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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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Hassani II, Quadri I, Yadav A, Bouchard S, Raoult D, Hacène H, Desnues C. Assessment of diversity of archaeal communities in Algerian chott. Extremophiles 2023; 27:2. [PMID: 36469177 DOI: 10.1007/s00792-022-01287-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 11/23/2022] [Indexed: 12/12/2022]
Abstract
Halophilic archaea are the dominant type of microorganisms in hypersaline environments. The diversity of halophilic archaea in Zehrez-Chergui (Saharian chott) was analyzed and compared by both analysis of a library of PCR amplified 16S rRNA genes and by cultivation approach. This work, represents the first of its type in Algeria. A total cell count was estimated at 3.8 × 103 CFU/g. The morphological, biochemical, and physiological characterizations of 45 distinct strains, suggests that all of them might be members of the class Halobacteria. Among stains, 23 were characterized phylogenetically and are related to 6 genera of halophilic archaea.The dominance of the genus Halopiger, has not been reported yet in other hypersaline environments. The 100 clones obtained by the molecular approach, were sequenced, and analyzed. The ribosomal library of 61 OTUs showed that the archaeal diversity included uncultured haloarcheon, Halomicrobium, Natronomonas, Halomicroarcula, Halapricum, Haloarcula, Halosimplex, Haloterrigena, Halolamina, Halorubellus, Halorussus and Halonotius. The results of rarefaction analysis indicated that the analysis of an increasing number of clones would have revealed additional diversity. Surprisingly, no halophilic archaea were not shared between the two approaches. Combining both types of methods was considered the best approach to acquire better information on the characteristics of soil halophilic archaea.
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Affiliation(s)
- Imene Ikram Hassani
- Laboratoire de Biologie Cellulaire et Moléculaire, Faculté de Biologie, USTHB Université, Bab Ezzouar, Algeria.
| | - Inès Quadri
- Laboratoire de Biologie Cellulaire et Moléculaire, Faculté de Biologie, USTHB Université, Bab Ezzouar, Algeria
| | - Archana Yadav
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Sonia Bouchard
- Faculté de Médecine, Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD 198, Inserm U1095, 27 Boulevard Jean Moulin, 13385, Marseille, France
| | - Didier Raoult
- Faculté de Médecine, Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD 198, Inserm U1095, 27 Boulevard Jean Moulin, 13385, Marseille, France
| | - Hocine Hacène
- Laboratoire de Biologie Cellulaire et Moléculaire, Faculté de Biologie, USTHB Université, Bab Ezzouar, Algeria
| | - Christelle Desnues
- Faculté de Médecine, Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD 198, Inserm U1095, 27 Boulevard Jean Moulin, 13385, Marseille, France
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Natronococcus pandeyae sp. nov., a Novel Haloarchaeon from Sambhar Salt Lake. Curr Microbiol 2022; 79:51. [PMID: 34982242 DOI: 10.1007/s00284-021-02740-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 12/06/2021] [Indexed: 11/03/2022]
Abstract
A halophilic archaeon, designated strain LS1_42T, was isolated from Sambhar Salt Lake, Rajasthan, India. Cells were non-motile, coccoid, Gram-stain-variable and present in irregular clusters with light pink pigmented colonies. The strain was strictly aerobic and able to grow without Mg2+. Growth of the strain LS1_42T was observed at 25-45 °C, pH 7.0-11.0 and NaCl concentrations of 10-35% (w/v). The nearest phylogenetic neighbor of strain LS1_42T was Natronococcus amylolyticus Ah-36T based on 16S rRNA and rpoB' genes with similarity of 95.4% and 91.9%, respectively. Phylogenetic analysis based on 16S rRNA gene, rpoB' gene and whole-genome sequences indicate that the strain LS1_42T belongs to the genus Natronococcus and is closely related to N. amylolyticus. The genome size was 5.38 Mb with 98.9% completeness. The DNA G + C content of the strain LS1_42T was 63.0 mol%. The average nucleotide identity, average amino acid identity and DNA-DNA hybridization values between LS1_42T and N. amylolyticus Ah-36T were 81.3%, 77.7% and 24.8%, respectively. The major polar lipids detected were phosphatidylglycerol and phosphatidylglycerol phosphate methyl ester. On the basis of phenotypic, chemotaxonomic and genome-based analysis, strain LS1_42T represents a novel species within the genus Natronococcus, for which the name Natronococcus pandeyae sp. nov. is proposed. The type strain is LS1_42T (MCC 3654T = JCM 33003T = KCTC 4280T = CGMCC 1.16738T).
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Boya BR, Kumar P, Lee JH, Lee J. Diversity of the Tryptophanase Gene and Its Evolutionary Implications in Living Organisms. Microorganisms 2021; 9:microorganisms9102156. [PMID: 34683477 PMCID: PMC8537960 DOI: 10.3390/microorganisms9102156] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/09/2021] [Accepted: 10/12/2021] [Indexed: 12/11/2022] Open
Abstract
Tryptophanase encoded by the gene tnaA is a pyridoxal phosphate-dependent enzyme that catalyses the conversion of tryptophan to indole, which is commonly used as an intra- and interspecies signalling molecule, particularly by microbes. However, the production of indole is rare in eukaryotic organisms. A nucleotide and protein database search revealed tnaA is commonly reported in various Gram-negative bacteria, but that only a few Gram-positive bacteria and archaea possess the gene. The presence of tnaA in eukaryotes, particularly protozoans and marine organisms, demonstrates the importance of this gene in the animal kingdom. Here, we document the distribution of tnaA and its acquisition and expansion among different taxonomic groups, many of which are usually categorized as non-indole producers. This study provides an opportunity to understand the intriguing role played by tnaA, and its distribution among various types of organisms.
