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Park M, Kim J. Arthrobacter horti sp. nov., isolated from mountain soil. Int J Syst Evol Microbiol 2024; 74. [PMID: 39008344 DOI: 10.1099/ijsem.0.006459] [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: 07/16/2024] Open
Abstract
Gram-stain-positive, aerobic, rod-shaped strains, YJM1T and YJM12S, were isolated from Maebong Mountain, Dogok-dong, Gangnam-gu, Seoul, Republic of Korea. Strains YJM1T and YJM12S exhibited growth at 5-35 °C (optimum, 20-30 °C) and pH 6-9 (optimum, pH 7) and in 0-4 % (w/v) NaCl. Strains YJM1T and YJM12S showed highest 16S rRNA gene sequence similarity to the following members of the genus Arthrobacter: A. nanjingensis A33T (98.3 %/98.2 % similarity), A. woluwensis NBRC 107840T (98.2 %/98.1 %), A. humicola KV-653T (97.3 %), A. oryzae KV-651T (97.3 %), and A. globiformis NBRC 12137T (97.2 %). The strains grew well on Reasoner's 2A, nutrient, Mueller-Hinton, yeast-dextrose, and glucose-peptone-meat extract agars. The major polar lipids of strain YJM1T were phosphatidylglycerol, diphosphatidylglycerol, and phosphatidylinositol. The primary respiratory quinone of strain YJM1T was MK-9(H2), and the major fatty acids of strains YJM1T and YJM12S were anteiso-C15 : 0, anteiso-C17 : 0, iso-C15 : 0, and iso-C16 : 0. The DNA G+C content, based on the whole genome sequence of strain YJM1T, was 68.3 mol%. Average nucleotide identity values and digital DNA-DNA hybridization values between strain YJM1T and the reference strains ranged from 75.0 to 92.7 % and from 21.0 to 65.3 %, respectively. Strain YJM1T exhibited antimicrobial activity against Bacillus subtilis and Escherichia coli. Considering the chemotaxonomic, phenotypic, genotypic, and phylogenetic results, we propose the strain YJM1T represents a novel species in the genus Arthrobacter and suggest the name Arthrobacter horti sp. nov. (type strain YJM1T=KACC 23300T=JCM 36483T).
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Affiliation(s)
- Mingyeong Park
- Department of Life Science, College of Natural Sciences, Kyonggi University, Suwon, Kyonggi-Do 16227, Republic of Korea
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You Y, Woo CY, Kim J. Pedobacter montanisoli sp. nov., isolated from soil. Int J Syst Evol Microbiol 2023; 73. [PMID: 37216277 DOI: 10.1099/ijsem.0.005887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023] Open
Abstract
A white-pigmented, non-motile, Gram-stain-negative, rod-shaped bacterium, designated CYS-01T, was obtained from soil sampled at Suwon, Gyeonggi-do, Republic of Korea. Cells were strictly aerobic, grew optimally at 28 °C. Phylogenetic analysis based on its 16S rRNA gene sequence revealed that strain CYS-01T formed a lineage within the family Sphingobacteriaceae and clustered with members of the genus Pedobacter. The closest relatives were Pedobacter xixiisoli CGMCC 1.12803T (95.70 % sequence similarity), Pedobacter ureilyticus THG-T11T (95.35 %), Pedobacter helvus P-25T (95.28 %), Pedobacter chitinilyticus CM134L-2T (94.94 %), Pedobacter nanyangensis Q-4T (94.73 %) and Pedobacter zeaxanthinifaciens TDMA-5T (94.07 %). The principal respiratory quinone was MK-7 and the major polar lipids were phosphatidylethanolamine, an unidentified aminolipid, unidentified lipids and an unidentified glycolipid. The predominant cellular fatty acids were iso-C15 : 0, summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c) and iso-C17 : 0 3-OH. The DNA G+C content was 36.6 mol%. Based on the results of genomic, chemotaxonomic, phenotypic and phylogenetic analyses, strain CYS-01T represents novel species in the genus Pedobacter, for which the name Pedobacter montanisoli sp. nov. is proposed. The type strain is CYS-01T (=KACC 22655T=NBRC 115630T).
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Affiliation(s)
- Yelim You
- Department of Life Science, College of Natural Sciences, Kyonggi University, Suwon, Kyonggi-Do 16227, Republic of Korea
| | - Chae Yung Woo
- Department of Life Science, College of Natural Sciences, Kyonggi University, Suwon, Kyonggi-Do 16227, Republic of Korea
| | - Jaisoo Kim
- Department of Life Science, College of Natural Sciences, Kyonggi University, Suwon, Kyonggi-Do 16227, Republic of Korea
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Vasilyeva L, Grouzdev D, Koziaeva V, Berestovskaya Y, Novikov A, Pimenov N. Prosthecodimorpha staleyi gen. nov., sp. nov., Novel Prosthecate Bacteria within the Family Ancalomicrobiaceae and Reclassification of the Polyphyletic Genus Prosthecomicrobium. Microbiology (Reading) 2022. [DOI: 10.1134/s0026261722601105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Woo CY, Kim J. Variovorax terrae sp. nov. Isolated from Soil with Potential Antioxidant Activity. J Microbiol Biotechnol 2022; 32:855-861. [PMID: 35791077 PMCID: PMC9628916 DOI: 10.4014/jmb.2205.05018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/15/2022] [Accepted: 06/27/2022] [Indexed: 12/15/2022]
Abstract
A white-pigmented, non-motile, gram-negative, and rod-shaped bacterium, designated CYS-02T, was isolated from soil sampled at Suwon, Gyeonggi-do, Republic of Korea. Cells were strictly aerobic, grew optimally at 20-28ºC and hydrolyzed Tween 40. Phylogenetic analysis based on 16S rRNA gene sequence indicated that strain CYS-02T formed a lineage within the family Comamonadaceae and clustered as members of the genus Variovorax. The closest members were Variovorax guangxiensis DSM 27352T (98.6% sequence similarity), Variovorax paradoxus NBRC 15149T (98.5%), and Variovorax gossypii JM-310T (98.3%). The principal respiratory quinone was Q-8 and the major polar lipids contain phosphatidylethanolamine (PE), phosphatidylethanolamine (PG), and diphosphatidylglycerol (DPG). The predominant cellular fatty acids were C16:0, summed feature 3 (C16:1ω7c and/or C16:1ω6c) and summed feature 8 (C18:1ω7c and/or C18:1ω6c). The DNA GC content was 67.7 mol%. The ANI and dDDH values between strain CYS-02T and the closest members in the genus Variovorax were ≤ 79.0 and 22.4%, respectively, and the AAI and POCP values between CYS-02T and the other related species in the family Comamonadaceae were > 70% and > 50%, respectively. The genome of strain CYS-02T showed a putative terpene biosynthetic cluster responsible for antioxidant activity which was supported by DPPH radical scavenging activity test. Based on genomic, phenotypic and chemotaxonomic analyses, strain CYS-02T was classified into a novel species in the genus Variovorax, for which the name Variovorax terrae sp. nov., has been proposed. The type strain is CYS-02T (= KACC 22656T = NBRC 115645 [corrected] T).
