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Ruan L, Wang E, Jiang X, Mao D, Cheng D, He J, Jiang J, Shen Q. Yanghanlia caeni gen. nov., sp. nov., a novel taxon within the family Alcaligenaceae isolated from sludge of a pesticide-manufacturing factory. Int J Syst Evol Microbiol 2024; 74. [PMID: 38767617 DOI: 10.1099/ijsem.0.006394] [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: 05/22/2024] Open
Abstract
A Gram-stain-negative bacterium, designated LG-2T, was isolated from sludge collected at a pesticide-manufacturing factory in Jiangsu Province, PR China. Cells of strain LG-2T were strictly aerobic, non-motile and spherical. Growth was observed at 15-42 °C (optimum, 30 °C), pH 6.0-9.0 (optimum, pH 7.0) and 0-3.0 % (w/v) NaCl (optimum, 1.0 %). LG-2T showed 95.5-96.9 % 16S rRNA sequence similarity to type strains in the genera Pusillimonas, Bordetella, Parapusillimonas, Candidimonas and Paracandidimonas of the family Alcaligenaceae. The phylogenomic tree indicated that strain LG-2T was clustered in the family Alcaligenaceae and formed a clade with Paracandidimonas soli IMT-305T, while the phylogenetic trees based on 16S rRNA gene sequences indicated that strain LG-2T formed a distinct clade within the family Alcaligenaceae. The average nucleotide identity, digital DNA-DNA hybridization and average amino acid identity values between LG-2T and its closely related type strains in the genera Pusillimonas, Bordetella, Parapusillimonas, Candidimonas and Paracandidimonas were 70.8-75.3, 18.9-23.7 and 59.6 %-69.3 %, respectively. The major cellular fatty acids were C16 : 0, C17 : 0 cyclo, summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c) and summed feature 2 (C12 : 0 aldehyde and/or unknown 10.928). The predominant menaquinone was Q-8. The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, two aminophospholipids, three aminolipids and nine unknown polar lipids. The genome size of strain LG-2T was 3.2 Mb and the DNA G+C content was 63.4 mol%. On the basis of the phenotypic, phylogenetic and genomic results from this study, strain LG-2T represents a novel species of a new genus in the family Alcaligenaceae, for which the name Yanghanlia caeni gen. nov., sp. nov. is proposed, with strain LG-2T (=KCTC 8084T= CCTCC AB 2023123T) as the type strain.
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Affiliation(s)
- Luyao Ruan
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Enyi Wang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Xueting Jiang
- Biological Experiment Center, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Dongmei Mao
- Biological Experiment Center, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Dan Cheng
- Biological Experiment Center, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Jian He
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
- Agricultural Microbial Resources Protection and Germplasm Innovation and Utilization Center of Jiangsu Province, Nanjing, Jiangsu 210095, PR China
| | - Jiandong Jiang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Qirong Shen
- Agricultural Microbial Resources Protection and Germplasm Innovation and Utilization Center of Jiangsu Province, Nanjing, Jiangsu 210095, PR China
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
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Subramanian P, Kim Y, Naito H, Asano T, Hamada M, Weon HY, Kwon SW, Heo J. Gracilibacillus salinarum sp. nov. and Gracilibacillus caseinilyticus sp. nov., halotolerant bacteria isolated from a saltern environment. Int J Syst Evol Microbiol 2023; 73. [PMID: 37787383 DOI: 10.1099/ijsem.0.005965] [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: 10/04/2023] Open
Abstract
Two aerobic, Gram-stain-positive, spore-forming motile bacterial strains, designated SSPM10-3T and SSWR10-1T, were isolated from salterns in Jeollanam province of South Korea. Both strains were halotolerant and grew well in 5 % NaCl but not in 20 and 25% NaCl, respectively. Optimal growth was observed with 5 % NaCl, at 30 °C and at pH 7.0-8.0. On the basis of the results of phylogenetic analysis using 16S rRNA gene sequence, both the strains were placed within the genus Gracilibacillus with Gracilibacillus massiliensis (98.65 % similarity) as their nearest neighbour. Menaquinone-7 (MK-7) (97 %) was the major isoprenoid quinone in both strains and major cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0 and anteiso-C17 : 0. Orthologous average nucleotide identity with usearch (OrthoANIu) and digital DNA-DNA hybridisation (dDDH) percentage comparison indicated that SSPM10-3T and SSWR10-1T exhibited highest similarity with G. massiliensis Awa-1T at 74.27 % and 21.0 and 74.23 % and 20.0 %, respectively. The DNA G+C contents of the strains were 39.1 % (SSPM10-3T) and 38.5 % (SSWR10-1T). Members of the genus Gracilibacillus, both strains were distinct from each other with respect to their ability to produce urease, β-glucosidase, assimilation of inulin and methyl-α-d-glucopyranoside and degradation of casein. Compared with each other, ANI and d4 dDDH calculations were only 88.2 % and 36.3 %, well below the cut-off values for species delineation for each index. On the basis of their phenotypic, physiological, biochemical and phylogenetic characteristics,SSPM10-3T and SSWR10-1T represent distinct novel species for which names Gracilibacillus salinarum SSPM10-3T and Gracilibacillus caseinilyticus SSWR10-1T are proposed. The type strains are SSPM10-3T (=KACC 21933T =NBRC 115502T) and SSWR10-1T (=KACC 21934T =NBRC 115503T).
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Affiliation(s)
- Parthiban Subramanian
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Yiseul Kim
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeollabuk-do, Republic of Korea
| | - Hanako Naito
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation, 2-5-8, Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Tomomi Asano
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation, 2-5-8, Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Moriyuki Hamada
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation, 2-5-8, Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Hang-Yeon Weon
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeollabuk-do, Republic of Korea
| | - Soon-Wo Kwon
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeollabuk-do, Republic of Korea
| | - Jun Heo
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeollabuk-do, Republic of Korea
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A culture-based and culture-independent approach to the study of landfill leachate bacterial and archaeal communities. Anaerobe 2022; 77:102626. [PMID: 35977655 DOI: 10.1016/j.anaerobe.2022.102626] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 07/14/2022] [Accepted: 08/09/2022] [Indexed: 11/20/2022]
Abstract
The landfill is a convenient and affordable method of municipal solid waste (MSW) management. Landfill leachate contains a heavy load of pollutants and pathogens. Discharge of untreated leachate is the leading cause of surface and groundwater contamination and a threat to public and environmental health. To develop an efficient leachate treatment technology, an in-depth understanding of landfill chemistry and microbiology is essential. In the present manuscript, we conducted a comparative study of three different landfill leachate samples using cultivation-based and culture-independent molecular studies. We cultivated 85 species of aerobic, anaerobic bacteria and archaea from leachate represented by a total of 200 strains using extensive culturomics approaches. Twelve out of 200 cultivated strains of bacteria showed very low 16S rRNA gene sequence similarity (84-98.6%) with their closest relatives and could be the potential novel taxa, the first time cultivated from leachate. Members of the six genera only have 2-5 representatives from past studies from other habitats but first time cultivated from leachate. In addition to bacteria, we also cultivated and characterized different groups of methanogenic archaea. Our chemistry data indicate that leachate is a highly stressed ecosystem with an assemblage of many toxic wastes like sulfur, zinc, mercury, chromium, etc. 16S rRNA gene-based amplicon analysis showed the dominance of (30-55%) methanogens and haloarachaea. Our data suggest that archaea are the significant regulators of leachate ecology, and more in-depth studies with multiple leachate samples are required to understand their role in leachate nutrient cycling and the development of effective leachate treatment technology.
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Zhu J, Che J, Jiang X, Ma M, Guan D, Li L, Cao F, Zhao B, Kang Y, Zhao J, Kong D, Zhou Y, Ruan Z, Li J. Leucobacter chinensis sp. nov., with plant growth-promoting potential isolated from field soil after seven-years continuous maize cropping. Int J Syst Evol Microbiol 2022; 72. [PMID: 35939329 DOI: 10.1099/ijsem.0.005417] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
A novel Gram-stain-positive, aerobic, non-motile and rod-shaped bacterium, designated strain NC76-1T, was isolated from soil from a field that had undergone seven years continuous maize cropping from Liuba town located in Zhangye city, Gansu province, PR China. Colonies of strain NC76-1T were white, opaque and circular with a convex shape. The isolate was found to be able to grow at 10-40 °C (optimum 30 °C), pH 6.0 to 12.0 (optimum 7.0-8.0) and with 0-5.0 % (w/v) NaCl (optimum 0%). On the basis of the results of 16S rRNA gene sequence analysis, the strain fell within the clade of the genus Leucobacter, showing the highest sequence similarities with Leucobacter iarius 40T (97.4%), Leucobacter aridicollis CIP 108388T (97.0%), Leucobacter chromiireducens subsp. solipictus TAN 31504T (96.7%) and Leucobacter denitrificans M1T8B10T (96.7%). The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between NC76-1T and its closest relatives, L. iarius 40T, L. aridicollis CIP 108388T, L. chromiireducens subsp. solipictus TAN 31504T and L. denitrificans M1T8B10T were ≤73.5 % and 20.3%, respectively. The genomic DNA G+C content of NC76-1T was 61.5 mol%. It presented MK-11 as the predominant menaquinone. The major cellular fatty acids were anteiso-C15 : 0 (49.2 %) and iso-C16 : 0 (35.7%). The major polar lipids were found to be diphosphatidyglycerol, phosphatidylglycerol, phosphatidylethanolamine, aminoglycolipid, five glycolipid and one unidentified lipids. The cell wall amino acids were 2,4-diaminobutyric acid, alanine, glutamic acid, glycine and threonine. On the basis of the phylogenetic, phenotypic and chemotaxonomic characteristics, strain NC76-1T is concluded to represent a novel species within the genus Leucobacter, for which the name Leucobacter chinensis sp. nov. is proposed. The type strain is NC76-1T (GDMCC 1.2286T= JCM 34651T).