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Chauhan AK, Choudhury B. Synthetic dyes degradation using lignolytic enzymes produced from Halopiger aswanensis strain ABC_IITR by Solid State Fermentation. CHEMOSPHERE 2021; 273:129671. [PMID: 33517115 DOI: 10.1016/j.chemosphere.2021.129671] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Revised: 11/01/2020] [Accepted: 01/13/2021] [Indexed: 06/12/2023]
Abstract
The present work focuses on studying the degradation of industrial synthetic dyes, which poses serious health hazards and a drastic impact on the environment. Currently available enzymatic processes have higher production and operational costs. However, most enzymes are active at acidic pH, which limits its application in textile dye degradation. This problem can be overcome by lignolytic enzymes obtained from halo-alkaliphile through Solid State Fermentation (SSF) using wheat bran (agro-byproduct) as a substrate. The major lignolytic enzymes studied were Lignin Peroxidase (LiP), Manganese Peroxidase (MnP), and laccase. The results demonstrated the highest activity of 215.4 ± 1.57 of LiP, 36.8 ± 2.38 of MnP, and 8.34 ± 0.21 IU/gds of laccase. Crude enzymes were used to treat synthetic dyes (mainly azo dyes), and their potential for its degradation was confirmed by spectrophotometric, GC-MS, and HPLC analysis. The highest decolorization of 82-93% of Malachite Green (MG) was achieved in LiP and MnP mediated reaction system within 2 hours. The laccase reaction system showed degradation of 53.87% of methyl orange without adding any redox mediator. After obtaining these results, the crude LiP and MnP in the reaction system were further subjected to decolorization at a higher MG concentration of 100-600 mg/L without a redox mediator. As a result, both LiP and MnP decolorized MG by 72-89%. Further, GC-MS analysis of MG biodegradation products confirmed the formation of less toxic low molecular weight products such as benzaldehyde and methanone.
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Affiliation(s)
- Ajay Kumar Chauhan
- Department of Biotechnology, Indian Institute of Technology, Roorkee, Uttarakhand, 24667, India
| | - Bijan Choudhury
- Department of Biotechnology, Indian Institute of Technology, Roorkee, Uttarakhand, 24667, India.
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Bachran M, Kluge S, Lopez-Fernandez M, Cherkouk A. Microbial Diversity in an Arid, Naturally Saline Environment. MICROBIAL ECOLOGY 2019; 78:494-505. [PMID: 30593603 DOI: 10.1007/s00248-018-1301-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 11/23/2018] [Indexed: 06/09/2023]
Abstract
The Arava Valley in is a rock desert within the Great African Rift valley. Soil from this area is covered with a salt crust. Here, we report microbial diversity from arid, naturally saline samples collected near Ein Yahav from the Arava Valley by culture-independent as well as culture-dependent analysis. High-throughput sequencing of the hypervariable region V4 of the 16S rRNA gene revealed that the microbial community consists of halophiles from the domain Bacteria as well as Archaea. Bacterial diversity was mainly represented by the genus Salinimicrobium of the order Flavobacteriales within the phylum Bacteroidetes, from the gammaproteobacterial orders Alteromonadales and Oceanospirillales as well as representatives from the order Bacillales of the phylum Firmicutes. Archaeal diversity was dominated by euryarchaeal Halobacteria from the orders Halobacteriales, Haloferacales, and Natrialbales. But more than 40% of the sequences affiliated with Archaea were assigned to unknown or unclassified archaea. Even if taxonomic resolution of the 16S rRNA gene V4 region for Archaea is limited, this study indicates the need of further and more detailed studies of Archaea. By using culture-dependent analysis, bacteria of the order Bacillales as well as archaea from all three halobacterial orders Halobacteriales, Haloferacales, and Natrialbales including potentially novel species from the genera Halorubrum and Haloparvum were isolated.
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Affiliation(s)
- Madlen Bachran
- Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstraße 400, 01328, Dresden, Germany
| | - Sindy Kluge
- Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstraße 400, 01328, Dresden, Germany
| | - Margarita Lopez-Fernandez
- Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstraße 400, 01328, Dresden, Germany.
| | - Andrea Cherkouk
- Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstraße 400, 01328, Dresden, Germany.
