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Straková D, Sánchez-Porro C, de la Haba RR, Ventosa A. Natrinema salsiterrestre sp. nov., an extremely halophilic archaeon isolated from a hypersaline soil. Int J Syst Evol Microbiol 2023; 73. [PMID: 37578894 DOI: 10.1099/ijsem.0.005960] [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: 08/16/2023] Open
Abstract
An extremely halophilic archaeal strain, designated S1CR25-10T, was isolated from hypersaline soil sampled in the Odiel Saltmarshes Natural Area in Southwestern Spain (Huelva) and subjected to a polyphasic taxonomic characterization. The cells were Gram-stain-negative, motile and their colonies were pink-pigmented. It was a strictly aerobic haloarchaeon that could grow at 25-55 °C (optimum, 37 °C), at pH 6.0-9.0 (optimum, pH 7.0-8.0) and in the presence of 12-30 % (w/v) total salts (optimum, 20-25 %, w/v). The phylogenetic analysis based on the comparison of the 16S rRNA gene sequences revealed that strain S1CR25-10T belongs to the genus Natrinema, with 98.9 % similarity to Natrinema salinisoli SLN56T. In addition, the values of orthologous average nucleotide identity, digital DNA-DNA hybridization and average amino acid identity were below the threshold limits accepted for prokaryotic species delineation, with N. salinisoli SLN56T showing the highest relatedness values (92.6 % and 48.4 %, respectively). The major polar lipids were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate and a glycolipid chromatographically identical to sulfated diglycosyl diether. The DNA G+C content of the isolate was 63.8 mol%. Based on the phylogenetic, phenotypic and chemotaxonomic characterization and the whole genome results, strain S1CR25-10T represents a new species within the genus Natrinema, for which the name Natrinema salsiterrestre sp. nov., with type strain S1CR25-10T (=CECT 30623T=CCM 9251T), is proposed.
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Affiliation(s)
- Dáša Straková
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, Spain
| | - Cristina Sánchez-Porro
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, Spain
| | - Rafael R de la Haba
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, Spain
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, Spain
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Cui C, Han D, Hou J, Cui HL. Genome-based classification of the class Halobacteria and description of Haladaptataceae fam. nov. and Halorubellaceae fam. nov. Int J Syst Evol Microbiol 2023; 73. [PMID: 37486319 DOI: 10.1099/ijsem.0.005984] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2023] Open
Abstract
Currently, there are four mainstream taxonomic opinions on the classification of the class Halobacteria at the family and order levels. The International Committee on Systematics of Prokaryotes Subcommittee on the Taxonomy of Halobacteria (ICSP), List of Prokaryotic names with Standing in Nomenclature (LPSN) and National Centre for Biotechnology Information (NCBI) adopted taxonomies have three to four orders and up to eight families, while the Genome Taxonomy Database (GTDB) taxonomy proposes only one order with nine families. To resolve the taxonomic inconsistency, phylogenomic analyses based on concatenated single-copy orthologous proteins and 122 concatenated conserved single-copy marker proteins were conducted to infer the taxonomic status of the current representatives of the class Halobacteria at the family and order levels. The current 76 genera with validly published names of the class Halobacteria were able to be assigned into eight families in one order. On the basis of these results, it is proposed that the current species with validly published names of the class Halobacteria should be remerged into the order Halobacteriales, then assigned to eight families, Haladaptataceae, Haloarculaceae, Halobacteriaceae, Halococcaceae, Haloferacaceae, Natronoarchaeaceae, Natrialbaceae and Halorubellaceae. Thus, Haladaptataceae fam. nov. is described based on Haladaptatus, Halomicrococcus and Halorussus and Halorubellaceae fam. nov. is proposed incorporating Haloarchaeobius and Halorubellus, respectively.
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Affiliation(s)
- Can Cui
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, PR China
| | - Dong Han
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang 212004, PR China
| | - Jing Hou
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, PR China
| | - Heng-Lin Cui
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, PR China
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Bao CX, Li SY, Xin YJ, Hou J, Cui HL. Natrinema halophilum sp. nov., Natrinema salinisoli sp. nov., Natrinema amylolyticum sp. nov. and Haloterrigena alkaliphila sp. nov., four extremely halophilic archaea isolated from salt mine, saline soil and salt lake. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005385] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Four halophilic archaeal strains, YPL8T, SLN56T, LT61T and KZCA68T, were isolated from a salt mine, saline soil and a salt lake located in different regions of China. Sequence similarities of 16S rRNA and rpoB′ genes among strains YPL8T, SLN56T, LT61T and the current members of
Natrinema
were 94.1–98.2 % and 89.3–95.1 %, respectively, while these values among strain KZCA68T and the current members of
Haloterrigena
were 97.2–97.4 % and 91.7–91.9 %, respectively. The average nucleotide identity, in silico DNA–DNA hybridization and average amino acid identity values among these four strains and their closely related species were all lower than the threshold values for species boundary. All four strains were unable to hydrolyse casein, gelatin, or Tween 80. Strain YPL8T contained phosphatidic acid (PA), phosphatidylglycerol (PG), phosphatidylglycerol phosphate methyl ester (PGP-Me), sulfated mannosyl glucosyl diether (S-DGD-1), disulfated mannosyl glucosyl diether (S2-DGD) and sulfated mannosyl glucosyl diether-phosphatidic acid (S-DGD-PA). Strain SLN56T contained PA, PG, phosphatidylglycerol sulphate (PGS), PGP-Me, S-DGD-1, S2-DGD and S-DGD-PA. Strain LT61T contained PA, PG, PGS, PGP-Me, S-DGD-1 and S2-DGD. The phospholipids of strain KZCA68T were PA, PG and PGP-Me. These results showed that strains YPL8T (=CGMCC 1.13883T=JCM 31181T), SLN56T (=CGMCC 1.14945T=JCM 30832T) and LT61T (=CGMCC 1.14942T=JCM 30668T) represent novel species of the genus
Natrinema
, for which the names, Natrinema halophilum sp. nov., Natrinema salinisoli sp. nov. and Natrinema amylolyticum sp. nov. are proposed. Strain KZCA68T (=CGMCC 1.17211T=JCM 34158T) represents a novel species of
Haloterrigena
, for which the name Haloterrigena alkaliphila sp. nov. is proposed.
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Affiliation(s)
- Chen-Xi Bao
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, PR China
| | - Si-Ya Li
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, PR China
| | - Yu-Jie Xin
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, PR China
| | - Jing Hou
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, PR China
| | - Heng-Lin Cui
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, PR China
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Liu BB, Salam N, Narsing Rao MP, Cheng S, Xie YG, Wang LY, Zhang YR, Yu XY, Guo SX, Li WJ. Haloterrigena gelatinilytica sp. nov., a new extremely halophilic archaeon isolated from salt-lake. Arch Microbiol 2022; 204:176. [PMID: 35166931 DOI: 10.1007/s00203-022-02783-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 01/24/2022] [Accepted: 01/27/2022] [Indexed: 12/01/2022]
Abstract
Two extremely halophilic strains, designated SYSU A558-1T and SYSU A121-1, were isolated from a saline sediment sample collected from Aiding salt-lake, China. Cells of strains SYSU A558-1T and SYSU A121-1 were Gram-stain-negative, coccoid, and non-motile. The strains were aerobic and grew at NaCl concentration of 10-30% (optimum, 20-22%), at 20-55 °C (optimum, 37-42 °C) and at pH 6.5-8.5 (optimum, 7.0-8.0). Cells lysed in distilled water. The polar lipids were phosphatidyl choline, phosphatidylglycerol phosphate methyl ester, disulfated diglycosyl diether-1 and unidentified glycolipid. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that the two strains SYSU A558-1T and SYSU A121-1 were closely related to the membranes of the genus Haloterrigena. Phylogenetic and phylogenomic trees of strains SYSU A558-1T and SYSU A121-1 demonstrated a robust clade with Haloterrigena turkmenica, Haloterrigena salifodinae and Haloterrigena salina. The genomic DNA G + C content of strains SYSU A558-1T and SYSU A121-1 were 65.8 and 65.0%, respectively. Phenotypic, phylogenetic, chemotaxonomic and genome analysis suggested that the two strains SYSU A558-1T and SYSU A121-1 represent a novel species of the genus Haloterrigena, for which the name Haloterrigena gelatinilytica sp. nov. is proposed. The type strain is SYSU A558-1T (= KCTC 4259T = CGMCC 1.15953T).
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Affiliation(s)
- Bing-Bing Liu
- Henan Key Laboratory of Industrial Microbial Resources and Fermentation Technology, College of Biological and Chemical Engineering, Nanyang Institute of Technology, Nanyang, 473004, People's Republic of China
| | - Nimaichand Salam
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Manik Prabhu Narsing Rao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Shuang Cheng
- Henan Key Laboratory of Industrial Microbial Resources and Fermentation Technology, College of Biological and Chemical Engineering, Nanyang Institute of Technology, Nanyang, 473004, People's Republic of China
| | - Yuan-Guo Xie
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Lai-You Wang
- Henan Key Laboratory of Industrial Microbial Resources and Fermentation Technology, College of Biological and Chemical Engineering, Nanyang Institute of Technology, Nanyang, 473004, People's Republic of China
| | - Yuan-Ru Zhang
- Henan Key Laboratory of Industrial Microbial Resources and Fermentation Technology, College of Biological and Chemical Engineering, Nanyang Institute of Technology, Nanyang, 473004, People's Republic of China
| | - Xin-Yuan Yu
- Henan Key Laboratory of Industrial Microbial Resources and Fermentation Technology, College of Biological and Chemical Engineering, Nanyang Institute of Technology, Nanyang, 473004, People's Republic of China
| | - Shu-Xian Guo
- Henan Key Laboratory of Industrial Microbial Resources and Fermentation Technology, College of Biological and Chemical Engineering, Nanyang Institute of Technology, Nanyang, 473004, People's Republic of China.
| | - Wen-Jun Li
- Henan Key Laboratory of Industrial Microbial Resources and Fermentation Technology, College of Biological and Chemical Engineering, Nanyang Institute of Technology, Nanyang, 473004, People's Republic of China. .,State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China. .,State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürümqi, 830011, People's Republic of China.
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de la Haba RR, Minegishi H, Kamekura M, Shimane Y, Ventosa A. Phylogenomics of Haloarchaea: The Controversy of the Genera Natrinema-Haloterrigena. Front Microbiol 2021; 12:740909. [PMID: 34690986 PMCID: PMC8530250 DOI: 10.3389/fmicb.2021.740909] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 08/25/2021] [Indexed: 02/03/2023] Open
Abstract
The haloarchaeal genera Natrinema and Haloterrigena were described almost simultaneously by two different research groups and some strains studied separately were described as different species of these genera. Furthermore, the description of additional species were assigned to either Natrinema or Haloterrigena, mainly on the basis of the phylogenetic comparative analysis of single genes (16S rRNA gene and more recently rpoB’ gene), but these species were not adequately separated or assigned to the corresponding genus. Some studies suggested that the species of these two genera should be unified into a single genus, while other studies indicated that the genera should remain but some of the species should be reassigned. In this study, we have sequenced or collected the genomes of the type strains of species of Natrinema and Haloterrigena and we have carried out a comparative genomic analysis in order to clarify the controversy related to these two genera. The phylogenomic analysis based on the comparison of 525 translated single-copy orthologous genes and the Overall Genome Relatedness Indexes (i.e., AAI, POCP, ANI, and dDDH) clearly indicate that the species Haloterrigena hispanica, Haloterrigena limicola, Haloterrigena longa, Haloterrigena mahii, Haloterrigena saccharevitans, Haloterrigena thermotolerans, and Halopiger salifodinae should be transferred to the genus Natrinema, as Natrinema hispanicum, Natrinema limicola, Natrinema longum, Natrinema mahii, Natrinema saccharevitans, Natrinema thermotolerans, and Natrinema salifodinae, respectively. On the contrary, the species Haloterrigena turkmenica, Haloterrigena salifodinae, and Haloterrigena salina will remain as the only representative species of the genus Haloterrigena. Besides, the species Haloterrigena daqingensis should be reclassified as a member of the genus Natronorubrum, as Natronorubrum daqingense. At the species level, Haloterrigena jeotgali and Natrinema ejinorense should be considered as a later heterotypic synonyms of the species Haloterrigena (Natrinema) thermotolerans and Haloterrigena (Natrinema) longa, respectively. Synteny analysis and phenotypic features also supported those proposals.
