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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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C 50 carotenoids extracted from Haloterrigena thermotolerans strain K15: antioxidant potential and identification. Folia Microbiol (Praha) 2021; 67:71-79. [PMID: 34510323 DOI: 10.1007/s12223-021-00905-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 08/02/2021] [Indexed: 10/20/2022]
Abstract
Halophilic archaea are one of the microorganism groups that have adapted to living in high saline environments and are important in terms of their potential use in biotechnology industry. One of the most important compounds they have, carotenoid, is used in food, cosmetics, and medical industries. The selected strain was identified as an extremely halophilic and thermophilic archaeon, Haloterrigena thermotolerans K15, based on morphological, biochemical, and physiological evidence as well as 16S rRNA analysis and screened by a scanning electron microscope and an atomic force microscope for the first time. The carotenoid contents of H. thermotolerans K15 isolated from Salt Lake (Tuz Gölü, Turkey) were determined by RP-HPLC-DAD and their isomers were characterized according to UV-Vis spectra by cis peak intensity and spectral fine structure. In addition to all-trans bacterioruberin as a major carotenoid, many isomers of the bacterioruberin such as monoanhydrobacterioruberin and bisanhydrobacterioruberin were also found. The antioxidant activity of carotenoid extract from H. thermotolerans was analyzed by the 2,2-diphenyl-1-picrylhydrazyl radical scavenging method. The carotenoid extract showed antioxidant activity statistically significantly higher than ascorbic acid and butylated hydroxytoluene as reference compounds (p < 0.05). This is the first study about carotenoid characterization and antioxidant activity of H. thermotolerans K15. The obtained results suggest the potential use of H. thermotolerans K15 products as a substitute for synthesized chemical carotenoids and antioxidants.
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3
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Ziko L, Saqr AHA, Ouf A, Gimpel M, Aziz RK, Neubauer P, Siam R. Antibacterial and anticancer activities of orphan biosynthetic gene clusters from Atlantis II Red Sea brine pool. Microb Cell Fact 2019; 18:56. [PMID: 30885206 PMCID: PMC6423787 DOI: 10.1186/s12934-019-1103-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 03/06/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Cancer and infectious diseases are problematic because of continuous emergence of drug resistance. One way to address this enormous global health threat is bioprospecting the unlikeliest environments, such as extreme marine niches, which have tremendous biodiversity that is barely explored. One such environment is the Red Sea brine pool, Atlantis II Deep (ATII). Here, we functionally screened a fosmid library of metagenomic DNA isolated from the ATII lower convective layer (LCL) for antibacterial and anticancer activities. RESULTS Selected clones, 14-7E and 10-2G, displayed antibacterial effects on the marine strain Bacillus sp. Cc6. Moreover, whole cell lysates from 14-7E and 10-2G exhibited decreased cell viability against MCF-7 (39.1% ± 6.6, 42% ± 8.1 at 50% v/v) and U2OS cells (35.7% ± 1.9, 79.9% ± 5.9 at 50% v/v), respectively. By sequencing the insert DNA from 14-7E and 10-2G, we identified two putative orphan biosynthetic gene clusters. Both clusters harbored putative ATP-binding cassette (ABC) transporter permeases and S-adenosylmethionine-related genes. Interestingly, the biosynthetic gene cluster identified on 14-7E is of archaeal origin and harbors a putative transcription factor. Several identified genes may be responsible for the observed antibacterial and anticancer activities. The 14-7E biosynthetic gene cluster may be encoding enzymes producing a specialized metabolite (effect of detected genes involved in C-C bond formation and glycosylation). The bioactivity may also be due to predicted subtilases encoded by this cluster. The 10-2G cluster harbored putative glycosyltransferase and non-ribosomal peptide synthase genes; thus the observed activity of this clone could be caused by a bioactive peptide. CONCLUSIONS The ATII LCL prokaryotic metagenome hosts putative orphan biosynthetic gene clusters that confer antibiotic and anticancer effects. Further biochemical studies should characterize the detected bioactive components, and the potential use of 14-7E metabolite for antibiosis and 10-2G metabolite as a selective anti-breast cancer drug.
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Affiliation(s)
- Laila Ziko
- Graduate Program of Biotechnology, School of Sciences and Engineering, The American University in Cairo, New Cairo, Cairo, 11835, Egypt
| | - Al-Hussein A Saqr
- Department of Biology, School of Sciences and Engineering, The American University in Cairo, SSE (Parcel 7), Second Floor, Office: Room 2194, AUC Avenue, New Cairo, Cairo, 11835, Egypt
| | - Amged Ouf
- Graduate Program of Biotechnology, School of Sciences and Engineering, The American University in Cairo, New Cairo, Cairo, 11835, Egypt
- Department of Biology, School of Sciences and Engineering, The American University in Cairo, SSE (Parcel 7), Second Floor, Office: Room 2194, AUC Avenue, New Cairo, Cairo, 11835, Egypt
| | - Matthias Gimpel
- Chair of Bioprocess Engineering, Department of Biotechnology, Technische Universität Berlin, Ackerstrasse 76, ACK24, 13355, Berlin, Germany
| | - Ramy K Aziz
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, 11562, Egypt
| | - Peter Neubauer
- Chair of Bioprocess Engineering, Department of Biotechnology, Technische Universität Berlin, Ackerstrasse 76, ACK24, 13355, Berlin, Germany
| | - Rania Siam
- Graduate Program of Biotechnology, School of Sciences and Engineering, The American University in Cairo, New Cairo, Cairo, 11835, Egypt.
