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Lee H, Chaudhary DK, Kim DU. Sphingomonas flavescens sp. nov., isolated from soil. Arch Microbiol 2024; 206:119. [PMID: 38396312 DOI: 10.1007/s00203-024-03851-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 01/11/2024] [Accepted: 01/17/2024] [Indexed: 02/25/2024]
Abstract
An aerobic bacterium, designated as PT-12T, was isolated from soil collected from agriculture field, and its taxonomic position was validated through a comprehensive polyphasic methodology. The strain was identified as Gram-stain-negative, non-motile, rod-shaped, and catalase- and oxidase-positive. The yellow-colored colonies showed growth ability at temperature range of 18-37 °C, NaCl content of 0-1.0% (w/v), and at a pH of 6.0-8.0. The 16S rRNA gene and phylogenetic analysis showed that strain PT-12T affiliated with the genus Sphingomonas in the family Sphingomonadaceae, and displayed the highest 16S rRNA nucleotide sequence similarity with Sphingomonas limnosediminicola 03SUJ6T (98.4%). The genome size of strain PT-12T was 2,656,862 bp and the DNA G + C content estimated from genome was 63.5%. The highest values of average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) were observed between strain PT-12T and Sphingomonas segetis YJ09T, accounting to 76.2% and 20.2%, respectively. In addition, both ANI and dDDH values between strain PT-12T and other phylogenetically related neighbors ranged between 69.6% and 76.2% and 18.4% and 20.2%, respectively. Chemotaxonomic features exhibited Q-10 as the only ubiquinone; homospermidine as the major polyamine; summed feature 8 (C18:1ω7c and/or C18:1ω6c), C16:0, and 10-methyl C18:0 as the notable fatty acids; and phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine, and sphingoglycolipid as dominating polar lipids. Overall, the comprehensive polyphasic data supported that strain PT-12T represents a novel bacterial species within the genus Sphingomonas. Accordingly, we propose the name Sphingomonas flavescens sp. nov. The type strain is PT-12T (= KCTC 92114T = NBRC 115717T).
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Affiliation(s)
- Hyosun Lee
- Department of Biological Science, College of Science and Engineering, Sangji University, Wonju, 26339, Republic of Korea
| | - Dhiraj Kumar Chaudhary
- Department of Biomaterials, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai, 600077, India
| | - Dong-Uk Kim
- Department of Biological Science, College of Science and Engineering, Sangji University, Wonju, 26339, Republic of Korea.
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Siddiqi MZ, Rajivgandhi G, Faiq M, Im WT. Isolation and Characterization of Sphingomonas telluris, Sphingomonas caseinilyticus Isolated from Wet Land Soil. Curr Microbiol 2023; 80:264. [PMID: 37386175 DOI: 10.1007/s00284-023-03339-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 05/22/2023] [Indexed: 07/01/2023]
Abstract
Two novel bacterial strains, designated as SM33T and NSE70-1T, were isolated from wet soil in South Korea. To get the taxonomic positions, the strains were characterized. The genomic information (both 16S rRNA gene and draft genome sequence analysis) show that both novel isolates (SM33T and NSE70-1T) belong to the genus Sphingomonas. SM33T share the highest 16s rRNA gene similarity (98.2%) with Sphingomonas sediminicola Dae20T. In addition, NSE70-1T show 96.4% 16s rRNA gene similarity with Sphingomonas flava THG-MM5T. The draft genome of strains SM33T and NSE70-1T consist of a circular chromosome of 3,033,485 and 2,778,408 base pairs with DNA G+C content of 63.9, and 62.5%, respectively. Strains SM33T and NSE70-1T possessed the ubiquinone Q-10 as the major quinone, and a fatty acid profile with C16:0, C18:1 2-OH, C16:1 ω7c/C16:1 ω6c (summed feature 3) and C18:1 ω7c/C18:1 ω6c (summed feature 8) as major fatty acids. The major polar lipids of SM33T and NSE70-1T were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, sphingoglycolipid and phosphatidylcholine, respectively. Moreover, genomic, physiological, and biochemical results allowed the phenotypic and genotypic differentiation of strains SM33T and NSE70-1T from their closest and other species of the genus Sphingomonas with validly published names. Therefore, the SM33T and NSE70-1T represent novel species of the genus Sphingomonas, for which the name Sphingomonas telluris sp. nov. (type strain SM33T = KACC 22222T = LMG 32193T), and Sphingomonas caseinilyticus (type strain NSE70-1T = KACC 22411T = LMG 32495T).