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Affiliation(s)
- Rafael R de la Haba
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, Spain
| | - Hiroaki Minegishi
- Department of Applied Chemistry, Faculty of Science and Engineering, Toyo University, Kawagoe, Japan
| | | | - Yasuhiro Shimane
- Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, Spain
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6
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Haloterrigena salifodinae sp. nov., an extremely halophilic archaeon isolated from a subterranean rock salt. Antonie van Leeuwenhoek 2019; 112:1317-1329. [DOI: 10.1007/s10482-019-01264-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 04/08/2019] [Indexed: 10/27/2022]
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7
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Pestov NB, Kalinovsky DV, Larionova TD, Zakirova AZ, Modyanov NN, Okkelman IA, Korneenko TV. Properties of a cryptic lysyl oxidase from haloarchaeon Haloterrigena turkmenica. PeerJ 2019; 7:e6691. [PMID: 30984480 PMCID: PMC6452851 DOI: 10.7717/peerj.6691] [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: 01/02/2018] [Accepted: 02/26/2019] [Indexed: 11/20/2022] Open
Abstract
Background Lysyl oxidases (LOX) have been extensively studied in mammals, whereas properties and functions of recently found homologues in prokaryotic genomes remain enigmatic. Methods LOX open reading frame was cloned from Haloterrigena turkmenica in an E. coli expression vector. Recombinant Haloterrigena turkmenica lysyl oxidase (HTU-LOX) proteins were purified using metal affinity chromatography under denaturing conditions followed by refolding. Amine oxidase activity has been measured fluorometrically as hydrogen peroxide release coupled with the oxidation of 10-acetyl-3,7-dihydroxyphenoxazine in the presence of horseradish peroxidase. Rabbit polyclonal antibodies were obtained and used in western blotting. Results Cultured H. turkmenica has no detectable amine oxidase activity. HTU-LOX may be expressed in E. coli with a high protein yield. The full-length protein gives no catalytic activity. For this reason, we hypothesized that the hydrophobic N-terminal region may interfere with proper folding and its removal may be beneficial. Indeed, truncated His-tagged HTU-LOX lacking the N-terminal hydrophobic signal peptide purified under denaturing conditions can be successfully refolded into an active enzyme, and a larger N-terminal truncation further increases the amine oxidase activity. Refolding is optimal in the presence of Cu2+ at pH 6.2 and is not sensitive to salt. HTU-LOX is sensitive to LOX inhibitor 3-aminopropionitrile. HTU-LOX deaminates usual substrates of mammalian LOX such as lysine-containing polypeptides and polymers. The major difference between HTU-LOX and mammalian LOX is a relaxed substrate specificity of the former. HTU-LOX readily oxidizes various primary amines including such compounds as taurine and glycine, benzylamine being a poor substrate. Of note, HTU-LOX is also active towards several aminoglycoside antibiotics and polymyxin. Western blotting indicates that epitopes for the anti-HTU-LOX polyclonal antibodies coincide with a high molecular weight protein in H. turkmenica cells. Conclusion H. turkmenica contains a lysyl oxidase gene that was heterologously expressed yielding an active recombinant enzyme with important biochemical features conserved between all known LOXes, for example, the sensitivity to 3-aminopropionitrile. However, the native function in the host appears to be cryptic. Significance This is the first report on some properties of a lysyl oxidase from Archaea and an interesting example of evolution of enzymatic properties after hypothetical horizontal transfers between distant taxa.
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Affiliation(s)
- Nikolay B Pestov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | | | | | - Alia Z Zakirova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Nikolai N Modyanov
- Department of Physiology and Pharmacology, University of Toledo, Toledo, OH, United States of America
| | - Irina A Okkelman
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
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Rasooli M, Naghoni A, Amoozegar MA, Mirfeizi L, Moshtaghi Nikou M, Shahzadeh Fazeli SA, Minegishi H, Ventosa A. Natrinema soli sp. nov., a novel halophilic archaeon isolated from a hypersaline wetland. Int J Syst Evol Microbiol 2017. [PMID: 28650314 DOI: 10.1099/ijsem.0.001909] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An extremely halophilic archaeon, designated strain 5-3T, was isolated from a soil sample of Meighan wetland in Iran. Strain 5-3T was strictly aerobic, catalase-positive and oxidase-negative. Cells were Gram-stain-negative, non-motile and ovoid. Colonies of strain 5-3T were cream-coloured. The isolate showed optimum growth at 4.0 M NaCl, 40 °C and pH 7.0. The major polar lipids of the strain were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, two unknown phospholipids and three glycolipids (including one that was chromatographically identical to S2-DGD). The major respiratory quinone was menaquinone MK-8. The G+C content of the genomic DNA was 61.5 mol%. The closest relative was Natrinema salaciae JCM 17869T with 97.3 % similarity in the orthologous 16S rRNA gene sequence. Analysis of 16S rRNA and rpoB' gene sequences indicated that strain 5-3T is a member of the genus Natrinema in the family Natrialbaceae and forms a distinct cluster. On the basis of phylogenetic analysis, and phenotypic and chemotaxonomic characteristics, a novel species of the family Natrialbaceae, Natrinema soli sp. nov., is proposed. The type strain is 5-3T (=IBRC-M 11063T=LMG 29247T).
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Affiliation(s)
- Mehrnoosh Rasooli
- Microorganisms Bank, Iranian Biological Resource Centre (IBRC), ACECR, Tehran, Iran
| | - Ali Naghoni
- Microorganisms Bank, Iranian Biological Resource Centre (IBRC), ACECR, Tehran, Iran
| | - Mohammad Ali Amoozegar
- Extremophiles Laboratory, Department of Microbiology, Faculty of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
| | - Leila Mirfeizi
- Microorganisms Bank, Iranian Biological Resource Centre (IBRC), ACECR, Tehran, Iran
| | | | - Seyed Abolhassan Shahzadeh Fazeli
- Microorganisms Bank, Iranian Biological Resource Centre (IBRC), ACECR, Tehran, Iran.,Department of Molecular and Cellular Biology, Faculty of Basic Sciences and Advanced Technologies in Biology, University of Science and Culture, Tehran, Iran
| | - Hiroaki Minegishi
- Department of Applied Chemistry, Faculty of Science and Engineering, Toyo University, Kawagoe-shi, Saitama, Japan
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
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Amoozegar MA, Siroosi M, Atashgahi S, Smidt H, Ventosa A. Systematics of haloarchaea and biotechnological potential of their hydrolytic enzymes. MICROBIOLOGY-SGM 2017; 163:623-645. [PMID: 28548036 DOI: 10.1099/mic.0.000463] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Halophilic archaea, also referred to as haloarchaea, dominate hypersaline environments. To survive under such extreme conditions, haloarchaea and their enzymes have evolved to function optimally in environments with high salt concentrations and, sometimes, with extreme pH and temperatures. These features make haloarchaea attractive sources of a wide variety of biotechnological products, such as hydrolytic enzymes, with numerous potential applications in biotechnology. The unique trait of haloarchaeal enzymes, haloenzymes, to sustain activity under hypersaline conditions has extended the range of already-available biocatalysts and industrial processes in which high salt concentrations inhibit the activity of regular enzymes. In addition to their halostable properties, haloenzymes can also withstand other conditions such as extreme pH and temperature. In spite of these benefits, the industrial potential of these natural catalysts remains largely unexplored, with only a few characterized extracellular hydrolases. Because of the applied impact of haloarchaea and their specific ability to live in the presence of high salt concentrations, studies on their systematics have intensified in recent years, identifying many new genera and species. This review summarizes the current status of the haloarchaeal genera and species, and discusses the properties of haloenzymes and their potential industrial applications.
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Affiliation(s)
- Mohammad Ali Amoozegar
- Extremophiles Laboratory, Department of Microbiology, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
| | - Maryam Siroosi
- Extremophiles Laboratory, Department of Microbiology, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
| | - Siavash Atashgahi
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, Spain
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10
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Haloterrigena mahii sp. nov., an extremely halophilic archaeon from a solar saltern. Int J Syst Evol Microbiol 2017; 67:1333-1338. [DOI: 10.1099/ijsem.0.001811] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Halocin C8: an antimicrobial peptide distributed among four halophilic archaeal genera: Natrinema, Haloterrigena, Haloferax, and Halobacterium. Extremophiles 2017; 21:623-638. [DOI: 10.1007/s00792-017-0931-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 03/24/2017] [Indexed: 11/26/2022]
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Santorelli M, Maurelli L, Pocsfalvi G, Fiume I, Squillaci G, La Cara F, Del Monaco G, Morana A. Isolation and characterisation of a novel alpha-amylase from the extreme haloarchaeon Haloterrigena turkmenica. Int J Biol Macromol 2016; 92:174-184. [PMID: 27377461 DOI: 10.1016/j.ijbiomac.2016.07.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Revised: 06/30/2016] [Accepted: 07/01/2016] [Indexed: 10/21/2022]
Abstract
An extracellular halophilic alpha-amylase (AmyA) was produced by the haloarchaeon Haloterrigena turkmenica grown in medium enriched with 0.2% (w/v) starch. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and size exclusion chromatography (SEC) analyses showed a major band at 66.0kDa and a peak of 54.0kDa, respectively. Analysis of tryptic fragments of the protein present in the major SDS-PAGE band by nano-LC-ESI-MS/MS led to identification of the alpha-amylase catalytic region, encoded by the htur2110 gene, as the protein possessing the described activity. Optimal values for activity were 55°C, pH 8.5 and 2M NaCl, and high thermostability was showed at 55°C and 3M NaCl. AmyA activity was enhanced by Triton X-100 and was not influenced by n-hexane and chloroform. Starch hydrolysis produced different oligomers with maltose as the smallest end-product. The efficiency of AmyA in degrading starch contained in agronomic residues was tested in grape cane chosen as model substrate. Preliminary results showed that starch was degraded making the enzyme a potential candidate for utilization of agro-industrial waste in fuel and chemicals production. AmyA is one of the few investigated amylases produced by haloarchaea, and the first alpha-amylase described among microorganisms belonging to the genus Haloterrigena.
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Affiliation(s)
- Marco Santorelli
- Department of Chemical, Materials and Production Engineering, University of Naples "Federico II", P.le Tecchio 80, 80125 Napoli, Italy
| | - Luisa Maurelli
- Institute of Biosciences and Bioresources, National Research Council of Italy, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Gabriella Pocsfalvi
- Institute of Biosciences and Bioresources, National Research Council of Italy, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Immacolata Fiume
- Institute of Biosciences and Bioresources, National Research Council of Italy, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Giuseppe Squillaci
- Institute of Agro-environmental and Forest Biology, National Research Council of Italy, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Francesco La Cara
- Institute of Agro-environmental and Forest Biology, National Research Council of Italy, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Giovanni Del Monaco
- Institute of Biosciences and Bioresources, National Research Council of Italy, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Alessandra Morana
- Institute of Agro-environmental and Forest Biology, National Research Council of Italy, Via Pietro Castellino 111, 80131 Naples, Italy.
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Corral P, de la Haba RR, Sánchez-Porro C, Ali Amoozegar M, Thane Papke R, Ventosa A. Halorubrum halodurans sp. nov., an extremely halophilic archaeon isolated from a hypersaline lake. Int J Syst Evol Microbiol 2015; 66:435-444. [PMID: 26537912 DOI: 10.1099/ijsem.0.000738] [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
Two extremely halophilic archaea, strains Cb34T and C170, belonging to the genus Halorubrum, were isolated from the brine of the hypersaline lake Aran-Bidgol in Iran. Cells of the two strains were motile, pleomorphic rods, stained Gram-variable and produced red-pigmented colonies. Strains Cb34T and C170 required 25 % (w/v) salts, pH 7.0 and 37 °C for optimal growth under aerobic conditions; 0.3 M Mg2+ was required. Cells of both isolates were lysed in distilled water and hypotonic treatment with < 10 % NaCl provoked cell lysis. Phylogenetic analysis based on 16S rRNA gene sequence similarities showed that these two strains were closely related to Halorubrum cibi B31T (98.8 %) and other members of the genus Halorubrum. In addition, studies based on the rpoB' gene revealed that strains Cb34T and C170 are placed among the species of Halorubrum and are closely related to Halorubrum cibi B31T, with rpoB' gene sequence similarity less than or equal to 95.7 %. The polar lipid patterns of both strains consisted of phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate and sulfated mannosyl glucosyl diether. The DNA G+C content was 62.1-62.4 mol%. DNA-DNA hybridization studies confirmed that strains Cb34T and C170 constitute a distinct species. Data obtained in this study show that the two strains represent a novel species, for which the name Halorubrum halodurans sp. nov. is proposed. The type strain is Cb34T ( = CECT 8745T = IBRC-M 10233T).