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Affiliation(s)
- Jie Zhu
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China.,School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, PR China
| | - Juan Che
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China.,College of Life Science, Xinjiang Normal University, Urumqi, 830046, PR China
| | - Xin Jiang
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China.,Laboratory of Quality and Safety Risk Assessment for Microbial Products (Beijing), Ministry of Agriculture, Beijing 100081, PR China
| | - Mingchao Ma
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China.,Laboratory of Quality and Safety Risk Assessment for Microbial Products (Beijing), Ministry of Agriculture, Beijing 100081, PR China
| | - Dawei Guan
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Li Li
- Laboratory of Quality and Safety Risk Assessment for Microbial Products (Beijing), Ministry of Agriculture, Beijing 100081, PR China
| | - Fengming Cao
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China.,Laboratory of Quality and Safety Risk Assessment for Microbial Products (Beijing), Ministry of Agriculture, Beijing 100081, PR China
| | - Baisuo Zhao
- Laboratory of Quality and Safety Risk Assessment for Microbial Products (Beijing), Ministry of Agriculture, Beijing 100081, PR China
| | - Yaowei Kang
- Life Sciences Collage of Zhaoqing University, Zhaoqing 526061, PR China
| | - Ji Zhao
- School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, PR China
| | - Delong Kong
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Yiqing Zhou
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Zhiyong Ruan
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Jun Li
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China.,Laboratory of Quality and Safety Risk Assessment for Microbial Products (Beijing), Ministry of Agriculture, Beijing 100081, PR China
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Huang XX, Xu L, Sun JQ. Gracilibacillus suaedae sp. nov., an indole acetic acid-producing endophyte isolated from a root of Suaeda salsa. Int J Syst Evol Microbiol 2021; 71. [PMID: 34878379 DOI: 10.1099/ijsem.0.005140] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive, facultatively anaerobic, spore-forming, motile with unipolar biflagella, rod-shaped, indole acetic acid-producing bacterium, named LD4P30T, was isolated from a root of Suaeda salsa collected in Inner Mongolia, northern China. Strain LD4P30T grew at pH 6.0-11.0 (optimum, pH 7.0), 10-40 °C (35 °C) and in the presence of 1-15% (w/v) NaCl (5%). The strain was positive for oxidase and negative for catalase. The major cellular fatty acids of strain LD4P30T were iso-C15:0, C15:1 ω5c and anteiso-C15:0; the major polar lipids were diphosphatidylglycerol and phosphatidylglycerol; and menaquinone-7 was the only respiratory quinone. The genomic DNA G+C content was 36.7 mol%. A phylogenetic tree based on 16S rRNA gene sequences showed that strain LD4P30T clustered with Gracilibacillus thailandensis TP2-8T, Gracilibacillus saliphilus YIM 91119T and Gracilibacillus lacisalsi BH312T, and showed 99.0, 98.9, 98.0 and <97.7% 16S rRNA gene similarity to G. thailandensis TP2-8T, G. saliphilus YIM 91119T, G. lacisalsi BH312T and all other current type strains, respectively. The digital DNA-DNA hybridization and average nucleotide identity based on blast values between strain LD4P30T and G. saliphilus YIM 91119T, G. thailandensis TP2-8T and G. lacisalsi BH312T were 44.9, 44.7 and 44.4%, and 91.1, 91.0 and 90.8%, respectively. Based on its phenotypic, physiological and phylogenetic characteristics, strain LD4P30T represents a novel species, for which the name Gracilibacillus suaedae is proposed. The type strain is LD4P30T (=CGMCC 1.17697T=KCTC 82375T).
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Affiliation(s)
- Xiao-Xian Huang
- Lab for Microbial Resources, Inner Mongolia Key Laboratory of Environmental Pollution Prevention and Waste Resource Recycle & Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, PR China
| | - Lian Xu
- Jiangsu Key Lab for Organic Solid Waste Utilization, Educational Ministry Engineering Center of Resource-saving Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Ji-Quan Sun
- Lab for Microbial Resources, Inner Mongolia Key Laboratory of Environmental Pollution Prevention and Waste Resource Recycle & Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, PR China
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Deutch CE, Farden AM, DiCesare ES. Characterization of β-galactosidase and α-galactosidase activities from the halophilic bacterium Gracilibacillus dipsosauri. ANN MICROBIOL 2021. [DOI: 10.1186/s13213-021-01657-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Purpose
Gracilibacillus dipsosauri strain DD1 is a salt-tolerant Gram-positive bacterium that can hydrolyze the synthetic substrates o-nitrophenyl-β-d-galactopyranoside (β-ONP-galactose) and p-nitrophenyl-α-d-galactopyranoside (α-PNP-galactose). The goals of this project were to characterize the enzymes responsible for these activities and to identify the genes encoding them.
Methods
G. dipsosauri strain DD1 was grown in tryptic soy broth containing various carbohydrates at 37 °C with aeration. Enzyme activities in cell extracts and whole cells were measured colorimetrically by hydrolysis of synthetic substrates containing nitrophenyl moieties. Two enzymes with β-galactosidase activity and one with α-galactosidase activity were partially purified by ammonium sulfate fractionation, ion-exchange chromatography, and gel-filtration chromatography from G. dipsosauri. Coomassie Blue-stained bands corresponding to each activity were excised from nondenaturing polyacrylamide gels and subjected to peptide sequencing after trypsin digestion and HPLC/MS analysis.
Result
Formation of β-galactosidase and α-galactosidase activities was repressed by d-glucose and not induced by lactose or d-melibiose. β-Galactosidase I had hydrolytic and transgalactosylation activity with lactose as the substrate but β-galactosidase II showed no activity towards lactose. The α-galactosidase had hydrolytic and transgalactosylation activity with d-melibiose but not with d-raffinose. β-Galactosidase I had a lower Km with β-ONP-galactose as the substrate (0.693 mmol l−1) than β-galactosidase II (1.662 mmol l−1), was active at more alkaline pH, and was inhibited by the product d-galactose. β-Galactosidase II was active at more acidic pH, was partially inhibited by ammonium salts, and showed higher activity with α-PNP-arabinose as a substrate. The α-galactosidase had a low Km with α-PNP-galactose as the substrate (0.338 mmol l−1), a pH optimum of about 7, and was inhibited by chloride-containing salts. β-Galactosidase I activity was found to be due to the protein A0A317L6F0 (encoded by gene DLJ74_04930), β-galactosidase II activity to the protein A0A317KZG3 (encoded by gene DLJ74_12640), and the α-galactosidase activity to the protein A0A317KU47 (encoded by gene DLJ74_17745).
Conclusions
G. dipsosauri forms three intracellular enzymes with different physiological properties which are responsible for the hydrolysis of β-ONP-galactose and α-PNP-galactose. BLAST analysis indicated that similar β-galactosidases may be formed by G. ureilyticus, G. orientalis, and G. kekensis and similar α-galactosidases by these bacteria and G. halophilus.
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Rhodobacter kunshanensis sp. nov., a Novel Bacterium Isolated from Activated Sludge. Curr Microbiol 2021; 78:3791-3797. [PMID: 34383131 DOI: 10.1007/s00284-021-02628-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 07/28/2021] [Indexed: 10/20/2022]
Abstract
Strain HX-7-19T was isolated from the activated sludge collected from an abandoned herbicide manufacturing plant in Kunshan, China. Cells were Gram-reaction-negative, rod-shaped, and non-motile. The phylogenetic analysis based on 16S rRNA gene indicated that strain HX-7-19T formed a clade with Rhodobacter blasticus CGMCC 1.3365T (96.3% sequence similarity). The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain HX-7-19T and R. blasticus CGMCC 1.3365T were 76.2% and 20.3%, respectively. The genomic DNA G + C content of strain HX-7-19T was 65.9%. The major fatty acids (> 10% of the total fatty acids) were C18:1 ω7c and C18:1 ω7c 11-methyl. The major respiratory quinone was quinone Q-10. The major polar lipid profile consists of phosphatidylglycerol (PG), diphosphatidyl-glycerol (DPG), phosphatidylethanolamine (PE), and phosphatidylcholine (PC). Photosynthesis pigments bacteriochlorophyll a and carotenoids were formed and photosynthesis genes pufL and pufM were detected. On the basis of phenotypic and phylogenetic evidences, strain HX-7-19T is considered as a novel species in the genus Rhodobacter, for which the name Rhodobacter kunshanensis sp. nov. is proposed. The type strain is HX-7-19T (= KCTC 72471T = CCTCC AB 2020148T).
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Ngom I, Hasni I, Senghor B, Lo C, Armstrong N, Sokhna C, Raoult D, Fournier PE, Lagier JC. Description of Gracilibacillus phocaeensis sp. nov., a new halophilic bacterium isolated from Senegalian human stool. New Microbes New Infect 2020; 38:100799. [PMID: 33294194 PMCID: PMC7695981 DOI: 10.1016/j.nmni.2020.100799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 10/05/2020] [Accepted: 10/19/2020] [Indexed: 10/24/2022] Open
Abstract
Using the taxonogenomics method, we describe Gracilibacillus phocaeensis strain Marseille-P3801, a new species previously isolated from a salty stool of a 20-year-old man from N'Diop, Senegal. It is a Gram-positive, aerobic and motile bacillus. The major fatty acids are C15:0-anteiso (59%), C16:0 (16%) and C17:0-anteiso (11%). Strain Marseille-P3801 exhibits a 98.45% sequence similarity with Gracilibacillus thailandensis strain TP2-8, the phylogenetically closest species. Its genome is 4.66 Mb with 39.6 mol% G + C content.