- Department of Biology, School of Sciences and Engineering, The American University in Cairo, SSE (Parcel 7), Second Floor, Office: Room 2194, AUC Avenue, New Cairo, Cairo, 11835, Egypt.
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Carroll CS, Moore MM. Ironing out siderophore biosynthesis: a review of non-ribosomal peptide synthetase (NRPS)-independent siderophore synthetases. Crit Rev Biochem Mol Biol 2018; 53:356-381. [DOI: 10.1080/10409238.2018.1476449] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Affiliation(s)
| | - Margo M. Moore
- Department of Biological Sciences, Simon Fraser University, Burnaby, Canada
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Sorokin DY, Khijniak TV, Kostrikina NA, Elcheninov AG, Toshchakov SV, Bale NJ, Damsté JSS, Kublanov IV. Natronobiforma cellulositropha gen. nov., sp. nov., a novel haloalkaliphilic member of the family Natrialbaceae (class Halobacteria) from hypersaline alkaline lakes. Syst Appl Microbiol 2018; 41:355-362. [PMID: 29752017 PMCID: PMC6052348 DOI: 10.1016/j.syapm.2018.04.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Revised: 04/13/2018] [Accepted: 04/18/2018] [Indexed: 11/24/2022]
Abstract
Six strains of extremely halophilic and alkaliphilic euryarchaea were enriched and isolated in pure culture from surface brines and sediments of hypersaline alkaline lakes in various geographical locations with various forms of insoluble cellulose as growth substrate. The cells are mostly flat motile rods with a thin monolayer cell wall while growing on cellobiose. In contrast, the cells growing with cellulose are mostly nonmotile cocci covered with a thick external EPS layer. The isolates, designated AArcel, are obligate aerobic heterotrophs with a narrow substrate spectrum. All strains can use insoluble celluloses, cellobiose, a few soluble glucans and xylan as their carbon and energy source. They are extreme halophiles, growing within the range from 2.5 to 4.8 M total Na+ (optimum at 4 M) and obligate alkaliphiles, with the pH range for growth from 7.5 to 9.9 (optimum at 8.5–9). The core archaeal lipids of strain AArcel5T were dominated by C20–C20 dialkyl glycerol ether (DGE) (i.e. archaeol) and C20–C25 DGE in nearly equal proportion. The 16S rRNA gene analysis indicated that all six isolates belong to a single genomic species mostly related to the genera Saliphagus-Natribaculum-Halovarius. Taking together a substantial phenotypic difference of the new isolates from the closest relatives and the phylogenetic distance, it is concluded that the AArcel group represents a novel genus-level branch within the family Natrialbaceae for which the name Natronobiforma cellulositropha gen. nov., sp. nov. is proposed with AArcel5T as the type strain (JCM 31939T = UNIQEM U972T).
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Affiliation(s)
- Dimitry Y Sorokin
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia; Department of Biotechnology, TU Delft, The Netherlands.
| | - Tatiana V Khijniak
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Nadezhda A Kostrikina
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Alexander G Elcheninov
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | | | - Nicole J Bale
- Department of Marine Microbiology and Biogeochemistry, NIOZ Netherlands Institute for Sea Research, and Utrecht University, The Netherlands
| | - Jaap S Sinninghe Damsté
- Department of Marine Microbiology and Biogeochemistry, NIOZ Netherlands Institute for Sea Research, and Utrecht University, The Netherlands; Department of Earth Sciences - Geochemistry, Faculty of Geosciences, Utrecht University, Utrecht, The Netherlands
| | - Ilya V Kublanov
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia; Immanuel Kant Baltic Federal University, Kaliningrad, Russia
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6
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Saliphagus infecundisoli gen. nov., sp. nov., an extremely halophilic archaeon isolated from a saline soil. Int J Syst Evol Microbiol 2017; 67:4154-4160. [DOI: 10.1099/ijsem.0.002270] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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7
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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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8
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Mehrshad M, Amoozegar MA, Makhdoumi A, Rasooli M, Asadi B, Schumann P, Ventosa A. Halovarius luteus gen. nov., sp. nov., an extremely halophilic archaeon from a salt lake. Int J Syst Evol Microbiol 2015; 65:2420-2425. [DOI: 10.1099/ijs.0.000279] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An extremely halophilic archaeon, strain DA50T, was isolated from a brine sample of Urmia lake, a hypersaline environment in north-west Iran. Strain DA50T was orange-pigmented, motile, pleomorphic and required at least 2.5 M NaCl but not MgCl2 for growth. Optimal growth was achieved at 4.0 M NaCl and 0.3 M MgCl2. The optimum pH and temperature for growth were pH 7.0 and 45 °C, while it was able to grow over a pH range of 6.5–8.0 and a temperature range of 25–50 °C. Analysis of 16S rRNA gene sequences revealed that strain DA50T is a member of the family Halobacteriaceae, showing a low level of similarity with other members of this family. Highest similarities, 94.4, 94.0 and 93.9 %, were obtained with the 16S rRNA gene sequences of the type strains of Natrialba aegyptia, Halobiforma lacisalsi and Halovivax asiaticus, respectively. Polar lipid analyses revealed that strain DA50T contains phosphatidylglycerol and phosphatidylglycerol phosphate methyl ester. Four unidentified glycolipids and two minor phospholipids were also observed. The only quinone present was MK-8(II-H2). The G+C content of its DNA was 62.3 mol%. On the basis of the data obtained, the new isolate could not be classified in any recognized genus. Strain DA50T is thus considered to represent a novel species of a new genus within the family Halobacteriaceae, order Halobacteriales, for which the name Halovarius luteus gen. nov., sp. nov. is proposed. The type strain of Halovarius luteus is DA50T ( = IBRC-M 10912T = CECT 8510T).