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Affiliation(s)
- Paulina Corral
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
| | - Rafael R de la Haba
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
| | - Cristina Sánchez-Porro
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
| | - Mohammad Ali Amoozegar
- Department of Microbiology, Faculty of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
| | - R Thane Papke
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
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14
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Production and properties of an exopolysaccharide synthesized by the extreme halophilic archaeon Haloterrigena turkmenica. Appl Microbiol Biotechnol 2015; 100:613-23. [DOI: 10.1007/s00253-015-6991-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2015] [Revised: 08/01/2015] [Accepted: 09/07/2015] [Indexed: 10/23/2022]
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15
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Cha IT, Lee MH, Kim BY, Cho YJ, Kim DW, Yim KJ, Song HS, Seo MJ, Rhee JK, Choi JS, Choi HJ, Yoon C, Roh SW, Nam YD. Genome sequence of the haloarchaeon Haloterrigena jeotgali type strain A29(T) isolated from salt-fermented food. Stand Genomic Sci 2015; 10:49. [PMID: 26380637 PMCID: PMC4572444 DOI: 10.1186/s40793-015-0047-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 07/21/2015] [Indexed: 11/10/2022] Open
Abstract
Haloterrigena jeotgali is a halophilic archaeon within the family Natrialbaceae that was isolated from shrimp jeotgal, a traditional Korean salt-fermented food. A29T is the type strain of H. jeotgali, and is a Gram-negative staining, non-motile, rod-shaped archaeon that grows in 10 %–30 % (w/v) NaCl. We present the annotated H. jeotgali A29T genome sequence along with a summary of its features. The 4,131,621 bp genome with a GC content of 64.9 % comprises 4,215 protein-coding genes and 127 RNA genes. The sequence can provide useful information on genetic mechanisms that enable haloarchaea to endure a hypersaline environment.
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Affiliation(s)
- In-Tae Cha
- Biological Disaster Analysis Team, Korea Basic Science Institute, Daejeon, 305-806 Republic of Korea.,Division of Bioengineering, Incheon National University, Incheon, 406-772 Republic of Korea
| | - Mi-Hwa Lee
- Research Group of Gut Microbiome, Korea Food Research Institute, Sungnam, 463-746 Republic of Korea
| | - Byung-Yong Kim
- ChunLab Inc., Seoul National University, Seoul, 151-742 Republic of Korea
| | - Yong-Joon Cho
- ChunLab Inc., Seoul National University, Seoul, 151-742 Republic of Korea
| | - Dae-Won Kim
- Systems Biology Team, Center for Immunity and Pathology, Korea National Institute of Health, Cheongju, 361-951 Republic of Korea
| | - Kyung June Yim
- Biological Disaster Analysis Team, Korea Basic Science Institute, Daejeon, 305-806 Republic of Korea
| | - Hye Seon Song
- Biological Disaster Analysis Team, Korea Basic Science Institute, Daejeon, 305-806 Republic of Korea
| | - Myung-Ji Seo
- Division of Bioengineering, Incheon National University, Incheon, 406-772 Republic of Korea
| | - Jin-Kyu Rhee
- Department of Food Science and Engineering, Ewha Womans University, Seoul, 120-750 South Korea
| | - Jong-Soon Choi
- Biological Disaster Analysis Team, Korea Basic Science Institute, Daejeon, 305-806 Republic of Korea.,Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, 305-764 Republic of Korea
| | - Hak-Jong Choi
- World Institute of Kimchi, Gwangju, 503-360 Republic of Korea
| | - Changmann Yoon
- Biological Disaster Analysis Team, Korea Basic Science Institute, Daejeon, 305-806 Republic of Korea
| | - Seong Woon Roh
- Biological Disaster Analysis Team, Korea Basic Science Institute, Daejeon, 305-806 Republic of Korea.,Korea University of Science and Technology, Daejeon, 305-350 Republic of Korea
| | - Young-Do Nam
- Research Group of Gut Microbiome, Korea Food Research Institute, Sungnam, 463-746 Republic of Korea.,Korea University of Science and Technology, Daejeon, 305-350 Republic of Korea
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16
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Corral P, de la Haba RR, Sánchez-Porro C, Amoozegar MA, Papke RT, Ventosa A. Halorubrum persicum sp. nov., an extremely halophilic archaeon isolated from sediment of a hypersaline lake. Int J Syst Evol Microbiol 2015; 65:1770-1778. [PMID: 25744586 DOI: 10.1099/ijs.0.000175] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An extremely halophilic archaeon belonging to the genus Halorubrum, strain C49T, was isolated from sediment of the hypersaline lake Aran-Bidgol in Iran. Phylogenetic analysis based on 16S rRNA gene sequence similarities showed that strain C49T was closely related to Halorubrum saccharovorum JCM 8865T (99.5 %) and other species of the genus Halorubrum. Studies based on multilocus sequence analysis revealed that strain C49T is placed among the species of Halorubrum; the strain constituted a defined branch in comparison with the type strains of species of Halorubrum, while the 16S rRNA gene sequence divergence could not define the status of the newly isolated strain. For optimum growth, strain C49T required 20 % (w/v) salts at pH 7.0 and 37 °C under aerobic conditions. Mg2+ was not required. The cells were pleomorphic rods, motile and stained Gram-variable. Colonies of the strain were pink. Hypotonic treatment with <12 % NaCl provoked cell lysis. The polar lipid pattern of strain C49T consisted of phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester derived from both C20C20 and C20C25 archaeol, phosphatidylglycerol sulfate and sulfated mannosyl glucosyl diether. The DNA G+C content was 64.2 mol%. DNA-DNA hybridization studies and average nucleotide identity confirmed that strain C49T constitutes a distinct genospecies. Data obtained in this study show that strain C49T represents a novel species, for which the name Halorubrum persicum sp. nov. is proposed. The type strain is C49T ( = IBRC-M 10232T = JCM 30541T).
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Affiliation(s)
- Paulina Corral
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
| | - Rafael R de la Haba
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
| | - Cristina Sánchez-Porro
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
| | - Mohammad Ali Amoozegar
- Department of Microbiology, Faculty of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
| | - R Thane Papke
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
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17
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Corral P, Corcelli A, Ventosa A. Halostagnicola bangensis sp. nov., an alkaliphilic haloarchaeon from a soda lake. Int J Syst Evol Microbiol 2014; 65:754-759. [PMID: 25479949 DOI: 10.1099/ijs.0.000006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An extremely haloalkaphilic archaeon, strain T26(T), belonging to the genus Halostagnicola, was isolated from sediment of the soda lake Bange in the region of Tibet, China. Phylogenetic analysis based on 16S rRNA gene sequence similarities showed that strain T26(T) was closely related to Halostagnicola alkaliphila 167-74(T) (98.4 %), Halostagnicola larsenii XH-48(T) (97.5 %) and Halostagnicola kamekurae 194-10(T) (96.8 %). Strain T26(T) grew optimally in media containing 25 % (w/v) salts, at pH 9.0 and 37 °C in aerobic conditions. Mg(2+) was not required for growth. The cells were motile, pleomorphic and Gram-stain-variable. Colonies of this strain were pink pigmented. Hypotonic treatment caused cell lysis. The polar lipids of the isolate consisted of C20C20 and C20C25 derivatives of phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and minor phospholipids components. Glycolipids were not detected, in contrast to the two neutrophilic species of this genus. The genomic DNA G+C content of strain T26(T) was 60.1 mol% and DNA-DNA hybridization showed a relatedness of 19 and 17 % with Halostagnicola alkaliphila CECT 7631(T) and Halostagnicola larsenii CECT 7116(T), respectively. The comparison of 16S rRNA gene sequences, detailed phenotypic characterization, polar lipid profile and DNA-DNA hybridization studies revealed that strain T26(T) belongs to the genus Halostagnicola, and represents a novel species for which the name Halostagnicola bangensis sp. nov. is proposed. The type strain is T26(T) ( = CECT 8219(T) = IBRC-M 10759(T) = JCM 18750(T)).
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Affiliation(s)
- Paulina Corral
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
| | - Angela Corcelli
- Department of Basic Medical Sciences, Neurosciences and Sensory Organs, University of Bari Aldo Moro, 70124 Bari, Italy
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
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18
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Gupta RS, Naushad S, Baker S. Phylogenomic analyses and molecular signatures for the class Halobacteria and its two major clades: a proposal for division of the class Halobacteria into an emended order Halobacteriales and two new orders, Haloferacales ord. nov. and Natrialbales ord. nov., containing the novel families Haloferacaceae fam. nov. and Natrialbaceae fam. nov. Int J Syst Evol Microbiol 2014; 65:1050-1069. [PMID: 25428416 DOI: 10.1099/ijs.0.070136-0] [Citation(s) in RCA: 235] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Halobacteria constitute one of the largest groups within the Archaea. The hierarchical relationship among members of this large class, which comprises a single order and a single family, has proven difficult to determine based upon 16S rRNA gene trees and morphological and physiological characteristics. This work reports detailed phylogenetic and comparative genomic studies on >100 halobacterial (haloarchaeal) genomes containing representatives from 30 genera to investigate their evolutionary relationships. In phylogenetic trees reconstructed on the basis of 32 conserved proteins, using both neighbour-joining and maximum-likelihood methods, two major clades (clades A and B) encompassing nearly two-thirds of the sequenced haloarchaeal species were strongly supported. Clades grouping the same species/genera were also supported by the 16S rRNA gene trees and trees for several individual highly conserved proteins (RpoC, EF-Tu, UvrD, GyrA, EF-2/EF-G). In parallel, our comparative analyses of protein sequences from haloarchaeal genomes have identified numerous discrete molecular markers in the form of conserved signature indels (CSI) in protein sequences and conserved signature proteins (CSPs) that are found uniquely in specific groups of haloarchaea. Thirteen CSIs in proteins involved in diverse functions and 68 CSPs that are uniquely present in all or most genome-sequenced haloarchaea provide novel molecular means for distinguishing members of the class Halobacteria from all other prokaryotes. The members of clade A are distinguished from all other haloarchaea by the unique shared presence of two CSIs in the ribose operon protein and small GTP-binding protein and eight CSPs that are found specifically in members of this clade. Likewise, four CSIs in different proteins and five other CSPs are present uniquely in members of clade B and distinguish them from all other haloarchaea. Based upon their specific clustering in phylogenetic trees for different gene/protein sequences and the unique shared presence of large numbers of molecular signatures, members of clades A and B are indicated to be distinct from all other haloarchaea because of their uniquely shared evolutionary histories. Based upon these results, it is proposed that clades A and B be recognized as two new orders, Natrialbales ord. nov. and Haloferacales ord. nov., within the class Halobacteria, containing the novel families Natrialbaceae fam. nov. and Haloferacaceae fam. nov. Other members of the class Halobacteria that are not members of these two orders will remain part of the emended order Halobacteriales in an emended family Halobacteriaceae.
