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Jiang L, Seo J, Peng Y, Jeon D, Lee JH, Kim CY, Lee J. A nostoxanthin-producing bacterium, Sphingomonas nostoxanthinifaciens sp. nov., alleviates the salt stress of Arabidopsis seedlings by scavenging of reactive oxygen species. Front Microbiol 2023; 14:1101150. [PMID: 36846770 PMCID: PMC9950776 DOI: 10.3389/fmicb.2023.1101150] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 01/18/2023] [Indexed: 02/12/2023] Open
Abstract
A novel, nostoxanthin-producing, endophytic bacterium, designated as AK-PDB1-5T, was isolated from the needle-like leaves of the Korean fir (Abies koreana Wilson) collected from Mt. Halla in Jeju, South Korea. A 16S rRNA sequence comparison indicated that the closest phylogenetic neighbors were Sphingomonas crusticola MIMD3T (95.6%) and Sphingomonas jatrophae S5-249T (95.3%) of the family Sphingomonadaceae. Strain AK-PDB1-5T had a genome size of 4,298,284 bp with a 67.8% G + C content, and digital DNA-DNA hybridization and OrthoANI values with the most closely related species of only 19.5-21% and 75.1-76.8%, respectively. Cells of the strain AK-PDB1-5T were Gram-negative, short rods, oxidase- and catalase-positive. Growth occurred at pH 5.0-9.0 (optimum pH 8.0) in the absence of NaCl at 4-37°C (optimum 25-30°C). Strain AK-PDB1-5T contained C14:0 2OH, C16:0 and summed feature 8 as the major cellular fatty acids (> 10%), while sphingoglycolipid, phosphatidylethanolamine, phosphatidylglycerol, phospholipids and lipids were found to be the major polar lipids. The strain produces a yellow carotenoid pigment; natural products prediction via AntiSMASH tool found zeaxanthin biosynthesis clusters in the entire genome. Biophysical characterization by ultraviolet-visible absorption spectroscopy and ESI-MS studies confirmed the yellow pigment was nostoxanthin. In addition, strain AK-PDB1-5T was found significantly promote Arabidopsis seedling growth under salt conditions by reducing reactive oxygen species (ROS). Based on the polyphasic taxonomic analysis results, strain AK-PDB1-5T was determined to be a novel species in the genus Sphingomonas with the proposed name Sphingomonas nostoxanthinifaciens sp. nov. The type strain is AK-PDB1-5T (= KCTC 82822T = CCTCC AB 2021150T).
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Affiliation(s)
- Lingmin Jiang
- Biological Resource Center, Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, Republic of Korea
| | - Jiyoon Seo
- Biological Resource Center, Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, Republic of Korea
| | - Yuxin Peng
- Biological Resource Center, Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, Republic of Korea
| | - Doeun Jeon
- Biological Resource Center, Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, Republic of Korea
| | - Ju Huck Lee
- Biological Resource Center, Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, Republic of Korea
| | - Cha Young Kim
- Biological Resource Center, Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, Republic of Korea
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2
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Park C, Kim M, Lee BH, Lee KE, Park W. Sphingomonas changnyeongensis sp. nov. isolated from the Hapcheon–Changnyeong barrage area in the Nakdong river. Int J Syst Evol Microbiol 2020; 70:6091-6097. [DOI: 10.1099/ijsem.0.004503] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
The novel bacterial strain C33T was isolated from a freshwater sample collected from the Hapcheon–Changnyeong barrage. The Gram-negative, motile, yellow-pigmented strain C33T was characterized as a rod-shaped and strictly aerobic bacterium. A 16S-rRNA phylogenetic analysis revealed that this strain was most closely related to
Sphingomonas changbaiensis
V2M44T,
Sphingomonas tabacisoli
X1-8T, and
Sphingomonas flavalba
ZLT-5T with 97.1, 97.0, and 95.0 % 16S-rRNA sequence similarities, respectively. The genomic DNA GC content of strain C33T was estimated at 65.0 mol%. The average nucleotide identity of strain C33T relative to
S. changbaiensis
V2M44T and
S. flavalba
ZLT-5T was found to be 77.0 and 75.6%, with average amino-acid identities of 69.9, and 66.7%, and the digital DNA–DNA hybridization values of 21.3 and 17.7 %, respectively. The cells grew at 19–37 °C and pH 6–9 with 0–0.5 % (w/v) NaCl (optimum: 28 °C, pH 6.5, and 0 % NaCl). The major component identified in the polyamine pattern was sym-homospermidine, and the main ubiquinone was Q-10. The predominant polar lipids characterized were diphophatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidyldimethylethanolamine, and sphingoglycolipid. Iso-C15 : 0, C15 : 0 anteiso, and summed feature 3 (C16 : 1
ω6c and/or C16 : 1
ω7c) were found to be the primary cellular fatty acids in strain C33T. Based on these genotypic and phenotypic characteristics, strain C33T was classified as a novel species of the genus
Sphingomonas
; and the name Sphingomonas changnyeongensis sp. nov. is proposed (=KACC 21511T=JCM 33880T).