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Affiliation(s)
- Maliheh Mehrshad
- 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
| | - Mohammad Ali Amoozegar
- Microorganisms Bank, Iranian Biological Resource Centre (IBRC), ACECR, Tehran, Iran
- 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
| | - Ali Makhdoumi
- Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Mehrnoosh Rasooli
- Microorganisms Bank, Iranian Biological Resource Centre (IBRC), ACECR, Tehran, Iran
| | - Basaer Asadi
- 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
| | - Peter Schumann
- Leibniz Institute DSMZ (German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
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9
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Amoozegar MA, Makhdoumi-Kakhki A, Mehrshad M, Rasooli M, Fazeli SAS, Spröer C, Ventosa A. Halovivax cerinus sp. nov., an extremely halophilic archaeon from a hypersaline lake. Int J Syst Evol Microbiol 2015; 65:65-70. [DOI: 10.1099/ijs.0.069757-0] [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
An extremely halophilic archaeon, strain IC35T, was isolated from a mud sample of the Aran-Bidgol salt lake in Iran. The novel strain was cream, non-motile, rod-shaped and required at least 2.5 M NaCl, but not MgCl2, for growth. Optimal growth was achieved with 3.4 M NaCl and 0.1 M MgCl2. The optimum pH and temperature for growth were pH 7.0 (grew over a pH range of 6.5–9.0) and 40 °C (grew over a temperature range of 30–50 °C), respectively. Analysis of 16S rRNA gene sequences revealed that strain IC35T clustered with species of the genus
Halovivax
, with sequence similarities of 97.3 %, 96.6 % and 96.3 %, respectively, to
Halovivax limisalsi
IC38T,
Halovivax asiaticus
EJ-46T and
Halovivax ruber
XH-70T. The rpoB′ gene similarities between the novel strain and
Halovivax limisalsi
IBRC-M 10022T,
Halovivax ruber
JCM 13892T and
Halovivax asiaticus
JCM 14624T were 90.2 %, 90.2 % and 89.9 %, respectively. The polar lipid pattern of strain IC35T consisted of phosphatidylglycerol and phosphatidylglycerol phosphate methyl ester; six unknown glycolipids and two minor phospholipids were also observed. The only quinone present was MK-8 (II-H2). The G+C content of the genomic DNA was 63.2 mol%. DNA–DNA hybridization studies (29 % hybridization with
Halovivax limisalsi
IBRC-M 10022T), as well as biochemical and physiological characterization, allowed strain IC35T to be differentiated from other species of the genus
Halovivax
. A novel species, Halovivax
cerinus sp. nov., is therefore proposed to accommodate this strain. The type strain is IC35T ( = IBRC-M 10256T = KCTC 4050T).
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Affiliation(s)
- 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
| | - Ali Makhdoumi-Kakhki
- Department of Biology, Faculty of Sciences, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Maliheh Mehrshad
- Microorganisms Bank, Iranian Biological Resource Centre (IBRC), ACECR Tehran, Iran
- 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
| | - Mehrnoosh Rasooli
- Microorganisms Bank, Iranian Biological Resource Centre (IBRC), ACECR Tehran, Iran
| | | | - Cathrin Spröer
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
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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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Amoozegar MA, Makhdoumi-Kakhki A, Mehrshad M, Riazi S, Ventosa A. Halovivax limisalsi sp. nov., an extremely halophilic archaeon from hypersaline mud. Int J Syst Evol Microbiol 2014; 64:3422-3426. [DOI: 10.1099/ijs.0.063297-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, cream‐pigmented, motile, extremely halophilic archaeon, designated strain IC38T, was isolated from a saline mud sample taken from a hypersaline lake, Aran-Bidgol, in Iran. The strain required at least 2.5 M NaCl for growth. However, MgCl2 was not required. Optimal growth occurred with 4.3 M NaCl and 0.2 M MgCl2. The optimum pH and temperature for growth were pH 7.0 and 35 °C, respectively, and strain IC38T was able to grow over a pH range of 6.5–9.0, and a temperature range of 25–45 °C. Analysis of the 16S rRNA gene sequence revealed that strain IC38T clustered with the two species of the genus
Halovivax
,
Halovivax asiaticus
EJ-46T and
Halovivax ruber
XH-70T, with sequence similarities of 96.4 % and 96.1 %, respectively. The similarities between the rpoB′ gene of the novel strain and
Halovivax asiaticus
and
Halovivax ruber
were 90.7 % and 90.3 %, respectively. The polar lipid pattern of strain IC38T consisted of phosphatidylglycerol and phosphatidylglycerol phosphate methyl ester. Three unidentified glycolipids and two minor phospholipids were also observed. The DNA G+C content of strain IC38T was 62.6 mol%. On the basis of the phylogenetic analysis, as well as the biochemical and physiological characteristics, the new isolate is suggested to be a representative of a novel species of the genus
Halovivax
, for which the name
Halovivax
limisalsi sp. nov. is proposed. The type strain of
Halovivax
limisalsi is IC38T ( = IBRC-M 10022T = KCTC 4051T).