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Sucrose Metabolism in Haloarchaea: Reassessment Using Genomics, Proteomics, and Metagenomics. Appl Environ Microbiol 2019; 85:AEM.02935-18. [PMID: 30658981 DOI: 10.1128/aem.02935-18] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 01/10/2019] [Indexed: 12/21/2022] Open
Abstract
The canonical pathway for sucrose metabolism in haloarchaea utilizes a modified Embden-Meyerhof-Parnas pathway (EMP), in which ketohexokinase and 1-phosphofructokinase phosphorylate fructose released from sucrose hydrolysis. However, our survey of haloarchaeal genomes determined that ketohexokinase and 1-phosphofructokinase genes were not present in all species known to utilize fructose and sucrose, thereby indicating that alternative mechanisms exist for fructose metabolism. A fructokinase gene was identified in the majority of fructose- and sucrose-utilizing species, whereas only a small number possessed a ketohexokinase gene. Analysis of a range of hypersaline metagenomes revealed that haloarchaeal fructokinase genes were far more abundant (37 times) than haloarchaeal ketohexokinase genes. We used proteomic analysis of Halohasta litchfieldiae (which encodes fructokinase) and identified changes in protein abundance that relate to growth on sucrose. Proteins inferred to be involved in sucrose metabolism included fructokinase, a carbohydrate primary transporter, a putative sucrose hydrolase, and two uncharacterized carbohydrate-related proteins encoded in the same gene cluster as fructokinase and the transporter. Homologs of these proteins were present in the genomes of all haloarchaea that use sugars for growth. Enzymes involved in the semiphosphorylative Entner-Doudoroff pathway also had higher abundances in sucrose-grown H. litchfieldiae cells, consistent with this pathway functioning in the catabolism of the glucose moiety of sucrose. The study revises the current understanding of fundamental pathways for sugar utilization in haloarchaea and proposes alternatives to the modified EMP pathway used by haloarchaea for sucrose and fructose utilization.IMPORTANCE Our ability to infer the function that microorganisms perform in the environment is predicated on assumptions about metabolic capacity. When genomic or metagenomic data are used, metabolic capacity is inferred from genetic potential. Here, we investigate the pathways by which haloarchaea utilize sucrose. The canonical haloarchaeal pathway for fructose metabolism involving ketohexokinase occurs only in a small proportion of haloarchaeal genomes and is underrepresented in metagenomes. Instead, fructokinase genes are present in the majority of genomes/metagenomes. In addition to genomic and metagenomic analyses, we used proteomic analysis of Halohasta litchfieldiae (which encodes fructokinase but lacks ketohexokinase) and identified changes in protein abundance that related to growth on sucrose. In this way, we identified novel proteins implicated in sucrose metabolism in haloarchaea, comprising a transporter and various catabolic enzymes (including proteins that are annotated as hypothetical).
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Sorokin DY, Elcheninov AG, Toshchakov SV, Bale NJ, Sinninghe Damsté JS, Khijniak TV, Kublanov IV. Natrarchaeobius chitinivorans gen. nov., sp. nov., and Natrarchaeobius halalkaliphilus sp. nov., alkaliphilic, chitin-utilizing haloarchaea from hypersaline alkaline lakes. Syst Appl Microbiol 2019; 42:309-318. [PMID: 30638904 PMCID: PMC6542413 DOI: 10.1016/j.syapm.2019.01.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 12/30/2018] [Accepted: 01/02/2019] [Indexed: 11/04/2022]
Abstract
Two groups of alkaliphilic haloarchaea from hypersaline alkaline lakes in Central Asia, Egypt and North America were enriched and isolated in pure culture using chitin as growth substrate. These cultures, termed AArcht, were divided into two groups: group 1 which includes eleven isolates from highly alkaline soda lakes and group 2 which contains a single isolate obtained from the alkaline hypersaline Searles Lake. The colonies of chitin-utilizing natronoarchaea were red-pigmented and surrounded by large zones of chitin hydrolysis. The free cells of both groups were mostly flat nonmotile rods, while the cells that attached to chitin or formed colonies on chitin plates were mostly coccoid. The isolates are obligate aerobic saccharolytic archaea utilizing chitin and chitosane (less actively) as the only sugar polymers as well as a few hexoses as their carbon and energy source. Both groups are extremely halophilic, growing optimally at 3.5–4 M total Na+, but they differ in their pH profiles: the main group 1 isolates are obligately alkaliphilic, while the single group 2 strain (AArcht-SlT) is alkalitolerant. The core archaeal lipids in both groups are dominated by C20–C20 and C20–C25 dialkyl glycerol ethers (DGE) in approximately equal proportion. Phylogenetic analysis indicated that the isolates form an independent genus-level lineage within the family Natrialbaceae with 3 species-level subgroups. The available genomes of the closest cultured relatives of the AArcht strains, belonging to the genera Natrialba and Halopiger, do not encode any chitinase-related genes. On the basis of their unique phenotypic properties and distinct phylogeny, we suggest that the obligate alkaliphilic AArcht isolates (group 1) with an identical phenotype are classified into a new genus and species Natrarchaeobius chitinivorans gen. nov., sp. nov., with strain AArcht4T as the type strain (JCM 32476T = UNIQEM U966T), while the facultatively alkaliphilic strain AArcht-SlT (group 2) — as a new species Natrarchaeobius halalkaliphilus sp. nov. (JCM 32477T = UNIQEM U969T).
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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.
| | - Alexander G Elcheninov
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Stepan V Toshchakov
- 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, The Netherlands
| | - Jaap S Sinninghe Damsté
- Department of Marine Microbiology and Biogeochemistry, NIOZ Netherlands Institute for Sea Research, The Netherlands; Department of Earth Sciences - Geochemistry, Faculty of Geosciences, Utrecht University, Utrecht, The Netherlands
| | - Tatiana V Khijniak
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Ilya V Kublanov
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia
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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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Williams TJ, Allen M, Tschitschko B, Cavicchioli R. Glycerol metabolism of haloarchaea. Environ Microbiol 2016; 19:864-877. [PMID: 27768817 DOI: 10.1111/1462-2920.13580] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Haloarchaea are heterotrophic members of the Archaea that thrive in hypersaline environments, often feeding off the glycerol that is produced as an osmolyte by eucaryotic Dunaliella during primary production. In this study we analyzed glycerol metabolism genes in closed genomes of haloarchaea and examined published data describing the growth properties of haloarchaea and experimental data for the enzymes involved. By integrating the genomic data with knowledge from the literature, we derived an understanding of the ecophysiology and evolutionary properties of glycerol catabolic pathways in haloarchaea.