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Affiliation(s)
- Radhey S Gupta
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada L8N 3Z5
| | - Sohail Naushad
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada L8N 3Z5
| | - Sheridan Baker
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada L8N 3Z5
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19
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PH1: an archaeovirus of Haloarcula hispanica related to SH1 and HHIV-2. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2013; 2013:456318. [PMID: 23585730 PMCID: PMC3622292 DOI: 10.1155/2013/456318] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Accepted: 01/07/2013] [Indexed: 11/24/2022]
Abstract
Halovirus PH1 infects Haloarcula hispanica and was isolated from an Australian salt lake. The burst size in single-step growth conditions was 50–100 PFU/cell, but cell density did not decrease until well after the rise (4–6 hr p.i.), indicating that the virus could exit without cell lysis. Virions were round, 51 nm in diameter, displayed a layered capsid structure, and were sensitive to chloroform and lowered salt concentration. The genome is linear dsDNA, 28,064 bp in length, with 337 bp terminal repeats and terminal proteins, and could transfect haloarchaeal species belonging to five different genera. The genome is predicted to carry 49 ORFs, including those for structural proteins, several of which were identified by mass spectroscopy. The close similarity of PH1 to SH1 (74% nucleotide identity) allowed a detailed description and analysis of the differences (divergent regions) between the two genomes, including the detection of repeat-mediated deletions. The relationship of SH1-like and pleolipoviruses to previously described genomic loci of virus and plasmid-related elements (ViPREs) of haloarchaea revealed an extensive level of recombination between the known haloviruses. PH1 is a member of the same virus group as SH1 and HHIV-2, and we propose the name halosphaerovirus to accommodate these viruses.
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20
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Genome sequence of Halorubrum sp. strain T3, an extremely halophilic archaeon harboring a virus-like element. J Bacteriol 2013; 194:6608-9. [PMID: 23144373 DOI: 10.1128/jb.01528-12] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Halorubrum sp. strain T3, harboring a virus-like element, was isolated from a sample collected from a solar saltern in Yunnan, China. Several strains of Halorubrum pleomorphic viruses were reported in this genus recently; however, the virus-host interaction in haloarchaea remains unclear. To explore this issue, here we present the genome sequence of Halorubrum sp. strain T3 (3,168,011 bp, 68.48% G+C content).
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21
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Albuquerque L, Taborda M, La Cono V, Yakimov M, da Costa MS. Natrinema salaciae sp. nov., a halophilic archaeon isolated from the deep, hypersaline anoxic Lake Medee in the Eastern Mediterranean Sea. Syst Appl Microbiol 2012; 35:368-73. [DOI: 10.1016/j.syapm.2012.06.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2012] [Revised: 06/19/2012] [Accepted: 06/21/2012] [Indexed: 10/28/2022]
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22
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Makhdoumi-Kakhki A, Amoozegar MA, Ventosa A. Halovenus aranensis gen. nov., sp. nov., an extremely halophilic archaeon from Aran-Bidgol salt lake. Int J Syst Evol Microbiol 2012; 62:1331-1336. [DOI: 10.1099/ijs.0.031419-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel red-pigmented halophilic archaeon, strain EB27T, was isolated from Aran-Bidgol salt lake, a hypersaline playa in Iran. Cells of strain EB27T were non-motile and pleomorphic (rods to triangular or disc-shaped). Strain EB27T required at least 2.5 M NaCl and 0.1 M MgCl2 for growth. Optimal growth was achieved at 4 M NaCl and 0.5 M MgCl2. The optimum pH and temperature for growth were pH 7.5 and 40 °C; it was able to grow at pH 6.0–8.0 and 25–50 °C. 16S rRNA gene sequence analysis showed that strain EB27T is a member of the family
Halobacteriaceae
; however, levels of 16S rRNA gene sequence similarity were as low as 90.0, 89.3 and 89.1 % to the most closely related haloarchaeal taxa, namely
Halalkalicoccus tibetensis
DS12T,
Halosimplex carlsbadense
2-9-1T and
Halorhabdus utahensis
AX-2T, respectively. The DNA G+C content of strain EB27T was 61 mol%. Strain EB27T contained phosphatidylglycerol and phosphatidylglycerol phosphate methyl ester, common phospholipids found in haloarchaea, together with two minor phospholipids. The only quinone present was MK-8(II-H2). Physiological, biochemical and phylogenetic differences between strain EB27T and recognized genera of extremely halophilic archaea suggest that this strain represents a novel species in a new genus within the family
Halobacteriaceae
, for which the name Halovenus aranensis gen. nov., sp. nov. is proposed. The type strain of Halovenus aranensis, the type species of the new genus, is strain EB27T ( = IBRC-M 10015T = CGMCC 1.11001T).
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Affiliation(s)
- A. Makhdoumi-Kakhki
- Microorganisms Bank, Iranian Biological Resource Centre (IBRC), ACECR Tehran, Iran
- Extremophile Laboratory, Department of Microbiology, School of Biology, College of Science, University of Tehran, Tehran, Iran
| | - M. A. Amoozegar
- Microorganisms Bank, Iranian Biological Resource Centre (IBRC), ACECR Tehran, Iran
- Extremophile Laboratory, Department of Microbiology, School of Biology, College of Science, University of Tehran, Tehran, Iran
| | - A. Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, Spain
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23
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Makhdoumi-Kakhki A, Amoozegar MA, Bagheri M, Ramezani M, Ventosa A. Haloarchaeobius iranensis gen. nov., sp. nov., an extremely halophilic archaeon isolated from a saline lake. Int J Syst Evol Microbiol 2012; 62:1021-1026. [DOI: 10.1099/ijs.0.033167-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain EB21T was isolated from a brine sample from Aran-Bidgol salt lake, a saline playa in Iran. Strain EB21T was an orange–red-pigmented, motile rod and required at least 2 M NaCl but not MgCl2 for growth. Optimal growth was achieved at 3.5 M NaCl and 0.2 M MgCl2. The optimum pH and temperature for growth were pH 7.5 and 40 °C, while it was able to grow at pH 6.0–8.0 and 25–55 °C. Analysis of the 16S rRNA gene sequence revealed that strain EB21T is a member of the family
Halobacteriaceae
, showing low levels of similarity to other members of the family. The highest sequence similarities, 91.8, 91.7 and 91.5 %, were obtained with the 16S rRNA gene sequences of the type strains of
Halobiforma lacisalsi
,
Haloterrigena thermotolerans
and
Halalkalicoccus tibetensis
, respectively. Polar lipid analyses revealed that strain EB21T contains phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and phosphatidylglycerol sulfate. Three unidentified glycolipids and one minor phospholipid were also observed. The only quinone present was MK-8(II-H2). The G+C content of its DNA was 67.7 mol%. On the basis of the data obtained, the new isolate could not be classified in any recognized genus. Strain EB21T is thus considered to represent a novel species in a new genus within the family
Halobacteriaceae
, order
Halobacteriales
, for which the name Haloarchaeobius iranensis gen. nov., sp. nov. is proposed. The type strain of Haloarchaeobius iranensis is EB21T ( = IBRC-M 10013T = KCTC 4048T).
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Affiliation(s)
- A. Makhdoumi-Kakhki
- Extremophile Laboratory, Department of Microbiology, School of Biology, College of Science, University of Tehran, Tehran, Iran
| | - M. A. Amoozegar
- Microorganisms Bank, Iranian Biological Resource Centre (IBRC), ACECR Tehran, Iran
- Extremophile Laboratory, Department of Microbiology, School of Biology, College of Science, University of Tehran, Tehran, Iran
| | - M. Bagheri
- Microorganisms Bank, Iranian Biological Resource Centre (IBRC), ACECR Tehran, Iran
| | - M. Ramezani
- Microorganisms Bank, Iranian Biological Resource Centre (IBRC), ACECR Tehran, Iran
| | - A. Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Seville, Sevilla, Spain
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24
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Ozcan B, Ozyilmaz G, Cihan A, Cokmus C, Caliskan M. Phylogenetic analysis and characterization of lipolytic activity of halophilic archaeal isolates. Microbiology (Reading) 2012. [DOI: 10.1134/s0026261712020105] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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25
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Shimane Y, Hatada Y, Minegishi H, Mizuki T, Echigo A, Miyazaki M, Ohta Y, Usami R, Grant WD, Horikoshi K. Natronoarchaeum mannanilyticum gen. nov., sp. nov., an aerobic, extremely halophilic archaeon isolated from commercial salt. Int J Syst Evol Microbiol 2010; 60:2529-2534. [DOI: 10.1099/ijs.0.016600-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain YSM-123T was isolated from commercial salt made from Japanese seawater in Niigata prefecture. Optimal NaCl and Mg2+ concentrations for growth were 4.0–4.5 M and 5 mM, respectively. The isolate was a mesophilic and slightly alkaliphilic haloarchaeon, whose optimal growth temperature and pH were 37 °C and pH 8.0–9.0. Phylogenetic analysis based on 16S rRNA gene sequence analysis suggested that strain YSM-123T is a member of the phylogenetic group defined by the family Halobacteriaceae, but there were low similarities to type strains of other genera of this family (≤90 %); for example, Halococcus (similarity <89 %), Halostagnicola (<89 %), Natronolimnobius (<89 %), Halobiforma (<90 %), Haloterrigena (<90 %), Halovivax (<90 %), Natrialba (<90 %), Natronobacterium (<90 %) and Natronococcus (<90 %). The G+C content of the DNA was 63 mol%. Polar lipid analysis revealed the presence of phosphatidylglycerol, phosphatidylglycerophosphate methyl ester, disulfated diglycosyl diether and an unknown glycolipid. On the basis of the data presented, we propose that strain YSM-123T should be placed in a new genus and species, Natronoarchaeum mannanilyticum gen. nov., sp. nov. The type strain of Natronoarchaeum mannanilyticum is strain YSM-123T (=JCM 16328T =CECT 7565T).
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Affiliation(s)
- Yasuhiro Shimane
- Bio-Nano Electronics Research Center, Toyo University, 2100 Kujirai, Kawagoe-shi, Saitama 350-8585, Japan
- Toyo University, 2100 Kujirai, Kawagoe-shi, Saitama 350-8585, Japan
- Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Yuji Hatada
- Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Hiroaki Minegishi
- Bio-Nano Electronics Research Center, Toyo University, 2100 Kujirai, Kawagoe-shi, Saitama 350-8585, Japan
- Toyo University, 2100 Kujirai, Kawagoe-shi, Saitama 350-8585, Japan
| | - Toru Mizuki
- Bio-Nano Electronics Research Center, Toyo University, 2100 Kujirai, Kawagoe-shi, Saitama 350-8585, Japan
- Toyo University, 2100 Kujirai, Kawagoe-shi, Saitama 350-8585, Japan
| | - Akinobu Echigo
- Bio-Nano Electronics Research Center, Toyo University, 2100 Kujirai, Kawagoe-shi, Saitama 350-8585, Japan
- Toyo University, 2100 Kujirai, Kawagoe-shi, Saitama 350-8585, Japan
| | - Masayuki Miyazaki
- Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Yukari Ohta
- Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Ron Usami
- Bio-Nano Electronics Research Center, Toyo University, 2100 Kujirai, Kawagoe-shi, Saitama 350-8585, Japan
- Toyo University, 2100 Kujirai, Kawagoe-shi, Saitama 350-8585, Japan
| | - William D. Grant
- Department of Infection, Immunity and Inflammation, University of Leicester, Room 144, Maurice Shock Medical Sciences Building, Leicester, UK
| | - Koki Horikoshi
- Toyo University, 2100 Kujirai, Kawagoe-shi, Saitama 350-8585, Japan
- Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
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Wang S, Yang Q, Liu ZH, Sun L, Wei D, Zhang JZ, Song JZ, Yuan HF. Haloterrigena daqingensis sp. nov., an extremely haloalkaliphilic archaeon isolated from a saline–alkaline soil. Int J Syst Evol Microbiol 2010; 60:2267-2271. [DOI: 10.1099/ijs.0.013995-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A haloalkaliphilic archaeon, strain JX313T, was isolated from a saline–alkaline soil from Daqing, Heilongjiang Province, China. Its morphological, physiological and biochemical features and 16S rRNA gene sequence were determined. Colonies of the strain were orange–red and cells were non-motile cocci and Gram-stain-variable. The strain required at least 1.7 M NaCl for growth, with optimal growth occurring in 2.0–2.5 M NaCl. Growth was observed at 20–50 °C and pH 8.0–10.5, with optimal growth at 35 °C and pH 10.0. The G+C content of its genomic DNA was 59.3 mol%. Phylogenetic analysis of 16S rRNA gene sequences showed that strain JX313T is associated with the genera Haloterrigena and Natrinema and is most closely related to Haloterrigena salina XH-65T (96.2 % sequence similarity) and Haloterrigena hispanica FP1T (96.2 %). DNA–DNA hybridization experiments revealed that the relatedness of strain JX313T to type strains of related species of the genus Haloterrigena or Natrinema was less than 50 %. Furthermore, the cellular polar lipids of strain JX313T, identified as phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and mannose-2,6-disulfate (1→2)-glucose glycerol diether (S2-DGD), were consistent with the polar lipid characteristics of the genus Haloterrigena. Therefore, phylogenetic analysis, phenotypic assessment and chemotaxonomic data showed that JX313T represents a novel species within the genus Haloterrigena, for which the name Haloterrigena daqingensis sp. nov. is proposed. The type strain is JX313T (=CGMCC 1.8909T =NBRC 105739T).