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Affiliation(s)
- 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
| | - Ali Makhdoumi-Kakhki
- Department of Biology, Faculty of Sciences, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Maliheh Mehrshad
- Microorganisms Bank, Iranian Biological Resource Centre (IBRC), ACECR Tehran, Iran
- 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
| | - Siavash Riazi
- 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
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
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Complete Genome Sequence of Salinarchaeum sp. Strain HArcht-Bsk1T, Isolated from Hypersaline Lake Baskunchak, Russia. GENOME ANNOUNCEMENTS 2013; 1:1/4/e00505-13. [PMID: 23868130 PMCID: PMC3715672 DOI: 10.1128/genomea.00505-13] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The complete genome sequence of a novel halophilic archaeon, Salinarchaeum sp. strain HArcht-Bsk1T, was determined using next-generation sequencing. The genome comprises a 3,255,260-bp circular chromosome with a G+C content of 66.7%. Automatic annotation of the genome revealed a single rRNA operon, 45 tRNAs, and 3,013 protein-coding gene sequences.
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Zhang WJ, Han D, Qiu XX, Zhao ML, Mou YZ, Cui HL, Li ZR. Halobellus rarus sp. nov., a halophilic archaeon from an inland salt lake of China. Antonie van Leeuwenhoek 2013; 104:377-84. [PMID: 23828176 DOI: 10.1007/s10482-013-9960-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2013] [Accepted: 06/24/2013] [Indexed: 11/25/2022]
Abstract
Two halophilic archaeal strains, YC21(T) and YC77, were isolated from an inland salt lake of China. Both have pleomorphic rod-shaped cells that lyse in distilled water, stain Gram-negative and form red-pigmented colonies. They are neutrophilic, require at least 2.1 M NaCl for growth under the optimum growth temperature of 37 °C. The major polar lipids of the two strains were phosphatidylglycerol (PG), phosphatidylglycerol phosphate methyl ester (PGP-Me), phosphatidylglycerol sulfate (PGS), two major glycolipids (GL1 and GL2) chromatographically identical to sulfated mannosyl glucosyl diether (S-DGD-1) and mannosyl glucosyl diether (DGD-1), respectively. Trace amounts of two unidentified lipids (GL0-1 and GL0-2) were also detected. The 16S rRNA gene sequences of the two strains are 99.9 % identical, show 94.0-98.9 % similarity to the closest relative members of Halobellus of the family Halobacteriaceae. The rpoB' gene similarity between strains YC21(T) and YC77 is 99.8 % and show 90.3-95.3 % similarity to the closest relative members of Halobellus. The DNA G+C content of strains YC21(T) and YC77 were 66.1 and 66.2 mol%, respectively. The DNA-DNA hybridization value between strain YC20(T) and strain YC77 was 89 %, and the two strains showed low DNA-DNA relatedness with Halobellus limi TBN53(T), the most related member of Halobellus. The phenotypic, chemotaxonomic and phylogenetic properties suggest that strains YC21(T) and YC77 represent a novel species of the genus Halobellus, for which the name Halobellus rarus sp. nov. is proposed. The type strain is YC21(T) (=CGMCC 1.12121(T) = JCM 18362(T)).
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Affiliation(s)
- Wen-Jiao Zhang
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Jingkou District, Zhenjiang, People's Republic of China
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Qiu XX, Mou YZ, Zhao ML, Zhang WJ, Han D, Ren M, Cui HL. Halobellus inordinatus sp. nov., from a marine solar saltern and an inland salt lake of China. Int J Syst Evol Microbiol 2013; 63:3975-3980. [PMID: 23728369 DOI: 10.1099/ijs.0.053066-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two halophilic archaeal strains, YC20(T) and XD15, were isolated from a marine solar saltern and an inland salt lake in China. Both had pleomorphic cells that lysed in distilled water, stained Gram-negative and formed red-pigmented colonies. They were neutrophilic, requiring at least 100 g NaCl l(-1) and 0.5-95 g MgCl2 l(-1) for growth at the optimum growth temperature of 37 °C. The major polar lipids of the two strains were phosphatidylglycerol (PG), phosphatidylglycerol phosphate methyl ester (PGP-Me), phosphatidylglycerol sulfate (PGS) and two major glycolipids chromatographically identical to sulfated mannosyl glucosyl diether (S-DGD-1) and mannosyl glucosyl diether (DGD-1), respectively. Trace amounts of two unidentified glycolipids were also detected. The 16S rRNA gene sequences of the two strains were 99.5 % identical and showed 94.0-95.9 % similarity to the most closely related members of the genus Halobellus of the family Halobacteriaceae. The rpoB' gene sequence similarity between strains YC20(T) and XD15 was 98.2 % and these sequences showed 89.6-92.8 % similarity to those of the most closely related members of the genus Halobellus. The DNA G+C contents of strains YC20(T) and XD15 were 65.8 mol% and 65.4 mol%, respectively. The DNA-DNA hybridization value between strain YC20(T) and strain XD15 was 92 %, and the two strains showed low DNA-DNA relatedness to members of the genus Halobellus. The phenotypic, chemotaxonomic and phylogenetic properties suggest that strains YC20(T) and XD15 represent a novel species of the genus Halobellus, for which the name Halobellus inordinatus sp. nov. is proposed. The type strain is YC20(T) ( = CGMCC 1.12120(T) = JCM 18361(T)) and the other strain is XD15 ( = CGMCC 1.12236 = JCM 18648).