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Affiliation(s)
- I.I. Ngom
- Aix-Marseille Université, IRD, APHM, MEPHI, France
- IHU-Méditerranée Infection, France
| | - I. Hasni
- Aix-Marseille Université, IRD, APHM, MEPHI, France
- IHU-Méditerranée Infection, France
- Amoeba R&D Department, Chassieu, France
| | - B. Senghor
- Aix-Marseille Université, IRD, APHM, MEPHI, France
- IHU-Méditerranée Infection, France
| | - C.I. Lo
- IHU-Méditerranée Infection, France
- Aix-Marseille Université, IRD, APHM, SSA, VITROME, Marseille, France
| | - N. Armstrong
- Aix-Marseille Université, IRD, APHM, MEPHI, France
- IHU-Méditerranée Infection, France
| | - C. Sokhna
- IHU-Méditerranée Infection, France
- Aix-Marseille Université, IRD, APHM, SSA, VITROME, Marseille, France
| | - D. Raoult
- Aix-Marseille Université, IRD, APHM, MEPHI, France
- IHU-Méditerranée Infection, France
| | - P.-E. Fournier
- IHU-Méditerranée Infection, France
- Aix-Marseille Université, IRD, APHM, SSA, VITROME, Marseille, France
| | - J.-C. Lagier
- Aix-Marseille Université, IRD, APHM, MEPHI, France
- IHU-Méditerranée Infection, France
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He SW, Wang X, Guo HB, Han JG, Thin KK, Gao JS, Ma LA, Zhang XX. Gracilibacillus oryzae sp. nov., isolated from rice seeds. Int J Syst Evol Microbiol 2020; 70:5467-5472. [PMID: 32894210 DOI: 10.1099/ijsem.0.004427] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive, facultatively anaerobic, endospore-forming bacterium, designated strain TD8T, was isolated from surface-sterilized rice seeds (Oryza sativa L.). Phylogenetic analysis of the 16S rRNA gene indicated that strain TD8T should be placed within the genus Gracilibacillus (95.2-99.0 % sequence similarity); it exhibited highest similarities to Gracilibacillus ureilyticus CGMCC 1.7727T (99.0 %), 'Gracilibacillus xinjiangensis' CGMCC 1.12449T (98.9 %) and Gracilibacillus dipsosauri CGMCC 1.3642T (97.5 %). Chemotaxonomic analysis showed that menaquinone-7 (MK-7) was the major isoprenoid quinone. Diphosphatidylglycerol, phosphatidylglycerol and one unidentified phospholipid were the major cellular polar lipids, and the major fatty acids were anteiso-C15 : 0, anteiso-C17 : 0, iso-C15 : 0, C16 : 0 and iso-C16 : 0, which supported the allocation of the strain to the genus Gracilibacillus. The digital DNA-DNA hybridization value between strain TD8T and Gracilibacillus ureilyticus CGMCC 1.7727T was lower than 70 % (22.60 %), and the average nucleotide identity score was 79.54±5.09 %, suggesting that strain TD8T represented a novel species in the genus Gracilibacillus. The genomic DNA G+C content was 37.5 %. Based on physiological and biochemical characteristics and genotypic data, strain TD8T represents a novel species of the genus Gracilibacillus, for which the name Gracilibacillus oryzae sp. nov. is proposed. The type strain is TD8T (=ACCC 61556T=CICC 24889T=JCM 33537T).
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Affiliation(s)
- Shan-Wen He
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China.,College of Life Science, The Yangtze University, Jingzhou 434025, PR China
| | - Xing Wang
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - He-Bao Guo
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Ji-Gang Han
- Shanghai Academy of Landscape Architecture Science and Planning, Shanghai 200232, PR China
| | - Kyu Kyu Thin
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Ju-Sheng Gao
- Qiyang Agro-ecosystem of National Field Experimental Station, Institute of Agricultural Resources and Regional, Chinese Academy of Agricultural Sciences, Qiyang 426182, PR China.,Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Li-An Ma
- College of Life Science, The Yangtze University, Jingzhou 434025, PR China
| | - Xiao-Xia Zhang
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
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10
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Gracilibacillus salitolerans sp. nov., a moderate halophile isolated from saline soil in Northwest China. Int J Syst Evol Microbiol 2020; 70:3701-3710. [DOI: 10.1099/ijsem.0.004224] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
A moderately halophilic strain, designated SCU50T, was recovered from a saline soil sample and characterized by a polyphasic approach. The 16S rRNA gene sequence analysis showed that strain SCU50T belonged to the genus
Gracilibacillus
and was most closely related to
Gracilibacillus thailandensis
TP2-8T (98.1 % similarity) and
Gracilibacillus orientalis
XH-63T (97.7 %). Genomic average nucleotide identity and digital DNA–DNA hybridization analyses confirmed the separate species status of the new isolate relative to other recognized
Gracilibacillus
species. The genome size was about 5.09 Mbp and the DNA G+C content was 36.7 mol%. The strain grew optimally at 10–15 % (w/v) NaCl, pH 6.5–7.5 and 25–30 °C. It contained anteiso-C15 : 0, iso-C15 : 0 and anteiso-C17 : 0 as the dominant fatty acids and menaquinone-7 as the major respiratory quinone. The polar lipid profile was examined and found to comprise diphosphatidylglycerol, phosphatidylglycerol, one unidentified phospholipid and one unidentified lipid. The cell-wall peptidoglycan type was A1γ based on meso-diaminopimelic acid. Combining the data from phenotypic, chemotaxonomic, genomic and phylogenetic characterization, it was concluded that strain SCU50T should be assigned as representing a novel species within the genus
Gracilibacillus
. Thus, a novel taxon named Gracilibacillus salitolerans sp. nov. was first established, with SCU50T (=CGMCC 1.17336T=KCTC 43107T) as the type strain.
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11
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Deutch CE, Yang S. Genomic sequencing of Gracilibacillus dipsosauri reveals key properties of a salt-tolerant α-amylase. Antonie Van Leeuwenhoek 2020; 113:1049-1059. [PMID: 32318981 DOI: 10.1007/s10482-020-01417-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 04/09/2020] [Indexed: 11/26/2022]
Abstract
Gracilibacillus dipsosauri is a moderately-halophilic Gram-positive bacterium which forms an extracellular α-amylase that is induced by starch, repressed by D-glucose, and active in 2.0 M KCl. Previous studies showed that while enzyme activity could be measured with the synthetic substrate 2-chloro-4-nitrophenyl-α-D-maltotrioside (CNPG3), other assays were inconsistent and the protein showed aberrant mobility during nondenaturing gel electrophoresis. To clarify the properties of this enzyme, the genome of G. dipsosauri was sequenced and was found to be 4.19 Mb in size with an overall G+C content of 36.9%. A gene encoding an α-amylase composed of 691 amino acids was identified. The protein was a member of the glycosyl hydrolase 13 family, which had a molecular mass of 77,396 daltons and a pI of 4.39 due to an unusually large number of aspartate and glutamate residues (95/691 or 13.7%). BLAST analysis of the amino acid sequence revealed significant matches to other proteins with cyclodextrin glycosyltransferase activity. Partial purification of the protein from G. dipsosauri showed that fractions catalyzing the hydrolysis of CNPG3 and p-nitrophenyl-D-maltoheptoside also catalyzed the formation of β-cyclodextrin but not α-cyclodextrin or γ-cyclodextrin. Formation of β-cyclodextrin was not stimulated by high salt concentrations but did occur with rice, potato, wheat, and corn starches and amylopectin. These studies explain the unusual features of the α-amylase from G. dipsosauri and indicate it should be classified as EC 2.4.1.19. The availability of the complete genomic sequence of G. dipsosauri will provide the basis for studies on other enzymes from this halophile which may be useful for biotechnology.
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Affiliation(s)
- Charles E Deutch
- Microbion Research, 8931 W. Deanna Dr., Peoria, AZ, 85382, USA.
- School of Mathematical and Natural Sciences, Arizona State University, Glendale, AZ, 85306, USA.
| | - Shanshan Yang
- Bioinformatics Core Facility, Knowledge Enterprise, Arizona State University, Tempe, AZ, 85281, USA
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12
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Peng Q, Sheng M, Yang Z, Ni H, Li Q, Li Y, He J. Extensimonas perlucida sp. nov., a Novel Bacterium Isolated from Sludge. Curr Microbiol 2020; 77:1316-1320. [PMID: 32060766 DOI: 10.1007/s00284-020-01911-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 01/30/2020] [Indexed: 11/26/2022]
Abstract
A bacterium, designated HX2-24 T, was isolated from activated sludge treating pesticide-manufacturing wastewater. Colonies of the strain on nutrient agar were circular, transparent, and colorless. Strain HX2-24 T shared 98.1% 16S rRNA gene sequence similarity with Extensimonas vulgaris S4T, and less than 97% similarities with other type strains. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the strain formed a clade with E. vulgaris S4T. The major cellular fatty acids were C16:0, summed feature 3 (C16:1ω7c and/or C16:1ω6c) and C17:0 cyclo, the major polar lipids were phosphatidylethanolamine (PE), phosphatidylglycerol (PG), diphosphatidylglycerol (DPG), aminophospholipid (APL), glycophospholipid (GPL), and aminoglycolipid (AGL). The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between HX2-24 T and E. vulgaris S4T were 92% and 41%, respectively. The G + C content of strain HX2-24 T was 64.4 mol%. Thus, based on the phenotypic, chemotaxonomic, and genotypic characteristics, strain HX2-24 T represents a novel species in the genus Extensimonas, for which the name Extensimonas perlucida HX2-24 T sp. nov. is proposed. The type strain is HX2-24 T (= KCTC 72472 T = CCTCC AB 2019178 T).
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Affiliation(s)
- Qian Peng
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Mengyao Sheng
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Zhou Yang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Haiyan Ni
- College of Life Science, Jiangxi Normal University, Jiangxi, 330022, People's Republic of China
| | - Qinfen Li
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, People's Republic of China
| | - Yi Li
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, People's Republic of China.
| | - Jian He
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.