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Affiliation(s)
- Chulwoo Park
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Minkyung Kim
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Byoung-Hee Lee
- National Institute of Biological Resources, Incheon, 22689, Republic of Korea
| | - Ki-Eun Lee
- National Institute of Biological Resources, Incheon, 22689, Republic of Korea
| | - Woojun Park
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, 02841, Republic of Korea
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3
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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: 223] [Impact Index Per Article: 55.8] [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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Regar RK, Gaur VK, Bajaj A, Tambat S, Manickam N. Comparative microbiome analysis of two different long-term pesticide contaminated soils revealed the anthropogenic influence on functional potential of microbial communities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 681:413-423. [PMID: 31108361 DOI: 10.1016/j.scitotenv.2019.05.090] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 05/07/2019] [Accepted: 05/07/2019] [Indexed: 05/17/2023]
Abstract
Microbial communities play a crucial role in bioremediation of pollutants in contaminated ecosystem. In addition to pure culture isolation and bacterial 16S rRNA based community studies, the focus has now shifted employing the omics technologies enormously for understanding the microbial diversity and functional potential of soil samples. Our previous report on two pesticide-contaminated sites revealed the diversity of both culturable and unculturable bacteria. In the present study, we have observed distinct taxonomic and functional communities in contaminated soil with respect to an uncontaminated soil as control by using shotgun metagenomic sequencing method. Our data demonstrated that Proteobacteria, Actinobacteria, Firmicutes, Bacteroidetes, and Acidobacteria significantly dominated the microbial diversity with their cumulative abundance percentage in the range of 98.61, 87.38, and 80.52 for Hindustan Insecticides Limited (HIL), India Pesticides Limited (IPL), and control respectively. Functional gene analysis demonstrated the presence of large number of both substrate specific upper pathway and common lower pathway degradative genes. Relatively lower number of genes was found encoding the degradation of styrene, atrazine, bisphenol, dioxin, and naphthalene. When three bacteria were augumentated with rhamnolipid (20-100 μM) and Triton X-100 (84-417 μM) surfactants in HIL soil, an enhanced degradation to 76%, 70%, and 58% of HCH, Endosulfan, and DDT respectively was achieved. The overall data obtained from two heavily contaminated soil suggest the versatility of the microbial communities for the xenobiotic pollutant degradation which may help in exploiting their potential applications in bioremediation.
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Affiliation(s)
- Raj Kumar Regar
- Environmental Biotechnology Division, CSIR-Indian Institute of Toxicology Research, Vishvigyan Bhavan, 31 Mahatma Gandhi Marg, Lucknow, Uttar Pradesh, India; Department of Biochemistry, School of Dental Sciences, Babu Banarsi Das University, Lucknow, Uttar Pradesh, India
| | - Vivek Kumar Gaur
- Environmental Biotechnology Division, CSIR-Indian Institute of Toxicology Research, Vishvigyan Bhavan, 31 Mahatma Gandhi Marg, Lucknow, Uttar Pradesh, India; Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, Lucknow, India
| | - Abhay Bajaj
- Environmental Biotechnology Division, CSIR-Indian Institute of Toxicology Research, Vishvigyan Bhavan, 31 Mahatma Gandhi Marg, Lucknow, Uttar Pradesh, India
| | - Subodh Tambat
- Bionivid Technology Pvt. Ltd., Bengaluru, Karnataka, India
| | - Natesan Manickam
- Environmental Biotechnology Division, CSIR-Indian Institute of Toxicology Research, Vishvigyan Bhavan, 31 Mahatma Gandhi Marg, Lucknow, Uttar Pradesh, India.
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5
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Zhou XK, Mi QL, Yao JH, Wu H, Liu XM, Li YD, Duan YQ, Chen JH, Dang LZ, Mo MH, Li XM, Li WJ. Sphingomonas tabacisoli sp. nov., a member of the genus Sphingomonas, isolated from rhizosphere soil of Nicotiana tabacum L. Int J Syst Evol Microbiol 2018; 68:2574-2579. [PMID: 29944093 DOI: 10.1099/ijsem.0.002879] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-staining-negative, aerobic, motile and rod-shaped bacterium, designated strain X1-8T, was isolated from rhizosphere soil of Nicotiana tabacum L. collected from the tobacco produce base located in Kunming, south-west PR China. Cells showed oxidase-negative and catalase-positive reactions and were motile by means of peritrichous flagella. Growth occurred at 25-40 °C and pH 6.0-8.0 with optimal growth at 30-35 °C, pH 7.0. The major respiratory lipoquinone was Q-10. C16 : 0 and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) were identified as major cellular fatty acids. The profile of polar lipids contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine, sphingoglycolipid, phosphatidylcholine and one unidentified glycolipid. The major polyamine was sym-homospermidine. The genomic DNA G+C content was 66.5 mol%. The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that X1-8T should be affiliated to the genus Sphingomonasand formed a clade with most closely related species Sphingomonas changbaiensisNBRC 104936T. The results of 16S rRNA gene sequences similarity analysis indicated that X1-8T had the highest similarity with S. changbaiensisNBRC 104936T (98.4 %) and lower than 96.0 % with other species of the genus Sphingomonas. DNA-DNA hybridization data indicated that X1-8T represented a novel genomic species of the genus Sphingomonas. The characteristics determined in the polyphasic taxonomic study indicated that X1-8T represents a novel species of the genus Sphingomonas, for which the name Sphingomonas tabacisoli sp. nov. (type strain X1-8T=KCTC 62032T=CGMCC 1.16275T) is proposed.