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Affiliation(s)
- Chae Yung Woo
- Department of Life Science, College of Natural Sciences, Kyonggi University, Suwon 16227, Republic of Korea
| | - Jaisoo Kim
- Department of Life Science, College of Natural Sciences, Kyonggi University, Suwon 16227, Republic of Korea,Corresponding author Phone: +82-31-249-9648 Fax: +82-31-249-9604 E-mail:
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Dahal RH, Kim J, Chaudhary DK, Le TTN, Kim DU, Jang H, Kim J. Genome mining revealed polyhydroxybutyrate biosynthesis by Ramlibacter agri sp. nov., isolated from agriculture soil in Korea. Antonie van Leeuwenhoek 2022; 115:563-572. [PMID: 35305190 DOI: 10.1007/s10482-022-01721-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 02/16/2022] [Indexed: 11/25/2022]
Abstract
A white-colony-forming, facultative anaerobic, motile and Gram-stain-negative bacterium, designated G-1-2-2 T was isolated from soil of agriculture field near Kyonggi University, Republic of Korea. Strain G-1-2-2 T synthesized the polyhydroxybutyrate and could grow at 10-35 °C. The phylogenetic analysis based on 16S rRNA gene sequence showed that, strain G-1-2-2 T formed a lineage within the family Comamonadaceae and clustered as a member of the genus Ramlibacter. The 16S rRNA gene sequence of strain G-1-2-2 T showed high sequence similarities with Ramlibacter ginsenosidimutans BXN5-27 T (97.9%), Ramlibacter monticola G-3-2 T (97.9%) and Ramlibacter alkalitolerans CJ661T (97.5%). The sole respiratory quinone was ubiquinone-8 (Q-8). The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, and an unidentified phospholipid. The principal cellular fatty acids were C16:0, cyclo-C17:0, summed feature 3 (C16:1ω7c and/or C16:1ω6c) and summed feature 8 (C18:1ω7c and/or C18:1ω6c). The genome of strain G-1-2-2 T was 7,200,642 bp long with 13 contigs, 6,647 protein-coding genes, and DNA G + C content of 68.9%. The average nucleotide identity and in silico DNA-DNA hybridization values between strain G-1-2-2 T and close members were ≤ 81.2 and 24.1%, respectively. The genome of strain G-1-2-2 T showed eight putative biosynthetic gene clusters responsible for various secondary metabolites. Genome mining revealed the presence of atoB, atoB2, phaS, phbB, phbC, and bhbD genes in the genome which are responsible for polyhydroxybutyrate biosynthesis. Based on these data, strain G-1-2-2 T represents a novel species in the genus Ramlibacter, for which the name Ramlibacter agri sp. nov. is proposed. The type strain is G-1-2-2 T (= KACC 21616 T = NBRC 114389 T).
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Affiliation(s)
- Ram Hari Dahal
- Department of Life Science, College of Natural Sciences, Kyonggi University, Suwon, Kyonggi-Do, 16227, Republic of Korea
- Department of Microbiology, School of Medicine, Kyungpook National University, Daegu, 41944, Republic of Korea
| | - Jungmin Kim
- Department of Microbiology, School of Medicine, Kyungpook National University, Daegu, 41944, Republic of Korea
| | - Dhiraj Kumar Chaudhary
- Department of Environmental Engineering, Korea University Sejong Campus, Sejong City, 30019, Republic of Korea
| | - Thi Tuyet Nhan Le
- Department of Life Science, College of Natural Sciences, Kyonggi University, Suwon, Kyonggi-Do, 16227, Republic of Korea
| | - Dong-Uk Kim
- Department of Biological Science, College of Science and Engineering, Sangji University, Wonju, Republic of Korea
| | - Hyein Jang
- School of Cosmetic Science and Beauty Biotechnology, Semyung University, Jecheon, Republic of Korea.
| | - Jaisoo Kim
- Department of Life Science, College of Natural Sciences, Kyonggi University, Suwon, Kyonggi-Do, 16227, Republic of Korea.
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Bedics A, Banerjee S, Bóka K, Tóth E, Benedek T, Kriszt B, Táncsics A. Pinisolibacter aquiterrae sp. nov., a novel aromatic hydrocarbon-degrading bacterium isolated from benzene-, and xylene-degrading enrichment cultures, and emended description of the genus Pinisolibacter. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005229] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two Gram-reaction-negative strains, designated as B13T and MA2-2, were isolated from two different aromatic hydrocarbon-degrading enrichment cultures and characterized using a polyphasic approach to determine their taxonomic position. The two strains had identical 16S rRNA gene sequences and were most closely related to
Pinisolibacter ravus
E9T (97.36 %) and
Siculibacillus lacustris
SA-279T (96.33 %). Cells were facultatively aerobic rods and motile with a single polar flagellum. The strains were able to degrade ethylbenzene as sole source of carbon and energy. The assembled genome of strain B13T had a total length of 4.91 Mb and the DNA G+C content was 68.8 mol%. The predominant fatty acids (>5 % of the total) of strains B13T and MA2-2 were C18 : 1
ω7c/C18 : 1
ω6c, C16 : 1
ω7c/C16 : 1
ω6c and C16 : 0. The major ubiquinone of strain B13T was Q10, while the major polar lipids were phosphatidyl-N-methylethanolamine, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and a phospholipid. Based on phenotypic characteristics and phylogenetic data, it is concluded that strains B13T and MA2-2 are members of the genus
Pinisolibacter
and represent a novel species for which the name Pinisolibacter aquiterrae sp. nov. is proposed. The type strain of the species is strain B13T (=LMG 32346T=NCAIM B.02665T).