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13
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Anaerophilus nitritogenes gen. nov., sp. nov., isolated from salt lake sediment in Xinjiang Province, China. Antonie van Leeuwenhoek 2019; 113:417-425. [PMID: 31713080 DOI: 10.1007/s10482-019-01351-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 10/18/2019] [Indexed: 10/25/2022]
Abstract
An obligately anaerobic, nitrate-reducing bacterial strain (MJB2T) was isolated from sediments of saline in Xinjiang province of China. Cells were Gram-stain-positive rods and motile by means of flagella and formed endospores. The novel strain MJB2T was able to grow at 15-37 °C (optimum 28-30 °C), pH 5.8-9.4 (optimum 7.8) and with 1.0-7.0% NaCl (optimum 5.0-6.0%, w/v). Sulfate, sulfite, thiosulfate, elemental sulfur, nitrite and Fe(III) were not used as terminal electron acceptors. Oxidase and catalase reactions were positive. H2S was producted from L-cystine. Complex substrates such as beef extract, peptone and yeast extract can be used as sole energy sources. The DNA G+C content was 29.4 mol%. The major cellular fatty acids (> 10%) were C14:0, C16:1 cis 7 and C16:1 cis 9. The main polar lipids consisted of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, three unidentified amino lipids, one unidentified amino glycolipid, two unidentified glycolipid, one unidentified aminophospholipid and two unidentified lipids. No respiratory quinones were detected. According to phylogenetic analysis based on 16S rRNA gene sequences, strain MJB2T was affiliated to the family Clostridiaceae (order Clostridiales) with highest 16S rRNA gene sequence similarity of 95.3% to Crassaminicella profunda Ra1766HT. Strain MJB2T exhibited 74.9% ANI values to C. profunda Ra1766HT. In silico DNA-DNA relatedness value between strain MJB2T and C. profunda Ra1766HT was 19.5%. The distinct biochemical, chemotaxonomic and phylogenetic differences from the previously described taxa supported that strain MJB2T represents a novel species of a new genus, for which the name Anaerophilus nitritogenes gen. nov., sp. nov. is proposed. The type strain is MJB2T (=KCTC 15800T=MCCC 1K03631T).
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14
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Han SB, Hou XJ, Yu YH, Ju Z, Zhang R, Wang RJ, Ye YH, Ren YH, Zhang WY, Wu M. Description of Wenzhouxiangella salilacus sp. nov., a moderate halophilic bacterium isolated from a salt lake in Xinjiang Province, China. Antonie van Leeuwenhoek 2018; 112:847-855. [PMID: 30569387 DOI: 10.1007/s10482-018-01216-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 12/11/2018] [Indexed: 10/27/2022]
Abstract
A Gram-stain negative, non-motile, strictly aerobic and rod-shaped bacterium, designated as 15181T, was isolated from a salt lake in Xinjiang Province, China. Strain 15181T was able to grow at 10-40 °C (optimum 37 °C), pH 6.0-8.5 (optimum 7.0) and with 1-14% NaCl (optimum 4%, w/v). According to phylogenetic analysis based on 16S rRNA gene sequences, strain 15181T was assigned to the genus Wenzhouxiangella with high 16S rRNA gene sequence similarity of 97.4% to Wenzhouxiangella sediminis XDB06T, followed by Wenzhouxiangella marina KCTC 42284T (95.9%). Strain 15181T exhibited ANI values of 80.0% and 72.0% to W. sediminis XDB06T and W. marina KCTC 42284T, respectively. The in silico DDH analysis revealed that strain 15181T shared 19.1% and 18.7% DNA relatedness with W. sediminis XDB06T and W. marina KCTC 42284T, respectively. Chemotaxonomic analysis showed that the sole respiratory quinone was ubiquinone-8, the major fatty acids included iso-C15:0, iso-C16:0 and summed feature 9 (C16:0 10-methyl and/or iso-C17:1ω9c). The major polar lipids included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, two unidentified glycolipids, two unidentified phospholipids, two unidentified aminophospholipids and an unidentified lipid. On the basis of phenotypic, genotypic and chemotaxonomic characteristics presented in this study, strain 15181T is concluded to represent a novel species in the genus Wenzhouxiangella, for which the name Wenzhouxiangella salilacus sp. nov. is proposed. The type strain is 15181T (=KCTC 62172T=MCCC 1K03442T).
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Affiliation(s)
- Shuai-Bo Han
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Xin-Jun Hou
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Yang-Huan Yu
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Zhao Ju
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Ran Zhang
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Rui-Jun Wang
- Ocean College, Zhejiang University, Zhoushan, 316000, People's Republic of China
| | - Yang-Hui Ye
- Ocean College, Zhejiang University, Zhoushan, 316000, People's Republic of China
| | - Yan-Hu Ren
- Ocean College, Zhejiang University, Zhoushan, 316000, People's Republic of China
| | - Wei-Yan Zhang
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, 315211, People's Republic of China.
| | - Min Wu
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, People's Republic of China.
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15
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Han SB, Yu YH, Ju Z, Li Y, Zhang R, Hou XJ, Ma XY, Yu XY, Sun C, Wu M. Rhodohalobacter barkolensis sp. nov., isolated from a saline lake and emended description of the genus Rhodohalobacter. Int J Syst Evol Microbiol 2018; 68:1949-1954. [DOI: 10.1099/ijsem.0.002775] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Shuai-Bo Han
- College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Yang-Huan Yu
- College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Zhao Ju
- College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Yu Li
- College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Ran Zhang
- College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Xin-Jun Hou
- College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Xin-Yuan Ma
- College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Xiao-Yun Yu
- College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Cong Sun
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, PR China
| | - Min Wu
- College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
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16
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Diop A, Seck EH, Dubourg G, Armstrong N, Blanc-Tailleur C, Raoult D, Fournier PE. Genome sequence and description of Gracilibacillus timonensis sp. nov. strain Marseille-P2481 T , a moderate halophilic bacterium isolated from the human gut microflora. Microbiologyopen 2018; 8:e00638. [PMID: 29675845 PMCID: PMC6485780 DOI: 10.1002/mbo3.638] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 01/31/2018] [Accepted: 03/09/2018] [Indexed: 12/19/2022] Open
Abstract
Microbial culturomics represents an ongoing revolution in the characterization of the human gut microbiota. By using three culture media containing high salt concentrations (10, 15, and 20% [w/v] NaCl), we attempted an exhaustive exploration of the halophilic microbial diversity of the human gut and isolated strain Marseille‐P2481 (= CSUR P2481 = DSM 103076), a new moderately halophilic bacterium. This bacterium is a Gram‐positive, strictly aerobic, spore‐forming rod that is motile by use of a flagellum and exhibits catalase, but not oxidase activity. Strain Marseille‐P2481 was cultivated in media containing up to 20% (w/v) NaCl, with optimal growth being obtained at 37°C, pH 7.0–8.0, and 7.5% [w/v] NaCl). The major fatty acids were 12‐methyl‐tetradecanoic acid and hexadecanoic acid. Its draft genome is 4,548,390 bp long, composed of 11 scaffolds, with a G+C content of 39.8%. It contains 4,335 predicted genes (4,266 protein coding including 89 pseudogenes and 69 RNA genes). Strain Marseille‐P2481 showed 96.57% 16S rRNA sequence similarity with Gracilibacillus alcaliphilus strain SG103T, the phylogenetically closest species with standing in nomenclature. On the basis of its specific features, strain Marseille‐P2481T was classified as type strain of a new species within the genus Gracilibacillus for which the name Gracilibacillus timonensis sp. nov. is formally proposed.
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Affiliation(s)
- Awa Diop
- URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095, Aix-Marseille Université, Institut hospitalo-universitaire Mediterranee-infection, Marseille, France
| | - El Hadji Seck
- URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095, Aix-Marseille Université, Institut hospitalo-universitaire Mediterranee-infection, Marseille, France
| | - Gregory Dubourg
- URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095, Aix-Marseille Université, Institut hospitalo-universitaire Mediterranee-infection, Marseille, France
| | - Nicholas Armstrong
- URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095, Aix-Marseille Université, Institut hospitalo-universitaire Mediterranee-infection, Marseille, France
| | - Caroline Blanc-Tailleur
- URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095, Aix-Marseille Université, Institut hospitalo-universitaire Mediterranee-infection, Marseille, France
| | - Didier Raoult
- URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095, Aix-Marseille Université, Institut hospitalo-universitaire Mediterranee-infection, Marseille, France.,Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Pierre-Edouard Fournier
- URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095, Aix-Marseille Université, Institut hospitalo-universitaire Mediterranee-infection, Marseille, France
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17
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Yuan N, Zeng Y, Feng H, Yu Z, Huang Y. Altererythrobacter xixiisoli sp. nov., isolated from wetland soil. Int J Syst Evol Microbiol 2017; 67:3655-3659. [PMID: 28879849 DOI: 10.1099/ijsem.0.002198] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, coccoid, yellow, non-motile, aerobic bacterium, designated strain S36T, was isolated from soil of the Xixi wetland in Zhejiang province, PR China. Phylogenetic analysis, based on 16S rRNA gene sequences, revealed that strain S36T could represent a novel species of genus Altererythrobacter showing highest similarity to Altererythrobacter atlanticus 26DY36T (96.31 % 16S rRNA gene sequence similarity). The temperature, pH and NaCl concentration ranges for growth were 10-37 °C (optimum 32 °C), pH 5.0-10.0 (optimum pH 7.0) and 0.5-3 % (optimum 1 %, w/v), respectively. The predominant respiratory quinone of strain S36T was Q-10. The major fatty acids were C16 : 0, C17 : 1ω6c, C18 : 1ω7c and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH). The G+C content of the genomic DNA was 62.7 mol%. These data all support the affiliation of strain S36T to the genus Altererythrobacter. The polar lipids profile of strain S36T comprised diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, two unidentified phospholipids and two unidentified glycolipids. The results of physiological and biochemical tests allowed differentiation of strain S36T from other members of the genus Altererythrobacter. Therefore, strain S36T represents a novel species of the genus Altererythrobacter, for which the name Altererythrobacter xixiisoli sp. nov. is proposed; the type strain is S36T (=CGMCC 1.12804T=NBRC 110413T).