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Affiliation(s)
- Shuang Wang
- Department of Life Science and Engineering, Harbin Institute of Technology, Harbin 150001, PR China
| | - Qian Yang
- Department of Life Science and Engineering, Harbin Institute of Technology, Harbin 150001, PR China
| | - Zhi-Hua Liu
- Department of Life Science and Engineering, Harbin Institute of Technology, Harbin 150001, PR China
| | - Lei Sun
- Soil Fertilizer and Environment Energy Institute of Heilongjiang Academy of Agricultural Sciences, Harbin 150086, PR China
| | - Dan Wei
- Soil Fertilizer and Environment Energy Institute of Heilongjiang Academy of Agricultural Sciences, Harbin 150086, PR China
| | - Jun-Zheng Zhang
- Department of Life Science and Engineering, Harbin Institute of Technology, Harbin 150001, PR China
| | - Jin-Zhu Song
- Department of Life Science and Engineering, Harbin Institute of Technology, Harbin 150001, PR China
| | - Hai-Feng Yuan
- Nature and Ecology Institute, Heilongjiang Academy of Sciences, Harbin 150040, PR China
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Grant WD, Heaphy S. Metagenomics and recovery of enzyme genes from alkaline saline environments. ENVIRONMENTAL TECHNOLOGY 2010; 31:1135-1143. [PMID: 20718296 DOI: 10.1080/09593331003646661] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Enzymes functioning at alkaline pH are widely used in the detergent industry as additives to improve the stain removal properties of domestic and industrial cleaning products. This industry provides by far the major mass market for enzymes. With constantly changing formulations in detergents and concerns over energy demands, new and improved enzymes are constantly in demand. Soda lakes host dense populations of alkali-loving microbes and, as such, provide vast reservoirs of potentially useful enzymes for such an industry. Traditional recovery methods for new enzymes have involved the isolation of microbes, preferably from a compatible chemical environment such as a soda lake, followed by screening of the isolates for useful enzymic activity. At least two commercially significant enzymes originating from soda lake microbes have been marketed following this route. However, the failure to cultivate more than a small percentage of microbes from most environments necessarily markedly reduces the recovery of new enzymes. In recent years, interest has focussed on more comprehensive recovery methods based around detecting appropriate enzyme genes in nucleic acids extracted from potentially useful sites, thus maximizing coverage of the whole genetic resource in a particular biotope. Here we review progress to date in soda lake biotopes and discuss ways the field may develop in the future.
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Affiliation(s)
- William D Grant
- Department of Infection, Immunity and Inflammation, The University of Leicester, Leicester LE1 9HN, UK.
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Saunders E, Tindall BJ, Fähnrich R, Lapidus A, Copeland A, Del Rio TG, Lucas S, Chen F, Tice H, Cheng JF, Han C, Detter JC, Bruce D, Goodwin L, Chain P, Pitluck S, Pati A, Ivanova N, Mavromatis K, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Brettin T, Rohde M, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC. Complete genome sequence of Haloterrigena turkmenica type strain (4k). Stand Genomic Sci 2010; 2:107-16. [PMID: 21304683 PMCID: PMC3035258 DOI: 10.4056/sigs.681272] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Haloterrigena turkmenica (Zvyagintseva and Tarasov 1987) Ventosa et al. 1999, comb. nov. is the type species of the genus Haloterrigena in the euryarchaeal family Halobacteriaceae. It is of phylogenetic interest because of the yet unclear position of the genera Haloterrigena and Natrinema within the Halobacteriaceae, which created some taxonomic problems historically. H. turkmenica, was isolated from sulfate saline soil in Turkmenistan, is a relatively fast growing, chemoorganotrophic, carotenoid-containing, extreme halophile, requiring at least 2 M NaCl for growth. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of the genus Haloterrigena, but the eighth genome sequence from a member of the family Halobacteriaceae. The 5,440,782 bp genome (including six plasmids) with its 5,287 protein-coding and 63 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
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Minegishi H, Kamekura M, Itoh T, Echigo A, Usami R, Hashimoto T. Further refinement of the phylogeny of the Halobacteriaceae based on the full-length RNA polymerase subunit B' (rpoB') gene. Int J Syst Evol Microbiol 2009; 60:2398-2408. [PMID: 19946058 DOI: 10.1099/ijs.0.017160-0] [Citation(s) in RCA: 151] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A considerable number of species of the Halobacteriaceae possess multiple copies of the 16S rRNA gene that exhibit more than 5 % divergence, complicating phylogenetic interpretations. Two additional problems have been pointed out: (i) the genera Haloterrigena and Natrinema show a very close relationship, with some species being shown to overlap in phylogenetic trees reconstructed by the neighbour-joining method, and (ii) alkaliphilic and neutrophilic species of the genus Natrialba form definitely separate clusters in neighbour-joining trees, suggesting that these two clusters could be separated into two genera. In an attempt to solve these problems, the RNA polymerase B' subunit has been used as an additional target molecule for phylogenetic analysis, using partial sequences of 1305 bp. In this work, a primer set was designed that consistently amplified the full-length RNA polymerase B' subunit gene (rpoB') (1827-1842 bp) from 85 strains in 27 genera of the Halobacteriaceae. Differences in sequence length were found within the first 15 to 31 nt, and their downstream sequences (1812 bp) were aligned unambiguously without any gaps or deletions. Phylogenetic trees reconstructed from nucleotide sequences and deduced amino acid sequences by the maximum-likelihood method demonstrated that multiple species/strains in most genera individually formed cohesive clusters. Two discrepancies were observed: (i) the two species of Natronolimnobius were placed in definitely different positions, in that Natronolimnobius innermongolicus was placed in the Haloterrigena/Natrinema cluster, while Natronolimnobius baerhuensis was closely related to Halostagnicola larsenii, and (ii) Natronorubrum tibetense was segregated from the three other Natronorubrum species in the protein tree, while all four species formed a cluster in the gene tree, although supported by a bootstrap value of less than 50 %. The six Haloterrigena species/strains and the five species of Natrinema formed a large cluster in both trees, with Halopiger xanaduensis and Nln. innermongolicus located in the cluster in the protein tree and Nln. innermongolicus in the gene tree. Hpg. xanaduensis broke into the cluster of the genus Halobiforma, instead of the Haloterrigena/Natrinema cluster, in the gene tree. The six Natrialba species formed a tight cluster with two subclusters, of neutrophilic species and alkaliphilic species, in both trees. Overall, our data strongly suggest that (i) Nln. innermongolicus is a member of Haloterrigena/Natrinema, (ii) Nrr. tibetense might represent a new genus and (iii) the two genera Haloterrigena and Natrinema might constitute a single genus. As more and more novel species and genera are proposed in the family Halobacteriaceae, the full sequence of the rpoB' gene may provide a supplementary tool for determining the phylogenetic position of new isolates.
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Affiliation(s)
- Hiroaki Minegishi
- Bio-Nano Electronics Research Center, Toyo University, Kawagoe-shi, Saitama, Japan
| | | | - Takashi Itoh
- Japan Collection of Micro-organisms, RIKEN BioResource Center, Wako-shi, Saitama, Japan
| | - Akinobu Echigo
- Bio-Nano Electronics Research Center, Toyo University, Kawagoe-shi, Saitama, Japan
| | - Ron Usami
- Graduate School of Interdisciplinary New Science, Toyo University, Kawagoe-shi, Saitama, Japan
- Bio-Nano Electronics Research Center, Toyo University, Kawagoe-shi, Saitama, Japan
| | - Tetsuo Hashimoto
- Institute of Biological Sciences, University of Tsukuba, Tsukuba-shi, Ibaraki, Japan
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Pappa A, Sánchez-Porro C, Lazoura P, Kallimanis A, Perisynakis A, Ventosa A, Drainas C, Koukkou AI. Bacillus halochares sp. nov., a halophilic bacterium isolated from a solar saltern. Int J Syst Evol Microbiol 2009; 60:1432-1436. [PMID: 19671720 DOI: 10.1099/ijs.0.014233-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel halophilic bacterium, designated strain MSS4(T), was isolated from the solar salterns of Mesolongi, Greece. The micro-organism, a motile, Gram-stain-positive, aerobic rod, proliferated at salinities of 1.0-4.0 M NaCl, with optimal growth at 2.5 M NaCl. Endospores were not observed. Strain MSS4(T) showed optimal growth at 37 degrees C and pH 8.0. The G+C content of its DNA was 47.2 mol%. The polar lipid pattern of strain MSS4(T) consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidic acid and phosphatidylethanolamine. It possessed anteiso-C(15 : 0), C(18 : 0), C(16 : 0) and anteiso-C(17 : 0) as the major fatty acids (altogether representing 84.7 % of the total). The predominant isoprenoid quinone was MK-7. The cell-wall peptidoglycan contained meso-diaminopimelic acid. 16S rRNA gene sequence analysis showed that the new isolate has 96.1 % similarity to Bacillus qingdaonensis CM1(T) and Bacillus aidingensis 17-5(T), 95.5 % to Bacillus salarius BH169(T) and lower similarity to other Bacillus species. These results justify the assignment of strain MSS4(T) to a novel species within the genus Bacillus, for which the name Bacillus halochares sp. nov. is proposed. The type strain is MSS4(T) (=LMG 24571(T) =DSM 21373(T)).
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Affiliation(s)
- A Pappa
- Sector of Organic Chemistry and Biochemistry, Department of Chemistry, University of Ioannina, 45110 Ioannina, Greece
| | - C Sánchez-Porro
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
| | - P Lazoura
- Sector of Organic Chemistry and Biochemistry, Department of Chemistry, University of Ioannina, 45110 Ioannina, Greece
| | - A Kallimanis
- Sector of Organic Chemistry and Biochemistry, Department of Chemistry, University of Ioannina, 45110 Ioannina, Greece
| | - A Perisynakis
- Sector of Organic Chemistry and Biochemistry, Department of Chemistry, University of Ioannina, 45110 Ioannina, Greece
| | - A Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
| | - C Drainas
- Sector of Organic Chemistry and Biochemistry, Department of Chemistry, University of Ioannina, 45110 Ioannina, Greece
| | - A I Koukkou
- Sector of Organic Chemistry and Biochemistry, Department of Chemistry, University of Ioannina, 45110 Ioannina, Greece
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31
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Amoozegar MA, Sanchez-Porro C, Rohban R, Hajighasemi M, Ventosa A. Piscibacillus halophilus sp. nov., a moderately halophilic bacterium from a hypersaline Iranian lake. Int J Syst Evol Microbiol 2009; 59:3095-9. [DOI: 10.1099/ijs.0.012013-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Roh SW, Nam YD, Chang HW, Kim KH, Sung Y, Kim MS, Oh HM, Bae JW. Haloterrigena jeotgali sp. nov., an extremely halophilic archaeon from salt-fermented food. Int J Syst Evol Microbiol 2009; 59:2359-63. [DOI: 10.1099/ijs.0.008243-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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33
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Sánchez-Porro C, de la Haba RR, Soto-Ramírez N, Márquez MC, Montalvo-Rodríguez R, Ventosa A. Description of Kushneria aurantia gen. nov., sp. nov., a novel member of the family Halomonadaceae, and a proposal for reclassification of Halomonas marisflavi as Kushneria marisflavi comb. nov., of Halomonas indalinina as Kushneria indalinina comb. nov. and of Halomonas avicenniae as Kushneria avicenniae comb. nov. Int J Syst Evol Microbiol 2009; 59:397-405. [PMID: 19196785 DOI: 10.1099/ijs.0.001461-0] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An aerobic, moderately halophilic, Gram-negative, motile, non-sporulating rod-shaped bacterium, designated strain A10(T), was isolated from the surface of leaves of the black mangrove Avicennia germinans and was subjected to a polyphasic taxonomic study. Strain A10(T) was able to grow at NaCl concentrations in the range 5-17.5 % (w/v) with optimum growth at 10 % (w/v) NaCl. Growth occurred at temperatures of 20-40 degrees C (optimal growth at 37 degrees C) and pH 5.5-8.5 (optimal growth at pH 7.0-8.0). The major respiratory quinone was ubiquinone 9. The major fatty acids were C(16 : 0), C(18 : 1)omega7c, C(19 : 0) cyclo omega8c and C(12 : 0) 3-OH. The polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, and unidentified phospholipids, glycolipids and an aminoglycolipid. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain A10(T) is closely related to Halomonas avicenniae MW2a(T) (95.7 % sequence similarity), Halomonas marisflavi SW32(T) (95.2 %) and Halomonas indalinina GC2.1(T) (95.0 %). Strain A10(T) formed a coherent phylogenetic branch with these three species, separated from other species of Halomonas and closely related genera (with 16S rRNA gene sequence similarities below 94.0 %). A complete 23S rRNA gene sequence comparison of strain A10(T) with closely related species confirmed the phylogenetic position of the novel isolate, forming a branch with the species Halomonas avicenniae, Halomonas indalinina and Halomonas marisflavi, separated from other species of the genera belonging to the family Halomonadaceae (showing sequence similarities below 91.7 %). DNA-DNA hybridization studies between strain A10(T) and Halomonas avicenniae MW2a(T), Halomonas marisflavi DSM 15357(T) and Halomonas indalinina CG2.1(T) were 21, 17 and 10 %, respectively. These levels of DNA-DNA relatedness were low enough to classify strain A10(T) as representing a genotypically distinct species. Overall, the phenotypic, genotypic, chemotaxonomic and phylogenetic results demonstrated that strain A10(T) represents a new genus and species. The name Kushneria aurantia gen. nov., sp. nov. is proposed, with strain A10(T) (=CCM 7415(T)=CECT 7220(T)) as the type strain. This is the type species of the new proposed genus, which belongs to the family Halomonadaceae. In addition, our data support the placement of the species Halomonas marisflavi, Halomonas indalinina and Halomonas avicenniae within this new genus, as Kushneria marisflavi comb. nov., Kushneria indalinina comb. nov. and Kushneria avicenniae comb. nov., respectively.
