, AAI and dDDH values of strains SYSU D00720T and SYSU D00722 to S. lutea KCTC 23642T were both 73.2, 69.9 and 19.2 %, respectively. Based on phylogenetic, phenotypic and chemotaxonomic distinctiveness, strains SYSU D00720T and SYSU D00722 represent a novel species of the genus Sphingomonas, for which the name Sphingomonas arenae sp. nov. is proposed. The type strain is SYSU D00720T (=MCCC 1K05154T=NBRC 115061T).
Collapse
Affiliation(s)
- Lei Dong
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Shuai Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Wen-Hui Lian
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Qi-Chuang Wei
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Osama Abdalla Abdelshafy Mohamad
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, PR China
| | - Wael N Hozzein
- Zoology Department, College of Science, King Saud University, Riyadh 999088, Saudi Arabia
- Botany and Microbiology Department, Faculty of Science, Beni-Suef University, Beni-Suef 62511, Egypt
| | - Iftikhar Ahmed
- National Culture Collection of Pakistan (NCCP), Bio-Resources Conservation Institute (BCI), National Agricultural Research Centre (NARC), Park Road, Islamabad 45500, Pakistan
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, PR China
| |
Collapse
|