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Affiliation(s)
- Xing-Xing Qiu
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Yun-Zhuang Mou
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Mei-Lin Zhao
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Wen-Jiao Zhang
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Dong Han
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Min Ren
- Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin of Xinjiang Production and Construction Corps, Tarim University, Alar 843300, PR China
| | - Heng-Lin Cui
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China
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Saralov AI, Baslerov RV, Reutskikh EM, Kuznetsov BB. Halarchaeum solikamskense sp. nov., a thermotolerant neutrophilic haloarchaeon from the foamy products of flotation enrichment of potassium minerals. Microbiology (Reading) 2012. [DOI: 10.1134/s0026261712050141] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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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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17
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Cui HL, Yang X, Mou YZ. Salinarchaeum laminariae gen. nov., sp. nov.: a new member of the family Halobacteriaceae isolated from salted brown alga Laminaria. Extremophiles 2011; 15:625-31. [PMID: 21901373 DOI: 10.1007/s00792-011-0393-0] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2011] [Accepted: 08/22/2011] [Indexed: 11/29/2022]
Abstract
Halophilic archaeal strains R26(T) and R22 were isolated from the brown alga Laminaria produced at Dalian, Liaoning Province, China. Cells from the two strains were pleomorphic rods and Gram negative, and colonies were red pigmented. Strains R26(T) and R22 were able to grow at 20-50°C (optimum 37°C) in 1.4-5.1 M NaCl (optimum 3.1-4.3 M) at pH 5.5-9.5 (optimum pH 8.0-8.5) and neither strain required Mg(2+) for growth. Cells lyse in distilled water and the minimum NaCl concentration required to prevent cell lysis was 8% (w/v) for strain R26(T) and 12% (w/v) for strain R22. The major polar lipids of the two strains were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and minor phosphatidylglycerol sulfate; glycolipids were not detected. Phylogenetic analyses based on 16S rRNA genes and rpoB' genes revealed that strains R26(T) and R22 formed a distinct clade with the closest relative, Natronoarchaeum mannanilyticum. The DNA G+C content of strains R26(T) and R22 was 65.8 and 66.4 mol%, respectively. The DNA-DNA hybridization value between strains R26(T) and R22 was 89%. The phenotypic, chemotaxonomic and phylogenetic properties suggest that the strains R26(T) and R22 represent a novel species in a new genus within the family Halobacteriaceae, for which the name Salinarchaeum laminariae gen. nov., sp. nov. is proposed. The type strain is R26(T) (type strain R26(T) = CGMCC 1.10590(T) = JCM 17267(T), reference strain R22 = CGMCC 1.10589).
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Affiliation(s)
- Heng-Lin Cui
- School of Food and Biological Engineering, Jiangsu University, Jingkou District, Zhenjiang, People's Republic of China.
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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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Cui HL, Gao X, Yang X, Xu XW. Halorussus rarus gen. nov., sp. nov., a new member of the family Halobacteriaceae isolated from a marine solar saltern. Extremophiles 2010; 14:493-9. [PMID: 20824294 DOI: 10.1007/s00792-010-0329-0] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2010] [Accepted: 08/25/2010] [Indexed: 11/24/2022]
Abstract
Two halophilic archaeal strains TBN4(T) and TBN5 were isolated from Taibei marine solar saltern in Jiangsu, China. Both strains showed light red-pigmented colonies and their cells were rod, motile and Gram-stain-negative. They were able to grow at 25-50°C (optimum 37°C), at 1.4-4.3 M NaCl (optimum 2.1 M NaCl), at 0-1.0 M MgCl(2) (optimum 0.005 M MgCl(2)) and at pH 6.0-9.0 (optimum pH 7.0). Their cells lyse in distilled water and minimal NaCl concentration to prevent cell lysis is 8% (w/v). The major polar lipids of the two strains were PG (phosphatidylglycerol), PGP-Me (phosphatidylglycerol phosphate methyl ester), PGS (phosphatidylglycerol sulfate) and five glycolipids chromatographically identical to S-TGD-1 (sulfated galactosyl mannosyl glucosyl diether), S-DGD-1 (sulfated mannosyl glucosyl diether), TGD-1 (galactosyl mannosyl glucosyl diether), DGD-1 (mannosyl glucosyl diether) and DGD-2 (an unknown diglycosyl diether). Phylogenetic analysis revealed that TBN4(T) and strain TBN5 formed a distinct clade with genus Haladaptatus (showing 90.0-90.9% 16S rRNA gene similarities). The DNA G + C content of strain TBN4(T) and strain TBN5 are 66.1 and 65.4 mol%, respectively. The DNA-DNA hybridization value between strain TBN4(T) and strain TBN5 was 94.3%. The phenotypic, chemotaxonomic and phylogenetic properties suggest that strain TBN4(T) and strain TBN5 represent a novel species in a new genus within the family Halobacteriaceae, for which the name Halorussus rarus gen. nov., sp. nov. is proposed. The type strain is TBN4(T) (=CGMCC 1.10122(T) = JCM 16429(T)).