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Affiliation(s)
- Cristina Sánchez-Porro
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
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Oren A, Arahal DR, Ventosa A. Emended descriptions of genera of the family Halobacteriaceae. Int J Syst Evol Microbiol 2009; 59:637-42. [DOI: 10.1099/ijs.0.008904-0] [Citation(s) in RCA: 116] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Gutiérrez MC, Castillo AM, Kamekura M, Ventosa A. Haloterrigena salina sp. nov., an extremely halophilic archaeon isolated from a salt lake. Int J Syst Evol Microbiol 2009; 58:2880-4. [PMID: 19060076 DOI: 10.1099/ijs.0.2008/001602-0] [Citation(s) in RCA: 63] [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 novel extremely halophilic strain, designated XH-65(T), isolated from the salt lake Xilinhot in Inner Mongolia, PR China, was subjected to a polyphasic taxonomic characterization. Strain XH-65(T) is neutrophilic, non-motile and requires at least 2.5 M NaCl for growth, with an optimum at 3.4 M NaCl, and grows at pH 6.0-9.0, with optimum growth at pH 7.5. Strain XH-65(T) grows at 25-50 degrees C, with optimal growth at 37 degrees C. Magnesium is not required for growth. On the basis of 16S rRNA gene sequence analysis, strain XH-65(T) was shown to belong to the genus Haloterrigena and was related to Haloterrigena turkmenica VKM B-1734(T) (98.1 % sequence similarity), Haloterrigena saccharevitans AB14(T) (96.9 %), Haloterrigena thermotolerans PR5(T) (96.3 %), Haloterrigena limicola AX-7(T) (95.8 %) and Haloterrigena hispanica FP1(T) (95.7 %). DNA-DNA hybridization revealed 37 % relatedness between strain XH-65(T) and Htg. turkmenica VKM B-1734(T). The polar lipid composition revealed the presence of phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and mannose-2,6-disulfate (1-->2)-glucose glycerol diether (S(2)-DGD). The results of the DNA-DNA hybridization and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain XH-65(T) from the six Haloterrigena species with validly published names. Therefore, strain XH-65(T) represents a novel species, for which the name Haloterrigena salina sp. nov. is proposed, with the type strain XH-65(T) (=CGMCC 1.6203(T) =JCM 13891(T)).
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Affiliation(s)
- M C Gutiérrez
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, Spain.
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Pesenti PT, Sikaroodi M, Gillevet PM, Sánchez-Porro C, Ventosa A, Litchfield CD. Halorubrum californiense sp. nov., an extreme archaeal halophile isolated from a crystallizer pond at a solar salt plant in California, USA. Int J Syst Evol Microbiol 2009; 58:2710-5. [PMID: 19060045 DOI: 10.1099/ijs.0.2008/002410-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A motile, rod-shaped, pink-pigmented, extremely halophilic archaeon, strain SF3-213(T), was isolated from a crystallizer pond at the Cargill Solar Salt Plant, Newark, California (USA). Analysis of the almost-complete 16S rRNA gene sequence showed that the isolate was phylogenetically related to species of the genus Halorubrum, with a close relationship to Halorubrum trapanicum NRC 34021(T) (98.6 % similarity), Halorubrum sodomense ATCC 33755(T) (98.3 %) and Halorubrum xinjiangense AS 1.3527(T) (98.2 %). The polar lipids of strain SF3-213(T) were C(20)C(20) derivatives of phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate and a sulfated diglycosyl-diether. Strain SF3-213(T) grew in 2.5-5.0 M NaCl. The temperature and pH ranges for growth were 25-42 degrees C and 6.8-8.5, respectively. Optimal growth occurred at 3.5-4.5 M NaCl, 37 degrees C and pH 7.3. Mg(2+) was required for growth. The DNA G+C content was 69.4 mol%. DNA-DNA hybridization values lower than 70 % were obtained between strain SF3-213(T) and the closely related species of the genus Halorubrum. Based on the data presented in this study, strain SF3-213(T) represents a novel species for which the name Halorubrum californiense sp. nov. is proposed; the type strain is SF3-213(T) (=CECT 7256(T)=DSM 19288(T)=JCM 14715(T)).
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Affiliation(s)
- Peter T Pesenti
- Department of Environmental Science and Policy, George Mason University, Manassas, VA 20110, USA
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Porter K, Dyall-Smith ML. Transfection of haloarchaea by the DNAs of spindle and round haloviruses and the use of transposon mutagenesis to identify non-essential regions. Mol Microbiol 2009; 70:1236-45. [PMID: 19006816 DOI: 10.1111/j.1365-2958.2008.06478.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Spindle-shaped halovirus His2 and spherical halovirus SH1 represent ecologically dominant virus morphotypes in high-salt environments. Both have linear dsDNA genomes with inverted terminal repeat sequences and terminal proteins, and probably replicate using protein priming. As a first step towards conventional genetic analyses on these viruses, we show that purified viral DNAs can transfect host cells. Intact terminal proteins were essential for this process. Despite the narrow host ranges of these viruses, at least under laboratory conditions, their DNAs were able to transfect a wide range of haloarchaeal species, demonstrating that the cytoplasms of diverse haloarchaea possess all the factors necessary for viral DNA synthesis and virion assembly. Transposon mutagenesis of viral DNAs was then used in conjunction with transfection to produce recombinant viruses, and to then map the insertion sites to identify non-essential genes. The inserts in 34 His2 mutants were mapped precisely, and most clustered in a few, specific regions, particularly in the inverted terminal repeats and near the ends of ORFs. The results are consistent with the small genome size and densely packed, often overlapping ORFs that are transcribed as long operons. This study is the first demonstration of transfection and transposon mutagenesis in protein-primed archaeal viruses.
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Affiliation(s)
- Kate Porter
- Biota Holdings Ltd., 10/585 Blackburn Road, Notting Hill, Victoria 3168, Australia
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Kharroub K, Lizama C, Aguilera M, Boulahrouf A, Campos V, Ramos-Cormenzana A, Monteoliva-Sánchez M. Halomicrobium katesii sp. nov., an extremely halophilic archaeon. Int J Syst Evol Microbiol 2008; 58:2354-8. [PMID: 18842855 DOI: 10.1099/ijs.0.65662-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two extremely halophilic archaea, strains Al-5(T) and K-1, were isolated from Lake Tebenquiche (Atacama Saltern, Chile) and Ezzemoul sabkha (Algeria), respectively. Cells of the two strains were short-rod-shaped and Gram-negative; colonies were orange-pigmented. They grew optimally at 37-40 degrees C and pH 7.0-7.5 in the presence of 25 % (w/v) NaCl. Magnesium was not required. Polar lipid analysis revealed the presence of phosphatidylglycerol and phosphatidylglycerophosphate methyl ester, the absence of phosphatidylglycerosulfate, and the presence of sulfated diglycosyl diether and diether diglycosyl as the sole glycolipids. DNA G+C contents of strains Al-5(T) and K-1 were 52.4 and 52.9 mol% (T(m) method), respectively. 16S rRNA gene sequence comparison with database sequences showed that strains Al-5(T) and K-1 were most closely related to Halomicrobium mukohataei DSM 12286(T) (similarities of 97.5 and 96.9 %, respectively). DNA-DNA hybridization indicated that strains Al-5(T) and K-1 were members of a single species. However, DNA-DNA relatedness to Halomicrobium mukohataei was 55.7+/-2.5 %. A comparative analysis of phenotypic characteristics and DNA-DNA hybridization between the isolates and Halomicrobium mukohataei DSM 12286(T) supported the conclusion that Al-5(T) and K-1 represent a novel species within the genus Halomicrobium, for which the name Halomicrobium katesii sp. nov. is proposed. The type strain is Al-5(T) (=CECT 7257(T)=DSM 19301(T)).
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Affiliation(s)
- Karima Kharroub
- Departamento de Microbiología, Facultad de Farmacia Campus de Cartuja s/n, 18071 Granada, Spain
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Sánchez-Porro C, Tokunaga H, Tokunaga M, Ventosa A. Chromohalobacter japonicus sp. nov., a moderately halophilic bacterium isolated from a Japanese salty food. Int J Syst Evol Microbiol 2007; 57:2262-2266. [PMID: 17911293 DOI: 10.1099/ijs.0.65212-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-negative, non-spore-forming, rod-shaped, motile bacterium, designated strain 43T, was isolated from a Japanese salty food and then subjected to a polyphasic taxonomic study. Strain 43T is moderately halophilic, growing at NaCl concentrations in the range 5–25 % (w/v), with optimum growth between 7.5 and 12.5 % (w/v) NaCl. Growth occurs at temperatures from 15 to 42 °C (optimally at 28–37 °C) and at pH 5.5–9.0 (optimally at pH 7.0–8.0). A phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain 43T belongs to the genus Chromohalobacter. The closest relatives were Chromohalobacter canadensis ATCC 43984T (99.3 % 16S rRNA gene sequence similarity), Chromohalobacter beijerinckii ATCC 19372T (99.1 %), Chromohalobacter sarecensis LV4T (98.3 %), Chromohalobacter nigrandesensis LTS-4NT (97.9 %) and Chromohalobacter marismortui ATCC 17056T (97.9 %). The DNA G+C content was 62.9 mol%, which is within the range described for the genus Chromohalobacter. DNA–DNA hybridization studies between strain 43T and C. canadensis CECT 5385T and C. beijerinckii DSM 7218T showed 38 and 49 % relatedness, respectively; lower DNA–DNA hybridization percentages were obtained with respect to other related Chromohalobacter species. The major fatty acids of strain 43T were C16 : 0, C19 : 0 cyclo ω8c and C12 : 0 3-OH. Overall, the phenotypic, genotypic and phylogenetic results demonstrated that strain 43T represents a novel species within the genus Chromohalobacter. The name Chromohalobacter japonicus sp. nov. is proposed, with strain 43T (=CECT 7219T =CCM 7416T) as the type strain.