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Affiliation(s)
- Muhammad Zubair Siddiqi
- Department of Biotechnology, Hankyong National University, 327 Jungang-ro, Anseong-si, Gyeonggi-do, 17579, Republic of Korea
- AceEMzyme Co., Ltd., Academic Industry Cooperation, Room 403, 327 Jungang-ro, Anseong-si, Gyeonggi-do, 17579, Republic of Korea
- HK Ginseng Research Center, 327 Jungang-no, Anseong-si, Gyeonggi-do, 17579, Republic of Korea
| | - Govindan Rajivgandhi
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat Sen University, Guangzhou, 510275, People's Republic of China
| | - Muhammad Faiq
- Department of Food Science and Technology, The University of Agriculture, Peshawar, 25130, Khyber Pakhtunkhwa, Pakistan
| | - Wan-Taek Im
- Department of Biotechnology, Hankyong National University, 327 Jungang-ro, Anseong-si, Gyeonggi-do, 17579, Republic of Korea.
- AceEMzyme Co., Ltd., Academic Industry Cooperation, Room 403, 327 Jungang-ro, Anseong-si, Gyeonggi-do, 17579, Republic of Korea.
- HK Ginseng Research Center, 327 Jungang-no, Anseong-si, Gyeonggi-do, 17579, Republic of Korea.
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3
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Liu B, Wan Y, Chen E, Huang M, Chen X, Ni H, He J. Sphingomonas caeni sp. nov., a phenolic acid-degrading bacterium isolated from activated sludge. Antonie Van Leeuwenhoek 2023:10.1007/s10482-023-01837-w. [PMID: 37156982 DOI: 10.1007/s10482-023-01837-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 04/25/2023] [Indexed: 05/10/2023]
Abstract
A Gram-stain-negative, rod-shaped, polar flagellated or stalked and non-spore-forming bacterium, designated LB-2T, was isolated from activated sludge. Growth was observed at 20-30 °C (optimum 28 °C), pH 6.0-8.0 (optimum pH 7.0) and salinity of 0-0.5% (w/v; optimum 0.5%). Phylogenetic analysis based on the 16S rRNA gene indicated that strain LB-2T belongs to the genus Sphingomonas and showed the highest sequence similarity (96.7%) and less than 96.7% similarities to other type strains. The genome size of strain LB-2T was 4.10 Mb, with 66.8 mol% G + C content. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strains LB-2T and S. canadensis FWC47T were 77.8% and 21%, respectively. The predominant cellular fatty acids were summed feature 8 (C18:1ω7c and/or C18 : 1ω6c) and C16:0. The major polar lipids were aminolipid, glycolipid, sphingoglycolipid, phosphatidylcholine, phosphatidylglycerol, four unidentified lipids, glycophospholipid, phosphatidylethanolamine and diphosphatidylglycerol. The predominant respiratory quinone was Q-10 and the major polyamine was sym-homospermidine. On the basis of phenotypic, genotypic and phylogenetic evidences, strain LB-2T represents a novel species in the genus Sphingomonas, for which the name Sphingomonas caeni sp. nov. is proposed. The type strain is LB-2T (GDMCC 1.3630T = NBRC 115,102T).