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Affiliation(s)
- Xing-Kui Zhou
- 1State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, PR China
| | - Qi-Li Mi
- 2China Tobacco Yunnan Industrial Co. Ltd., Kunming 650231, PR China
| | - Jian-Hua Yao
- 2China Tobacco Yunnan Industrial Co. Ltd., Kunming 650231, PR China
| | - Heng Wu
- 2China Tobacco Yunnan Industrial Co. Ltd., Kunming 650231, PR China
| | - Xiu-Ming Liu
- 2China Tobacco Yunnan Industrial Co. Ltd., Kunming 650231, PR China
| | - Yuan-Dong Li
- 2China Tobacco Yunnan Industrial Co. Ltd., Kunming 650231, PR China
| | - Yan-Qing Duan
- 2China Tobacco Yunnan Industrial Co. Ltd., Kunming 650231, PR China
| | - Jian-Hua Chen
- 2China Tobacco Yunnan Industrial Co. Ltd., Kunming 650231, PR China
| | - Li-Zhi Dang
- 2China Tobacco Yunnan Industrial Co. Ltd., Kunming 650231, PR China
| | - Ming-He Mo
- 1State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, PR China
- 3Biocontrol Engineering Research Center of Crop Disease and Pest, Yunnan Province 650091, PR China
| | - Xue-Mei Li
- 2China Tobacco Yunnan Industrial Co. Ltd., Kunming 650231, PR China
| | - Wen-Jun Li
- 1State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, PR China
- 4State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
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6
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Lin SY, Hameed A, Hsu YH, Liu YC, Hung MH, Lai WA, Young CC. Sphingomonas colocasiae sp. nov., isolated from taro (Colocasia esculanta). Int J Syst Evol Microbiol 2017; 68:133-140. [PMID: 29116039 DOI: 10.1099/ijsem.0.002471] [Citation(s) in RCA: 7] [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 polyphasic approach was used to characterize an aerobic, Gram-stain-negative, rod-shaped bacterium (designed as strain CC-MHH0539T) isolated from the chopped tuber of taro (Colocasia esculanta) in Taiwan. Strain CC-MHH0539T was able to grow at 15-30 °C (optimum, 25 °C), at pH 6.0-9.0 (optimum, 7.0) and with 0-1 % (w/v) NaCl. Strain CC-MHH0539T showed highest 16S rRNA gene sequence similarity to Sphingomonas laterariae LNB2T (96.8 %), Sphingobium boeckii 469T (96.5 %), Sphingomonas faucium E62-3T (96.4 %) and Sphingosinicella vermicomposti YC7378T (96.2 %) and <96.1 % similarity to other sphingomonads. Strain CC-MHH0539T was found to cluster mainly with the clade that accommodated members of the genus Sphingomonas. The dominant cellular fatty acids were C16 : 0, C16 : 1ω5c, C14 : 0 2-OH, C16 : 1ω7c/C16 : 1ω6c and C18 : 1ω7c/C18 : 1ω6c. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, two sphingoglycolipids and two unidentified phospholipids were detected in strain CC-MHH0539T. The DNA G+C content was 69.5 mol%. The respiratory quinone system and predominant polyamine was ubiquinone 10 (Q-10) and sym-homospermidine, respectively, which is in line with Sphingomonas representatives. Based on the distinct phylogenetic, phenotypic and chemotaxonomic traits, strain CC-MHH0539T is considered to represent a novel species of the genus Sphingomonas, for which the name Sphingomonas colocasiae sp. nov. is proposed. The type strain is CC-MHH0539T (=BCRC 80933T=JCM 31229T).