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MESH Headings
- Bacterial Typing Techniques
- Base Composition
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Fatty Acids/analysis
- Food Microbiology
- Genes, rRNA
- Halomonadaceae/chemistry
- Halomonadaceae/classification
- Halomonadaceae/isolation & purification
- Halomonadaceae/physiology
- Hydrogen-Ion Concentration
- Japan
- Locomotion/physiology
- Molecular Sequence Data
- Nucleic Acid Hybridization
- Phylogeny
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Sodium Chloride/metabolism
- Temperature
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Affiliation(s)
- Cristina Sánchez-Porro
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
| | - Hiroko Tokunaga
- Laboratory of Applied and Molecular Microbiology, Faculty of Agriculture, Kagoshima University, Kagoshima 890-0065, Japan
| | - Masao Tokunaga
- Laboratory of Applied and Molecular Microbiology, Faculty of Agriculture, Kagoshima University, Kagoshima 890-0065, Japan
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
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41
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Gutiérrez MC, Castillo AM, Kamekura M, Xue Y, Ma Y, Cowan DA, Jones BE, Grant WD, Ventosa A. Halopiger xanaduensis gen. nov., sp. nov., an extremely halophilic archaeon isolated from saline Lake Shangmatala in Inner Mongolia, China. Int J Syst Evol Microbiol 2007; 57:1402-1407. [PMID: 17625165 DOI: 10.1099/ijs.0.65001-0] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain SH-6(T) was isolated from the sediment of Lake Shangmatala, a saline lake in Inner Mongolia (China). Cells were pleomorphic. The organism was neutrophilic and required at least 2.5 M (15 %) NaCl, but not MgCl(2), for growth; optimal growth occurred at 4.3 M (25 %) NaCl. The G+C content of its DNA was 63.1 mol%. 16S rRNA gene sequence analysis revealed that strain SH-6(T) is a member of the family Halobacteriaceae, but there was a low level of similarity with other members of this family. Highest sequence similarity (94.6 %) was obtained with the 16S rRNA genes of the type strains of Natronolimnobius innermongolicus and Natronolimnobius baerhuensis. Polar lipid analyses revealed that strain SH-6(T) contains phosphatidylglycerol and phosphatidylglyceromethylphosphate, derived from both C(20)C(20) and C(20)C(25) glycerol diethers together with the glycolipid S(2)-DGD-1. On the basis of the data obtained, the new isolate could not be classified in any recognized genus. Strain SH-6(T) is thus considered to represent a novel species in a new genus within the family Halobacteriaceae, order Halobacteriales, for which the name Halopiger xanaduensis gen. nov., sp. nov. is proposed. The type strain of Halopiger xanaduensis is SH-6(T) (=CECT 7173(T)=CGMCC 1.6379(T)=JCM 14033(T)).
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MESH Headings
- Base Composition
- China
- DNA, Archaeal/chemistry
- DNA, Archaeal/isolation & purification
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/isolation & purification
- Genes, rRNA
- Geologic Sediments/microbiology
- Halobacteriaceae/chemistry
- Halobacteriaceae/classification
- Halobacteriaceae/isolation & purification
- Halobacteriaceae/physiology
- Magnesium Chloride/metabolism
- Microscopy, Phase-Contrast
- Molecular Sequence Data
- Phospholipids/analysis
- Phylogeny
- RNA, Archaeal/genetics
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Sodium Chloride/metabolism
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Affiliation(s)
- M C Gutiérrez
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
| | - A M Castillo
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
| | - M Kamekura
- Noda Institute for Scientific Research, 399 Noda, Noda-shi, Chiba-ken 278-0037, Japan
| | - Y Xue
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 100080 Beijing, China
| | - Y Ma
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 100080 Beijing, China
| | - D A Cowan
- Department of Biotechnology, University of the Western Cape, Bellville 7535, Cape Town, South Africa
| | - B E Jones
- Genencor International BV, Archimedesweg 30, 2333 CN Leiden, The Netherlands
| | - W D Grant
- Department of Infection, Immunity and Inflammation, University of Leicester, Leicester LE1 9HN, UK
| | - A Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
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42
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Soto-Ramírez N, Sánchez-Porro C, Rosas S, González W, Quiñones M, Ventosa A, Montalvo-Rodríguez R. Halomonas avicenniae sp. nov., isolated from the salty leaves of the black mangrove Avicennia germinans in Puerto Rico. Int J Syst Evol Microbiol 2007; 57:900-905. [PMID: 17473230 DOI: 10.1099/ijs.0.64818-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-negative, short rod to oval-shaped bacterium (strain MW2a(T)) was isolated from the surface of leaves of the black mangrove Avicennia germinans and subjected to a polyphasic taxonomic study. Strain MW2a(T) was moderately halophilic, growing at NaCl concentrations in the range 0-25 % (w/v) with optimum growth at 5 % (w/v) NaCl. Growth occurred at 12-40 degrees C (optimum, 30-35 degrees C) and at pH 5.0-9.0 (optimum, pH 7.0-8.0). Strain MW2a(T) was strictly aerobic. Phylogenetic analysis based on the 16S rRNA gene showed that the strain belongs to the genus Halomonas. The closest relative was Halomonas marisflavi, with 98.6 % 16S rRNA gene sequence similarity. The DNA G+C content of strain MW2a(T) was 61.5 mol%, which is in the range of values for Halomonas species. DNA-DNA hybridization with H. marisflavi showed a relatedness of 42 % and lower values were obtained with respect to other related Halomonas species. The major fatty acids were C(16 : 0), C(19 : 0) cyclo omega8c, C(18 : 1)omega7c and C(12 : 0) 3-OH. Overall, the phenotypic, genotypic and phylogenetic results presented in this study demonstrate that strain MW2a(T) represents a novel species within the genus Halomonas. The name Halomonas avicenniae sp. nov. is proposed, with strain MW2a(T) (=CECT 7193(T)=CCM 7396(T)) as the type strain.
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MESH Headings
- Avicennia/microbiology
- Base Composition
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Environmental Microbiology
- Fatty Acids/analysis
- Genes, rRNA/genetics
- Gentian Violet
- Halomonas/chemistry
- Halomonas/classification
- Halomonas/isolation & purification
- Halomonas/physiology
- Hydrogen-Ion Concentration
- Molecular Sequence Data
- Nucleic Acid Hybridization
- Phenazines
- Phylogeny
- Plant Leaves/microbiology
- Puerto Rico
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Sodium Chloride/metabolism
- Temperature
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Affiliation(s)
- Nelís Soto-Ramírez
- Biology Department Box 9012, University of Puerto Rico, Mayagüez 00681, Puerto Rico
| | - Cristina Sánchez-Porro
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
| | - Soniris Rosas
- Biology Department Box 9012, University of Puerto Rico, Mayagüez 00681, Puerto Rico
| | - Wildaomaris González
- Biology Department Box 9012, University of Puerto Rico, Mayagüez 00681, Puerto Rico
| | - Marian Quiñones
- Biology Department Box 9012, University of Puerto Rico, Mayagüez 00681, Puerto Rico
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
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43
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Romano I, Poli A, Finore I, Huertas FJ, Gambacorta A, Pelliccione S, Nicolaus G, Lama L, Nicolaus B. Haloterrigena hispanica sp. nov., an extremely halophilic archaeon from Fuente de Piedra, southern Spain. Int J Syst Evol Microbiol 2007; 57:1499-1503. [PMID: 17625183 DOI: 10.1099/ijs.0.64895-0] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An extremely halophilic archaeon belonging to the order Halobacteriales was isolated from Fuente de Piedra salt lake, Spain. This strain, designated FP1T, was a pleomorphic coccoid, neutrophilic and required at least 15 % (w/v) NaCl for growth. Strain FP1T grew at 37–60 °C, with optimal growth at 50 °C. Mg2+ was not required, but growth was observed with up to 10 % (w/v) MgSO4. Polar lipid analysis revealed the presence of mannose-6-sulfate(1-2)-glucose glycerol diether as a major glycolipid. Both C20C20 and C20C25 core lipids were present. The genomic DNA G+C content was 62.0 mol%. Phylogenetic analysis based on comparison of 16S rRNA gene sequences demonstrated that the isolate was most closely related to species of the genus Haloterrigena. DNA–DNA reassociation values between strain FP1T and the most closely related species of the genus Haloterrigena (Haloterrigena thermotolerans, Haloterrigena saccharevitans and Haloterrigena limicola) were lower than 29 %. It is therefore considered that strain FP1T represents a novel species of the genus Haloterrigena, for which the name Haloterrigena hispanica sp. nov. is proposed. The type strain is FP1T (=DSM 18328T=ATCC BAA-1310T).
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MESH Headings
- Base Composition
- DNA, Archaeal/chemistry
- DNA, Archaeal/isolation & purification
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/isolation & purification
- Genes, rRNA
- Glycolipids/analysis
- Halobacteriaceae/chemistry
- Halobacteriaceae/classification
- Halobacteriaceae/isolation & purification
- Halobacteriaceae/physiology
- Magnesium Chloride/metabolism
- Molecular Sequence Data
- Nucleic Acid Hybridization
- Phylogeny
- RNA, Archaeal/genetics
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Sodium Chloride/metabolism
- Spain
- Temperature
- Water Microbiology
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Affiliation(s)
- Ida Romano
- Istituto di Chimica Biomolecolare, Comprensorio ex Olivetti, via Campi Flegrei 34, 80078 Pozzuoli, Napoli, Italy
| | - Annarita Poli
- Istituto di Chimica Biomolecolare, Comprensorio ex Olivetti, via Campi Flegrei 34, 80078 Pozzuoli, Napoli, Italy
| | - Ilaria Finore
- Istituto di Chimica Biomolecolare, Comprensorio ex Olivetti, via Campi Flegrei 34, 80078 Pozzuoli, Napoli, Italy
| | - F Javier Huertas
- CSIC, Estacion Experimental del Zaidin, Department of Earth Sciences and Environmental Chemistry, Profesor Albareda 1, 18008 Granada, Spain
| | - Agata Gambacorta
- Istituto di Chimica Biomolecolare, Comprensorio ex Olivetti, via Campi Flegrei 34, 80078 Pozzuoli, Napoli, Italy
| | - Salvatore Pelliccione
- Istituto di Chimica Biomolecolare, Comprensorio ex Olivetti, via Campi Flegrei 34, 80078 Pozzuoli, Napoli, Italy
| | - Giancarlo Nicolaus
- Istituto di Ricerche di Biologia Molecolare Angeletti IRBM, Pomezia, Roma, Italy
| | - Licia Lama
- Istituto di Chimica Biomolecolare, Comprensorio ex Olivetti, via Campi Flegrei 34, 80078 Pozzuoli, Napoli, Italy
| | - Barbara Nicolaus
- Istituto di Chimica Biomolecolare, Comprensorio ex Olivetti, via Campi Flegrei 34, 80078 Pozzuoli, Napoli, Italy
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44
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Gallego V, Sánchez-Porro C, García MT, Ventosa A. Roseomonas aquatica sp. nov., isolated from drinking water. Int J Syst Evol Microbiol 2006; 56:2291-2295. [PMID: 17012549 DOI: 10.1099/ijs.0.64379-0] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain TR53(T), a Gram-negative, non-motile, non-spore-forming and strictly aerobic coccobacillus, isolated from the drinking water distribution system of Seville, Spain, was subjected to polyphasic taxonomic analysis using a combination of phenotypic, genotypic and phylogenetic features. Phylogenetic analysis of 16S rRNA gene sequences showed that strain TR53(T) had highest similarity to members of the genus Roseomonas, with sequence similarity values between 95.7 % (to Roseomonas genomospecies 5 strain ATCC 49960) and 94.0 % (to Roseomonas gilardii subsp. rosea ATCC 49956(T)). On the basis of its phenotypic characteristics, 16S rRNA gene sequence data and DNA G+C content (68.6 mol%), strain TR53(T) represents a novel species of the genus Roseomonas, for which the name Roseomonas aquatica sp. nov. is proposed. The type strain of Roseomonas aquatica is TR53(T) (=CECT 7131(T)=JCM 13556(T)).