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Affiliation(s)
- Bin Liu
- College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Yingying Wan
- College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China
| | - E Chen
- The Environmental Monitoring Center of Gansu Province, Lanzhou, 730020, China
| | - Mingzhu Huang
- College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China
| | - Xuelan Chen
- College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China
| | - Haiyan Ni
- College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China.
| | - Jian He
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
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Liu H, Jiang S, Ou J, Tang J, Lu Y, Wei Y. Investigation of soil microbiota reveals variable dominant species at different land areas in China. BIOTECHNOL BIOTEC EQ 2022. [DOI: 10.1080/13102818.2022.2071634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Affiliation(s)
- Hai Liu
- Criminal technology corps of Henan Provincial Public Security Bureau, Zhengzhou, Henan Province, China
| | - Shan Jiang
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, PR China
| | - Jintao Ou
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan, People’s Republic of China
- Laboratory of Synthetic Biology, Zhengzhou University, Zhengzhou, Henan, People’s Republic of China
| | - Jinfeng Tang
- Laboratory of Synthetic Biology, Zhengzhou University, Zhengzhou, Henan, People’s Republic of China
- Key Laboratory for Water Quality and Conservation of Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Linköping University – Guangzhou University Research Center on Urban Sustainable Development, Guangzhou, People’s Republic of China
| | - Yang Lu
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, People’s Republic of China
| | - Yongjun Wei
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan, People’s Republic of China
- Laboratory of Synthetic Biology, Zhengzhou University, Zhengzhou, Henan, People’s Republic of China
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Wei DW, Yang Y, Zeng Y, Wang C, Feng J. Sphingomonas baiyangensis sp. nov., isolated from water in Baiyang Lake. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-stain-negative, short-rod-shaped, orange-pigmented bacterial strain, designated L-1–4 w-11T, was isolated from Baiyang Lake in China. The strain grew at 15–35 °C (optimum 30 °C) and pH 7–8 (optimum pH 7) in TSA medium. The predominant polar lipids of strain L-1–4 w-11T were sphingoglycolipid, phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, one unidentified glycolipid and three unidentified lipids; the major cellular fatty acids were C17 : 1ω6c and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c); and the major respiratory quinone was ubiquinone 10 (Q-10). Strain L-1–4 w-11T showed the highest 16S rRNA gene sequence similarity to
Sphingomonas japonica
JCM 15438T (98.3 %) and
S. spermidinifaciens
GDMCC 1.657T (98.0 %). The draft genome size of strain L-1–4 w-11T was 3.3 Mbp, and the G+C content was 67.8 mol%. Digital DNA–DNA hydridization and average nucleotide identity values between the genome sequences of strain L-1–4 w-11T and
S. spermidinifaciens
GDMCC 1.657T (76.9 and 21.0 %),
S. japonica
JCM 15438T (76.0 and 19.9 %) and
S. paucimobilis
CGMCC 1.12825T (72.8 and 19.6 %) were far below the thresholds for prokaryotic conspecific assignment. With the evidence from the phylogenetic, chemotaxonomic and genotypic analyses, we propose that strain L-1–4 w-11T represents a novel
Sphingomonas
species with the name S. baiyangensis sp. nov. The type strain is L-1–4 w-11T (=CGMCC 1.13572T=JCM 33962T).
