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Straková D, Sánchez-Porro C, de la Haba RR, Ventosa A. Decoding the Genomic Profile of the Halomicroarcula Genus: Comparative Analysis and Characterization of Two Novel Species. Microorganisms 2024; 12:334. [PMID: 38399738 PMCID: PMC10892550 DOI: 10.3390/microorganisms12020334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 01/24/2024] [Accepted: 01/28/2024] [Indexed: 02/25/2024] Open
Abstract
The genus Halomicroarcula, classified within the family Haloarculaceae, presently comprises eight haloarchaeal species isolated from diverse saline habitats, such as solar salterns, hypersaline soils, marine salt, and marine algae. Here, a detailed taxogenomic study and comparative genomic analysis of the genus Halomicroarcula was carried out. In addition, two strains, designated S1CR25-12T and S3CR25-11T, that were isolated from hypersaline soils located in the Odiel Saltmarshes in Huelva (Spain) were included in this study. The 16S rRNA and rpoB' gene sequence analyses affiliated the two strains to the genus Halomicroarcula. Typically, the species of the genus Halomicroarcula possess multiple heterogeneous copies of the 16S rRNA gene, which can lead to misclassification of the taxa and overestimation of the prokaryotic diversity. In contrast, the application of overall genome relatedness indexes (OGRIs) augments the capacity for the precise taxonomic classification and categorization of prokaryotic organisms. The relatedness indexes of the two new isolates, particularly digital DNA-DNA hybridization (dDDH), orthologous average nucleotide identity (OrthoANI), and average amino acid identity (AAI), confirmed that strains S1CR25-12T (= CECT 30620T = CCM 9252T) and S3CR25-11T (= CECT 30621T = CCM 9254T) constitute two novel species of the genus Halomicroarcula. The names Halomicroarcula saliterrae sp. nov. and Halomicroarcula onubensis sp. nov. are proposed for S1CR25-12T and S3CR25-11T, respectively. Metagenomic fragment recruitment analysis, conducted using seven shotgun metagenomic datasets, revealed that the species belonging to the genus Halomicroarcula were predominantly recruited from hypersaline soils found in the Odiel Saltmarshes and the ponds of salterns with high salt concentrations. This reinforces the understanding of the extreme halophilic characteristics associated with the genus Halomicroarcula. Finally, comparing pan-genomes across the twenty Halomicroarcula and Haloarcula species allowed for the identification of commonalities and differences between the species of these two related genera.
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Affiliation(s)
| | | | | | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain; (D.S.); (C.S.-P.); (R.R.d.l.H.)
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2
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Martinez Pastor M, Sakrikar S, Hwang S, Hackley R, Soborowski A, Maupin-Furlow J, Schmid A. TroR is the primary regulator of the iron homeostasis transcription network in the halophilic archaeon Haloferax volcanii. Nucleic Acids Res 2024; 52:125-140. [PMID: 37994787 PMCID: PMC10783522 DOI: 10.1093/nar/gkad997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 10/10/2023] [Accepted: 10/23/2023] [Indexed: 11/24/2023] Open
Abstract
Maintaining the intracellular iron concentration within the homeostatic range is vital to meet cellular metabolic needs and reduce oxidative stress. Previous research revealed that the haloarchaeon Halobacterium salinarum encodes four diphtheria toxin repressor (DtxR) family transcription factors (TFs) that together regulate the iron response through an interconnected transcriptional regulatory network (TRN). However, the conservation of the TRN and the metal specificity of DtxR TFs remained poorly understood. Here we identified and characterized the TRN of Haloferax volcanii for comparison. Genetic analysis demonstrated that Hfx. volcanii relies on three DtxR transcriptional regulators (Idr, SirR, and TroR), with TroR as the primary regulator of iron homeostasis. Bioinformatics and molecular approaches revealed that TroR binds a conserved cis-regulatory motif located ∼100 nt upstream of the start codon of iron-related target genes. Transcriptomics analysis demonstrated that, under conditions of iron sufficiency, TroR repressed iron uptake and induced iron storage mechanisms. TroR repressed the expression of one other DtxR TF, Idr. This reduced DtxR TRN complexity relative to that of Hbt. salinarum appeared correlated with natural variations in iron availability. Based on these data, we hypothesize that variable environmental conditions such as iron availability appear to select for increasing TRN complexity.