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Affiliation(s)
- Nate Yuan
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Yanhua Zeng
- Department of Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Hao Feng
- Department of Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Zhiliang Yu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Yili Huang
- Department of Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, PR China
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18
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Gracilibacillus aidingensis sp. nov., a novel moderately halophilic bacterium isolated from Aiding salt lake. Arch Microbiol 2017. [PMID: 28624973 DOI: 10.1007/s00203-017-1399-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
A novel Gram-positive, aerobe, moderately halophilic bacterium was isolated from saline soil of Aiding lake in Xinjiang, north-west of China, designated strain YIM 98001T. Cells were rod-shaped, motile and grew at 5-20% (w/v) NaCl (optimum 10%), pH 6-10 (optimum pH 7.0) and 4-45 °C (optimum 37 °C). The major cellular fatty acids were anteiso C15:0, anteiso C17:0, iso C15:0. The predominant respiratory quinone was MK-7. Diphosphatidylglycerol, phosphatidylglycerol, phosphoglycolipid were the major polar lipids. Meso-diaminopimelic acid was the diagnostic diamino acid of the cell-wall peptidoglycan. The G+C content was 36.46 mol%. 16S rRNA gene sequence analysis showed that the strain belongs to the family Bacillaceae, with the highest sequence similarity to the type strain Gracilibacillus thailandensis TP2-8T (96.84%), followed by Gracilibacillus saliphilus YIM 91119T (96.78%) and Gracilibacillus ureilyticus MF38T (96.57%), thus confirming the affiliation of strain YIM 98001T to the genus Gracilibacillus. The polyphasic approach indicates that strain YIM 98001T represents a novel species of the genus Gracilibacillus, for which the name Gracilibacillus aidingensis is proposed. The type strain is YIM 98001T (=KCTC 42683T = DSMZ 104330T).
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19
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Diop A, Khelaifia S, Armstrong N, Labas N, Fournier PE, Raoult D, Million M. Microbial culturomics unravels the halophilic microbiota repertoire of table salt: description of Gracilibacillus massiliensis sp. nov. MICROBIAL ECOLOGY IN HEALTH AND DISEASE 2016; 27:32049. [PMID: 27760679 PMCID: PMC5071648 DOI: 10.3402/mehd.v27.32049] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 09/22/2016] [Indexed: 01/12/2023]
Abstract
Background Microbial culturomics represents an ongoing revolution in the characterization of environmental and human microbiome. Methods By using three media containing high salt concentration (100, 150, and 200 g/L), the halophilic microbial culturome of a commercial table salt was determined. Results Eighteen species belonging to the Terrabacteria group were isolated including eight moderate halophilic and 10 halotolerant bacteria. Gracilibacillus massiliensis sp. nov., type strain Awa-1T (=CSUR P1441=DSM 29726), is a moderately halophilic gram-positive, non-spore-forming rod, and is motile by using a flagellum. Strain Awa-1T shows catalase activity but no oxidase activity. It is not only an aerobic bacterium but also able to grow in anaerobic and microaerophilic atmospheres. The draft genome of G. massiliensis is 4,207,226 bp long, composed of 13 scaffolds with 36.05% of G+C content. It contains 3,908 genes (3,839 protein-coding and 69 RNA genes). At least 1,983 (52%) orthologous proteins were not shared with the closest phylogenetic species. Hundred twenty-six genes (3.3%) were identified as ORFans. Conclusions Microbial culturomics can dramatically improve the characterization of the food and environmental microbiota repertoire, deciphering new bacterial species and new genes. Further studies will clarify the geographic specificity and the putative role of these new microbes and their related functional genetic content in environment, health, and disease.
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Affiliation(s)
- Awa Diop
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, AMU UM 63, CNRS UMR7278, IRD 198, INSERM U1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
| | - Saber Khelaifia
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, AMU UM 63, CNRS UMR7278, IRD 198, INSERM U1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
| | - Nicholas Armstrong
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, AMU UM 63, CNRS UMR7278, IRD 198, INSERM U1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
| | - Noémie Labas
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, AMU UM 63, CNRS UMR7278, IRD 198, INSERM U1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
| | - Pierre-Edouard Fournier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, AMU UM 63, CNRS UMR7278, IRD 198, INSERM U1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
| | - Didier Raoult
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, AMU UM 63, CNRS UMR7278, IRD 198, INSERM U1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France.,Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Matthieu Million
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, AMU UM 63, CNRS UMR7278, IRD 198, INSERM U1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France;
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20
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Oh YJ, Lee HW, Lim SK, Kwon MS, Lee J, Jang JY, Park HW, Nam YD, Seo MJ, Choi HJ. Gracilibacillus kimchii sp. nov., a halophilic bacterium isolated from kimchi. J Microbiol 2016; 54:588-593. [PMID: 27572507 DOI: 10.1007/s12275-016-6349-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 08/03/2016] [Accepted: 08/06/2016] [Indexed: 10/21/2022]
Abstract
A novel halophilic bacterium, strain K7(T), was isolated from kimchi, a traditional Korean fermented food. The strain is Gram-positive, motile, and produces terminal endospores. The isolate is facultative aerobic and grows at salinities of 0.0-25.0% (w/v) NaCl (optimum 10-15% NaCl), pH 5.5-8.5 (optimum pH 7.0-7.5), and 15-42°C (optimum 37°C). The predominant isoprenoid quinone in the strain is menaquinone-7 and the peptidoglycan of the strain is meso-diaminopimelic acid. The major fatty acids of the strain are anteisio-C15:0, iso-C15:0, and, C16:0 (other components were < 10.0%), while the major polar lipids are diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, and three unidentified lipids. A phylogenetic analysis of 16S rRNA gene sequence similarity showed that the isolated strain was a cluster of the genus Gracilibacillus. High levels of gene sequence similarity were observed between strain K7(T) and Gracilibacillus orientalis XH-63(T) (96.5%), and between the present strain and Gracilibacillus xinjiangensis (96.5%). The DNA G+C content of this strain is 37.7 mol%. Based on these findings, strain K7(T) is proposed as a novel species: Gracilibacillus kimchii sp. nov. The type strain is K7(T) (KACC 18669(T); JCM 31344(T)).
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Affiliation(s)
- Young Joon Oh
- Microbiology and Functionality Research Group, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
| | - Hae-Won Lee
- Hygienic Safety and Analysis Center, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
| | - Seul Ki Lim
- Microbiology and Functionality Research Group, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
| | - Min-Sung Kwon
- Microbiology and Functionality Research Group, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
| | - Jieun Lee
- Microbiology and Functionality Research Group, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
| | - Ja-Young Jang
- Microbiology and Functionality Research Group, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
| | - Hae Woong Park
- Advanced Process Technology Research Group, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
| | - Young-Do Nam
- Research Group of Gut Microbiome, Korea Food Research Institute, Seongnam, 13539, Republic of Korea
| | - Myung-Ji Seo
- Division of Bioengineering, Incheon National University, Incheon, 22012, Republic of Korea
| | - Hak-Jong Choi
- Microbiology and Functionality Research Group, World Institute of Kimchi, Gwangju, 61755, Republic of Korea.
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Han SB, Su Y, Hu J, Wang RJ, Sun C, Wu D, Zhu XF, Wu M. Terasakiella brassicae sp. nov., isolated from the wastewater of a pickle-processing factory, and emended descriptions of Terasakiella pusilla and the genus Terasakiella. Int J Syst Evol Microbiol 2016; 66:1807-1812. [DOI: 10.1099/ijsem.0.000946] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Shuai-Bo Han
- College of Life Sciences, Zhejiang University, Hangzhou 310058, PRChina
| | - Yue Su
- Ocean College, Zhejiang University, Hangzhou 310058, PRChina
| | - Jing Hu
- College of Life Sciences, Zhejiang University, Hangzhou 310058, PRChina
| | - Rui-Jun Wang
- Ocean College, Zhejiang University, Hangzhou 310058, PRChina
| | - Cong Sun
- College of Life Sciences, Zhejiang University, Hangzhou 310058, PRChina
| | - Dildar Wu
- Department of Biology, Xinjiang Normal University, Urumqi 830054, PRChina
| | - Xu-Fen Zhu
- College of Life Sciences, Zhejiang University, Hangzhou 310058, PRChina
| | - Min Wu
- College of Life Sciences, Zhejiang University, Hangzhou 310058, PRChina
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Zhang WY, Hu J, Zhang XQ, Zhu XF, Wu M. Bacillus salitolerans sp. nov., a novel bacterium isolated from a salt mine in Xinjiang province, China. Antonie van Leeuwenhoek 2015; 108:443-51. [DOI: 10.1007/s10482-015-0497-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 05/27/2015] [Indexed: 11/30/2022]
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Huang Y, Zeng Y, Feng H, Wu Y, Xu X. Croceicoccus naphthovorans sp. nov., a polycyclic aromatic hydrocarbons-degrading and acylhomoserine-lactone-producing bacterium isolated from marine biofilm, and emended description of the genus Croceicoccus. Int J Syst Evol Microbiol 2015; 65:1531-1536. [DOI: 10.1099/ijs.0.000132] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A polycyclic aromatic hydrocarbons-degrading and acylhomoserine-lactone-producing marine bacterium, designated strain PQ-2T, was isolated from marine biofilm collected from a boat shell at a harbour of Zhoushan island in Zhejiang Province, PR China. Strain PQ-2T is Gram-stain-negative, yellow-pigmented, non-motile and short rod-shaped. Optimal growth of strain PQ-2T was observed at 32 °C, at pH 7.0 and in 2 % (w/v) NaCl. The 16S rRNA gene sequence of strain PQ-2T showed highest similarity to
Croceicoccus marinus
E4A9T (96.3 %) followed by
Novosphingobium malaysiense
MUSC 273T (95.6 %) and
Altererythrobacter marinus
H32T (95.6 %). Phylogenetic analysis with all species of the family
Erythrobacteraceae
with validly published names revealed that strain PQ-2T formed a phyletic line with
Croceicoccus marinus
E4A9T that was distinct from other members of the family
Erythrobacteraceae
. The sole respiratory quinone was ubiquinone 10 (Q-10). The predominant fatty acids were C18 : 1ω7c, C17 : 1ω6c and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH). The genomic DNA G+C content was 61.7 mol%. In the polar lipid profile, phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol, one unidentified phospholipid and one sphingoglycolipid were the major compounds; and another sphingoglycolipid was present in a minor amount. Based on the genotypic and phenotypic data, strain PQ-2T represents a novel species of the genus
Croceicoccus
, for which the name Croceicoccus
naphthovorans sp. nov. is proposed. The type strain is PQ-2T ( = CGMCC 1.12805T = NBRC 110381T). In addition, emended descriptions for the genus
Croceicoccus
and the species
C. marinus
are given.