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Affiliation(s)
- Timothy J Williams
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, 2052, New South Wales, Australia
| | - Michelle Allen
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, 2052, New South Wales, Australia
| | - Bernhard Tschitschko
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, 2052, New South Wales, Australia
| | - Ricardo Cavicchioli
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, 2052, New South Wales, Australia
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Minegishi H, Shimogaki R, Enomoto S, Echigo A, Kondo Y, Nagaoka S, Shimane Y, Kamekura M, Itoh T, Ohkuma M, Nunoura T, Takai K, Usami R. Halopiger thermotolerans sp. nov., a thermo-tolerant haloarchaeon isolated from commercial salt. Int J Syst Evol Microbiol 2016; 66:4975-4980. [PMID: 27562780 DOI: 10.1099/ijsem.0.001455] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three thermo-tolerant halophilic archaeal strains, SR-441T, SR-412 and SR-188, were isolated from commercial salt samples. Cells were non-motile pleomorphic rod-shaped, and stained Gram-negative. Colonies were pink-pigmented. The three strains were able to grow with 1.7-4.6 M NaCl (optimum, 2.5 M), at pH 6.5-9.0 (optimum, pH 8.0) and at 35-60 °C (optimum, 45 °C). The orthologous 16S rRNA gene sequence similarities amongst the three strains were 98.8-99.3 %, and the level of DNA-DNA relatedness was 71-74 and 72-75 % (reciprocally). The closest relative was Halopiger aswanensis JCM 11628T with 98.6 %-99.1 % similarity in the orthologous 16S rRNA gene sequences, followed by two more Halopiger species, Halopiger xanaduensis JCM 14033T (98.5 %-99.1 %) and Halopiger salifodinae JCM 9578T (95.5 %-95.6 %). DNA-DNA relatednesses between the three strains and H. aswanensis JCM 11628T and H. xanaduensis JCM 14033T were 61 and 54 %, respectively. The polar lipids of the three novel strains were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, and bis-sulfated diglycosyl archaeol-1. The most distinctive feature of the three strains was the ability to grow at 60 °C, while the maximum growth temperature of H. aswanensis is 55 °C. Based on phenotypic and phylogenetic analyses, the isolates are considered to represent a novel species of the genus Halopiger, for which the name Halopiger thermotolerans sp. nov. is proposed. The type strain is SR-441T (=JCM 19583T=KCTC 4248T) isolated from solar salt produced in Australia. SR-412 (=JCM 19582) and SR-188 (=JCM 19581) isolated from commercial salt samples are additional strains of the species.
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Affiliation(s)
- Hiroaki Minegishi
- Faculty of Science and Engineering, Toyo University, 2100 Kujirai, Kawagoe-shi, Saitama 350-8585, Japan
- Research Institute of Industrial Technology, 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
| | - Ryuta Shimogaki
- Faculty of Science and Engineering, Toyo University, 2100 Kujirai, Kawagoe-shi, Saitama 350-8585, Japan
| | - Shigeaki Enomoto
- Faculty of Science and Engineering, Toyo University, 2100 Kujirai, Kawagoe-shi, Saitama 350-8585, Japan
| | - Akinobu Echigo
- Research Institute of Industrial Technology, Toyo University, 2100 Kujirai, Kawagoe-shi, Saitama 350-8585, Japan
- Faculty of Science and Engineering, Toyo University, 2100 Kujirai, Kawagoe-shi, Saitama 350-8585, Japan
| | - Yusuke Kondo
- Faculty of Science and Engineering, Toyo University, 2100 Kujirai, Kawagoe-shi, Saitama 350-8585, Japan
| | - Shuhei Nagaoka
- Faculty of Science and Engineering, Toyo University, 2100 Kujirai, Kawagoe-shi, Saitama 350-8585, Japan
| | - Yasuhiro Shimane
- Japan Agency for Marine-Earth Science and Technology, 2-15, Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Masahiro Kamekura
- Halophiles Research Institute, 677-1 Shimizu, Noda-shi, Chiba 278-0043, Japan
| | - Takashi Itoh
- RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba-shi, Ibaraki 305-0074, Japan
| | - Moriya Ohkuma
- RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba-shi, Ibaraki 305-0074, Japan
| | - Takuro Nunoura
- Japan Agency for Marine-Earth Science and Technology, 2-15, Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Ken Takai
- Japan Agency for Marine-Earth Science and Technology, 2-15, Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Ron Usami
- Research Institute of Industrial Technology, Toyo University, 2100 Kujirai, Kawagoe-shi, Saitama 350-8585, Japan
- Faculty of Science and Engineering, Toyo University, 2100 Kujirai, Kawagoe-shi, Saitama 350-8585, Japan
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12
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Song HS, Cha IT, Rhee JK, Yim KJ, Kim AY, Choi JS, Baek SJ, Seo MJ, Park SJ, Nam YD, Roh SW. Halostella salina gen. nov., sp. nov., an extremely halophilic archaeon isolated from solar salt. Int J Syst Evol Microbiol 2016; 66:2740-2746. [PMID: 27118259 DOI: 10.1099/ijsem.0.001118] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel halophilic archaeon designated strain CBA1114T was isolated from solar salt in the Republic of Korea. Strain CBA1114T, cells of which were coccoid and Gram-stain-negative, grew in the presence of 15-30 % (w/v) NaCl (optimum, 20 %) and at 20-50 °C (optimum, 40 °C) and pH 7.0-9.0 (optimum, pH 8.0). Strain CBA1114T required Mg2+ for growth. Strain CBA1114T had three 16S rRNA genes, rrnA, rrnB and rrnC; levels of similarity between the sequences were 99.7-99.9 %. The 16S rRNA gene sequence of strain CBA1114T showed 91.7 % similarity to that of Haloterrigena thermotolerans PR5T. In multilocus sequence analysis (MLSA), five housekeeping genes, atpB, EF-2, radA, rpoB' and secY, were found to be closely related to those of the members of the genera Halorientalis(89.7 % similarity of the atpB gene sequence), Halomicroarcula(91.9 %, EF-2), Haloterrigena(85.4 %, radA), Natronoarchaeum(89.2 %, rpoB') and Natrinema(75.7 %, secY). A phylogenetic tree generated from the results of MLSA of the five housekeeping genes showed that strain CBA1114T was closely related to species of the genus Halorientalis in the family Halobacteriaceae. The major polar lipids were identified as phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and unidentified lipids. The G+C content of the genomic DNA of strain CBA1114T was 68.1 mol%. According to the results of phylogenetic, phenotypic and chemotaxonomic analyses, we designate strain CBA1114T (=JCM 30111T=KCTC 4206T) as the type strain of Halostella salina gen. nov., sp. nov., a novel species of a new genus within the family Halobacteriaceae.