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Affiliation(s)
| | - Saaz Sakrikar
- Center for Genomics and System Biology at NYU Department of Biology, New York University, NY, NY 10003, USA
| | - Sungmin Hwang
- Division of Practical Research, Honam National Institute of Biological Resources, Jeollanam-do, Mokpo-si 58762, Republic of Korea
| | - Rylee K Hackley
- Department of Biology, Duke University, Durham, NC 27708, USA
- University Program in Genetics and Genomics, Duke University, Durham, NC 27708, USA
| | - Andrew L Soborowski
- Department of Biology, Duke University, Durham, NC 27708, USA
- Computational Biology and Bioinformatics graduate program, Duke University, Durham, NC 27708, USA
| | - Julie A Maupin-Furlow
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL 32611, USA
- Genetics Institute, University of Florida, Gainesville, FL 32611, USA
| | - Amy K Schmid
- Department of Biology, Duke University, Durham, NC 27708, USA
- University Program in Genetics and Genomics, Duke University, Durham, NC 27708, USA
- Computational Biology and Bioinformatics graduate program, Duke University, Durham, NC 27708, USA
- Center for Genomics and Computational Biology, Duke University, Durham, NC 27708, USA
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3
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Straková D, Galisteo C, de la Haba RR, Ventosa A. Characterization of Haloarcula terrestris sp. nov. and reclassification of a Haloarcula species based on a taxogenomic approach. Int J Syst Evol Microbiol 2023; 73. [PMID: 37990990 DOI: 10.1099/ijsem.0.006157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2023] Open
Abstract
An extremely halophilic archaeon, strain S1AR25-5AT, was isolated from a hypersaline soil sampled in Odiel Saltmarshes Natural Area (Huelva, Spain). The cells were Gram-stain-negative, motile, pleomorphic rods. Cell growth was observed in the presence of 15-30 % (w/v) NaCl [optimum, 25 % (w/v) NaCl], at pH 6.0-9.0 (optimum, pH 6.5-7.5) and at 25-50 °C (optimum, 37 °C). Based on the 16S rRNA and rpoB' gene sequence comparisons, strain S1AR25-5AT was affiliated to the genus Haloarcula. Taxogenomic analysis, including comparison of the genomes and the phylogenomic tree based on the core-orthologous proteins, together with the genomic indices, i.e., orthologous average nucleotide identity, digital DNA-DNA hybridization and average amino acid identity, confirmed that strain S1AR25-5AT (=CCM 9249T=CECT 30619T) represents a new species of the genus Haloarcula, for which we propose the name Haloarcula terrestris sp. nov. The major polar lipids were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulphate and an unidentified glycolipid, which correlated with the lipid profile of species of the genus Haloarcula. In addition, based on the modern approach in description of species in taxonomy of prokaryotes, the above mentioned genomic indexes indicated that the species Haloarcula tradensis should be considered as a heterotypic synonym of Haloarcula argentinensis.
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Affiliation(s)
- Dáša Straková
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
| | - Cristina Galisteo
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
| | - Rafael R de la Haba
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
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Straková D, Sánchez-Porro C, de la Haba RR, Ventosa A. Natrinema salsiterrestre sp. nov., an extremely halophilic archaeon isolated from a hypersaline soil. Int J Syst Evol Microbiol 2023; 73. [PMID: 37578894 DOI: 10.1099/ijsem.0.005960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/16/2023] Open
Abstract
An extremely halophilic archaeal strain, designated S1CR25-10T, was isolated from hypersaline soil sampled in the Odiel Saltmarshes Natural Area in Southwestern Spain (Huelva) and subjected to a polyphasic taxonomic characterization. The cells were Gram-stain-negative, motile and their colonies were pink-pigmented. It was a strictly aerobic haloarchaeon that could grow at 25-55 °C (optimum, 37 °C), at pH 6.0-9.0 (optimum, pH 7.0-8.0) and in the presence of 12-30 % (w/v) total salts (optimum, 20-25 %, w/v). The phylogenetic analysis based on the comparison of the 16S rRNA gene sequences revealed that strain S1CR25-10T belongs to the genus Natrinema, with 98.9 % similarity to Natrinema salinisoli SLN56T. In addition, the values of orthologous average nucleotide identity, digital DNA-DNA hybridization and average amino acid identity were below the threshold limits accepted for prokaryotic species delineation, with N. salinisoli SLN56T showing the highest relatedness values (92.6 % and 48.4 %, respectively). The major polar lipids were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate and a glycolipid chromatographically identical to sulfated diglycosyl diether. The DNA G+C content of the isolate was 63.8 mol%. Based on the phylogenetic, phenotypic and chemotaxonomic characterization and the whole genome results, strain S1CR25-10T represents a new species within the genus Natrinema, for which the name Natrinema salsiterrestre sp. nov., with type strain S1CR25-10T (=CECT 30623T=CCM 9251T), is proposed.