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Affiliation(s)
- Shih-Yao Lin
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Asif Hameed
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Yi-Han Hsu
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - You-Cheng Liu
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Mei-Hua Hung
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Wei-An Lai
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC.,Agricultural Biotechnology Center, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Chiu-Chung Young
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung, Taiwan, ROC.,Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
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7
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Wübbeler JH, Oppermann-Sanio FB, Ockenfels A, Röttig A, Osthaar-Ebker A, Verbarg S, Poehlein A, Madkour MH, Al-Ansari AM, Almakishah NH, Daniel R, Steinbüchel A. Sphingomonas jeddahensis sp. nov., isolated from Saudi Arabian desert soil. Int J Syst Evol Microbiol 2017; 67:4057-4063. [PMID: 28905699 DOI: 10.1099/ijsem.0.002249] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Sphingomonas strain was isolated from a sample of desert soil collected near Jeddah in Saudi Arabia. A polyphasic approach was performed to characterize this strain, initially designated as G39T. Cells of strain G39T are motile, Gram-negative, catalase- and oxidase-positive. The strain is able to grow aerobically at 20-35 °C, pH 6.5-8 and tolerates up to 4 % (w/v) NaCl. Based on 16S rRNA gene sequence similarity, the closest relative type strains of G39T are Sphingomonas mucosissima DSM 17494T (98.6 %), S. dokdonensis DSM 21029T (98.4 %) and S. hankookensis DSM 23329T (97.4 %). Furthermore, the average nucleotide identities between the draft genome sequence of strain G39T and the genome sequences of all other available and related Sphingomonas species are significantly below the threshold of 94 %. The G+C content of the draft genome (3.12 Mbp) is 65.84 %. The prevalent (>5 %) cellular fatty acids of G39T were C18 : 1ω7c, C16 : 1ω7c and/or C16 : 1ω6c, C14 : 0 2-OH and C16 : 0. The only detectable respiratory quinone was ubiquinone-10 and the polar lipids profile is composed of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, sphingoglycolipid, as well as unidentified lipids, phospholipids and glycolipids. The results of the conducted polyphasic approach confirmed that this isolate represents a novel species of the genus Sphingomonas, for which the name Sphingomonas jeddahensis sp. nov. is proposed. The type strain of this species is G39T (=DSM 103790T=LMG 29955T).
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Affiliation(s)
- Jan Hendrik Wübbeler
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Corrensstraße 3, 48149 Münster, Germany
| | - Fred Bernd Oppermann-Sanio
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Corrensstraße 3, 48149 Münster, Germany
| | - Andrea Ockenfels
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Corrensstraße 3, 48149 Münster, Germany
| | - Annika Röttig
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Corrensstraße 3, 48149 Münster, Germany
| | - Alena Osthaar-Ebker
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Corrensstraße 3, 48149 Münster, Germany
| | - Susanne Verbarg
- Leibniz-Institut DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7b, 38124 Braunschweig, Germany
| | - Anja Poehlein
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, Grisebachstraße 8, 37077 Göttingen, Germany
| | - Mohamed H Madkour
- Environmental Sciences Department, Faculty of Meteorology, Environment and Arid Land Agriculture, King Abdulaziz University, 21589 Jeddah, Saudi Arabia
| | - Ahmed M Al-Ansari
- Environmental Sciences Department, Faculty of Meteorology, Environment and Arid Land Agriculture, King Abdulaziz University, 21589 Jeddah, Saudi Arabia
| | - Naief H Almakishah
- Environmental Sciences Department, Faculty of Meteorology, Environment and Arid Land Agriculture, King Abdulaziz University, 21589 Jeddah, Saudi Arabia
| | - Rolf Daniel
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, Grisebachstraße 8, 37077 Göttingen, Germany
| | - Alexander Steinbüchel
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Corrensstraße 3, 48149 Münster, Germany.,Environmental Sciences Department, Faculty of Meteorology, Environment and Arid Land Agriculture, King Abdulaziz University, 21589 Jeddah, Saudi Arabia
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8
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Chaudhary DK, Kim J. Sphingomonas olei sp. nov., with the ability to degrade aliphatic hydrocarbons, isolated from oil-contaminated soil. Int J Syst Evol Microbiol 2017; 67:2731-2738. [PMID: 28792375 DOI: 10.1099/ijsem.0.002010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A yellow-coloured, Gram-stain-negative, non-motile, rod-shaped bacterium, designated K-1-16T, that is capable of degrading aliphatic hydrocarbons was isolated from oil-contaminated soil at Biratnagar, Morang, Nepal. It was able to grow at 15-45 °C, at pH 5.5-9.5 and with 0-5 % (w/v) NaCl. This strain was taxonomically characterized by a polyphasic approach. Based on 16S rRNA gene sequence analysis, strain K-1-16T belongs to the genus Sphingomonas and is closely related to Sphingomonas mucosissima CP173-2T (98.6 % similarity), Sphingomonas dokdonensis DS-4T (97.9 %), Sphingomonas faeni MA-olkiT (97.9 %), Sphingomonas aurantiaca MA101bT (97.8 %) and Sphingomonas xinjiangensis 10-1-84T (96.6 %). The predominant respiratory quinone was ubiquinone Q-10 and the major polyamine was homospermidine. The polar lipid profile revealed the presence of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine, phosphatidyldimethylethanolamine and sphingoglycolipid. The predominant fatty acids of strain K-1-16T were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), C16 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C18 : 1ω7c 11-methyl and C14 : 0 2-OH. The genomic DNA G+C content was 64.8 mol%. Levels of DNA-DNA relatedness between strain K-1-16T and S. mucosissima DSM 17494T, S. dokdonensis KACC 17420T, S. faeni KCCM 41909T and S. aurantiaca KCCM 41908T were 49.7, 41.3, 43.7 and 36.7 %, respectively. The morphological, physiological, chemotaxonomic and phylogenetic analyses clearly distinguished this strain from its closest phylogenetic neighbours. Thus, strain K-1-16T represents a novel species of the genus Sphingomonas, for which the name Sphingomonas olei sp. nov. is proposed. The type strain is K-1-16T (=KEMB 9005-450T=KACC 19002T=JCM 31674T).