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Affiliation(s)
- Anna Bedics
- Department of Molecular Ecology, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, Gödöllő, Hungary
| | - Sinchan Banerjee
- Department of Molecular Ecology, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, Gödöllő, Hungary
| | - Károly Bóka
- Department of Plant Anatomy, Eötvös Loránd University, Budapest, Hungary
| | - Erika Tóth
- Department of Microbiology, Eötvös Loránd University, Budapest, Hungary
| | - Tibor Benedek
- Department of Molecular Ecology, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, Gödöllő, Hungary
| | - Balázs Kriszt
- Department of Environmental Safety, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, Gödöllő, Hungary
| | - András Táncsics
- Department of Molecular Ecology, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, Gödöllő, Hungary
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Abstract
A yellow-pigmented, non-motile, Gram-stain-negative, rod-shaped bacterium, designated II4T was obtained from soil sampled at Seongnam, Gyeonggi-do, Republic of Korea. Cells were strictly aerobic, grew optimally at 20–28 °C and hydrolysed casein. A phylogenetic analysis based on its 16S rRNA gene sequence revealed that strain II4T formed a lineage within the family
Xanthomonadaceae
and clustered as members of the genus
Lysobacter
. The closest members were
Lysobacter terrae
THG-A13T (97.88 % sequence similarity),
Lysobacter niabensis
GH34-4T (97.82 %),
Lysobacter oryzae
YC6269T (97.74%),
Lysobacter yangpyeongensis
GH19-3T (97.53 %) and
Lysobacter enzymogenes
ATCC 29487T (96.18 %). The principal respiratory quinone was Q-8 and the major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The predominant cellular fatty acids were summed feature 9 (C16 : 0 10-methyl and/or iso-C17 : 1
ω9c) and iso-C15 : 0 and iso-C16 : 0. The DNA G+C content was 68.2 mol%. The average nucleotide identity and in silico DNA–DNA hybridization relatedness values between strain II4T and its closely related genus members with possible full genome sequences were ≤79.6 and 23.7 %, respectively. Based on genomic, chemotaxonomic, phenotypic and phylogenetic data, strain II4T represents novel species in the genus
Lysobacter
, for which the name Lyobacter terrestris sp. nov. is proposed. The type strain is II4T (=KACC 21196T=NBRC 113956T).
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Affiliation(s)
- Chae Yung Woo
- Department of Life Science, College of Natural Sciences, Kyonggi University, Suwon, Kyonggi-Do 16227, Republic of Korea
| | - Jaisoo Kim
- Department of Life Science, College of Natural Sciences, Kyonggi University, Suwon, Kyonggi-Do 16227, Republic of Korea
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Dahal RH, Kim J, Chaudhary DK, Kim DU, Kim J. Description of antibiotic-producing novel bacteria Paraburkholderia antibiotica sp. nov. and Paraburkholderia polaris sp. nov. Int J Syst Evol Microbiol 2021; 71. [PMID: 34694983 DOI: 10.1099/ijsem.0.005060] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two white colony-forming, Gram-stain-negative, non-sporulating and motile bacteria, designated G-4-1-8T and RP-4-7T, were isolated from forest soil and Arctic soil, respectively. Both strains showed antimicrobial activity against Gram-negative pathogens (Pseudomonas aeruginosa and Escherichia coli) and could grow at a pH range of pH 4.0-11.0 (optimum, pH 7.0-9.0). Phylogenetic analyses based on their 16S rRNA gene sequences indicated that strains G-4-1-8T and RP-4-7T formed a lineage within the family Burkholderiaceae and were clustered as members of the genus Paraburkholderia. Strain G-4-1-8T showed the highest 16S rRNA sequence similarity to Paraburkholderia monticola JC2948T (98.1 %), while strain RP-4-7T showed the highest similarity to Paraburkholderia metrosideri DNBP6-1T (98.8 %). The only respiratory quinone in both strains was ubiquinone Q-8. Their principal cellular fatty acids were C16 : 0, cyclo-C17 : 0, summed feature 3 (iso-C15 :0 2-OH and/or C16 :1 ω7c) and summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c). Their major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and an unidentified aminophospholipid. The DNA G+C content of strains G-4-1-8T and RP-4-7T were 63.7 and 61.3 mol%, respectively, while their genome lengths were 7.44 and 9.67 Mb, respectively. The genomes of both strains showed at least 12 putative biosynthetic gene clusters. The average nucleotide identity and in silico DNA-DNA hybridization relatedness values between both strains and most closely related Paraburkholderia species were below the species threshold values. Based on a polyphasic study, these isolated strains represent novel species belonging to the genus Paraburkholderia, for which the names Paraburkholderia antibiotica sp. nov. (G-4-1-8T= KACC 21617T=NBRC 114603T) and Paraburkholderia polaris sp. nov. (RP-4-7T=KACC 21621T=NBRC 114605T) are proposed.
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Affiliation(s)
- Ram Hari Dahal
- Department of Life Science, College of Natural Sciences, Kyonggi University, Suwon, Kyonggi-Do 16227, Republic of Korea.,Department of Microbiology, School of Medicine, Kyungpook National University, Daegu 41944, Republic of Korea
| | - Jungmin Kim
- Department of Microbiology, School of Medicine, Kyungpook National University, Daegu 41944, Republic of Korea
| | - Dhiraj Kumar Chaudhary
- Department of Environmental Engineering, Korea University Sejong Campus, Sejong City 30019, Republic of Korea
| | - Dong-Uk Kim
- Department of Biological Science, College of Science and Engineering, Sangji University, Wonju, Republic of Korea
| | - Jaisoo Kim
- Department of Life Science, College of Natural Sciences, Kyonggi University, Suwon, Kyonggi-Do 16227, Republic of Korea
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Characterization of Terrihabitans soli gen. nov., sp. nov., a Novel 0.2 μm-Filterable Soil Bacterium Belonging to a Widely Distributed Lineage of Hyphomicrobiales (Rhizobiales). DIVERSITY 2021. [DOI: 10.3390/d13090422] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
We previously showed that novel filterable bacteria remain in “sterile” (<0.2 μm filtered) terrestrial environmental samples from Japan, China, and Arctic Norway. Here, we characterized the novel filterable strain IZ6T, a representative strain of a widely distributed lineage. Phylogenetic analysis showed that this strain was affiliated with the Rhizobiales (now proposed as Hyphomicrobiales) of Alphaproteobacteria, but distinct from any other type strains. Strain IZ6T shared the following chemotaxonomic features with the closest (but distantly) related type strain, Flaviflagellibacter deserti SYSU D60017T: ubiquinone-10 as the major quinone; phosphatidylethanolamine, phosphatidylcholine, and phosphatidylglycerol as major polar lipids; and slightly high G+C content of 62.2 mol%. However, the cellular fatty acid composition differed between them, and the unsaturated fatty acid (C18:1ω7c/C18:1ω6c) was predominantly found in our strain. Moreover, unlike methyrotrophs and nitrogen-fixers of the neighboring genera of Hyphomicrobiales (Rhizobiales), strain IZ6T cannot utilize a one-carbon compound (e.g., methanol) and fix atmospheric nitrogen gas. These findings were consistent with the genome-inferred physiological potential. Based on the phylogenetic, physiological, and chemotaxonomic traits, we propose that strain IZ6T represents a novel genus and species with the name Terrihabitans soli gen. nov., sp. nov. (=NBRC 106741T = NCIMB 15058T). The findings will provide deeper insight into the eco-physiology of filterable microorganisms.