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Affiliation(s)
- Dáša Straková
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, Spain
| | - Cristina Sánchez-Porro
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, Spain
| | - Rafael R de la Haba
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, Spain
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, Spain
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Durán-Viseras A, Sánchez-Porro C, Viver T, Konstantinidis KT, Ventosa A. Discovery of the Streamlined Haloarchaeon Halorutilus salinus, Comprising a New Order Widespread in Hypersaline Environments across the World. mSystems 2023; 8:e0119822. [PMID: 36943059 PMCID: PMC10134839 DOI: 10.1128/msystems.01198-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023] Open
Abstract
The class Halobacteria is one of the most diverse groups within the Euryarchaeota phylum, whose members are ubiquitously distributed in hypersaline environments, where they often constitute the major population. Here, we report the discovery and isolation of a new halophilic archaeon, strain F3-133T exhibiting ≤86.3% 16S rRNA gene identity to any previously cultivated archaeon, and, thus, representing a new order. Analysis of available 16S rRNA gene amplicon and metagenomic data sets showed that the new isolate represents an abundant group in intermediate-to-high salinity ecosystems and is widely distributed across the world. The isolate presents a streamlined genome, which probably accounts for its ecological success in nature and its fastidious growth in culture. The predominant osmoprotection mechanism appears to be the typical salt-in strategy used by other haloarchaea. Furthermore, the genome contains the complete gene set for nucleotide monophosphate degradation pathway through archaeal RuBisCO, being within the first halophilic archaea representatives reported to code this enzyme. Genomic comparisons with previously described representatives of the phylum Euryarchaeota were consistent with the 16S rRNA gene data in supporting that our isolate represents a novel order within the class Halobacteria for which we propose the names Halorutilales ord. nov., Halorutilaceae fam. nov., Halorutilus gen. nov. and Halorutilus salinus sp. nov. IMPORTANCE The discovery of the new halophilic archaeon, Halorutilus salinus, representing a novel order, family, genus, and species within the class Halobacteria and phylum Euryarchaeota clearly enables insights into the microbial dark matter, expanding the current taxonomical knowledge of this group of archaea. The in-depth comparative genomic analysis performed on this new taxon revealed one of the first known examples of an Halobacteria representative coding the archaeal RuBisCO gene and with a streamlined genome, being ecologically successful in nature and explaining its previous non-isolation. Altogether, this research brings light into the understanding of the physiology of the Halobacteria class members, their ecological distribution, and capacity to thrive in hypersaline environments.
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Affiliation(s)
- Ana Durán-Viseras
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, Spain
- School of Civil & Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Cristina Sánchez-Porro
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, Spain
| | - Tomeu Viver
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain
| | | | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, Spain
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Tang R, Yu Z, Li J. KINN: An alignment-free accurate phylogeny reconstruction method based on inner distance distributions of k-mer pairs in biological sequences. Mol Phylogenet Evol 2023; 179:107662. [PMID: 36375789 DOI: 10.1016/j.ympev.2022.107662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 10/10/2022] [Accepted: 11/02/2022] [Indexed: 11/13/2022]
Abstract
Alignment-based methods have faced disadvantages in sequence comparison and phylogeny reconstruction due to their high computational complexity. Alignment-free methods for sequence comparison and phylogeny inference have attracted a great deal of attention in recent years. Here, we explore an alignment-free approach that uses inner distance distributions of k-mer pairs in biological sequences for phylogeny inference. For every sequence in a dataset, our method transforms the sequence into a numeric feature vector consisting of features each representing a specific k-mer pair's contribution to the characterization of the sequentiality uniqueness of the sequence. This newly defined k-mer pair's contribution is an integration of the reverse Kullback-Leibler divergence, pseudo mode and the classic entropy of an inner distance distribution of the k-mer pair in the sequence. Our method has been tested on datasets of complete genome sequences, complete protein sequences, and gene sequences of rRNA of various lengths. Our method achieves the best performance in comparison with state-of-the-art alignment-free methods as measured by the Robinson-Foulds distance between the reference and the constructed phylogeny trees.
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Affiliation(s)
- Runbin Tang
- Hunan Key Laboratory for Computation and Simulation in Science and Engineering and Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education, Xiangtan University, Hunan 411105, China; School of Mathematical Sciences, Chongqing Normal University, Chongqing 401331, China
| | - Zuguo Yu
- Hunan Key Laboratory for Computation and Simulation in Science and Engineering and Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education, Xiangtan University, Hunan 411105, China.
| | - Jinyan Li
- Data Science Institute, University of Technology Sydney, Ultimo, NSW 2007, Australia.