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Affiliation(s)
- Hye Seon Song
- Biological Disaster Analysis Group, Korea Basic Science Institute, Daejeon 34133, South Korea.,Department of Food Science and Engineering, Ewha Womans University, Seoul 03760, South Korea
| | - In-Tae Cha
- Biological Disaster Analysis Group, Korea Basic Science Institute, Daejeon 34133, South Korea.,Division of Bioengineering, Incheon National University, Incheon 22012, South Korea
| | - Jin-Kyu Rhee
- Department of Food Science and Engineering, Ewha Womans University, Seoul 03760, South Korea
| | - Kyung June Yim
- Biological Disaster Analysis Group, Korea Basic Science Institute, Daejeon 34133, South Korea
| | - Ah Yoon Kim
- Biological Disaster Analysis Group, Korea Basic Science Institute, Daejeon 34133, South Korea
| | - Jong-Soon Choi
- Biological Disaster Analysis Group, Korea Basic Science Institute, Daejeon 34133, South Korea.,Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon 34134, South Korea
| | - Su Jeong Baek
- Biological Disaster Analysis Group, Korea Basic Science Institute, Daejeon 34133, South Korea.,Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon 34134, South Korea
| | - Myung-Ji Seo
- Division of Bioengineering, Incheon National University, Incheon 22012, South Korea
| | - Soo-Je Park
- Department of Biology, Jeju National University, Jeju 63243, South Korea
| | - Young-Do Nam
- Research Group of Gut Microbiome, Korea Food Research Institute, Sungnam 13539, South Korea
| | - Seong Woon Roh
- Biological Disaster Analysis Group, Korea Basic Science Institute, Daejeon 34133, South Korea
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Zhang WY, Hu J, Pan J, Sun C, Wu M, Xu XW. Draft genome sequence of Halopiger salifodinae KCY07-B2(T), an extremly halophilic archaeon isolated from a salt mine. Stand Genomic Sci 2015; 10:124. [PMID: 26664653 PMCID: PMC4675023 DOI: 10.1186/s40793-015-0113-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 11/24/2015] [Indexed: 12/13/2022] Open
Abstract
Halopiger salifodinae strain KCY07-B2(T), isolated from a salt mine in Kuche county, Xinjiang province, China, belongs to the family Halobacteriaceae. It is a strictly aerobic, pleomorphic, rod-shaped, Gram-negative and extremely halophilic archaeon. In this work, we report the features of the type strain KCY07-B2(T), together with the draft genome sequence and annotation. The draft genome sequence is composed of 83 contigs for 4,350,718 bp with 65.41 % G + C content and contains 4204 protein-coding genes and 50 rRNA genes.
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Affiliation(s)
- Wei-Yan Zhang
- />College of Life Sciences, Zhejiang University, Hangzhou, 310058 P. R. China
| | - Jing Hu
- />College of Life Sciences, Zhejiang University, Hangzhou, 310058 P. R. China
| | - Jie Pan
- />College of Life Sciences, Zhejiang University, Hangzhou, 310058 P. R. China
| | - Cong Sun
- />College of Life Sciences, Zhejiang University, Hangzhou, 310058 P. R. China
| | - Min Wu
- />College of Life Sciences, Zhejiang University, Hangzhou, 310058 P. R. China
| | - Xue-Wei Xu
- />Second Institute of Oceanography, State Oceanic Administration, Hangzhou, 310012 P. R. China
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14
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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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Adaptation, ecology, and evolution of the halophilic stromatolite archaeon Halococcus hamelinensis inferred through genome analyses. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2015; 2015:241608. [PMID: 25709556 PMCID: PMC4325475 DOI: 10.1155/2015/241608] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Revised: 12/04/2014] [Accepted: 12/10/2014] [Indexed: 01/26/2023]
Abstract
Halococcus hamelinensis was the first archaeon isolated from stromatolites. These geomicrobial ecosystems are thought to be some of the earliest known on Earth, yet, despite their evolutionary significance, the role of Archaea in these systems is still not well understood. Detailed here is the genome sequencing and analysis of an archaeon isolated from stromatolites. The genome of H. hamelinensis consisted of 3,133,046 base pairs with an average G+C content of 60.08% and contained 3,150 predicted coding sequences or ORFs, 2,196 (68.67%) of which were protein-coding genes with functional assignments and 954 (29.83%) of which were of unknown function. Codon usage of the H. hamelinensis genome was consistent with a highly acidic proteome, a major adaptive mechanism towards high salinity. Amino acid transport and metabolism, inorganic ion transport and metabolism, energy production and conversion, ribosomal structure, and unknown function COG genes were overrepresented. The genome of H. hamelinensis also revealed characteristics reflecting its survival in its extreme environment, including putative genes/pathways involved in osmoprotection, oxidative stress response, and UV damage repair. Finally, genome analyses indicated the presence of putative transposases as well as positive matches of genes of H. hamelinensis against various genomes of Bacteria, Archaea, and viruses, suggesting the potential for horizontal gene transfer.