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Dahal RH, Chaudhary DK, Kim DU, Kim J. Azohydromonas caseinilytica sp. nov., a Nitrogen-Fixing Bacterium Isolated From Forest Soil by Using Optimized Culture Method. Front Microbiol 2021; 12:647132. [PMID: 34093463 PMCID: PMC8175650 DOI: 10.3389/fmicb.2021.647132] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 04/13/2021] [Indexed: 11/20/2022] Open
Abstract
A bacterial strain, designated strain G-1-1-14T, was isolated from Kyonggi University forest soil during a study of previously uncultured bacterium. The cells of strain G-1-1-14T were motile by means of peritrichous flagella, Gram-stain-negative, rod-shaped, and able to grow autotrophically with hydrogen and fix nitrogen. Phylogenetic analysis based on 16S rRNA gene sequence indicated that strain G-1-1-14T belonged to the genus Azohydromonas. The closest species of strain G-1-1-14T were Azohydromonas ureilytica UCM-80T (98.4% sequence similarity), Azohydromonas lata IAM 12599T (97.5%), Azohydromonas riparia UCM-11T (97.1%), and Azohydromonas australica IAM 12664T (97.0%). The genome of strain G-1-1-14T was 6,654,139 bp long with 5,865 protein-coding genes. The genome consisted of N2-fixing genes (nifH) and various regulatory genes for CO2 fixation and H2 utilization. The principal respiratory quinone was ubiquinone-8, and the major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, and phosphatidylglycerol. The major fatty acids were summed feature 3 (iso-C15:0 2-OH and/or C16:1ω7c), C16:0, summed feature 8 (C18:1ω7c and/or C18:1ω6c), and cyclo-C17:0. The DNA G + C content was 69.9%. The average nucleotide identity (OrthoANI), in silico DNA–DNA hybridization (dDDH), and conventional DDH relatedness values were below the species demarcation values for novel species. Based on genomic, genetic, phylogenetic, phenotypic, and chemotaxonomic characterizations, strain G-1-1-14T represents a novel species within the genus Azohydromonas, for which the name Azohydromonas caseinilytica sp. nov. is proposed. The type strain is G-1-1-14T (= KACC 21615T = NBRC 114390T).
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Affiliation(s)
- Ram Hari Dahal
- Department of Life Sciences, College of Natural Sciences, Kyonggi University, Suwon-si, South Korea.,Department of Microbiology, School of Medicine, Kyungpook National University, Daegu, South Korea
| | - Dhiraj Kumar Chaudhary
- Department of Life Sciences, College of Natural Sciences, Kyonggi University, Suwon-si, South Korea.,Department of Environmental Engineering, Korea University Sejong Campus, Sejong City, South Korea
| | - Dong-Uk Kim
- Department of Biological Science, College of Science and Engineering, Sangji University, Wonju-si, South Korea
| | - Jaisoo Kim
- Department of Life Sciences, College of Natural Sciences, Kyonggi University, Suwon-si, South Korea
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Dahal RH, Chaudhary DK, Kim J. Genome insight and description of antibiotic producing Massilia antibiotica sp. nov., isolated from oil-contaminated soil. Sci Rep 2021; 11:6695. [PMID: 33758279 PMCID: PMC7988111 DOI: 10.1038/s41598-021-86232-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 03/05/2021] [Indexed: 01/08/2023] Open
Abstract
An ivory-coloured, motile, Gram-stain-negative bacterium, designated TW-1T was isolated from oil-contaminated experimental soil in Kyonggi University. The phylogenetic analysis based on 16S rRNA gene sequence revealed, strain TW-1T formed a lineage within the family Oxalobacteraceae and clustered as members of the genus Massilia. The closest members were M. pinisoli T33T (98.8% sequence similarity), M. putida 6NM-7T (98.6%), M. arvi THG-RS2OT (98.5%), M. phosphatilytica 12-OD1T (98.3%) and M. niastensis 5516S-1T (98.2%). The sole respiratory quinone is ubiquinone-8. The major cellular fatty acids are hexadeconic acid, cis-9, methylenehexadeconic acid, summed feature 3 and summed feature 8. The major polar lipids are phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. The DNA G + C content of the type strain is 66.3%. The average nucleotide identity (ANI) and in silico DNA–DNA hybridization (dDDH) relatedness values between strain TW-1T and closest members were below the threshold value for species demarcation. The genome size is 7,051,197 bp along with 46 contigs and 5,977 protein-coding genes. The genome showed 5 putative biosynthetic gene clusters (BGCs) that are responsible for different secondary metabolites. Cluster 2 showed thiopeptide BGC with no known cluster blast, indicating TW-1T might produce novel antimicrobial agent. The antimicrobial assessment also showed that strain TW-1T possessed inhibitory activity against Gram-negative pathogens (Escherichia coli and Pseudomonas aeruginosa). This is the first report of the species in the genus Massilia which produces antimicrobial compounds. Based on the polyphasic study, strain TW-1T represents novel species in the genus Massilia, for which the name Massilia antibiotica sp. nov. is proposed. The type strain is TW-1T (= KACC 21627T = NBRC 114363T).
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Affiliation(s)
- Ram Hari Dahal
- Department of Life Science, College of Natural Sciences, Kyonggi University, Suwon, Kyonggi-Do, 16227, Republic of Korea.,Department of Microbiology, School of Medicine, Kyungpook National University, Daegu, 41944, Republic of Korea
| | - Dhiraj Kumar Chaudhary
- Department of Life Science, College of Natural Sciences, Kyonggi University, Suwon, Kyonggi-Do, 16227, Republic of Korea.,Department of Environmental Engineering, Korea University Sejong Campus, Sejong City, 30019, Republic of Korea
| | - Jaisoo Kim
- Department of Life Science, College of Natural Sciences, Kyonggi University, Suwon, Kyonggi-Do, 16227, Republic of Korea.