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Phenotypic characteristics, phylogenetic analysis and characterization of alkaline proteases of marine bacteria Geomicrobium halophilum, Oceanobacillus oncorhynchi, and Oceanobacillus khimchii. Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-022-01095-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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8
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Durán-Viseras A, Sánchez-Porro C, Ventosa A. Genomic Insights Into New Species of the Genus Halomicroarcula Reveals Potential for New Osmoadaptative Strategies in Halophilic Archaea. Front Microbiol 2021; 12:751746. [PMID: 34803972 PMCID: PMC8600319 DOI: 10.3389/fmicb.2021.751746] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 10/11/2021] [Indexed: 12/02/2022] Open
Abstract
Metagenomic studies on prokaryotic diversity of hypersaline soils from the Odiel saltmarshes, South-west Spain, revealed a high proportion of genomic sequences not related to previously cultivated taxa, that might be related to haloarchaea with a high environmental and nutritional flexibility. In this study, we used a culturomics approach in order to isolate new haloarchaeal microorganisms from these hypersaline soils. Four haloarchaeal strains, designated strains F24AT, F28, F27T, and F13T, phylogenetically related to the genus Halomicroarcula, were isolated and characterized in detail. The phylogenomic tree based on the 100 orthologous single-copy genes present in the genomes of these four strains as well as those of the type strains of the species Halomicroarcula pellucida CECT 7537T, Halomicroarcula salina JCM 18369T and Halomicroarcula limicola JCM 18640T, that were determined in this study, revealed that these four new isolates clustered on three groups, with strains F24AT and F28 within a single cluster, and altogether with the species of Halomicroarcula. Additionally, Orthologous Average Nucleotide Identity (OrthoANI), digital DNA-DNA hybridization (dDDH) and Average Amino-acid Identity (AAI) values, likewise phenotypic characteristics, including their polar lipids profiles, permitted to determine that they represent three new species, for which we propose the names Halomicroarcula rubra sp. nov. (type strain F13T), Halomicroarcula nitratireducens sp. nov. (type strain F27T) and Halomicroarcula salinisoli sp. nov. (type strain F24AT). An in deep comparative genomic analysis of species of the genus Halomicroarcula, including their metabolism, their capability to biosynthesize secondary metabolites and their osmoregulatory adaptation mechanisms was carried out. Although they use a salt-in strategy, the identification of the complete pathways for the biosynthesis of the compatible solutes trehalose and glycine betaine, not identified before in any other haloarchaea, might suggest alternative osmoadaptation strategies for this group. This alternative osmoregulatory mechanism would allow this group of haloarchaea to be versatile and eco-physiologically successful in hypersaline environments and would justify the capability of the species of this genus to grow not only on environments with high salt concentrations [up to 30% (w/v) salts], but also under intermediate to low salinities.
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Affiliation(s)
- Ana Durán-Viseras
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, Spain
| | - Cristina Sánchez-Porro
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, Spain
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, Spain
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Complex Brines and Their Implications for Habitability. Life (Basel) 2021; 11:life11080847. [PMID: 34440591 PMCID: PMC8398403 DOI: 10.3390/life11080847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 08/09/2021] [Accepted: 08/11/2021] [Indexed: 11/16/2022] Open
Abstract
There is evidence that life on Earth originated in cold saline waters around scorching hydrothermal vents, and that similar conditions might exist or have existed on Mars, Europa, Ganymede, Enceladus, and other worlds. Could potentially habitable complex brines with extremely low freezing temperatures exist in the shallow subsurface of these frigid worlds? Earth, Mars, and carbonaceous chondrites have similar bulk elemental abundances, but while the Earth is depleted in the most volatile elements, the Icy Worlds of the outer solar system are expected to be rich in them. The cooling of ionic solutions containing substances that likely exist in the Icy Worlds could form complex brines with the lowest eutectic temperature possible for the compounds available in them. Indeed, here, we show observational and theoretical evidence that even elements present in trace amounts in nature are concentrated by freeze–thaw cycles, and therefore contribute significantly to the formation of brine reservoirs that remain liquid throughout the year in some of the coldest places on Earth. This is interesting because the eutectic temperature of water–ammonia solutions can be as low as ~160 K, and significant fractions of the mass of the Icy Worlds are estimated to be water substance and ammonia. Thus, briny solutions with eutectic temperature of at least ~160 K could have formed where, historically, temperature have oscillated above and below ~160 K. We conclude that complex brines must exist in the shallow subsurface of Mars and the Icy Worlds, and that liquid saline water should be present where ice has existed, the temperature is above ~160 K, and evaporation and sublimation have been inhibited.
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Effect of Carbon Sources in Carotenoid Production from Haloarcula sp. M1, Halolamina sp. M3 and Halorubrum sp. M5, Halophilic Archaea Isolated from Sonora Saltern, Mexico. Microorganisms 2021; 9:microorganisms9051096. [PMID: 34065163 PMCID: PMC8160830 DOI: 10.3390/microorganisms9051096] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 04/29/2021] [Accepted: 05/11/2021] [Indexed: 12/25/2022] Open
Abstract
The isolation and molecular and chemo-taxonomic identification of seventeen halophilic archaea from the Santa Bárbara saltern, Sonora, México, were performed. Eight strains were selected based on pigmentation. Molecular identification revealed that the strains belonged to the Haloarcula, Halolamina and Halorubrum genera. Neutral lipids (quinones) were identified in all strains. Glycolipid S-DGD was found only in Halolamina sp. strain M3; polar phospholipids 2,3-O-phytanyl-sn-glycerol-1-phosphoryl-3-sn-glycerol (PG), 2,3-di-O-phytanyl-sn-glycero-1-phospho-3′-sn-glycerol-1′-methyl phosphate (PGP-Me) and sodium salt 1-(3-sn-phosphatidyl)-rac-glycerol were found in all the strains; and one unidentified glyco-phospholipid in strains M1, M3 and M4. Strains M1, M3 and M5 were selected for further studies based on carotenoid production. The effect of glucose and succinic and glutamic acid on carotenoid production was assessed. In particular, carotenoid production and growth significantly improved in the presence of glucose in strains Haloarcula sp. M1 and Halorubrum sp. M5 but not in Halolamina sp. M3. Glutamic and succinic acid had no effect on carotenoid production, and even was negative for Halorubrum sp. M5. Growth was increased by glutamic and succinic acid on Haloarcula sp. M1 but not in the other strains. This work describes for first time the presence of halophilic archaea in the Santa Bárbara saltern and highlights the differences in the effect of carbon sources on the growth and carotenoid production of haloarchaea.