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Affiliation(s)
- Da-Wei Wei
- College of Life Science, University of Chinese Academy of Sciences, Beijing, PR China
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, PR China
| | - Yunzhen Yang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, PR China
| | - Yuan Zeng
- College of Life Science, University of Chinese Academy of Sciences, Beijing, PR China
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, PR China
| | - Chao Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, PR China
| | - Jie Feng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, PR China
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Floc’h JB, Hamel C, Laterrière M, Tidemann B, St-Arnaud M, Hijri M. Long-Term Persistence of Arbuscular Mycorrhizal Fungi in the Rhizosphere and Bulk Soils of Non-host Brassica napus and Their Networks of Co-occurring Microbes. FRONTIERS IN PLANT SCIENCE 2022; 13:828145. [PMID: 35283923 PMCID: PMC8914178 DOI: 10.3389/fpls.2022.828145] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 01/25/2022] [Indexed: 05/25/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF) are obligate plant symbionts that improve the nutrition and health of their host. Most, but not all the crops form a symbiosis with AMF. It is the case for canola (Brassica napus), an important crop in the Canadian Prairies that is known to not form this association. From 2008 to 2018, an experiment was replicated at three locations of the Canadian Prairies and it was used to assess the impact of canola on the community of AMF naturally occurring in three cropping systems, canola monoculture, or canola in two different rotation systems (2-years, canola-wheat and 3-years, barley-pea-canola). We sampled canola rhizosphere and bulk soils to: (i) determine diversity and community structure of AMF, we expected that canola will negatively impact AMF communities in function of its frequency in crop rotations and (ii) wanted to assess how these AMF communities interact with other fungi and bacteria. We detected 49 AMF amplicon sequence variants (ASVs) in canola rhizosphere and bulk soils, confirming the persistence of a diversified AMF community in canola-planted soil, even after 10 years of canola monoculture, which was unexpected considering that canola is among non-mycorrhizal plants. Network analysis revealed a broad range of potential interactions between canola-associated AMF and some fungal and bacterial taxa. We report for the first time that two AMF, Funneliformis mosseae and Rhizophagus iranicus, shared their bacterial cohort almost entirely in bulk soil. Our results suggest the existence of non-species-specific AMF-bacteria or AMF-fungi relationships that could benefit AMF in absence of host plants. The persistence of an AMF community in canola rhizosphere and bulk soils brings a new light on AMF ecology and leads to new perspectives for further studies about AMF and soil microbes interactions and AMF subsistence without mycotrophic host plants.
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Affiliation(s)
- Jean-Baptiste Floc’h
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, QC, Canada
- Quebec Research and Development Centre, Agriculture and Agri-Food Canada, Québec, QC, Canada
| | - Chantal Hamel
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, QC, Canada
- Quebec Research and Development Centre, Agriculture and Agri-Food Canada, Québec, QC, Canada
| | - Mario Laterrière
- Quebec Research and Development Centre, Agriculture and Agri-Food Canada, Québec, QC, Canada
| | - Breanne Tidemann
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB, Canada
| | - Marc St-Arnaud
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, QC, Canada
| | - Mohamed Hijri
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, QC, Canada
- African Genome Center, Mohammed VI Polytechnic University (UM6P), Ben Guerir, Morocco
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7
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Cha I, Kang H, Kim H, Joh K. Sphingomonas ginkgonis sp. nov., isolated from phyllosphere of Ginkgo biloba. Int J Syst Evol Microbiol 2019; 69:3224-3229. [PMID: 31343398 DOI: 10.1099/ijsem.0.003613] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain HMF7854T, isolated from a ginkgo tree, was an orange-pigmented, Gram-stain-negative, motile by means of a single flagellum, strictly aerobic, rod-shaped bacterium. The isolate grew optimally on Reasoner's 2A agar at 30 °C, pH 7.0-8.0 and 0 % NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain HMF7854T belonged to the genus Sphingomonas and was most closely related to Sphingomonasagri HKS-06T (96.8 % sequence similarity). The major fatty acids were C17 : 1 ω6c, summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0. The predominant isoprenoid quinone was ubiquinone-10. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, sphingoglycolipid, two unidentified lipids and two unidentified glycolipids. The genomic DNA G+C content was 68.4 mol%. Thus, based on its phylogenetic, phenotypic and chemotaxonomic data, strain HMF7854T represents a novel species of the genus Sphingomonas, for which the name Sphingomonasginkgonis sp. nov. is proposed. The type strain of the species is strain HMF7854T (=KCTC 62461T=NBRC 113337T).