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Affiliation(s)
- Dhiraj Kumar Chaudhary
- 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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9
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Lee JH, Kim DI, Choe HN, Lee SD, Seong CN. Sphingomonas limnosediminicola sp. nov. and Sphingomonas palustris sp. nov., isolated from freshwater environments. Int J Syst Evol Microbiol 2017; 67:2834-2841. [DOI: 10.1099/ijsem.0.002029] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Ji Hee Lee
- Department of Biology, College of Life Science and Natural Resources, Sunchon National University, Suncheon 57922, Republic of Korea
| | - Dae In Kim
- Department of Biology, College of Life Science and Natural Resources, Sunchon National University, Suncheon 57922, Republic of Korea
| | - Han Na Choe
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup 56212, Republic of Korea
| | - Soon Dong Lee
- Faculty of Science Education, Jeju National University, Jeju63243, Republic of Korea
| | - Chi Nam Seong
- Department of Biology, College of Life Science and Natural Resources, Sunchon National University, Suncheon 57922, Republic of Korea
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10
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Sphingomonas montana sp. nov., isolated from a soil sample from the Tanggula Mountain in the Qinghai Tibetan Plateau. Antonie van Leeuwenhoek 2017; 110:1659-1668. [PMID: 28755311 DOI: 10.1007/s10482-017-0915-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 07/19/2017] [Indexed: 10/19/2022]
Abstract
An orange pigmented, Gram-staining negative, aerobic, motile, rod-shaped bacterium isolated from a soil from the Tanggula Mountain, China was studied using a polyphasic approach. Based on 16S rRNA gene sequence similarity, strain W16RDT was found to be closely related to Sphingomonas prati DSM 103336T (99%), Sphingomonas fennica DSM 13665T (97.21%), followed by Sphingomonas laterariae DSM 25432T (96.44%), Sphingomonas haloaromaticamans CGMCC 1.10206 T (96.36%) and Sphingomonas formosensis DSM 24164T (96.06%). The strain was found to be catalase and oxidase positive and was found to grow optimally at temperatures of 20-25 °C, pH 8 and tolerated NaCl concentration up to 1% (w/v). The major fatty acids identified were summed feature eight comprising C18:1 ω 7c and/or C18:1 ω 6c (39.2%), summed feature three comprising of C16:1 ω7c and/or C16:1 ω6c (36.7%) and C16:0 (7.0%). The polar lipids detected were phosphatidylcholine, sphingoglycolipid, phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, phosphatidyldimethylethanolamine, phosphatidylmonomethylethanolamine, and three unidentified lipids. The strain possessed ubiquinone-10 (Q-10) as the predominant respiratory quinone. Along with other distinguishing characteristics, we also describe the draft genome of strain W16RDT. The final assembled draft genome sequence is 3,722,743 bp with 3390 coding and 48 RNA (45 tRNA and 3 rRNA) genes. The DNA G+C content of the genomic DNA was determined to be 67%. The DNA-DNA relatedness value between the strain W16RDT and its closest phylogenetic relatives S. prati DSM 103336T, S. fennica DSM 13665T, S. laterariae DSM 25432T, and S. haloaromaticamans CGMCC 1.10206T were 52.17, 47.60, 20.93 and 17.09% respectively. The strain W16RDT could be distinguished genotypically and phenotypically from the recognized species belonging to the genus Sphingomonas and thus represents a novel species, for which the name Sphingomonas montana sp. nov. is proposed. The type strain is W16RDT (=CGMCC 1.15646T = DSM 103337T).