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Affiliation(s)
- Yili Huang
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Yanhua Zeng
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Hao Feng
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Yuehong Wu
- Second Institute of Oceanography, State Oceanic Administration, Hangzhou 310012, PR China
| | - Xuewei Xu
- Second Institute of Oceanography, State Oceanic Administration, Hangzhou 310012, PR China
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Feng H, Zeng Y, Huang Y. Flavobacterium palustre sp. nov., isolated from wetland soil. Int J Syst Evol Microbiol 2015; 65:1003-1007. [PMID: 25563922 DOI: 10.1099/ijs.0.000054] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-staining-negative, non-motile, yellow-coloured, rod-shaped bacterium, designated S44(T), was isolated from bankside soil of Xixi wetland, located in Zhejiang province, China. Growth of strain S44(T) was observed at 6-37 °C (optimum, 28 °C) and at pH 6.0-9.0 (optimum, 7.0). No growth occurred in the presence of >2 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain S44(T) represented a member of the genus Flavobacterium, showing the highest sequence similarities to the sequences from Flavobacterium succinicans DSM 4002(T) (96.9 %), Flavobacterium reichenbachii WB 3.2-61(T) (96.6 %) and Flavobacterium glycines NCBI 105008(T) (96.5 %). The G+C content of the genomic DNA was 33.6 mol%. The predominant cellular fatty acids were C15 : 0, iso-C15 : 0, anteiso-C15 : 0 and summed feature 3 (comprising C16 : 1ω7c and/or iso-C15 : 0 2-OH), and the major respiratory quinone was menaquinone 6 (MK-6). The major polar lipids were phosphatidylethanolamine, two unknown aminolipids, two unknown aminophospholipids and four unknown polar lipids. On the basis of the phenotypic and genotypic data, it is proposed that the isolate S44(T) be classified as representing a novel species of the genus Flavobacterium, for which the name Flavobacterium palustre sp. nov. is proposed. The type strain is S44(T) ( = CGMCC 1.12811(T) = NBRC 110389(T)).
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Affiliation(s)
- Hao Feng
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, PR China
| | - Yanhua Zeng
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, PR China
| | - Yili Huang
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, PR China
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Aquibacillus salifodinae sp. nov., a novel bacterium isolated from a salt mine in Xinjiang province, China. Antonie van Leeuwenhoek 2014; 107:367-74. [DOI: 10.1007/s10482-014-0335-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2014] [Accepted: 11/14/2014] [Indexed: 10/24/2022]
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26
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Zeng Y, Feng H, Huang Y. Pedobacter xixiisoli sp. nov., isolated from bank soil. Int J Syst Evol Microbiol 2014; 64:3683-3689. [DOI: 10.1099/ijs.0.065946-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, rod-shaped, yellow, non-motile, aerobic bacterium (strain S27T) was isolated from bank soil of the Xixi wetland in Zhejiang province, PR China. Phylogenetic analysis, based on its 16S rRNA gene sequence, revealed that strain S27T could represent a novel species of the genus
Pedobacter
showing highest similarity to
Pedobacter koreensis
WPCB189T (95.45 %), followed by ‘Pedobacter zeaxanthinifaciens’ TDMA-5 (95.22 %). The temperature, pH and NaCl concentration ranges for growth were 6–37 °C (optimum 28 °C), pH 5.0–9.0 (optimum pH 7.5) and 0–3 % (w/v) [optimum 0.5 % (w/v)], respectively. The DNA G+C content was 36.1 mol%, MK-7 was the only respiratory quinone, and iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH) were the major fatty acids. These data all support the affiliation of strain S27T to the genus
Pedobacter
. The polar lipids of strain S27T comprised phosphatidylethanolamine, one unidentified aminophospholipid, four unidentified aminolipids and three unidentified lipids. However, strain S27T could be distinguished from other members of the genus
Pedobacter
due to its physiological and biochemical characteristics. Therefore, strain S27T represents a novel species of the genus
Pedobacter
, for which the name Pedobacter xixiisoli sp. nov. is proposed; the type strain is S27T ( = CGMCC 1.12803T = NBRC 110388T).
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Affiliation(s)
- Yanhua Zeng
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Hao Feng
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Yili Huang
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, PR China
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27
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Feng H, Zeng Y, Huang Y. Sphingobacterium paludis sp. nov., isolated from wetland soil. Int J Syst Evol Microbiol 2014; 64:3453-3458. [DOI: 10.1099/ijs.0.064915-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-stain-negative bacteria, designated S37T, was isolated from soil of the Xixi wetland, Zhejiang province, China. Cells of strain S37T were aerobic, non-motile rods. Growth occurred at 10–37 °C (optimum, 25 °C), pH 5.0–9.7 (optimum, pH 7.5) and with 0–6 % (w/v) NaCl (optimum, 0.5 %). Based on 16S rRNA gene sequence analysis, strain S37T was found to be a member of the genus
Sphingobacterium
and shared highest similarity with
Sphingobacterium composti
4M24T (95.78 %). The major fatty acids were summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c), iso-C15 : 0 and iso-C17 : 0 3-OH, and the DNA G+C content was 43.8 mol%. The predominant respiratory quinone was MK-7. Based on its phenotypic and chemotaxonomic characteristics and phylogenetic data, strain S37T represents a novel species of the genus
Sphingobacterium
, for which the name Sphingobacterium
paludis sp. nov. (type strain S37T = CGMCC 1.12801T = NBRC 110386T) is proposed.
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Affiliation(s)
- Hao Feng
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, PR China
| | - Yanhua Zeng
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, PR China
| | - Yili Huang
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, PR China
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Feng H, Zeng Y, Huang Y. Epilithonimonas xixisoli sp. nov., isolated from wetland bank-side soil. Int J Syst Evol Microbiol 2014; 64:4155-4159. [PMID: 25256707 DOI: 10.1099/ijs.0.065771-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-staining-negative, non-motile and rod-shaped bacterial strain containing flexirubin-type pigments, designated S31(T), was isolated from bank-side soil of the Xixi wetland in Zhejiang province, China. Growth occurred at 10-37 °C (optimum, 32 °C), pH 6-8 (optimum, pH 7) and with 0-2 % (w/v) NaCl (optimum, 1 %). Strain S31(T) shared highest 16S rRNA gene sequence similarities with Epilithonimonas lactis H1(T) (96.2 %) and Chryseobacterium molle DW3(T) (96.4 %). Phylogenetic analysis suggested that strain S31(T) was a member of the genus Epilithonimonas. The dominant respiratory quinone was MK-6 and the DNA G+C content was 33.3 mol%. The major fatty acids were iso-C15 : 0, summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c) and anteiso-C15 : 0. The major polar lipids of strain S31(T) were phosphatidylethanolamine, three unidentified aminolipids and four unidentified polar lipids. Based on its phenotypic and chemotaxonomic characteristics and phylogenetic data, strain S31(T) represents a novel species of the genus Epilithonimonas, for which the name Epilithonimonas xixisoli sp. nov. (type strain S31(T) = CGMCC 1.12802(T) = NBRC 110387(T)) is proposed.
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Affiliation(s)
- Hao Feng
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, PR China
| | - Yanhua Zeng
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, PR China
| | - Yili Huang
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, PR China
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Abstract
ABSTRACT
The family
Bacillaceae
constitutes a phenotypically diverse and globally ubiquitous assemblage of bacteria. Investigation into how evolution has shaped, and continues to shape, this family has relied on several widely ranging approaches from classical taxonomy, ecological field studies, and evolution in soil microcosms to genomic-scale phylogenetics, laboratory, and directed evolution experiments. One unifying characteristic of the
Bacillaceae
, the endospore, poses unique challenges to answering questions regarding both the calculation of evolutionary rates and claims of extreme longevity in ancient environmental samples.
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Hirota K, Hanaoka Y, Nodasaka Y, Yumoto I. Gracilibacillus alcaliphilus sp. nov., a facultative alkaliphile isolated from indigo fermentation liquor for dyeing. Int J Syst Evol Microbiol 2014; 64:3174-3180. [DOI: 10.1099/ijs.0.060871-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A facultatively alkaliphilic, lactic-acid-producing and halophilic strain, designated SG103T, was isolated from a fermented Polygonum indigo (Polygonum tinctorium Lour.) liquor sample for dyeing prepared in a laboratory. 16S rRNA gene sequence phylogeny suggested that SG103T is a member of the genus
Gracilibacillus
with the closest relatives being ‘Gracilibacillus
xinjiangensis’ J2 (similarity: 97.06 %),
Gracilibacillus thailandensis
TP2-8T (97.06 %) and
Gracilibacillus halotolerans
NNT (96.87 %). Cells of the isolate stained Gram-positive and were facultatively anaerobic straight rods that were motile by peritrichous flagella. The strain grew at temperatures between 13 and 48 °C with the optimum at 39 °C. It grew in the range pH 7–10 with the optimum at pH 9. The isoprenoid quinone detected was menaquinone-7 (MK-7) and the DNA G+C content was 41.3 mol%. The whole-cell fatty acid profile mainly (>10 %) consisted of iso-C15 : 0, anteiso-C15 : 0 and anteiso-C17 : 0. Unlike other reported species of the genus
Gracilibacillus
, the strain lacked diphosphatidylglycerol as a major polar lipid. DNA–DNA hybridization experiments with strains exhibiting greater than 96.87 % 16S rRNA gene sequence similarity, ‘G. xinjiangensis’ J2,
G. thailandensis
TP2-8T and
G. halotolerans
NNT, revealed 2±4 %, 4±9 % and 3±2 % relatedness, respectively. On the basis of the differences in phenotypic and chemotaxonomic characteristics, and the results of phylogenetic analyses based on 16S rRNA gene sequences and DNA–DNA relatedness data from reported species of the genus
Gracilibacillus
, strain SG103T merits classification as a members of a novel species, for which the name Gracilibacillus
alcaliphilus sp. nov. is proposed. The type strain is SG103T ( = JCM 17253T = NCIMB 14683T).