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Chaudhary DK, Dahal RH, Kim DU, Kim J. Novosphingobium olei sp. nov., with the ability to degrade diesel oil, isolated from oil-contaminated soil and proposal to reclassify Novosphingobium stygium as a later heterotypic synonym of Novosphingobium aromaticivorans. Int J Syst Evol Microbiol 2021; 71. [PMID: 33411666 DOI: 10.1099/ijsem.0.004628] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two yellow-pigmented, non-motile, Gram-stain-negative, and rod-shaped bacteria, designated TW-4T and TNP-2 were obtained from oil-contaminated soil. Both strains degrade diesel oil, hydrolyse aesculin, DNA, Tween 40 and Tween 60. A phylogenetic analysis based on its 16S rRNA gene sequence revealed that strain TW-4T formed a lineage within the family Erythrobacteraceae and clustered as members of the genus Novosphingobium. The closest members of strain TW-4T were Novosphingobium subterraneum DSM 12447T (97.9 %, sequence similarity), Novosphingobium lubricantis KSS165-70T (97.8 %), Novosphingobium taihuense T3-B9T (97.8 %), Novosphingobium aromaticivorans DSM 12444T (97.7 %), Novosphingobium flavum UCT-28T (97.7 %), and Novosphingobium bradum STM-24T (97.6 %). The sequence similarity for other members was ≤97.6 %. The genome of strain TW-4T was 4 683 467 bp long with 44 scaffolds and 4280 protein-coding genes. The sole respiratory quinone was Q-10. The major cellular fatty acids were summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c), summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), C16 : 0 and C14 : 0 2-OH. The major polar lipids were phosphatidylethanolamine (PE), phosphatidylglycerol (PG), diphosphatidylglycerol (DPG), phosphatidylcholine (PC), phosphatidyl-n-methylethanolamine (PME) and sphingoglycolipid (SGL). The DNA G+C content of the type strain was 65.0 %. The average nucleotide identity (ANIu) and in silico DNA-DNA hybridization (dDDH) relatedness values between strain TW-4T and closest members were below the threshold value for species delineation. Based on polyphasic taxonomic analyses, strain TW-4T represents novel species in the genus Novosphingobium, for which the name Novosphingobium olei sp. nov. is proposed. The type strain is TW-4T (=KACC 21628T=NBRC 114364T) and strain TNP-2 (=KACC 21629=NBRC 114365) represents an additional strain. Based on new data obtained in this study, it is also proposed to reclassify Novosphingobium stygium as a later heterotypic synonym of Novosphingobium aromaticivorans.
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Affiliation(s)
- Dhiraj Kumar Chaudhary
- Department of Environmental Engineering, College of Science and Technology, Korea University Sejong Campus, 2511 Sejong-ro, Sejong City, 30019, Republic of Korea.,Department of Life Science, College of Natural Sciences, Kyonggi University, Suwon, Kyonggi-Do 16227, Republic of Korea
| | - Ram Hari Dahal
- Department of Life Science, College of Natural Sciences, Kyonggi University, Suwon, Kyonggi-Do 16227, Republic of Korea
| | - Dong-Uk Kim
- Department of Biological Science, College of Science and Engineering, Sangji University, Wonju, Republic of Korea
| | - Jaisoo Kim
- Department of Life Science, College of Natural Sciences, Kyonggi University, Suwon, Kyonggi-Do 16227, Republic of Korea
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13
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Dahal RH, Chaudhary DK, Kim DU, Kim J. Chitinophaga fulva sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 2021; 71. [PMID: 33470923 DOI: 10.1099/ijsem.0.004646] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An aerobic, Gram-stain-negative, oxidase- and catalase-positive, non-motile, non-spore-forming, rod-shaped and yellow-coloured bacterium designated strain G-6-1-13T was isolated from Gwanggyo mountain forest soil. Strain G-6-1-13T could grow at 15-40 °C (optimum, 20-32 °C), pH 4.5-10.5 (optimum, pH 6.0-9.0), at 2 % (w/v) NaCl concentration, and produced flexirubin-type pigments. Phylogenetic analysis based on its 16S rRNA gene sequence showed that strain G-6-1-13T formed a lineage within the genus Chitinophaga that was distinct from other species of the genus. Closest member was Chitinophaga varians 10-7 W-9003T (98.6 % sequence similarity) followed by C. eiseniae DSM 22224T (98.4 %), C. qingshengii JN246T (97.6 %) and C. terrae KP01T (97.4%). The major cellular fatty acids were iso-C15 : 0, C16 : 1 ω5c, and summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1 ω6c). MK-7 was the sole respiratory quinone. The major polar lipids were phosphatidylethanolamine and an unidentified phospholipid. The DNA G+C content of strain G-6-1-13T was 48.7 mol%. Average nucleotide identity and in silico DNA-DNA hybridization were below the species threshold. On the basis of phenotypic, genotypic, phylogenetic and chemotaxonomic characterization, G-6-1-13T represents a novel species in the genus Chitinophaga, for which the name Chitinophaga fulva sp. nov. is proposed. The type strain is G-6-1-13T (=KACC 21624T=NBRC 114361T).
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Affiliation(s)
- Ram Hari Dahal
- Department of Microbiology, School of Medicine, Kyungpook National University, Daegu 14944, Republic of Korea.,Department of Life Science, College of Natural Sciences, Kyonggi University, Suwon, Kyonggi-Do 16227, Republic of Korea
| | - Dhiraj Kumar Chaudhary
- Department of Environmental Engineering, Korea University Sejong Campus, Sejong City 30019, Republic of Korea.,Department of Life Science, College of Natural Sciences, Kyonggi University, Suwon, Kyonggi-Do 16227, Republic of Korea
| | - Dong-Uk Kim
- Department of Biological Science, College of Science and Engineering, Sangji University, Wonju, Republic of Korea
| | - Jaisoo Kim
- Department of Life Science, College of Natural Sciences, Kyonggi University, Suwon, Kyonggi-Do 16227, Republic of Korea
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14
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Dahal RH, Lee H, Chaudhary DK, Kim DY, Son J, Kim J, Ka JO, Kim DU. Caenimonas soli sp. nov., isolated from soil. Arch Microbiol 2020; 203:1123-1129. [PMID: 33174135 DOI: 10.1007/s00203-020-02110-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 10/07/2020] [Accepted: 10/23/2020] [Indexed: 11/25/2022]
Abstract
A non-motile, Gram-stain-negative, rod-shaped bacterium, designated strain S4T, was obtained from soil sampled at Wonju, Gyeonggi-do, Republic of Korea. Cells were white-coloured, aerobic, grew optimally at 25-32 °C on R2A agar plate. A phylogenetic analysis based on its 16S rRNA gene sequence revealed that strain S4T formed a lineage within the family Comamonadaceae. The closest members were Caenimonas terrae SGM1-15T (98.1% sequence similarity), Caenimonas koreensis EMB320T (97.5%) and Ramlibacter solisilvae 5-10T (97.8%). The sequence similarities of strain S4T with other members of the family Comamonadaceae were ≤ 97.5%. The sole respiratory quinone was ubiquinone-8 (Q-8) and the principal polar lipid was phosphatidylethanolamine. The predominant cellular fatty acids were summed feature 3 (iso-C15 :0 2-OH/C16 :1 ω7c), C16:0 and summed feature 8 (C18:1 ω7c and/or C18:1 ω6c). The DNA G + C content was 65.1 mol%. In addition, the average nucleotide identity (ANIu) and in silico DNA-DNA hybridization (dDDH) relatedness values between strain S4T and Caenimonas koreensis were 77.6 and 21%, respectively. Based on genomic, chemotaxonomic, phenotypic, and phylogenetic analyses, strain S4T represents a novel species in the genus Caenimonas, for which the name Caenimonas soli sp. nov. is proposed. The type strain is S4T (= KCTC 72742T = NBRC 114610T).