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11
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Chaudhary DK, Kim J. Sphingomonas naphthae sp. nov., isolated from oil-contaminated soil. Int J Syst Evol Microbiol 2016; 66:4621-4627. [DOI: 10.1099/ijsem.0.001400] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Dhiraj Kumar Chaudhary
- 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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12
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Manandhar P, Zhang G, Hu Y, Lama A, Gao F, Gu Z. Sphingomonas prati sp. nov., isolated from alpine meadow soil. Int J Syst Evol Microbiol 2016; 66:4269-4275. [DOI: 10.1099/ijsem.0.001346] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Pooja Manandhar
- Key Laboratory of Alpine Ecology and Biodiversity, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, PR China
- University of Chinese Academy of Sciences, Beijing, PR China
| | - Gengxin Zhang
- Key Laboratory of Alpine Ecology and Biodiversity, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, PR China
| | - Yilun Hu
- Key Laboratory of Alpine Ecology and Biodiversity, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, PR China
- University of Chinese Academy of Sciences, Beijing, PR China
| | - Arun Lama
- School of Environment, Tsinghua University, Beijing, PR China
| | - Feng Gao
- Key Laboratory of Alpine Ecology and Biodiversity, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, PR China
- Hebei University of Engineering, Handan, PR China
| | - Zhengquan Gu
- University of Chinese Academy of Sciences, Beijing, PR China
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13
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Liu D, Jin X, Sun X, Song Y, Feng L, Wang G, Li M. Sphingomonas faucium sp. nov., isolated from canyon soil. Int J Syst Evol Microbiol 2016; 66:2847-2852. [DOI: 10.1099/ijsem.0.001064] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Dongmei Liu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Xin Jin
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Xuelian Sun
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Yali Song
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Liling Feng
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Gejiao Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Mingshun Li
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
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14
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Han L, Teng YW, Feng QQ, Zhang RG, Zhao XM, Lv J, Xie B. Description of Sphingomonas mohensis sp. nov., Isolated from Sediment. Curr Microbiol 2016; 73:386-392. [PMID: 27262460 DOI: 10.1007/s00284-016-1074-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2016] [Accepted: 04/25/2016] [Indexed: 11/24/2022]
Abstract
An aerobic, gram-reaction-negative, rod-shaped bacterium, designated strain Z6(T), was isolated from sediment collected at Mohe Basin, China. And its taxonomic position was investigated by applying a polyphasic approach. Growth occurs at 10-45 °C (optimum, 30 °C), at pH 6.0-11.0 (optimum, pH 7.0) and in the presence of 0-3.0 % (w/v) NaCl (optimum, 0 %). The polar lipid profile of strain Z6(T) revealed the presence of diphosphatidylglycerol, phosphatidylethanolamine, sphingoglycolipid and two unidentified phospholipids, and the major quinone was Q-10. The major fatty acids were C18:1 ω7c and/or C18:1 ω6c (summed feature 8) and C16:1 ω6c and/or C16:1 ω7c (summed feature 3). The predominant polyamine was homospermidine. The DNA G + C content of strain Z6(T) is 65.2 mol%. On the basis of the polyphasic evidence presented, strain Z6(T) represents a novel species of the genus Sphingomonas, for which the name Sphingomonas mohensis sp. nov. is proposed. The type strain is Z6(T) (=CGMCC 1.12891(T) = JCM 19983(T)).
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Affiliation(s)
- Lu Han
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai, 200241, People's Republic of China.,College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
| | - Yue-Wen Teng
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
| | - Qing-Qing Feng
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
| | - Ren-Gang Zhang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
| | - Xing-Min Zhao
- Oil and Gas Survey, China Geological Survey, Beijing, 100029, People's Republic of China
| | - Jie Lv
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
| | - Bing Xie
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai, 200241, People's Republic of China.
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15
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Jia L, Zheng Z, Feng X, Nogi Y, Yang A, Zhang Y, Han L, Lu Z, Lv J. Sphingomonas arantia sp. nov., isolated from Hoh Xil basin, China. Antonie van Leeuwenhoek 2015; 108:1341-1347. [PMID: 26363912 DOI: 10.1007/s10482-015-0586-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 09/08/2015] [Indexed: 10/23/2022]
Abstract
A Gram-negative, rod-shaped, non-motile, non-spore forming, aerobic, orange-pigmented bacterium, designated strain 6P(T), was isolated from a soil sample collected from the Hoh Xil basin, China. Strain 6P(T) grew optimally at 25 °C, pH 7.0-7.5 and NaCl concentration of 0-1 % (w/v). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain 6P(T) belongs to the genus Sphingomonas, with high sequence similarity (97.1 %) to Sphingomonas fennica. The DNA-DNA hybridization homology with S. fennica DSM 13665(T) was 45.3 %. The DNA G+C content of the novel strain is 65.3 mol%. The isolate contained Q-10 as the only respiratory quinone. The major polar lipids are diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), phosphatidylglycerol (PG), phosphatidylcholine (PC) and sphingoglycolipid (SGL). C18:1 ω7c and C16:1 ω7c are the major fatty acids. On the basis of the polyphasic evidence presented, strain 6P(T) represents a novel species of the genus Sphingomonas, for which the name Sphingomonas arantia sp. nov. is proposed. The type strain is 6P(T) (=CGMCC 1.12702(T) = JCM 19855(T)).
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Affiliation(s)
- Li Jia
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
| | - Zhong Zheng
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
| | - Xiaomin Feng
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
| | - Yuichi Nogi
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-EarthScience and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Japan
| | - Aichen Yang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
| | - Yali Zhang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
| | - Lu Han
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
- College of Resources and Environmental Science, East China Normal University, Shanghai, 200241, People's Republic of China
| | - Zhenquan Lu
- Oil and Gas Survey, China Geological Survey, Beijing, 100029, People's Republic of China
| | - Jie Lv
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China.