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Affiliation(s)
- Inseong Cha
- Department of Bioscience and Biotechnology, Hankuk University of Foreign Studies, Gyeonggi 17035, Republic of Korea
| | - Heeyoung Kang
- Department of Bioscience and Biotechnology, Hankuk University of Foreign Studies, Gyeonggi 17035, Republic of Korea
| | - Haneul Kim
- Department of Bioscience and Biotechnology, Hankuk University of Foreign Studies, Gyeonggi 17035, Republic of Korea
| | - Kiseong Joh
- Department of Bioscience and Biotechnology, Hankuk University of Foreign Studies, Gyeonggi 17035, Republic of Korea
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8
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Hetharua B, Min D, Liao H, Guo W, Lin X, Xu H, Tian Y. Sphingosinithalassobacter portus gen. nov., sp. nov., a novel member of the family Sphingomonadaceae isolated from surface seawater. Int J Syst Evol Microbiol 2019; 69:2834-2840. [PMID: 31274398 DOI: 10.1099/ijsem.0.003566] [Citation(s) in RCA: 8] [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 Gram-stain-negative strain, designated FM6T, was isolated from surface seawater sampled at the port in Xiamen, PR China. Strain FM6T showed less than 96.3 % 16S rRNA gene sequence similarity to the type strains of species with validly published names. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain FM6T belonged to the family Sphingomonadaceae and was closely related to species of the genera Sphingomonas (96.3 %) and Stakelama (96.0 %). Ubiquinone-10 was the predominant respiratory quinone. Cells were motile with a single polar flagellum. Growth occurred at temperatures from 20 to 45 °C (optimum, 30 °C), at pH values between pH 6.0 and 8.0 (optimum, pH 7.0) and in 0-4.0 % (w/v) NaCl (optimum, 1.0-1.5 %). Predominant polar lipids were sphingoglycolipid, phosphatidylcholine, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, five unidentified glycolipids and five unidentified polar lipids. The major fatty acids were summed feature 8 (containing C18 : 1ω7c and/or C18 : 1ω6c). The DNA G+C content of the type strain was 63.8 mol%. On the basis of the results of phylogenetic analysis, combined with phenotypic and chemotaxonomic data, strain FM6T is considered to represent a novel species in a new genus in the family Sphingomonadaceae for which the name Sphingosinithalassobacter portus gen. nov., sp. nov. is proposed. The type strain of Sphingosinithalassobacter portus gen. nov., sp. nov. is FM6T (=MCCC 1K03501T=JCM 32714T).
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Affiliation(s)
- Buce Hetharua
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, PR China
| | - Derong Min
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, PR China
| | - Hu Liao
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, PR China
| | - Wei Guo
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, PR China
| | - Xiaolan Lin
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, PR China
| | - Hong Xu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, PR China
| | - Yun Tian
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, PR China
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9
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Li YQ, Narsing Rao MP, Zhang H, Guo YM, Dong ZY, Alkhalifah DHM, Hozzein WN, Xiao M, Li WJ. Description of Sphingomonas mesophila sp. nov., isolated from Gastrodia elata Blume. Int J Syst Evol Microbiol 2019; 69:1030-1034. [PMID: 30735115 DOI: 10.1099/ijsem.0.003263] [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 Gram-staining-negative, strictly aerobic, non-motile strain, SYSUP0001T, was isolated from tubers of Gastrodia elata Blume. The 16S rRNA gene sequence result indicated that SYSUP0001T represents a member of the genus Sphingomonas, with the highest sequence similarity (97.7 %) to the type strain of Sphingomonasginsengisoli. SYSUP0001T grew at 14-37 °C and pH 6-8, with optimum growth at 28 °C and pH 7. Tolerance to NaCl was up to 3 % (w/v) with optimum growth in the absence of NaCl. The respiratory quinone was Q-10. The major fatty acids were C18 : 1ω7c, Summed feature 3 (C16 : 1ω7c/C16 : 1ω6c), and C16 : 0. The polar lipids were diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), phosphatidylglycerol (PG), sphingoglycolipid (SGL), phosphatidylcholine (PC) and four unidentified polar lipids (L). The DNA G+C content was 67.5 %. The average nucleotide identity (ANI) values between SYSUP0001T and closely related members of the genus Sphingomonas were below the cut-off level (95-96 %) for species delineation. On the basis of the phenotypic, phylogenetic and chemotaxonomic characterizations, SYSUP0001T represents a novel species of the genus Sphingomonas, for which the name Sphingomonasmesophila sp. nov. is proposed. The type strain is SYSUP0001T (=KCTC 62179 T=CGMCC 1.16462T).