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Affiliation(s)
- Ram Hari Dahal
- Department of Life Science, College of Natural Sciences, Kyonggi University, Suwon, Kyonggi-Do, 16227, Republic of Korea
| | - Hyosun Lee
- Department of Biological Science, College of Science and Engineering, Sangji University, Wonju, 26339, Republic of Korea
| | - Dhiraj Kumar Chaudhary
- Department of Environmental Engineering, Korea University, Sejong City, 30019, Republic of Korea
| | - Dae-Young Kim
- Department of Biological Science, College of Science and Engineering, Sangji University, Wonju, 26339, Republic of Korea
| | - Jigwan Son
- Department of Agricultural Biotechnology and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jaisoo Kim
- Department of Life Science, College of Natural Sciences, Kyonggi University, Suwon, Kyonggi-Do, 16227, Republic of Korea
| | - Jong-Ok Ka
- Department of Agricultural Biotechnology and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Dong-Uk Kim
- Department of Biological Science, College of Science and Engineering, Sangji University, Wonju, 26339, Republic of Korea.
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15
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Chryseobacterium cheonjiense sp. nov., isolated from forest soil. Arch Microbiol 2020; 203:725-731. [PMID: 33047174 DOI: 10.1007/s00203-020-02065-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 08/30/2020] [Accepted: 09/30/2020] [Indexed: 10/23/2022]
Abstract
A yellow-pigmented, non-motile and rod-shaped bacterium, designated RJ-7-14T was obtained from forest soil sampled at Cheonji-dong, Seogwipo-si, Jeju-do, South Korea. Cells were Gram-stain-negative and produced flexirubin type pigments. A phylogenetic analysis based on its 16S rRNA gene sequence revealed that strain RJ-7-14T formed a lineage within the family Weeksellaceae and clustered as members of the genus Chryseobacterium. The closest members were Chryseobacterium geocarposphaerae DSM 27617T (98.2% sequence similarity), Chryseobacterium hispalense DSM 25574T (98.0%) and Chryseobacterium nepalense KACC 18907T (98.0%). The sequence similarity for other members was < 98.0%. The genome was 4,276,416 bp long with 9 scaffolds and 3779 protein-coding genes. The sole respiratory quinone was MK-6. The major cellular fatty acids were iso-C15:0, summed feature 9 (iso-C17:1 ω9c and/or C16:0 10-methyl), summed feature 3 (iso-C15:0 2-OH and/or C16: 1ω7c) and iso-C17:0 3-OH. The major polar lipid was phosphatidylethanolamine (PE). The DNA G + C content of the type strain was 37.2 mol%. In addition, the average nucleotide identity (ANIu) and in silico DNA-DNA hybridization (dDDH) relatedness values between strain RJ-7-14T and phylogenetically closest members were ≤ 88.2% and ≤ 35.0%, respectively, which were below the threshold values of 95-96% (for ANI) and 70% (for dDDH), suggesting the allocation of novel strain to a new species. Based on genomic, chemotaxonomic, phenotypic and phylogenetic analyses, strain RJ-7-14T represents novel species in the genus Chryseobacterium, for which the name Chryseobacterium cheonjiense sp. nov. is proposed. The type strain is RJ-7-14T (= KACC 21625T = NBRC 114362T).
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16
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Chryseobacterium antibioticum sp. nov. with antimicrobial activity against Gram-negative bacteria, isolated from Arctic soil. J Antibiot (Tokyo) 2020; 74:115-123. [DOI: 10.1038/s41429-020-00367-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 08/06/2020] [Accepted: 08/16/2020] [Indexed: 11/09/2022]
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17
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Dahal RH, Chaudhary DK, Kim DU, Kim J. Zoogloea dura sp. nov., a N 2-fixing bacterium isolated from forest soil and emendation of the genus Zoogloea and the species Zoogloea oryzae and Zoogloea ramigera. Int J Syst Evol Microbiol 2020; 70:5312-5318. [PMID: 32841112 DOI: 10.1099/ijsem.0.004416] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A motile, Gram-stain-negative, rod-shaped bacterium, designated G-4-1-14T, was obtained from forest soil sampled at Gwanggyo mountain, Gyeonggi-do, Republic of Korea. Cells were colourless, aerobic, grew optimally at 28-35 °C and hydrolysed DNA and casein. Phylogenetic analysis based on its 16S rRNA gene sequence revealed that strain G-4-1-14T formed a lineage within the genus Zoogloea. The closest members were Zoogloea resiniphila ATCC 70068T (98.6 % sequence similarity), Zoogloea caeni EMB43T (98.2 %), Zoogloea oryzae A-7T (97.7 %), Zoogloea ramigera IAM 12136T (96.9 %) and Zoogloea oleivorans BucT (96.2 %). The major respiratory quinone was ubiquinone-8 and the principal polar lipids were phosphatidylethanolamine, phosphatidyl-N-methylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. The predominant cellular fatty acids were summed feature 3 (iso-C15 :0 2-OH/C16 : 1 ω7c) and C16 : 0. The DNA G+C content was 65.9 mol%. The average nucleotide identity and digital DNA-DNA hybridization relatedness values between strain G-4-1-14T and other type strains were ≤81.6 and ≤24.9 %, respectively, which are below the species demarcation thresholds. Based on the results of phenotypic, phylogenetic and genomic analyses, strain G-4-1-14T represents a novel species in the genus Zoogloea, for which the name Zoogloea dura sp. nov. is proposed. The type strain is G-4-1-14T (=KACC 21618T=NBRC 114358T). In addition, we propose emendation of the genus Zoogloea and the species Zoogloea oryzae and Zoogloea ramigera.