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Affiliation(s)
- Kikue Hirota
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan
| | - Yoshiko Hanaoka
- Laboratory of Environmental Microbiology, Graduate School of Agriculture, Hokkaido University, Kita-ku, Sapporo 060-8589, Japan
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan
| | - Yoshinobu Nodasaka
- Laboratory of Electron Microscopy, Graduate School of Dentistry, Hokkaido University, Kita-ku, Sapporo 060-8586, Japan
| | - Isao Yumoto
- Laboratory of Environmental Microbiology, Graduate School of Agriculture, Hokkaido University, Kita-ku, Sapporo 060-8589, Japan
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan
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Zhang X, Zhang WY, Shen AH, Huo YY, Zhu XF, Wu M. Halopelagius
longus sp. nov., a member of the family
Halobacteriaceae
isolated from a salt mine, and emended description of the genus
Halopelagius. Int J Syst Evol Microbiol 2013; 63:3585-3590. [DOI: 10.1099/ijs.0.051375-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A thermotolerant, extremely halophilic archaeon, BC12-B1T, was isolated from a salt mine in Baicheng county, Xinjiang province, China. Colonies were off-white–grey. The cells stained Gram-negative, were motile and irregularly long-rod-shaped (variation in both width and length) with abundant gas vesicles. The strain was able to grow at 20–55 °C (optimum, 48 °C), at pH 6.0–8.0 (optimum, 7.0–7.3), with 1.8–6.0 M NaCl (optimum, 3.0–3.5 M) and with 0.02–2.2 M Mg2+ (optimum, 0.1–0.2 M). Cells lysed in distilled water and the minimal NaCl concentration to prevent cell lysis was 8 % (w/v). Phylogenetic analysis based on the 16S rRNA gene sequences showed that strain BC12-B1T was most closely related to
Halopelagius inordinatus
RO5-2T (98.5 %) with less than 95 % sequence similarity to other described species. The genomic DNA G+C content of strain BC12-B1T was 64.0 mol%. The DNA–DNA hybridization value between strain BC12-B1T and
Hpl. inordinatus
RO5-2T was 43.6 %. The major polar lipids of strain BC12-B1T were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, four glycolipids and an unknown lipid. Based on phenotypic, chemotaxonomic and genotypic characteristics, strain BC12-B1T represents a novel species of the genus
Halopelagius
, for which the name
Halopelagius
longus sp. nov. is proposed. The type strain is BC12-B1T ( = CGMCC 1.12397T = JCM 18758T). An emended description of the genus
Halopelagius
is also provided.
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Affiliation(s)
- Xin Zhang
- College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
- College of Forestry and Biotechnology, Zhejiang Agricultural and Forestry University, Lin’an, 311300, PR China
| | - Wei-Yan Zhang
- College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Ai-Hua Shen
- Zhejiang Forestry Academy, Hangzhou 310023, PR China
| | - Ying-Yi Huo
- Second Institute of Oceanography, State Oceanic Administration, Hangzhou 310012, PR China
- Laboratory of Marine Ecosystem and Biogeochemistry, State Oceanic Administration, Hangzhou 310012, PR China
| | - Xu-Fen Zhu
- College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Min Wu
- College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
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Huang HQ, Wang Y, Yuan WD, Xiao C, Ye JJ, Liu M, Zhu J, Sun QG, Bao SX. Gracilibacillus marinus sp. nov., isolated from the northern South China Sea. Antonie van Leeuwenhoek 2013; 104:695-701. [PMID: 23942614 DOI: 10.1007/s10482-013-9977-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2013] [Accepted: 07/15/2013] [Indexed: 10/26/2022]
Abstract
Two gram-positive, aerobic, spore-forming, rod-shaped bacteria, designated HB09003(T) and HB12160, were isolated from seawater and sediment in the northern South China Sea, respectively. Cells were found to be motile by means of peritrichous flagella. The strains were found to grow with 0-15 % (w/v) NaCl, at 10-45 °C and pH 5.0-10.7, with an optimum of 3 % NaCl, 28 °C and pH 8.5, respectively. The predominant isoprenoid quinone of strain HB09003(T), selected as the representative strain, was identified as MK-7. This strain was found to possess anteiso-C15:0, iso-C15:0, anteiso-C17:0 and C16:0 as the major fatty acids. The G+C contents of strain HB09003(T) and HB12160 were determined to be 34.1 and 34.3 mol%, respectively. Analysis of the 16S rRNA gene sequences of the two strains showed an affiliation with the genus Gracilibacillus, with Gracilibacillus kekensis CGMCC 1.10681(T) (similarity of 97.4, 98.0 %, respectively) and Gracilibacillus ureilyticus CGMCC 1.7727(T) (similarity of 97.1, 97.8 %, respectively) as their closest relatives. The DNA-DNA hybridization values between strain HB09003(T) and the two type strains were 42.2 and 54.1 %, respectively. On the basis of phenotypic and genotypic data, strain HB09003(T) and HB12160 are proposed to represent a novel species of the genus Gracilibacillus, for which the name Gracilibacillus marinus sp. nov. is proposed. The type strain is HB09003(T) (=CGMCC 1.10343(T) = DSM 23372(T)).
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Affiliation(s)
- Hui-qin Huang
- Key Laboratory of Biology and Genetic Resources of Tropical Crops of Ministry of Agriculture, Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, People's Republic of China,
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Yang N, Ren B, Dai H, Liu Z, Zhou Y, Song F, Zhang L. Gracilibacillus xinjiangensis sp. nov., a new member of the genus Gracilibacillus isolated from Xinjiang region, China. Antonie van Leeuwenhoek 2013; 104:809-16. [PMID: 23921649 DOI: 10.1007/s10482-013-9992-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Accepted: 07/26/2013] [Indexed: 11/29/2022]
Abstract
A Gram-positive, endospore-forming, rod-shaped bacterium, designated isolate J2(T) was isolated from a soil sample from Xinjiang Uyghur Autonomous Region, China. The isolate was observed to grow at 16-46 °C and pH 6.5-8.0. Chemotaxonomic analysis showed menaquinone-7 (MK-7) to be the major isoprenoid quinone; diphosphatidylglycerol, phosphatidylglycerol, one aminophospholipid, two phosphoglycolipids and one glycolipid as the major cellular polar lipids; and anteiso-C15:0, iso-C15:0, anteiso-C17:0 and C16:0 as the major fatty acids. Comparative analyses of the 16S rRNA gene sequence showed that strain J2(T) is most closely related to Gracilibacillus ureilyticus (with 98.8 % similarity), Gracilibacillus dipsosauri (97.2 %), Gracilibacillus quinghaiensis (97.1 %) and Gracilibacillus thailandensis (97.0 %). The DNA-DNA reassociation values between strain J2(T) and G. ureilyticus MF38(T), G. dipsosauri DD1(T), G. quinghaiensis YIM-C229(T) and G. thailandensis TP2-8(T) were 29.8 ± 3.7, 23.0 ± 3.5, 15.8 ± 4.9 and 15.9 ± 5.0 %, respectively. The genomic DNA G+C content of strain J2(T) was determined to be 36.5 mol%. Based on these data, strain J2(T) is considered as a novel species of the genus Gracilibacillus, for which the name Gracilibacillus xinjiangensis sp. nov. is proposed. The type species is J2(T) (= CGMCC 1.12449(T) = JCM 18859(T)).
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Affiliation(s)
- Na Yang
- Chinese Academy of Sciences Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100190, People's Republic of China
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Zhang WY, Huo YY, Zhang XQ, Zhu XF, Wu M. Halolamina salifodinae sp. nov. and Halolamina salina sp. nov., two extremely halophilic archaea isolated from a salt mine. Int J Syst Evol Microbiol 2013; 63:4380-4385. [PMID: 23832972 DOI: 10.1099/ijs.0.050864-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two strictly aerobic, extremely halophilic archaea, strains WSY15-H1(T) and WSY15-H3(T), were isolated from a salt mine in Wensu county, Xinjiang province, China. Cells of the two strains were Gram-stain-negative, non-motile and pleomorphic. Colonies were pink- and red-pigmented, respectively. Strain WSY15-H1(T) grew at 20-45 °C (optimum 37-42 °C), 1.6-5.4 M NaCl (optimum 3.4-3.9 M), 0-2.0 M MgCl2 (optimum 0.1-0.5 M) and pH 6.0-9.0 (optimum 7.0), whereas strain WSY15-H3(T) grew at 20-50 °C (optimum 37 °C), 1.9-5.4 M NaCl (optimum 3.4 M), 0.02-2.5 M MgCl2 (optimum 0.5-1.0 M) and pH 6.0-7.5 (optimum 6.5). The minimal NaCl concentrations to prevent cell lysis were 9 % (w/v) for strain WSY15-H1(T) and 8 % (w/v) for strain WSY15-H3(T). The major polar lipids of the two isolates were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and phosphatidylglycerol sulfate, as well as nine glycolipids for strain WSY15-H1(T) and seven glycolipids for strain WSY15-H3(T); two of these glycolipids (GL1 and GL3) were chromatographically identical to bis-sulfated diglycosyl diether (S2-DGD-1) and sulfated diglycosyl diether (S-DGD-1), respectively. The genomic DNA G+C contents of strains WSY15-H1(T) and WSY15-H3(T) were 65.4 and 66.2 mol%. On the basis of 16S rRNA gene sequence analysis, strains WSY15-H1(T) and WSY15-H3(T) shared 97.0% similarity with each other and showed respectively 98.4 and 97.6% sequence similarity to Halolamina pelagica TBN21(T), which was the only type strain that had higher than 91% sequence similarity with the two isolates. Analysis of phylogenetic relationships and DNA-DNA relatedness indicated that strains WSY15-H1(T) and WSY15-H3(T) represent two novel lineages with closest affinity to H. pelagica TBN21(T). Based on phenotypic, chemotaxonomic and genotypic characteristics, two novel species of the genus Halolamina are proposed, Halolamina salifodinae sp. nov. (type strain WSY15-H1(T) = JCM 18548(T) = GCMCC 1.12371(T)) and Halolamina salina sp. nov. (type strain WSY15-H3(T) = JCM 18549(T) = GCMCC 1.12285(T)).