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Affiliation(s)
- Heng-Lin Cui
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Jingkou District, Zhenjiang, 212013, People's Republic of China.
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20
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Cui HL, Gao X, Yang X, Xu XW. Halolamina pelagica gen. nov., sp. nov., a new member of the family Halobacteriaceae. Int J Syst Evol Microbiol 2010; 61:1617-1621. [PMID: 20693359 DOI: 10.1099/ijs.0.026799-0] [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
Two extremely halophilic archaeal strains, TBN21(T) and TBN49, were isolated from the Taibei marine solar saltern near Lianyungang city, Jiangsu province, China. Cells of the two strains were pleomorphic and gram-negative and colonies were red. Strains TBN21(T) and TBN49 were able to grow at 25-50 °C (optimum 37 °C), at 1.4-5.1 M NaCl (optimum 3.4-3.9 M) and at pH 5.5-9.5 (optimum pH 7.0-7.5) and neither strain required Mg(2+) for growth. Cells lysed in distilled water and the minimal NaCl concentration to prevent cell lysis was 8 % (w/v). The major polar lipids of the two strains were phosphatidic acid, phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate and eight glycolipids; three of these glycolipids (GL3, GL4 and GL5) were chromatographically identical to sulfated mannosyl glucosyl diether (S-DGD-1), galactosyl mannosyl glucosyl diether (TGD-1) and mannosyl glucosyl diether (DGD-1), respectively. Phylogenetic analysis revealed that strains TBN21(T) and TBN49 formed a distinct clade with their closest relative, Halobaculum gomorrense JCM 9908(T) (89.0-89.5 % 16S rRNA gene sequence similarity). The DNA G+C contents of strains TBN21(T) and TBN49 were 64.8 and 62.7 mol%, respectively. DNA-DNA hybridization between strains TBN21(T) and TBN49 was 90.1 %. The phenotypic, chemotaxonomic and phylogenetic properties suggest that strains TBN21(T) and TBN49 represent a novel species in a new genus within the family Halobacteriaceae, for which the name Halolamina pelagica gen. nov., sp. nov. is proposed. The type strain of Halolamina pelagica is TBN21(T) ( = CGMCC 1.10329(T) = JCM 16809(T)).
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Affiliation(s)
- Heng-Lin Cui
- School of Food & Biological Engineering, Jiangsu University, Zhenjiang 212013, PR China
| | - Xia Gao
- School of Food & Biological Engineering, Jiangsu University, Zhenjiang 212013, PR China
| | - Xin Yang
- School of Food & Biological Engineering, Jiangsu University, Zhenjiang 212013, PR China
| | - Xue-Wei Xu
- Second Institute of Oceanography, State Oceanic Administration, Hangzhou 310012, PR China
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21
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Cui HL, Gao X, Sun FF, Dong Y, Xu XW, Zhou YG, Liu HC, Oren A, Zhou PJ. Halogranum rubrum gen. nov., sp. nov., a halophilic archaeon isolated from a marine solar saltern. Int J Syst Evol Microbiol 2009; 60:1366-1371. [PMID: 19671729 DOI: 10.1099/ijs.0.014928-0] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two extremely halophilic archaea, strains RO2-11(T) and HO2-1, were isolated from two Chinese marine solar salterns, Rudong solar saltern and Haimen solar saltern, respectively. Cells of the two strains were polymorphic and Gram-stain-negative; colonies were red-pigmented. The two strains grew at NaCl concentrations of 2.6-4.3 M (optimum 3.9 M) and required at least 0.1 M Mg2+ for growth. They were able to grow over a pH range of 6.0-8.0 and a temperature range of 20-50 degrees C, with optimal pH of 7.5 and optimal temperature of 37 degrees C. The major polar lipids of strain RO2-11(T) and strain HO2-1 were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and three glycolipids, two of them chromatographically identical to S-DGD-1 and DGD-1, the third unidentified. The 16S rRNA gene sequence similarity of strain RO2-11(T) and strain HO2-1 was 99.3 % and highest sequence similarity with the closest relative (Haloferax larsenii) was 91.4 %. Based on the data obtained, the two isolates could not be classified in any recognized genus of the family Halobacteriaceae. Strain RO2-11(T) and strain HO2-1 are thus considered to represent a novel species of a new genus within the family Halobacteriaceae, for which the name Halogranum rubrum gen. nov., sp. nov. is proposed. The type strain is RO2-11(T) (=CGMCC 1.7738(T) =JCM 15772(T)).