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16
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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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17
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Ikram HI, Catherine R, Caroline M, Didier R, Hocine H, Christelle D. Non-contiguous finished genome sequence and description of Halopiger goleamassiliensis sp. nov. Stand Genomic Sci 2014; 9:956-9. [PMID: 25197441 PMCID: PMC4149028 DOI: 10.4056/sigs.4618288] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Halopiger goleamassiliensis strain IIH3(T) sp. nov. is a novel, extremely halophilic archaeon within the genus Halopiger. This strain was isolated from an evaporitic sediment in El Golea Lake, Ghardaïa region (Algeria). The type strain is strain IIH3(T). H. goleamassiliensis is moderately thermophilic, neutrophilic, non-motile and coccus-shaped. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 3,906,923 bp long genome contains 3,854 protein-encoding genes and 49 RNA genes (1 gene is 16S rRNA, 1 gene is 23S rRNA, 3 genes are 5S rRNA, and 44 are tRNA genes).
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Affiliation(s)
- Hassani Imene Ikram
- USTHB Université, Laboratoire de Biologie Cellulaire et Moléculaire, Faculté de Biologie Algérie
| | | | | | | | - Hacène Hocine
- USTHB Université, Laboratoire de Biologie Cellulaire et Moléculaire, Faculté de Biologie Algérie
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18
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Popescu G, Dumitru L. Biosorption of Some Heavy Metals from Media with High Salt Concentrations by HalophilicArchaea. BIOTECHNOL BIOTEC EQ 2014. [DOI: 10.1080/13102818.2009.10818542] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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19
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Hassani II, Robert C, Michelle C, Raoult D, Hacène H, Desnues C. Non-contiguous finished genome sequence and description of Halopiger djelfamassiliensis sp. nov. Stand Genomic Sci 2013; 9:160-74. [PMID: 24501653 PMCID: PMC3910545 DOI: 10.4056/sigs.4578289] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Halopiger djelfamassiliensis strain IIH2T sp. nov. is the type strain of Halopiger djelfamassiliensis sp. nov., a new species within the genus Halopiger. This strain, whose genome is described here, was isolated from evaporitic sediment of the hypersaline Lake Zahrez Gharbi in the Djelfa region (Algeria). H. Djelfamassiliensis is a Gram-negative, polymorphic-shaped and strictly aerobic archaeon. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 3,771,216 bp long genome-contains 3,761 protein-coding and 51 RNA genes, including 4 rRNA genes.
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Affiliation(s)
- Ikram Imene Hassani
- USTHB Université, Laboratoire de Biologie Cellulaire et Moléculaire, Faculté de Biologie Algérie
| | | | - Caroline Michelle
- USTHB Université, Laboratoire de Biologie Cellulaire et Moléculaire, Faculté de Biologie Algérie
| | - Didier Raoult
- Aix-Marseille Université, Faculté de médecine, France
| | - Hocine Hacène
- USTHB Université, Laboratoire de Biologie Cellulaire et Moléculaire, Faculté de Biologie Algérie
| | - Christelle Desnues
- USTHB Université, Laboratoire de Biologie Cellulaire et Moléculaire, Faculté de Biologie Algérie
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Bacterial CS2 hydrolases from Acidithiobacillus thiooxidans strains are homologous to the archaeal catenane CS2 hydrolase. J Bacteriol 2013; 195:4046-56. [PMID: 23836868 DOI: 10.1128/jb.00627-13] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Carbon disulfide (CS(2)) and carbonyl sulfide (COS) are important in the global sulfur cycle, and CS(2) is used as a solvent in the viscose industry. These compounds can be converted by sulfur-oxidizing bacteria, such as Acidithiobacillus thiooxidans species, to carbon dioxide (CO(2)) and hydrogen sulfide (H2S), a property used in industrial biofiltration of CS(2)-polluted airstreams. We report on the mechanism of bacterial CS(2) conversion in the extremely acidophilic A. thiooxidans strains S1p and G8. The bacterial CS(2) hydrolases were highly abundant. They were purified and found to be homologous to the only other described (archaeal) CS(2) hydrolase from Acidianus strain A1-3, which forms a catenane of two interlocked rings. The enzymes cluster in a group of β-carbonic anhydrase (β-CA) homologues that may comprise a subclass of CS(2) hydrolases within the β-CA family. Unlike CAs, the CS(2) hydrolases did not hydrate CO(2) but converted CS(2) and COS with H(2)O to H(2)S and CO(2). The CS(2) hydrolases of A. thiooxidans strains G8, 2Bp, Sts 4-3, and BBW1, like the CS(2) hydrolase of Acidianus strain A1-3, exist as both octamers and hexadecamers in solution. The CS(2) hydrolase of A. thiooxidans strain S1p forms only octamers. Structure models of the A. thiooxidans CS(2) hydrolases based on the structure of Acidianus strain A1-3 CS(2) hydrolase suggest that the A. thiooxidans strain G8 CS(2) hydrolase may also form a catenane. In the A. thiooxidans strain S1p enzyme, two insertions (positions 26 and 27 [PD] and positions 56 to 61 [TPAGGG]) and a nine-amino-acid-longer C-terminal tail may prevent catenane formation.