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Birbir M, Caglayan P, Birbir Y. The Destructive Effects of Extremely Halophilic Archaeal Strains on Sheepskins, and Proposals for Remedial Curing Processes : Use of sterile brine or direct electric current to prevent red heat damage on salted sheepskins. JOHNSON MATTHEY TECHNOLOGY REVIEW 2020. [DOI: 10.1595/205651320x15943793010464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Proteolytic and lipolytic extremely halophilic archaea found in curing salt may contaminate skins during the brine curing process and damage skin structure. In the present study, three proteolytic and lipolytic extremely halophilic archaea were isolated from deteriorated salted sheepskins
and characterised using conventional and molecular methods. Each test strain (Haloarcula salaria AT1, Halobacterium salinarum 22T6, Haloarcula tradensis 7T3), a mixed culture of these strains and the mixed culture treated with 1.5 A direct current (DC) were used
for brine curing processes of fresh sheepskins and examined during 47 days of storage to evaluate the degree of destruction wreaked by these microorganisms. Both organoleptic properties and scanning electron microscopy (SEM) images of sheepskins proved that each separate test strain and the
mixed culture caused serious damage. However, the mixed culture of strains treated with electric current did not damage sheepskin structure. Therefore, we highly recommend sterilisation of brine using DC to prevent archaeal damage on cured hides and skins in the leather industry.
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Affiliation(s)
- Meral Birbir
- Division of Plant Diseases and Microbiology, Department of Biology, Faculty of Arts and Sciences, Marmara University Göztepe Campus, 34722 Kadıköy Istanbul, Turkey
| | - Pinar Caglayan
- Division of Plant Diseases and Microbiology, Department of Biology, Faculty of Arts and Sciences, Marmara University Göztepe Campus, 34722 Kadıköy Istanbul, Turkey
| | - Yasar Birbir
- Department of Electrical and Electronics Engineering, Faculty of Technology, Marmara University Göztepe Campus, 34722 Kadıköy Istanbul, Turkey
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12
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Durán-Viseras A, Andrei AŞ, Vera-Gargallo B, Ghai R, Sánchez-Porro C, Ventosa A. Culturomics-based genomics sheds light on the ecology of the new haloarchaeal genus Halosegnis. Environ Microbiol 2020; 23:3418-3434. [PMID: 32410366 DOI: 10.1111/1462-2920.15082] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 05/10/2020] [Accepted: 05/11/2020] [Indexed: 12/22/2022]
Abstract
The development of culture-independent techniques has revolutionized our understanding of microbial ecology, especially through the illustration of the vast gap between the environmentally abundant microbial diversity and that accessible through cultivation. However, culture-based approaches are not only crucial for understanding the evolutionary, metabolic and ecological milieu of microbial diversity but also for the development of novel biotechnological applications. In this study, we used a culturomics-based approach in order to isolate novel microbial taxa from hypersaline environments (i.e. Isla Cristina and Isla Bacuta salterns in Huelva, Spain). We managed to obtain axenic cultures of four haloarchaeal strains that belong to a new haloarchaeal genus and to obtain their genomic sequences. The phylogenomic and phylogenetic analyses (together with AAI, ANI and digital DDH indices) showed that the isolates constitute two new species, for which we propose the names Halosegnis longus sp. nov. and Halosegnis rubeus sp. nov. The genomic-based metabolic reconstructions indicated that members of this new haloarchaeal genus have photoheterotrophic aerobic lifestyle with a typical salt-in signature. 16S rRNA gene sequence reads abundance profiles and genomic recruitment analyses revealed that the Halosegnis genus has a worldwide geographical distribution, reaching high abundance (up to 8%) in habitats with intermediate salinities.