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Affiliation(s)
- Heng-Lin Cui
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, PR China
| | - Xia Gao
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, PR China
| | - Fang-Fang Sun
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, PR China
| | - Ying Dong
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, PR China
| | - Xue-Wei Xu
- Second Institute of Oceanography, State Oceanic Administration, Hangzhou 310012, PR China
| | - Yu-Guang Zhou
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Hong-Can Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Aharon Oren
- Institute of Life Sciences, and the Moshe Shilo Minerva Center for Marine Biogeochemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Pei-Jin Zhou
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
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Kebbouche-Gana S, Gana ML, Khemili S, Fazouane-Naimi F, Bouanane NA, Penninckx M, Hacene H. Isolation and characterization of halophilic Archaea able to produce biosurfactants. J Ind Microbiol Biotechnol 2009; 36:727-38. [PMID: 19266223 DOI: 10.1007/s10295-009-0545-8] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2008] [Accepted: 02/03/2009] [Indexed: 11/28/2022]
Abstract
Halotolerant microorganisms able to live in saline environments offer a multitude of actual or potential applications in various fields of biotechnology. This is why some strains of Halobacteria from an Algerian culture collection were screened for biosurfactant production in a standard medium using the qualitative drop-collapse test and emulsification activity assay. Five of the Halobacteria strains reduced the growth medium surface tension below 40 mN m(-1), and two of them exhibited high emulsion-stabilizing capacity. Diesel oil-in-water emulsions were stabilized over a broad range of conditions, from pH 2 to 11, with up to 35% sodium chloride or up to 25% ethanol in the aqueous phase. Emulsions were stable to three cycles of freezing and thawing. The components of the biosurfactant were determined; it contained sugar, protein and lipid. The two Halobacteria strains with enhanced biosurfactant producers, designated strain A21 and strain D21, were selected to identify by phenotypic, biochemical characteristics and by partial 16S rRNA gene sequencing. The strains have Mg(2+), and salt growth requirements are always above 15% (w/v) salts with an optimal concentration of 15-25%. Analyses of partial 16S rRNA gene sequences of the two strains suggested that they were halophiles belonging to genera of the family Halobacteriaceae, Halovivax (strain A21) and Haloarcula (strain D21). To our knowledge, this is the first report of biosurfactant production at such a high salt concentration.
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Affiliation(s)
- S Kebbouche-Gana
- Faculty of Biological Sciences, Laboratory of Microbiology, USTHB, Algiers, Algeria.
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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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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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Savage KN, Krumholz LR, Oren A, Elshahed MS. Halosarcina pallida gen. nov., sp. nov., a halophilic archaeon from a low-salt, sulfide-rich spring. Int J Syst Evol Microbiol 2008; 58:856-60. [DOI: 10.1099/ijs.0.65398-0] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Valenzuela-Encinas C, Neria-González I, Alcántara-Hernández RJ, Enríquez-Aragón JA, Estrada-Alvarado I, Hernández-Rodríguez C, Dendooven L, Marsch R. Phylogenetic analysis of the archaeal community in an alkaline-saline soil of the former lake Texcoco (Mexico). Extremophiles 2007; 12:247-54. [DOI: 10.1007/s00792-007-0121-y] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2007] [Accepted: 10/29/2007] [Indexed: 11/30/2022]
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Enache M, Itoh T, Kamekura M, Teodosiu G, Dumitru L. Haloferax prahovense sp. nov., an extremely halophilic archaeon isolated from a Romanian salt lake. Int J Syst Evol Microbiol 2007; 57:393-397. [PMID: 17267985 DOI: 10.1099/ijs.0.64674-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel halophilic archaeon, strain TL6T, was isolated from Telega Lake, a hypersaline environment in Prahova county, Romania. Strain TL6T was able to grow in media with a salt concentration of between 2.5 and 5.2 M, with optimum growth at a concentration of 3.5 M. The novel strain was able to grow at concentrations of 1 M MgCl2 or less, with an optimum of 0.4 M Mg2+. Growth of the novel strain occurred between pH 6.0 and 8.5, with an optimum of pH 7.0-7.5. The G+C content of the total DNA was 63.7 mol%. The 16S rRNA gene sequence of the novel strain was most closely related to species of the genus Haloferax (97.3-99.3 % sequence similarity). The lipid profile of the novel strain corresponded to that of other species belonging to the genus Haloferax. A comparative analysis of the phenotypic properties and DNA-DNA hybridization between the novel strain and other species of the genus Haloferax strongly supported the conclusion that strain TL6T represents a novel species within this genus, for which the name Haloferax prahovense sp. nov., is proposed. The type strain is TL6T (=JCM 13924T=DSM 18310T).