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Affiliation(s)
- Ram Hari Dahal
- Department of Life Science, College of Natural Sciences, Kyonggi University, Suwon, Kyonggi-Do 16227, Republic of Korea
| | - Dhiraj Kumar Chaudhary
- Department of Environmental Engineering, Korea University Sejong Campus, Sejong City 30019, Republic of Korea
| | - Dong-Uk Kim
- Department of Biological Science, College of Science and Engineering, Sangji University, Wonju, Republic of Korea
| | - Jaisoo Kim
- Department of Life Science, College of Natural Sciences, Kyonggi University, Suwon, Kyonggi-Do 16227, Republic of Korea
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18
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Dahal RH, Chaudhary DK, Kim DU, Kim J. Hymenobacter polaris sp. nov., a psychrotolerant bacterium isolated from an Arctic station. Int J Syst Evol Microbiol 2020; 70:4890-4896. [PMID: 32730196 DOI: 10.1099/ijsem.0.004356] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
A pink-pigmented, non-motile, Gram-stain-negative, rod-shaped bacterium, designated RP-2-7T, was obtained from soil sampled at the Arctic station, Spitsbergen, Svalbard, Norway. Cells were strictly aerobic, psychrotolerant, grew optimally at 15-20 °C and hydrolysed CM-cellulose. Phylogenetic analysis based on its 16S rRNA gene sequence revealed that strain RP-2-7T formed a lineage within the family Hymenobacteraceae and clustered with members of the genus Hymenobacter. Its closest relative was Hymenobacter marinus KJ035T (97.6 % sequence similarity). The sequence similarities to other strains were ≤96.9 %. The principal respiratory quinone was MK-7 and the major polar lipids were phosphatidylethanolamine and an unidentified aminophospholipid. The predominant cellular fatty acids were summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), anteiso-C15 : 0, iso-C15 : 0, C16 : 1 ω5c and summed featured 4 (iso-C17 : 1 I and/or anteiso-C17 : 1 B). The DNA G+C content was 62.8 mol%. In addition, the average nucleotide identity and in silico DNA-DNA hybridization relatedness values between strain RP-2-7T and closely related strains were lower than species demarcation thresholds. Based on the resuls of genomic, chemotaxonomic, phenotypic and phylogenetic analyses, strain RP-2-7T represents novel species in the genus Hymenobacter, for which the name Hymenobacter polaris sp. nov. is proposed. The type strain is RP-2-7T (=KACC 21670T=NBRC 114391T).
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Affiliation(s)
- Ram Hari Dahal
- Department of Life Science, College of Natural Sciences, Kyonggi University, Suwon, Kyonggi-Do 16227, Republic of Korea
| | - Dhiraj Kumar Chaudhary
- Department of Environmental Engineering, Korea University, Sejong City 30019, Republic of Korea
| | - Dong-Uk Kim
- Department of Biological Science, College of Science and Engineering, Sangji University, Wonju, Republic of Korea
| | - Jaisoo Kim
- Department of Life Science, College of Natural Sciences, Kyonggi University, Suwon, Kyonggi-Do 16227, Republic of Korea
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Hördt A, López MG, Meier-Kolthoff JP, Schleuning M, Weinhold LM, Tindall BJ, Gronow S, Kyrpides NC, Woyke T, Göker M. Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria. Front Microbiol 2020; 11:468. [PMID: 32373076 PMCID: PMC7179689 DOI: 10.3389/fmicb.2020.00468] [Citation(s) in RCA: 259] [Impact Index Per Article: 64.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 03/04/2020] [Indexed: 11/13/2022] Open
Abstract
The class Alphaproteobacteria is comprised of a diverse assemblage of Gram-negative bacteria that includes organisms of varying morphologies, physiologies and habitat preferences many of which are of clinical and ecological importance. Alphaproteobacteria classification has proved to be difficult, not least when taxonomic decisions rested heavily on a limited number of phenotypic features and interpretation of poorly resolved 16S rRNA gene trees. Despite progress in recent years regarding the classification of bacteria assigned to the class, there remains a need to further clarify taxonomic relationships. Here, draft genome sequences of a collection of genomes of more than 1000 Alphaproteobacteria and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa recognized as problematic long ago but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera and of a variety of genera to other families. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which are confirmed as valuable taxonomic markers. Similarly, analysis of the gene content was shown to provide valuable taxonomic insights in the class. Significant incongruities between 16S rRNA gene and whole genome trees were not found in the class. The incongruities that became obvious when comparing the results of the present study with existing classifications appeared to be caused mainly by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. Another probable cause of misclassifications in the past is the partially low overall fit of phenotypic characters to the sequence-based tree. Even though a significant degree of phylogenetic conservation was detected in all characters investigated, the overall fit to the tree varied considerably.