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Affiliation(s)
- Ana Durán-Viseras
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, 41012, Spain
| | - Adrian-Ştefan Andrei
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, České Budějovice, 370 05, Czech Republic
| | - Blanca Vera-Gargallo
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, 41012, Spain
| | - Rohit Ghai
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, České Budějovice, 370 05, Czech Republic
| | - Cristina Sánchez-Porro
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, 41012, Spain
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, 41012, Spain
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Mitra U, Bhattacharyya B, Mukhopadhyay T. PEER: A direct method for biosequence pattern mining through waits of optimal k-mers. Inf Sci (N Y) 2020. [DOI: 10.1016/j.ins.2019.12.072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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14
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Natronomonas salsuginis sp. nov., a New Inhabitant of a Marine Solar Saltern. Microorganisms 2020; 8:microorganisms8040605. [PMID: 32326357 PMCID: PMC7232251 DOI: 10.3390/microorganisms8040605] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Revised: 04/17/2020] [Accepted: 04/19/2020] [Indexed: 11/17/2022] Open
Abstract
A halophilic archaeon, strain F20-122T, was isolated from a marine saltern of Isla Bacuta (Huelva, Spain). Cells were Gram-stain-negative, aerobic, and coccoid in morphology. It grew at 25–50 °C (optimum 37 °C), pH 6.5–9.0 (optimum pH 8.0), and 10–30% (w/v) total salts (optimum 25% salts). The phylogenetic analyses based on the 16S rRNA and rpoB’ genes showed its affiliation with the genus Natronomonas and suggested its placement as a new species within this genus. The in silico DNA–DNA hybridization (DDH) and average nucleotide identity (ANI) analyses of this strain against closely related species supported its placement in a new taxon. The DNA G + C content of this isolate was 63.0 mol%. The polar lipids of strain F20-122T were phosphatidylglycerol phosphate methyl ester (PGP-Me), phosphatidylglycerol (PG), and phosphatidylglycerol sulfate (PGS). Traces of biphosphatidylglycerol (BPG) and other minor phospholipids and unidentified glycolipids were also present. Based on the phylogenetic, genomic, phenotypic, and chemotaxonomic characterization, we propose strain F20-122T (= CCM 8891T = CECT 9564T = JCM 33320T) as the type strain of a new species within the genus Natronomonas, with the name Natronomonas salsuginis sp. nov. Rhodopsin-like sequence analysis of strain F20-122T revealed the presence of haloarchaeal proton pumps, suggesting a light-mediated ATP synthesis for this strain and a maximum wavelength absorption in the green spectrum.
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Haloglomus irregulare gen. nov., sp. nov., a New Halophilic Archaeon Isolated from a Marine Saltern. Microorganisms 2020; 8:microorganisms8020206. [PMID: 32024278 PMCID: PMC7074781 DOI: 10.3390/microorganisms8020206] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 01/28/2020] [Accepted: 01/30/2020] [Indexed: 11/17/2022] Open
Abstract
A halophilic archaeal strain, designated F16-60T, was isolated from Isla Cristina marine saltern in Huelva, Spain. Cells were pleomorphic, irregular, non-motile, and Gram-stain-negative. It produced red-pigmented colonies on agar plates. Strain F16-60T was extremely halophilic (optimum at 30% (w/v) NaCl) and neutrophilic (optimum pH 7.5). Phylogenetic tree reconstructions based on 16S rRNA and rpoB´ gene sequences revealed that strain F16-60T was distinct from species of the related genera Natronomonas, Halomarina, and Halomicrobium, of the order Halobacteriales. The polar lipids are phosphatidylglycerol (PG), phosphatidylglycerol phosphate methyl ester (PGP-Me), phosphatidylglycerol sulfate (PGS), and one glycolipid chromatographically identical to sulfated mannosyl glucosyl diether (S-DGD-1). The DNA G+C content is 68.0 mol%. The taxonomic study, based on a combination of phylogenetic, genomic, chemotaxonomic, and phenotypic analyses, suggest that strain F16-60T (= CECT 9635T = JCM 33318T), represents a novel species of a new genus within the family Haloarculaceae and the order Halobacteriales, for which the name Haloglomus irregulare gen. nov., sp. nov. is proposed. Metagenomic fragment recruitment analysis revealed the worldwide distribution of members of this genus and suggested the existence of other closely related species to be isolated.