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Affiliation(s)
- Madalin Enache
- Institute of Biology of the Romanian Academy, Splaiul Independentei 296, PO Box 56-53, Bucharest 060031, Romania
- Japan Collection of Micro-organisms RIKEN BioResource Center, Wako-shi, Saitama-ken 351-0198, Japan
| | - Takashi Itoh
- Japan Collection of Micro-organisms RIKEN BioResource Center, Wako-shi, Saitama-ken 351-0198, Japan
| | - Masahiro Kamekura
- Halophiles Research Institute, 677-1 Shimizu, Noda-shi, Chiba-ken 278-0043, Japan
| | - Gabriela Teodosiu
- Institute of Biology of the Romanian Academy, Splaiul Independentei 296, PO Box 56-53, Bucharest 060031, Romania
| | - Lucia Dumitru
- Institute of Biology of the Romanian Academy, Splaiul Independentei 296, PO Box 56-53, Bucharest 060031, Romania
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Sharma AK, Walsh DA, Bapteste E, Rodriguez-Valera F, Ford Doolittle W, Papke RT. Evolution of rhodopsin ion pumps in haloarchaea. BMC Evol Biol 2007; 7:79. [PMID: 17511874 PMCID: PMC1885257 DOI: 10.1186/1471-2148-7-79] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2007] [Accepted: 05/18/2007] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND The type 1 (microbial) rhodopsins are a diverse group of photochemically reactive proteins that display a broad yet patchy distribution among the three domains of life. Recent work indicates that this pattern is likely the result of lateral gene transfer (LGT) of rhodopsin genes between major lineages, and even across domain boundaries. Within the lineage in which the microbial rhodopsins were initially discovered, the haloarchaea, a similar patchy distribution is observed. In this initial study, we assess the roles of LGT and gene loss in the evolution of haloarchaeal rhodopsin ion pump genes, using phylogenetics and comparative genomics approaches. RESULTS Mapping presence/absence of rhodopsins onto the phylogeny of the RNA polymerase B' subunit (RpoB') of the haloarchaea supports previous notions that rhodopsins are patchily distributed. The phylogeny for the bacteriorhodopsin (BR) protein revealed two discrepancies in comparison to the RpoB' marker, while the halorhodopsin (HR) tree showed incongruence to both markers. Comparative analyses of bacteriorhodopsin-linked regions of five haloarchaeal genomes supported relationships observed in the BR tree, and also identified two open reading frames (ORFs) that were more frequently linked to the bacteriorhodopsin gene than those genes previously shown to be important to the function and expression of BR. CONCLUSION The evidence presented here reveals a complex evolutionary history for the haloarchaeal rhodopsins, with both LGT and gene loss contributing to the patchy distribution of rhodopsins within this group. Similarities between the BR and RpoB' phylogenies provide supportive evidence for the presence of bacteriorhodopsin in the last common ancestor of haloarchaea. Furthermore, two loci that we have designated bacterio-opsin associated chaperone (bac) and bacterio-opsin associated protein (bap) are inferred to have important roles in BR biogenesis based on frequent linkage and co-transfer with bacteriorhodopsin genes.
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Affiliation(s)
- Adrian K Sharma
- Department of Biochemistry and Molecular Biology, Dalhousie University, 5850 College St., Halifax, Nova Scotia, B3H 1X5, Canada
| | - David A Walsh
- Department of Biochemistry and Molecular Biology, Dalhousie University, 5850 College St., Halifax, Nova Scotia, B3H 1X5, Canada
| | - Eric Bapteste
- Department of Biochemistry and Molecular Biology, Dalhousie University, 5850 College St., Halifax, Nova Scotia, B3H 1X5, Canada
| | - Francisco Rodriguez-Valera
- Unidad de Microbiologia, Centro de Biologia Molecular y Celular, Universidad Miguel Hernandez, Campus de San Juan, 03550 San Juan, Alicante, Spain
| | - W Ford Doolittle
- Department of Biochemistry and Molecular Biology, Dalhousie University, 5850 College St., Halifax, Nova Scotia, B3H 1X5, Canada
| | - R Thane Papke
- Department of Biochemistry and Molecular Biology, Dalhousie University, 5850 College St., Halifax, Nova Scotia, B3H 1X5, Canada
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Fendrihan S, Legat A, Pfaffenhuemer M, Gruber C, Weidler G, Gerbl F, Stan-Lotter H. Extremely halophilic archaea and the issue of long-term microbial survival. RE/VIEWS IN ENVIRONMENTAL SCIENCE AND BIO/TECHNOLOGY 2006; 5:203-218. [PMID: 21984879 PMCID: PMC3188376 DOI: 10.1007/s11157-006-0007-y] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Halophilic archaebacteria (haloarchaea) thrive in environments with salt concentrations approaching saturation, such as natural brines, the Dead Sea, alkaline salt lakes and marine solar salterns; they have also been isolated from rock salt of great geological age (195-250 million years). An overview of their taxonomy, including novel isolates from rock salt, is presented here; in addition, some of their unique characteristics and physiological adaptations to environments of low water activity are reviewed. The issue of extreme long-term microbial survival is considered and its implications for the search for extraterrestrial life. The development of detection methods for subterranean haloarchaea, which might also be applicable to samples from future missions to space, is presented.
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Affiliation(s)
- Sergiu Fendrihan
- Department of Microbiology, University of Salzburg, Billrothstr. 11, A-5020 Salzburg, Austria
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30
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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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