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Affiliation(s)
- Anton Hördt
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Marina García López
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Jan P. Meier-Kolthoff
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Marcel Schleuning
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Lisa-Maria Weinhold
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czechia
| | - Brian J. Tindall
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Sabine Gronow
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Nikos C. Kyrpides
- Department of Energy, Joint Genome Institute, Berkeley, CA, United States
| | - Tanja Woyke
- Department of Energy, Joint Genome Institute, Berkeley, CA, United States
| | - Markus Göker
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
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Dahal RH, Chaudhary DK, Kim DU, Kim J. Nine novel psychrotolerant species of the genus Pedobacter isolated from Arctic soil with potential antioxidant activities. Int J Syst Evol Microbiol 2020; 70:2537-2553. [DOI: 10.1099/ijsem.0.004071] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Fifteen isolates of the genus
Pedobacter
were obtained from Arctic soil samples. All isolates were Gram-stain-negative and rod-shaped. Cells were strictly aerobic, psychrotolerant and grew optimally at 15–20 °C. Phylogenetic analysis based on 16S rRNA gene sequences revealed that all the isolated strains formed a lineage within the family
Sphingobacteriaceae
and clustered as members of the genus
Pedobacter
. The sole respiratory quinone was MK-7 and the major polar lipid was phosphatidylethanolamine. The major cellular fatty acids were summed feature 3 (iso-C15 : 02-OH/C16 : 1ω7c/ω6c), iso-C15 : 0 and iso-C17 : 0 3-OH. The DNA G+C content of the novel strains was 33.9–41.8 mol%. In addition, the average nucleotide identity and in silico DNA–DNA hybridization relatedness values between the novel type strains and phylogenetically related type strains were below the threshold values used for species delineation. Based on genomic, chemotaxonomic, phenotypic, phylogenetic and phylogenomic analyses, the isolated strains represent novel species in the genus
Pedobacter
, for which the names Pedobacter cryotolerans sp. nov. (type strain AR-2-6T=KEMB 9005-717T=KACC 19998T=NBRC 113826T), Pedobacter cryophilus sp. nov. (type strain AR-3-17T=KEMB 9005-718T=KACC 19999T=NBRC 113827T), Pedobacter frigiditerrae sp. nov. (type strain RP-1-13T=KEMB 9005-720T=KACC 21147T=NBRC 113829T), Pedobacter psychroterrae sp. nov. (type strain RP-1-14T=KEMB 9005-721T=KACC 21148T=NBRC 113830T), Pedobacter hiemivivus sp. nov. (type strain RP-3-8T=KEMB 9005-724T=KACC 21152T=NBRC 113833T), Pedobacter frigidisoli sp. nov. (type strain RP-3-11T=KEMB 9005-725T=KACC 21153T=NBRC 113927T), Pedobacter frigoris sp. nov. (type strain RP-3-15T=KEMB 9005-726T=KACC 21154T=NBRC 113834T), Pedobacter psychrodurus sp. nov. (type strain RP-3-21T=KEMB 9005-728T=KACC 21156T=NBRC 113835T) and Pedobacter polaris sp. nov. (type strain RP-3-22T=KEMB 9005-729T=KACC 21157T=NBRC 113836T) are proposed.
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Affiliation(s)
- Ram Hari Dahal
- Department of Life Science, College of Natural Sciences, Kyonggi University, Suwon, Kyonggi-Do 16227, Republic of Korea
| | - Dhiraj Kumar Chaudhary
- Department of Life Science, College of Natural Sciences, Kyonggi University, Suwon, Kyonggi-Do 16227, Republic of Korea
| | - Dong-Uk Kim
- Department of Biological Science, College of Science and Engineering, Sangji University, Wonju, Republic of Korea
| | - Jaisoo Kim
- Department of Life Science, College of Natural Sciences, Kyonggi University, Suwon, Kyonggi-Do 16227, Republic of Korea
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21
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Dahal RH, Kim J. Glaciihabitans arcticus sp. nov., a psychrotolerant bacterium isolated from Arctic soil. Int J Syst Evol Microbiol 2019; 69:2492-2497. [DOI: 10.1099/ijsem.0.003520] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Ram Hari Dahal
- Department of Life Science, College of Natural Sciences, Kyonggi University, Suwon Gyeonggi-Do 16227, Republic of Korea
| | - Jaisoo Kim
- Department of Life Science, College of Natural Sciences, Kyonggi University, Suwon Gyeonggi-Do 16227, Republic of Korea
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Felföldi T, Márton Z, Szabó A, Mentes A, Bóka K, Márialigeti K, Máthé I, Koncz M, Schumann P, Tóth E. Siculibacillus lacustris gen. nov., sp. nov., a new rosette-forming bacterium isolated from a freshwater crater lake (Lake St. Ana, Romania). Int J Syst Evol Microbiol 2019; 69:1731-1736. [PMID: 30950779 DOI: 10.1099/ijsem.0.003385] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A new aerobic alphaproteobacterium, strain SA-279T, was isolated from a water sample of a crater lake. The 16S rRNA gene sequence analysis revealed that strain SA-279T formed a distinct lineage within the family Ancalomicrobiaceae and shared the highest pairwise similarity values with Pinisolibacterravus E9T (96.4 %) and Ancalomicrobiumadetum NBRC 102456T (94.2 %). Cells of strain SA-279T were rod-shaped, motile, oxidase and catalase positive, and capable of forming rosettes. Its predominant fatty acids were C18 : 1ω7c (69.0 %) and C16 : 1ω7c (22.7 %), the major respiratory quinone was Q-10, and the main polar lipids were phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylcholine, phosphatidylglycerol, an unidentified aminophospholipid and an unidentified lipid. The G+C content of the genomic DNA of strain SA-279T was 69.2 mol%. On the basis of the phenotypic, chemotaxonomic and molecular data, strain SA-279T is considered to represent a new genus and species within the family Ancalomicrobiaceae, for which the name Siculibacillus lacustris gen. nov., sp. nov. is proposed. The type strain is SA-279T (=DSM 29840T=JCM 31761T).
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Affiliation(s)
- Tamás Felföldi
- 2Department of Bioengineering, Sapientia Hungarian University of Transylvania, Piaţa Libertăţii 1, 530104 Miercurea Ciuc, Romania.,1Department of Microbiology, ELTE Eötvös Loránd University, Pázmány Péter stny. 1/c, 1117 Budapest, Hungary
| | - Zsuzsanna Márton
- 1Department of Microbiology, ELTE Eötvös Loránd University, Pázmány Péter stny. 1/c, 1117 Budapest, Hungary
| | - Attila Szabó
- 1Department of Microbiology, ELTE Eötvös Loránd University, Pázmány Péter stny. 1/c, 1117 Budapest, Hungary
| | - Anikó Mentes
- 1Department of Microbiology, ELTE Eötvös Loránd University, Pázmány Péter stny. 1/c, 1117 Budapest, Hungary
| | - Károly Bóka
- 3Department of Plant Anatomy, ELTE Eötvös Loránd University, Pázmány Péter stny. 1/c, 1117 Budapest, Hungary
| | - Károly Márialigeti
- 1Department of Microbiology, ELTE Eötvös Loránd University, Pázmány Péter stny. 1/c, 1117 Budapest, Hungary
| | - István Máthé
- 2Department of Bioengineering, Sapientia Hungarian University of Transylvania, Piaţa Libertăţii 1, 530104 Miercurea Ciuc, Romania
| | - Mihály Koncz
- 2Department of Bioengineering, Sapientia Hungarian University of Transylvania, Piaţa Libertăţii 1, 530104 Miercurea Ciuc, Romania.,†Present address: Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Temesvári krt. 62, 6726 Szeged, Hungary
| | - Peter Schumann
- 4Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Erika Tóth
- 1Department of Microbiology, ELTE Eötvös Loránd University, Pázmány Péter stny. 1/c, 1117 Budapest, Hungary
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