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Joulak I, Finore I, Nicolaus B, Leone L, Moriello AS, Attia H, Poli A, Azabou S. Evaluation of the production of exopolysaccharides by newly isolated Halomonas strains from Tunisian hypersaline environments. Int J Biol Macromol 2019; 138:658-666. [DOI: 10.1016/j.ijbiomac.2019.07.128] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Revised: 07/17/2019] [Accepted: 07/21/2019] [Indexed: 01/01/2023]
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Durán-Viseras A, Sánchez-Porro C, Ventosa A. Halorientalis pallida sp. nov., an extremely halophilic archaeon isolated from a marine saltern. Int J Syst Evol Microbiol 2019; 69:3636-3643. [PMID: 31460861 DOI: 10.1099/ijsem.0.003675] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
An extremely halophilic archaeon, strain F13-25T, was isolated from a marine saltern located in Isla Cristina, Huelva, on the south-west coast of Spain. The novel strain had pink-pigmented, non-motile, coccoid cells. Optimal growth was achieved at 25 % (w/v) NaCl, pH 7.5 and 37 °C. Strain F13-25T possessed two heterogeneous 16S rRNA genes (rrnA and rrnB) most closely related to Halorientalis persicus D108T (97.6-99.2 % sequence similarity) and Halorientalis regularis TNN28T (95.9-98.8 %). On the basis of the results of rpoB' gene sequence analysis, strain F13-25T was also closely related to Halorientalis persicus IBRC-M 10043T (89.9 %) and Halorientalis regularis TNN28T (92.3 %). Relatedness values, computed using the Genome-to-Genome Distance Calculator, between strain F13-25T and Halorientalis persicus IBRC-M 10043T and Halorientalis regularis IBRC-M 10760T were 34.6 and 36.2 %, respectively. Average nucleotide identity values based on orthoANI, ANIb and ANIm of strain F13-25T and Halorientalis persicus IBRC-M 10043T and Halorientalisregularis IBRC-M 10760T were 88.0 and 88.8, 87.1 and 87.6 %, and 89.2 and 89.6 %, respectively. All values were far below the threshold accepted for prokaryotic species delineation. The major polar lipids were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and one glycolipid chromatographically identical to sulfated diglycosyl diether. The DNA G+C content was 65.7 mol% (genome). The results of phylogenetic, phenotypic and chemotaxonomic analyses indicated that strain F13-25T represents a novel species of the genus Halorientalis, for which the name Halorientalis pallida sp. nov., with type strain F13-25T (=CECT 9384T=IBRC-M 11176T), is proposed.
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Affiliation(s)
- Ana Durán-Viseras
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
| | - Cristina Sánchez-Porro
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
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Durán-Viseras A, Andrei AS, Ghai R, Sánchez-Porro C, Ventosa A. New Halonotius Species Provide Genomics-Based Insights Into Cobalamin Synthesis in Haloarchaea. Front Microbiol 2019; 10:1928. [PMID: 31507553 PMCID: PMC6719526 DOI: 10.3389/fmicb.2019.01928] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 08/05/2019] [Indexed: 11/13/2022] Open
Abstract
Hypersaline aquatic and terrestrial ecosystems display a cosmopolitan distribution. These environments teem with microbes and harbor a plethora of prokaryotic lineages that evaded ecological characterization due to the prior inability to cultivate them or to access their genomic information. In order to close the current knowledge gap, we performed two sampling and isolation campaigns in the saline soils of the Odiel Saltmarshes and the salterns of Isla Cristina (Huelva, Spain). From the isolated haloarchaeal strains subjected to high-throughput phylogenetic screening, two were chosen (F15BT and F9-27T) for physiological and genomic characterization due of their relatedness to the genus Halonotius. Comparative genomic analyses were carried out between the isolated strains and the genomes of previously described species Halonotius pteroides CECT 7525T, Halonotius aquaticus F13-13T and environmentaly recovered metagenome-assembled representatives of the genus Halonotius. The topology of the phylogenomic tree showed agreement with the phylogenetic ones based on 16S rRNA and rpoB' genes, and together with average amino acid and nucleotide identities suggested the two strains as novel species within the genus. We propose the names Halonotius terrestris sp. nov. (type strain F15BT = CECT 9688T = CCM 8954T) and Halonotius roseus sp. nov. (type strain F9-27T = CECT 9745T = CCM 8956T) for these strains. Comparative genomic analyses within the genus highlighted a typical salt-in signature, characterized by acidic proteomes with low isoelectric points, and indicated heterotrophic aerobic lifestyles. Genome-scale metabolic reconstructions revealed that the newly proposed species encode all the necessary enzymatic reactions involved in cobalamin (vitamin B12) biosynthesis. Based on the worldwide distribution of the genus and its abundance in hypersaline habitats we postulate that its members perform a critical function by being able to provide "expensive" commodities (i.e., vitamin B12) to the halophilic microbial communities at large.
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Affiliation(s)
- Ana Durán-Viseras
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Seville, Seville, Spain
| | - Adrian-Stefan Andrei
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Academy of Sciences of the Czech Republic, České Budějovice, Czechia
| | - Rohit Ghai
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Academy of Sciences of the Czech Republic, České Budějovice, Czechia
| | - Cristina Sánchez-Porro
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Seville, Seville, Spain
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Seville, Seville, Spain
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19
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Rennó NO, Backhus R, Cooper C, Flatico JM, Fischer E, Greer LC, Krasowski MJ, Kremic T, Martínez GM, Prokop NF, Sweeney D, Vicente-Retortillo A. A Simple Instrument Suite for Characterizing Habitability and Weathering: The Modern Aqueous Habitat Reconnaissance Suite (MAHRS). ASTROBIOLOGY 2019; 19:849-866. [PMID: 30964330 DOI: 10.1089/ast.2018.1945] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The shallow subsurface of Mars is extremely interesting as a possible microbial habitat because it becomes temporarily wet, it is shielded from radiation, and mixing by aeolian processes could provide the sources of energy and nutrients necessary for sustaining microbial life in it. The Modern Aqueous Habitat Reconnaissance Suite (MAHRS) was developed primarily to search for potentially habitable environments in the shallow subsurface of Mars and to study weathering, but it can also be used to search for potentially habitable environments in the shallow subsurface of other planetary bodies such as the Icy Worlds. MAHRS includes an instrument developed to measure regolith wetness and search for brine in the shallow subsurface of Mars, where it is most likely to be found. The detection of brine can aid in our understanding not only of habitability but also of geochemistry and aqueous weathering processes. Besides the regolith wetness sensor, MAHRS includes an electric field sensor, an optical microscope, and a radiometer developed to characterize the near-surface environment and study mixing by aeolian processes. MAHRS was designed to aid in the selection of optimum areas for sample collection for return to Earth.