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Sphingomonas chloroacetimidivorans sp. nov., a chloroacetamide herbicide-degrading bacterium isolated from activated sludge. Antonie van Leeuwenhoek 2015; 108:703-10. [PMID: 26159664 DOI: 10.1007/s10482-015-0526-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 07/02/2015] [Indexed: 10/23/2022]
Abstract
Strain Y1(T), a Gram-negative, non-spore-forming, rod-shaped bacterium, was isolated from activated sludge. This strain is able to degrade several commonly used chloroacetamide herbicides, such as butachlor, acetochlor and alachlor. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain Y1(T) is a member of the genus Sphingomonas and shows high sequence similarities with S. starnbergensis 382(T) (95.7 %), S. sanxanigenens NX02(T) (95.7 %) and S. haloaromaticamans A175(T) (95.3 %), and shows low (<95 %) sequence similarities to all other Sphingomonas species. Chemotaxonomic analysis revealed that strain Y1(T) possesses Q-10 as the predominant ubiquinone, C14:0 2-OH as the major 2-hydroxy fatty acid and sym-homospermidine as the major polyamine. The main cellular fatty acids of strain Y1(T) were found to be C18:1 ω7c (38.2 %), C16:1 ω6c/C16:1 ω7c (28.5 %), C16: 0 (10.7 %) and C14:0 2-OH (14.3 %). The main polar lipids were determined to be diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, sphingoglycolipids (SGL1-SGL3), phosphatidyl dimethylethanolamine and aminophospholipid. The DNA G+C content was found to be 66 ± 0.4 mol%. Based on phylogenetic analysis, phenotypic characteristics and chemotaxonomic data, strain Y1(T) is considered to represent a novel species of the genus Sphingomonas, for which the name Sphingomonas chloroacetimidivorans sp. nov. is proposed. The type strain is Y1(T) (=CCTCC AB 2011178(T) = KACC 16607(T)).
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Lee KC, Kim KK, Kim JS, Kim DS, Ko SH, Yang SH, Kim SG, Lee JS. Sphingomonas vulcanisoli sp. nov., isolated from soil of a lava forest. Int J Syst Evol Microbiol 2015; 65:3320-3325. [PMID: 26296342 DOI: 10.1099/ijsem.0.000414] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, non-motile, yellow-pigmented and rod-shaped bacterial strain, designated SN6-13T, was isolated from soil of the Gotjawal, lava forest, located in Jeju, Republic of Korea. Cells of strain SN6-13T were oxidase- and catalase-positive. The isolate contained Q-10 as the predominant isoprenoid quinone, summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C16 : 0 as the major fatty acids, sym-homospermidine as the major polyamine and diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, sphingoglycolipid, ninhydrinphosphatidylglycerol and two unidentified aminophospholipids as the polar lipids. The DNA G+C content was 64.6 mol%. In phylogenetic analyses based on 16S rRNA gene sequencing, strain SN6-13T was most closely related to Sphingomonas laterariae LNB2T (95.4 % sequence similarity) and formed a separate lineage in the genus Sphingomonas. Based on phenotypic, chemotaxonomic and phylogenetic characteristics, it is concluded that strain SN6-13T represents a novel species of the genus Sphingomonas, for which the name Sphingomonas vulcanisoli sp. nov. is proposed. The type strain is SN6-13T ( = KCTC 42454T = CECT 8804T).
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Affiliation(s)
- Keun Chul Lee
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Republic of Korea
| | - Kwang Kyu Kim
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Republic of Korea
| | - Jong-Shik Kim
- Gyeongbuk Institute for Marine Bioindustry, Uljin, 767-813, Republic of Korea
| | - Dae-Shin Kim
- World Heritage and Mt. Hallasan Research Institute, Jeju Special Self-Governing Province, 690-816, Republic of Korea
| | - Suk-Hyung Ko
- World Heritage and Mt. Hallasan Research Institute, Jeju Special Self-Governing Province, 690-816, Republic of Korea
| | - Seung-Hoon Yang
- World Heritage and Mt. Hallasan Research Institute, Jeju Special Self-Governing Province, 690-816, Republic of Korea
| | - Song-Gun Kim
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Republic of Korea
| | - Jung-Sook Lee
- University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon 305-350, Republic of Korea.,Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Republic of Korea
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18
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Sharma A, Sangwan N, Negi V, Kohli P, Khurana JP, Rao DLN, Lal R. Pan-genome dynamics of Pseudomonas gene complements enriched across hexachlorocyclohexane dumpsite. BMC Genomics 2015; 16:313. [PMID: 25898829 PMCID: PMC4405911 DOI: 10.1186/s12864-015-1488-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Accepted: 03/25/2015] [Indexed: 11/16/2022] Open
Abstract