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Affiliation(s)
- Wei-Yan Zhang
- College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Ying-Yi Huo
- Second Institute of Oceanography, State Oceanic Administration, Hangzhou 310012, PR China.,Laboratory of Marine Ecosystem and Biogeochemistry, State Oceanic Administration, Hangzhou 310012, PR China
| | - Xin-Qi Zhang
- College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Xu-Fen Zhu
- College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Min Wu
- College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
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Zhang WY, Meng Y, Zhu XF, Wu M. Halopiger salifodinae sp. nov., an extremely halophilic archaeon isolated from a salt mine. Int J Syst Evol Microbiol 2013; 63:3563-3567. [PMID: 23563233 DOI: 10.1099/ijs.0.050971-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel extremely halophilic archaeon KCY07-B2(T) was isolated from a salt mine in Kuche county, Xinjiang province, China. Colonies were cream-pigmented and cells were pleomorphic rod-shaped. Strain KCY07-B2(T) was able to grow at 25-50 °C (optimum 37-45 °C) and pH 6.0-8.0 (optimum 7.0). The strain required at least 1.9 M NaCl for growth. MgCl2 was not required. Cells lysed in distilled water. Polar lipid analysis revealed the presence of phosphatidylglycerol and phosphatidylglycerol phosphate methyl ester, derived from both C20C20 and C20C25 glycerol diethers, together with five glyolipids. The bis-sulfated glycolipid S2-DGD-1 was present. The DNA G+C content was 62.5 mol%. Analysis of the 16S rRNA gene sequence revealed that strain KCY07-B2(T) was closely related to Halopiger xanaduensis SH-6(T) and Halopiger aswanensis 56(T) (95.8 % and 95.5 % similarity, respectively). On the basis of its phenotypic, chemotaxonomic and genotypic characteristics, strain KCY07-B2(T) is considered to represent a novel species of the genus Halopiger, for which the name Halopiger salifodinae sp. nov. is proposed. The type strain is KCY07-B2(T) ( = JCM 18547(T) = CGMCC 1.12284(T)).
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Affiliation(s)
- Wei-Yan Zhang
- College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Yuan Meng
- College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Xu-Fen Zhu
- College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Min Wu
- College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
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Zhang WY, Fang MX, Zhang WW, Xiao C, Zhang XQ, Yu ZP, Zhu XF, Wu M. Extensimonas vulgaris gen. nov., sp. nov., a member of the family Comamonadaceae. Int J Syst Evol Microbiol 2012; 63:2062-2068. [PMID: 23064351 DOI: 10.1099/ijs.0.038158-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel strain, named S4(T), was obtained from industrial wastewater in Xiaoshan, Zhejiang Province, China. Cells were Gram-negative, neutrophilic and non-spore-forming and moved by means of a polar flagellum. Normal cells were 0.8-0.9 × 1.3-1.9 µm and the cells elongated to 10-25 µm when cultivated at high temperatures. Strain S4(T) grew at 15-50 °C (optimum at 48 °C), pH 5.5-8.5 (optimum 7.0-7.5) and 0-2% (optimum 0.5%) (w/v) NaCl. Ubiquinone-8 was the predominant respiratory quinone. C16:0, summed feature 3 (C16:1ω7c and/or iso-C15:0 2-OH) and C17:0 cyclo were the major cellular fatty acids. The major 3-OH fatty acid was C10:0 3-OH. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and an unknown aminoglycolipid. The genomic DNA G+C content was 68.8 mol%. Based on 16S rRNA gene sequences alignment, the most closely related strains were members of the genera Comamonas (94.6-95.6% similarities), Giesbergeria (94.9-95.6%), Acidovorax (94.8-95.4%), Brachymonas (94.1-95.2%) and Macromonas (95.1%). Phylogenetic analysis showed the closest relatives of strain S4(T) were members of the genus Macromonas. Based on phenotypic and phylogenetic characteristics, we suggest that strain S4(T) represents a novel species of a new genus of the family Comamonadaceae, for which the name Extensimonas vulgaris gen. nov., sp. nov. is proposed. The type strain of Extensimonas vulgaris is S4(T) (=CGMCC 1.10977(T)=JCM 17803(T)).
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Affiliation(s)
- Wei-Yan Zhang
- College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Ming-Xu Fang
- College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Wen-Wu Zhang
- College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Chuan Xiao
- College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Xin-Qi Zhang
- College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Zhi-Ping Yu
- Environmental Science Research & Design Institute of Zhejiang Province, Hangzhou 310007, PR China
| | - Xu-Fen Zhu
- College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Min Wu
- College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
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Kim P, Lee JC, Park DJ, Shin KS, Kim JY, Kim CJ. Gracilibacillus bigeumensis sp. nov., a moderately halophilic bacterium from solar saltern soil. Int J Syst Evol Microbiol 2012; 62:1857-1863. [DOI: 10.1099/ijs.0.034264-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-staining-positive, moderately halophilic bacterium, designated strain BH097T, was isolated from solar saltern soil of Bigeum Island in south-west Korea. Cells were motile rods, producing spherical endospores at a terminal position in swollen sporangia. Strain BH097T was strictly aerobic, grew at pH 5.5–9.5 (optimum, pH 8.0), at 10–52 °C (optimum, 37 °C) and at salinities of 1–22 % (w/v) NaCl (optimum, 7 % NaCl). On the basis of 16S rRNA gene sequence analysis, strain BH097T was shown to belong to the genus
Gracilibacillus
within the phylum
Firmicutes
, and showed closest sequence similarity to
Gracilibacillus saliphilus
DSM 19802T (95.8 %),
Gracilibacillus thailandensis
TP2-8T (95.6 %),
Gracilibacillus boraciitolerans
DSM 17256T (95.5 %), ‘Gracilibacillus quinghaiensis’ DSM 17858 (95.4 %) and
Gracilibacillus halophilus
DSM 17856T (95.2 %). The DNA G+C content of this novel isolate was 37.9 mol%. The major cellular fatty acids of strain BH097T were anteiso-C15 : 0, iso-C15 : 0 and C16 : 0, and its polar lipid pattern consisted of diphosphatidylglycerol, phosphatidylglycerol two unknown phospholipids and a glycolipid. The isoprenoid quinone was MK-7, and the peptidoglycan type was A1γ, with meso-diaminopimelic acid as the diagnostic diamino acid. On the basis of polyphasic evidence from this study, strain BH097T represents a novel species of the genus
Gracilibacillus
for which the name Gracilibacillus
bigeumensis sp. nov. is proposed. The type strain is BH097T ( = KCTC 13130T = DSM 19028T).
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Affiliation(s)
- Pankyung Kim
- Department of Microbiology, Chungnam National University, Gung-dong 220, Yuseong-gu, Daejeon 305-764, Republic of Korea
| | - Jae-Chan Lee
- Microbial Resource Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Republic of Korea
| | - Dong-Jin Park
- Microbial Resource Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Republic of Korea
| | - Kee-Sun Shin
- Microbial Resource Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Republic of Korea
| | - Jeong-Yoon Kim
- Department of Microbiology, Chungnam National University, Gung-dong 220, Yuseong-gu, Daejeon 305-764, Republic of Korea
| | - Chang-Jin Kim
- Microbial Resource Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Republic of Korea
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Gao M, Liu ZZ, Zhou YG, Liu HC, Ma YC, Wang L, Chen SF, Ji XC. Gracilibacillus kekensis sp. nov., a moderate halophile isolated from Keke Salt Lake. Int J Syst Evol Microbiol 2011; 62:1032-1036. [PMID: 21685255 DOI: 10.1099/ijs.0.030858-0] [Citation(s) in RCA: 15] [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 novel moderately halophilic bacterium, designated strain K170(T), was isolated from Keke Salt Lake in Qinghai, China. The strain grew with 0-22 % (w/v) NaCl, at 4-50 °C and at pH 6-11, with optimum growth in 3 % (w/v) NaCl, at 40 °C and at pH 8. The predominant respiratory quinone was menaquinone 7 (MK-7). The polar lipids included diphosphatidylglycerol, phosphatidylglycerol, unidentified phospholipids, aminolipids and glycolipids. The major cellular fatty acids were anteiso-C(15 : 0), iso-C(15 : 0) and anteiso-C(17 : 0). The DNA G+C content was 35.8 mol%. Phylogenetic analysis based on the full-length 16S rRNA gene sequence revealed that strain K170(T) was a member of the genus Gracilibacillus. High levels of 16S rRNA gene sequence similarity were found between strain K170(T) and Gracilibacillus boraciitolerans DSM 17256(T) (97.3 %) and Gracilibacillus thailandensis JCM 15569(T) (97.1 %). 16S rRNA gene sequence similarities between strain K170(T) and the type strains of other recognized members of the genus Gracilibacillus were below 97 %. The DNA-DNA hybridization values of strain K170(T) with G. boraciitolerans DSM 17256(T) and G. thailandensis JCM 15569(T) were 21.9 % and 34.3 %, respectively. On the basis of these results, strain K170(T) is considered to represent a novel species of the genus Gracilibacillus, for which the name Gracilibacillus kekensis sp. nov. is proposed; the type strain is K170(T) ( = CGMCC 1.10681(T) = DSM 23178(T)).
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Affiliation(s)
- Miao Gao
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences/Ministry of Agriculture Key Laboratory of Crop Nutrition and Fertilization, Beijing 100081, PR China.,State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, PR China
| | - Zhan-Zhi Liu
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, PR China
| | - Yu-Guang Zhou
- China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Hong-Can Liu
- China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Yu-Chao Ma
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, PR China
| | - Lei Wang
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, PR China
| | - San-Feng Chen
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, PR China
| | - Xiao-Ci Ji
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, PR China
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