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Affiliation(s)
- Yan-Qiong Li
- Kunming Medical University Haiyuan College, Kunming, 650106, PR China
| | - Manik Prabhu Narsing Rao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat- Sen University, Guangzhou, PR China
| | - Hui Zhang
- Kunming Medical University Haiyuan College, Kunming, 650106, PR China
| | - Yan-Mei Guo
- Kunming Medical University Haiyuan College, Kunming, 650106, PR China
| | - Zhou-Yan Dong
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat- Sen University, Guangzhou, PR China
| | - Dalal Hussien M Alkhalifah
- Biology Department, Faculty of Science, Princess Nourah bint Abdulrahman University, Riyadh 11564, Kingdom of Saudi Arabia
| | - Wael N Hozzein
- Bioproducts Research Chair, Zoology Department, College of Science, King Saud University, Riyadh 11451, Kingdom of Saudi Arabia.,Department of Botany and Microbiology, Faculty of Science, Beni-Suef University, Beni Suef, Egypt
| | - Min Xiao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat- Sen University, Guangzhou, PR China
| | - Wen-Jun Li
- College of Fisheries, Henan Normal University, Xinxiang 453007, PR China.,State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat- Sen University, Guangzhou, PR China
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10
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Liu L, Hui N, Liang L, Zhang X, Sun Q, Li L. Sphingomonas deserti sp. nov., isolated from Mu Us Sandy Land soil. Int J Syst Evol Microbiol 2018; 69:441-446. [PMID: 30543503 DOI: 10.1099/ijsem.0.003168] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
A Gram-stain-negative, rod-shaped bacterium, designated as strain GL-C-18T, was isolated from soil sample collected at Mu Us Sandy Land, China, and its taxonomic position was investigated using a polyphasic approach. Growth was observed in the presence of 0-1 % (w/v) NaCl (optimum, 0 %), pH 6.0-9.0 (optimum, pH 7.0-8.0) and 20-37 °C. On the basis of 16S rRNA gene sequence similarity, strain GL-C-18T belonged to the family Sphingomonadaceae and was most closely related to Sphingosinicella vermicomposti YC7378T (95.7 %), Sphingomonas oligophenolica S213T (95.0 %) and Sphingobium boeckii 301T (94.8 %). The draft genome of strain GL-C-18T was 6.09 Mb, and the G+C content was 66.0 %. The average nucleotide identity value to Sphingosinicella vermicomposti YC7378T was 83.7 %. The predominant respiratory quinone was Q-10. The major fatty acids were C18 : 1ω7c, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16:0 and C14 : 0 2OH. The main polar lipids were sphingoglycolipid, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine. On the basis of chemotaxonomic, phylogenetic and phenotypic evidence, strain GL-C-18T represents a novel species of the genus Sphingomonas, for which the name Sphingomonasdeserti sp. nov. is proposed. The type strain is GL-C-18T (=ACCC 60076T=KCTC 62411T).
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Affiliation(s)
- Lei Liu
- 1State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, PR China
| | - Nan Hui
- 1State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, PR China
| | - Lixiong Liang
- 1State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, PR China
| | - Xiaoxia Zhang
- 2Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Qiwu Sun
- 1State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, PR China
| | - Lubin Li
- 1State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, PR China
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