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21
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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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22
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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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Zhang WY, Meng Y, Zhu XF, Wu M. Halopiger salifodinae sp. nov., an extremely halophilic archaeon isolated from a salt mine. Int J Syst Evol Microbiol 2013; 63:3563-3567. [PMID: 23563233 DOI: 10.1099/ijs.0.050971-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel extremely halophilic archaeon KCY07-B2(T) was isolated from a salt mine in Kuche county, Xinjiang province, China. Colonies were cream-pigmented and cells were pleomorphic rod-shaped. Strain KCY07-B2(T) was able to grow at 25-50 °C (optimum 37-45 °C) and pH 6.0-8.0 (optimum 7.0). The strain required at least 1.9 M NaCl for growth. MgCl2 was not required. Cells lysed in distilled water. Polar lipid analysis revealed the presence of phosphatidylglycerol and phosphatidylglycerol phosphate methyl ester, derived from both C20C20 and C20C25 glycerol diethers, together with five glyolipids. The bis-sulfated glycolipid S2-DGD-1 was present. The DNA G+C content was 62.5 mol%. Analysis of the 16S rRNA gene sequence revealed that strain KCY07-B2(T) was closely related to Halopiger xanaduensis SH-6(T) and Halopiger aswanensis 56(T) (95.8 % and 95.5 % similarity, respectively). On the basis of its phenotypic, chemotaxonomic and genotypic characteristics, strain KCY07-B2(T) is considered to represent a novel species of the genus Halopiger, for which the name Halopiger salifodinae sp. nov. is proposed. The type strain is KCY07-B2(T) ( = JCM 18547(T) = CGMCC 1.12284(T)).
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Affiliation(s)
- Wei-Yan Zhang
- College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Yuan Meng
- College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Xu-Fen Zhu
- College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Min Wu
- College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
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24
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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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Anderson I, Tindall BJ, Rohde M, Lucas S, Han J, Lapidus A, Cheng JF, Goodwin L, Pitluck S, Peters L, Pati A, Mikhailova N, Pagani I, Teshima H, Han C, Tapia R, Land M, Woyke T, Klenk HP, Kyrpides N, Ivanova N. Complete genome sequence of Halopiger xanaduensis type strain (SH-6(T)). Stand Genomic Sci 2012; 6:31-42. [PMID: 22675596 PMCID: PMC3368405 DOI: 10.4056/sigs.2505605] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Halopiger xanaduensis is the type species of the genus Halopiger and belongs to the euryarchaeal family Halobacteriaceae. H. xanaduensis strain SH-6, which is designated as the type strain, was isolated from the sediment of a salt lake in Inner Mongolia, Lake Shangmatala. Like other members of the family Halobacteriaceae, it is an extreme halophile requiring at least 2.5 M salt for growth. We report here the sequencing and annotation of the 4,355,268 bp genome, which includes one chromosome and three plasmids. This genome is part of a Joint Genome Institute (JGI) Community Sequencing Program (CSP) project to sequence diverse haloarchaeal genomes.
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Affiliation(s)
- Iain Anderson
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Brian J. Tindall
- Leibnitz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Manfred Rohde
- HZI – Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Susan Lucas
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - James Han
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Alla Lapidus
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Jan-Fang Cheng
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Lynne Goodwin
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Sam Pitluck
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Lin Peters
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Amrita Pati
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | - Ioanna Pagani
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Hazuki Teshima
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Cliff Han
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Roxanne Tapia
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Miriam Land
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Hans-Peter Klenk
- Leibnitz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Nikos Kyrpides
- DOE Joint Genome Institute, Walnut Creek, California, USA
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Capes MD, DasSarma P, DasSarma S. The core and unique proteins of haloarchaea. BMC Genomics 2012; 13:39. [PMID: 22272718 PMCID: PMC3287961 DOI: 10.1186/1471-2164-13-39] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2011] [Accepted: 01/24/2012] [Indexed: 11/10/2022] Open
Abstract
Background Since the first genome of a halophilic archaeon was sequenced in 2000, biologists have been advancing the understanding of genomic characteristics that allow for survival in the harsh natural environments of these organisms. An increase in protein acidity and GC-bias in the genome have been implicated as factors in tolerance to extreme salinity, desiccation, and high solar radiation. However, few previous attempts have been made to identify novel genes that would permit survival in such extreme conditions. Results With the recent release of several new complete haloarchaeal genome sequences, we have conducted a comprehensive comparative genomic analysis focusing on the identification of unique haloarchaeal conserved proteins that likely play key roles in environmental adaptation. Using bioinformatic methods, we have clustered 31,312 predicted proteins from nine haloarchaeal genomes into 4,455 haloarchaeal orthologous groups (HOGs). We assigned likely functions by association with established COG and KOG databases in NCBI. After identifying homologs in four additional haloarchaeal genomes, we determined that there were 784 core haloarchaeal protein clusters (cHOGs), of which 83 clusters were found primarily in haloarchaea. Further analysis found that 55 clusters were truly unique (tucHOGs) to haloarchaea and qualify as signature proteins while 28 were nearly unique (nucHOGs), the vast majority of which were coded for on the haloarchaeal chromosomes. Of the signature proteins, only one example with any predicted function, Ral, involved in desiccation/radiation tolerance in Halobacterium sp. NRC-1, was identified. Among the core clusters, 33% was predicted to function in metabolism, 25% in information transfer and storage, 10% in cell processes and signaling, and 22% belong to poorly characterized or general function groups. Conclusion Our studies have established conserved groups of nearly 800 protein clusters present in all haloarchaea, with a subset of 55 which are predicted to be accessory proteins that may be critical or essential for success in an extreme environment. These studies support core and signature genes and proteins as valuable concepts for understanding phylogenetic and phenotypic characteristics of coherent groups of organisms.