Background Phylogenetic heterogeneity across Pseudomonas genus is complemented by its diverse genome architecture enriched by accessory genetic elements (plasmids, transposons, and integrons) conferring resistance across this genus. Here, we sequenced a stress tolerant genotype i.e. Pseudomonas sp. strain RL isolated from a hexachlorocyclohexane (HCH) contaminated pond (45 mg of total HCH g−1 sediment) and further compared its gene repertoire with 17 reference ecotypes belonging to P. stutzeri, P. mendocina, P. aeruginosa, P. psychrotolerans and P. denitrificans, representing metabolically diverse ecosystems (i.e. marine, clinical, and soil/sludge). Metagenomic data from HCH contaminated pond sediment and similar HCH contaminated sites were further used to analyze the pan-genome dynamics of Pseudomonas genotypes enriched across increasing HCH gradient. Results Although strain RL demonstrated clear species demarcation (ANI ≤ 80.03%) from the rest of its phylogenetic relatives, it was found to be closest to P. stutzeri clade which was further complemented functionally. Comparative functional analysis elucidated strain specific enrichment of metabolic pathways like α-linoleic acid degradation and carbazole degradation in Pseudomonas sp. strain RL and P. stutzeri XLDN-R, respectively. Composition based methods (%codon bias and %G + C difference) further highlighted the significance of horizontal gene transfer (HGT) in evolution of nitrogen metabolism, two-component system (TCS) and methionine metabolism across the Pseudomonas genomes used in this study. An intact mobile class-I integron (3,552 bp) with a captured gene cassette encoding for dihydrofolate reductase (dhfra1) was detected in strain RL, distinctly demarcated from other integron harboring species (i.e. P. aeruginosa, P. stutzeri, and P. putida). Mobility of this integron was confirmed by its association with Tnp21-like transposon (95% identity) suggesting stress specific mobilization across HCH contaminated sites. Metagenomics data from pond sediment and recently surveyed HCH adulterated soils revealed the in situ enrichment of integron associated transposase gene (TnpA6100) across increasing HCH contamination (0.7 to 450 mg HCH g−1 of soil). Conclusions Unlocking the potential of comparative genomics supplemented with metagenomics, we have attempted to resolve the environment and strain specific demarcations across 18 Pseudomonas gene complements. Pan-genome analyses of these strains indicate at astoundingly diverse metabolic strategies and provide genetic basis for the cosmopolitan existence of this taxon. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1488-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Anukriti Sharma
- Department of Zoology, University of Delhi, New Delhi, 110007, India.
| | - Naseer Sangwan
- Department of Zoology, University of Delhi, New Delhi, 110007, India.
| | - Vivek Negi
- Department of Zoology, University of Delhi, New Delhi, 110007, India.
| | - Puneet Kohli
- Department of Zoology, University of Delhi, New Delhi, 110007, India.
| | - Jitendra Paul Khurana
- Interdisciplinary Centre for Plant Genomics & Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India.
| | - Desiraju Lakshmi Narsimha Rao
- All India Network Project on Soil Biodiversity and Biofertilizers, Indian Institute of Soil Science, Bhopal, 462038, India.
| | - Rup Lal
- Department of Zoology, University of Delhi, New Delhi, 110007, India.
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Sphingobium baderi sp. nov., isolated from a hexachlorocyclohexane dump site. Int J Syst Evol Microbiol 2013; 63:673-678. [DOI: 10.1099/ijs.0.039834-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, rod-shaped and white-coloured bacterial strain, designated LL03T, was isolated from hexachlorocyclohexane-contaminated soil at Spolana Neratovice, Czech Republic, where lindane was formerly produced. Strain LL03T was found to be a degrader of α-, γ- and δ-isomers of hexachlorocyclohexane, although no significant degradation activity was observed for the β-isomer. A neighbour-joining tree based on 16S rRNA gene sequences showed that strain LL03T occupied a distinct phylogenetic position in the
Sphingobium
cluster, showing the highest similarity with
Sphingobium wenxiniae
JZ-1T (99.2 %). The DNA G+C content of strain LL03T was 67.0 mol%. DNA–DNA relatedness values of strain LL03T with its close phylogenetic neighbours were below the threshold level of 70 %, supporting its identification as a representative of a novel species of the genus
Sphingobium
. The predominant respiratory quinone was ubiquinone Q-10. The polar lipid profile of strain LL03T also corresponded to those reported for other
Sphingobium
species (phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol, phosphatidylmonomethylethanolamine and sphingoglycolipid), supporting its identification as a member of the genus
Sphingobium
. Spermidine was identified as the major polyamine. The predominant fatty acids were 16 : 0, summed feature 3 (16 : 1ω7c and/or 16 : 1ω6c), summed feature 8 (18 : 1ω7c and/or 18 : 1ω6c) and 14 : 0 2-OH. The polar lipid pattern, the presence of spermidine and ubiquinone Q-10, the predominance of the cellular fatty acids C18 : 1ω7c, C16 : 0 and C14 : 0 2-OH and the G+C content of the genomic DNA supported the affiliation of the strain to the genus
Sphingobium
. The results obtained after DNA–DNA hybridization, biochemical and physiological tests clearly distinguished it from closely related species of the genus
Sphingobium
. Therefore, strain LL03T represents a novel species of the genus
Sphingobium
for which the name Sphingobium baderi LL03T sp. nov. is proposed; the type strain is LL03T ( = CCM 7981T = DSM 25433T).
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