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Affiliation(s)
- Virginia Gallego
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
| | - Cristina Sánchez-Porro
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
| | - Maria Teresa García
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
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45
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Castillo AM, Gutiérrez MC, Kamekura M, Ma Y, Cowan DA, Jones BE, Grant WD, Ventosa A. Halovivax asiaticus gen. nov., sp. nov., a novel extremely halophilic archaeon isolated from Inner Mongolia, China. Int J Syst Evol Microbiol 2006; 56:765-770. [PMID: 16585691 DOI: 10.1099/ijs.0.63954-0] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain EJ-46T, a novel pleomorphic, aerobic, extremely halophilic member of the Archaea was isolated from sediment of the saline Lake Ejinor, in Inner Mongolia, China. This organism was neutrophilic and required at least 15 % (2.5 M) NaCl for growth. MgCl2 was not required. The isolate was able to grow at pH 6.0-9.0. Optimum growth occurred in media containing 20 % (3.4 M) NaCl at pH 7.0-7.5. Polar lipid analysis revealed the presence of phosphatidylglycerol and phosphatidylglycerol phosphate methyl ester, derived from both C20C20 and C20C25 glycerol diethers. Four glycolipids were detected, one of which may be novel. The DNA G+C content was 60.3 mol%. 16S rRNA gene analysis revealed that strain EJ-46T was a member of the phylogenetic group defined by the family Halobacteriaceae, and the highest 16S rRNA gene similarity values of 94.9 and 94.8 % were obtained with the haloalkaliphilic species of the genus Natronococcus, Natronococcus occultus and Natronococcus amylolyticus, respectively. Based on the phenotypic, genotypic and phylogenetic analyses, it is proposed that the novel isolate should be classified as representing a new genus and species, for which the name Halovivax asiaticus gen. nov., sp. nov. is proposed. The type strain is EJ-46T (=CGMCC 1.4248T = CECT 7098T).
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Affiliation(s)
- A M Castillo
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
| | - M C Gutiérrez
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
| | - M Kamekura
- Noda Institute for Scientific Research, 399 Noda, Noda-shi, Chiba-ken 278-0037, Japan
| | - Y Ma
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 100080 Beijing, China
| | - D A Cowan
- Department of Biotechnology, University of the Western Cape, Bellville 7535, Cape Town, South Africa
| | - B E Jones
- Genencor International BV, Archimedesweg 30, 2333 CN Leiden, The Netherlands
| | - W D Grant
- Department of Infection, Immunity and Inflammation, University of Leicester, Leicester LE1 9HN, UK
| | - A Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
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46
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Gallego V, Sánchez-Porro C, García MT, Ventosa A. Massilia aurea sp. nov., isolated from drinking water. Int J Syst Evol Microbiol 2006; 56:2449-2453. [PMID: 17012578 DOI: 10.1099/ijs.0.64389-0] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-negative, motile, rod-shaped organism, strain AP13T, able to produce yellow-pigmented colonies, was isolated from the drinking water distribution system of Seville (Spain) and was characterized by using a polyphasic taxonomic approach. In 16S rRNA gene sequence comparisons, strain AP13T exhibited 96.9–95.6 % similarity with respect to the five recognized species of the genus Massilia. The DNA G+C content of strain AP13T was 66.0 mol%, a value that supports the affiliation of strain AP13T to the genus Massilia. DNA–DNA hybridization data and phenotypic properties confirmed that strain AP13T represents a novel species of the genus Massilia, for which the name Massilia aurea sp. nov. is proposed. The type strain is AP13T (=CECT 7142T=CCM 7363T=DSM 18055T=JCM 13879T).
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Affiliation(s)
- Virginia Gallego
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
| | - Cristina Sánchez-Porro
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
| | - Maria Teresa García
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
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47
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Cui HL, Tohty D, Zhou PJ, Liu SJ. Haloterrigena longa sp. nov. and Haloterrigena limicola sp. nov., extremely halophilic archaea isolated from a salt lake. Int J Syst Evol Microbiol 2006; 56:1837-1840. [PMID: 16902017 DOI: 10.1099/ijs.0.64372-0] [Citation(s) in RCA: 35] [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
Halophilic archaeal strains ABH32T and AX-7T were isolated from Aibi salt lake in Xin-Jiang, China, and were subjected to taxonomic studies. The cells of both strains were rod-shaped, and growth required at least 10 % (w/v) NaCl. The cellular polar lipids were identified as phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and mannose-2,6-disulfate (1→2)-glucose glycerol diether (S2-DGD). The isolates were different in that strain ABH32T did not require magnesium and had strong ability to assimilate sugars for growth, whereas strain AX-7T required magnesium and did not assimilate glucose, sucrose or maltose for growth. Both strain ABH32T and strain AX-7T were most closely related to members of the genera Haloterrigena and Natrinema. On the basis of phenotypic and genotypic characteristics, especially their cellular polar lipids, the two isolates were assigned to the genus Haloterrigena. Moreover, the DNA relatedness values for strains ABH32T and AX-7T with respect to members of the genus Haloterrigena were found to be well below 70 %. Thus, strains ABH32T and AX-7T represent two novel species within the genus Haloterrigena, for which the names Haloterrigena longa sp. nov. (type strain ABH32T=CGMCC 1.5334T=JCM 13562T) and Haloterrigena limicola sp. nov. (type strain AX-7T=CGMCC 1.5333T=JCM 13563T) are proposed.
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Affiliation(s)
- Heng-Lin Cui
- Graduate University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100080, People's Republic of China
| | - Dilbr Tohty
- College of Life Sciences, Xin-Jiang Normal University, Urumqi 830053, People's Republic of China
| | - Pei-Jin Zhou
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100080, People's Republic of China
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100080, People's Republic of China
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48
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Castillo AM, Gutiérrez MC, Kamekura M, Xue Y, Ma Y, Cowan DA, Jones BE, Grant WD, Ventosa A. Halostagnicola larsenii gen. nov., sp. nov., an extremely halophilic archaeon from a saline lake in Inner Mongolia, China. Int J Syst Evol Microbiol 2006; 56:1519-1524. [PMID: 16825623 DOI: 10.1099/ijs.0.64286-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain XH-48T was isolated from the sediment of Lake Xilinhot, a saline lake in Inner Mongolia (China). The organism is pleomorphic, neutrophilic and requires at least 2.5 M (15 %) NaCl, but not MgCl2, for growth; it exhibits optimal growth at 3.4 M (20 %) NaCl. The G+C content of its DNA is 61 mol%. 16S rRNA gene sequence analysis revealed that strain XH-48T is a member of the family Halobacteriaceae, but there were low levels of similarity with other members of this family. The highest sequence similarity values (94.5 and 93.3 %) were obtained with the 16S rRNA genes of Natrialba aegyptiaca and Natrialba asiatica, respectively. Polar lipid analyses revealed that strain XH-48T contains phosphatidylglycerol and phosphatidylglyceromethylphosphate, derived from both C20C20 and C20C25 glycerol diethers, and two unidentified glycolipids. On the basis of the data obtained, the novel isolate cannot be classified within any recognized genus. Strain XH-48T should be placed within a novel genus and species within the family Halobacteriaceae, order Halobacteriales, for which the name Halostagnicola larsenii gen. nov., sp. nov. is proposed. The type strain of Halostagnicola larsenii is strain XH-48T (=DSM 17691T=CGMCC 1.5338T=JCM 13463T=CECT 7116T).
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MESH Headings
- Aerobiosis
- Anaerobiosis
- Base Composition
- China
- DNA, Archaeal/chemistry
- DNA, Archaeal/isolation & purification
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/isolation & purification
- Enzymes/analysis
- Genes, rRNA
- Geologic Sediments/microbiology
- Halobacteriaceae/classification
- Halobacteriaceae/cytology
- Halobacteriaceae/genetics
- Halobacteriaceae/isolation & purification
- Halobacteriaceae/physiology
- Lipids/chemistry
- Lipids/isolation & purification
- Magnesium Chloride/metabolism
- Microscopy, Phase-Contrast
- Molecular Sequence Data
- Mongolia
- Phylogeny
- RNA, Archaeal/genetics
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Sodium Chloride/metabolism
- Water Microbiology
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Affiliation(s)
- A M Castillo
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Seville, 41012 Seville, Spain
| | - M C Gutiérrez
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Seville, 41012 Seville, Spain
| | - M Kamekura
- Noda Institute for Scientific Research, 399 Noda, Noda-shi, Chiba-ken 278-0037, Japan
| | - Y Xue
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 100080 Beijing, P. R. China
| | - Y Ma
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 100080 Beijing, P. R. China
| | - D A Cowan
- Department of Biotechnology, University of the Western Cape, Bellville 7535, Cape Town, South Africa
| | - B E Jones
- Genencor International BV, Archimedesweg 30, 2333 CN Leiden, The Netherlands
| | - W D Grant
- Department of Infection, Immunity and Inflammation, University of Leicester, Leicester LE1 9HN, UK
| | - A Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Seville, 41012 Seville, Spain
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Wright ADG. Phylogenetic relationships within the order Halobacteriales inferred from 16S rRNA gene sequences. Int J Syst Evol Microbiol 2006; 56:1223-1227. [PMID: 16738095 DOI: 10.1099/ijs.0.63776-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Phylogenetic relationships within the halophilic archaea were inferred from comparisons of the 16S rRNA gene sequences from 61 strains, representing 18 genera with validly published names within the orderHalobacteriales. Trees produced using distance-matrix (least-squares and neighbour-joining) methods affirm with strong bootstrap support that the members of the orderHalobacterialesare a monophyletic group. Ten genera were supported as monophyletic groups [Haloarcula,Halobiforma,Halococcus,Haloferax,Halorubrum,Halosimplex(multiple sequences from a single strain),Natrialba,Natrinema,NatronococcusandNatronorubrum] and eight genera were represented by a single strain (Halobacterium,Halobaculum,Halogeometricum,Halomicrobium,Halorhabdus,Halosimplex,NatronobacteriumandNatronomonas). The genusHaloterrigenawas always paraphyletic, and the phylogenetic placement of and sister groups toHalobacteriumandNatronomonascould not be resolved. Both treeing methods failed to resolve the deep branching patterns within the orderHalobacterialesand the relationships between the major clades. Additional representation from the currently monospecific genera and/or the use of other macromolecules may be required to resolve the relationships within the orderHalobacteriales.
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Affiliation(s)
- André-Denis Girard Wright
- CSIRO Livestock Industries, Centre for Environment and Life Sciences, Private Bag 5, Wembley, Western Australia 6913, Australia
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Bath C, Cukalac T, Porter K, Dyall-Smith ML. His1 and His2 are distantly related, spindle-shaped haloviruses belonging to the novel virus group, Salterprovirus. Virology 2006; 350:228-39. [PMID: 16530800 DOI: 10.1016/j.virol.2006.02.005] [Citation(s) in RCA: 127] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2005] [Revised: 01/31/2006] [Accepted: 02/02/2006] [Indexed: 11/16/2022]
Abstract
Spindle-shaped viruses are a dominant morphotype in hypersaline waters but their molecular characteristics and their relationship to other archaeal viruses have not been determined. Here, we describe the isolation, characteristics and genome sequence of His2, a spindle-shaped halovirus, and compare it to the previously reported halovirus His1. Their particle dimensions, host-ranges and buoyant densities were found to be similar but they differed in their stabilities to raised temperature, low salinity and chloroform. The genomes of both viruses were linear dsDNA, of similar size (His1, 14,464 bp; His2, 16,067 bp) and mol% G+C (approximately 40%), with long, inverted terminal repeat sequences. The genomic termini of both viruses are likely to possess bound proteins. They shared little nucleotide similarity and, except for their putative DNA polymerase ORFs, no significant similarity at the predicted protein level. A few of the 35 predicted ORFs of both viruses showed significant matches to sequences in GenBank, and these were always to proteins of haloarchaea. Their DNA polymerases showed 42% aa identity, and belonged to the type B group of replicases that use protein-priming. Purified His2 particles were composed of four main proteins (62, 36, 28 and 21 kDa) and the gene for the major capsid protein was identified. Hypothetical proteins similar to His2 VP1 are present in four haloarchaeal genomes but are not part of complete prophages. This, and other evidence, suggests a high frequency of recombination between haloviruses and their hosts. His1 and His2 are unlike fuselloviruses and have been placed in a new virus group, Salterprovirus.
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Affiliation(s)
- Carolyn Bath
- Department of Microbiology and Immunology, The University of Melbourne, Parkville, Victoria 3010, Australia
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