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Affiliation(s)
- Melinda D Capes
- Department of Microbiology and Immunology, Institute of Marine and Environmental Technology, University of Maryland, 701 East Pratt Street, Baltimore, MD 21202 USA
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Inoue K, Itoh T, Ohkuma M, Kogure K. Halomarina oriensis gen. nov., sp. nov., a halophilic archaeon isolated from a seawater aquarium. Int J Syst Evol Microbiol 2011; 61:942-946. [DOI: 10.1099/ijs.0.020677-0] [Citation(s) in RCA: 36] [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 halophilic archaeon, strain KeC-11T, was isolated from a seawater aquarium at the Ocean Research Institute, University of Tokyo, Japan. The strain was aerobic, Gram-negative and chemo-organotrophic, growing optimally at 37 °C, at pH 7.0–8.0 and in 2.7 M (16 %) NaCl. The strain required at least 10 mM magnesium ions for growth. Cells of strain KeC-11T were non-motile and generally irregular coccoids or discoids. The DNA G+C content of the isolate was 67.7 mol%. Phylogenetic tree reconstructions indicated that it was distantly related to the other recognized members of the family Halobacteriaceae, with the closest relative being Natronomonas pharaonis GabaraT (91 % sequence similarity). The strain contained C20C20 and C20C25 diether derivatives of phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, a glycolipid chromatographically identical to the glycosyl-mannosyl-glucosyl diether (TGD-2) and at least one unidentified glycolipid. Phenotypic characterization and phylogenetic data support the placement of isolate KeC-11T in a novel species in a new genus within the family Halobacteriaceae, for which the name Halomarina oriensis gen. nov., sp. nov. is proposed; the type strain is KeC-11T ( = JCM 16495T = KCTC 4074T).
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Affiliation(s)
- Kentaro Inoue
- Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba 277-8561, Japan
- Japan Collection of Microorganisms, RIKEN BioResource Center, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Ocean Research Institute, University of Tokyo, 1-15-1 Minamidai, Nakano-ku, Tokyo 164-8639, Japan
| | - Takashi Itoh
- Japan Collection of Microorganisms, RIKEN BioResource Center, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Moriya Ohkuma
- Japan Collection of Microorganisms, RIKEN BioResource Center, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Kazuhiro Kogure
- Ocean Research Institute, University of Tokyo, 1-15-1 Minamidai, Nakano-ku, Tokyo 164-8639, Japan
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Bowers KJ, Wiegel J. Temperature and pH optima of extremely halophilic archaea: a mini-review. Extremophiles 2011; 15:119-28. [DOI: 10.1007/s00792-010-0347-y] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2010] [Accepted: 12/08/2010] [Indexed: 11/25/2022]
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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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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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31
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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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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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Halophilic archaea isolated from man-made young (200 years) salt lakes in Slănic, Prahova, Romania. Open Life Sci 2008. [DOI: 10.2478/s11535-008-0034-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AbstractWe isolated a number of extremely halophilic archaea from four salt lakes (Red Bath, Green Bath, Shepherd Bath and Bride Cave) located in Slanic Prahova, Romania. The characterization of 12 representative isolates by polyphasic approach revealed that 11 strains were members of the genus Haloferax and only one was a member of the genus Haloarcula. The 11 Haloferax isolates possessed sulfated diglycosylarchaeol-1 as the major membrane glycolipid, and G+C contents of total DNA were 63.4–65.8 mol%. The predominant isolation of Haloferax species from the lakes may suggest that the underground salt deposit possesses Haloferax species as the major biota of ancient origin. To the best of the authors’ knowledge, this is the first paper on the survey of halophilic archaea of man-made young salt lakes.
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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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35
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Castillo AM, Gutiérrez MC, Kamekura M, Xue Y, Ma Y, Cowan DA, Jones BE, Grant WD, Ventosa A. Halorubrum ejinorense sp. nov., isolated from Lake Ejinor, Inner Mongolia, China. Int J Syst Evol Microbiol 2007; 57:2538-2542. [DOI: 10.1099/ijs.0.65241-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel halophilic archaeon, strain EJ-32T, was isolated from water from Lake Ejinor in Inner Mongolia, China. The taxonomy of strain EJ-32T was studied by using a polyphasic approach. On the basis of 16S rRNA gene sequence similarities, strain EJ-32T was shown to be phylogenetically related to Halorubrum coriense (97.9 %), Halorubrum trapanicum (97.9 %), Halorubrum sodomense (97.8 %), Halorubrum tebenquichense (97.8 %), Halorubrum xinjiangense (97.6 %), Halorubrum terrestre (97.4 %), Halorubrum distributum (97.1 %) and Halorubrum saccharovorum (96.4 %). Strain EJ-32T was found to be neutrophilic, non-motile and Gram-negative. It grew in medium containing saturation concentrations of NaCl and did not require magnesium for optimal growth. The G+C content of the DNA is 64.0 mol%. Values for DNA–DNA hybridization with respect to phylogenetically related Halorubrum species were ≤49 %, indicating that EJ-32T constitutes a different genospecies. The data show that strain EJ-32T represents a novel species of the genus Halorubrum, for which the name Halorubrum ejinorense sp. nov. is proposed. The type strain is EJ-32T (=CECT 7194T=CGMCC 1.6782T=JCM 14265T).
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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. Xue
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 100080 Beijing, People's Republic of China
| | - Y. Ma
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 100080 Beijing, People's Republic of 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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