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Affiliation(s)
- N O Rennó
- 1Department of Climate and Space Sciences and Engineering, University of Michigan, Ann Arbor, Michigan
| | - R Backhus
- 2Space Physics Research Laboratory, University of Michigan, Ann Arbor, Michigan
| | - C Cooper
- 2Space Physics Research Laboratory, University of Michigan, Ann Arbor, Michigan
| | | | - E Fischer
- 1Department of Climate and Space Sciences and Engineering, University of Michigan, Ann Arbor, Michigan
| | - L C Greer
- 4NASA Glenn Research Center, Cleveland, Ohio
| | | | - T Kremic
- 3Ohio Aerospace Institute, Cleveland, Ohio
| | - G M Martínez
- 1Department of Climate and Space Sciences and Engineering, University of Michigan, Ann Arbor, Michigan
| | - N F Prokop
- 4NASA Glenn Research Center, Cleveland, Ohio
| | - David Sweeney
- 1Department of Climate and Space Sciences and Engineering, University of Michigan, Ann Arbor, Michigan
| | - A Vicente-Retortillo
- 1Department of Climate and Space Sciences and Engineering, University of Michigan, Ann Arbor, Michigan
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20
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Durán-Viseras A, Ventosa A, Sánchez-Porro C. Halonotius aquaticus sp. nov., a new haloarchaeon isolated from a marine saltern. Int J Syst Evol Microbiol 2019; 69:1306-1312. [DOI: 10.1099/ijsem.0.003309] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Ana Durán-Viseras
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
| | - Cristina Sánchez-Porro
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
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21
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de la Haba RR, Corral P, Sánchez-Porro C, Infante-Domínguez C, Makkay AM, Amoozegar MA, Ventosa A, Papke RT. Genotypic and Lipid Analyses of Strains From the Archaeal Genus Halorubrum Reveal Insights Into Their Taxonomy, Divergence, and Population Structure. Front Microbiol 2018; 9:512. [PMID: 29662474 PMCID: PMC5890160 DOI: 10.3389/fmicb.2018.00512] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 03/06/2018] [Indexed: 11/13/2022] Open
Abstract
To gain a better understanding of how divergence occurs, and how taxonomy can benefit from studying natural populations, we isolated and examined 25 closely related Halorubrum strains obtained from different hypersaline communities and compared them to validly named species and other reference strains using five taxonomic study approaches: phylogenetic analysis using the 16S rRNA gene and multilocus sequencing analysis (MLSA), polar lipid profiles (PLP), average nucleotide identity (ANI) and DNA-DNA hybridization (DDH). 16S rRNA gene sequence could not differentiate the newly isolated strains from described species, while MLSA grouped strains into three major clusters. Two of those MLSA clusters distinguished candidates for new species. The third cluster with concatenated sequence identity equal to or greater than 97.5% was comprised of strains from Aran-Bidgol Lake (Iran) and solar salterns in Namibia and Spain, and two previously described species isolated from Mexico and Algeria. PLP and DDH analyses showed that Aran-Bidgol strains formed uniform populations, and that strains isolated from other geographic locations were heterogeneous and divergent, indicating that they may constitute different species. Therefore, applying only sequencing approaches and similarity cutoffs for circumscribing species may be too conservative, lumping concealed diversity into a single taxon. Further, our data support the interpretation that local populations experience unique evolutionary homogenization pressures, and once relieved of insular constraints (e.g., through migration) are free to diverge.
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Affiliation(s)
- Rafael R. de la Haba
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, Spain
| | - Paulina Corral
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, Spain
| | - Cristina Sánchez-Porro
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, Spain
| | - Carmen Infante-Domínguez
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, Spain
| | - Andrea M. Makkay
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, United States
| | - Mohammad A. Amoozegar
- 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, Sevilla, Spain
| | - R. Thane Papke
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, United States
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22
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Atanasova NS, Heiniö CH, Demina TA, Bamford DH, Oksanen HM. The Unexplored Diversity of Pleolipoviruses: The Surprising Case of Two Viruses with Identical Major Structural Modules. Genes (Basel) 2018; 9:genes9030131. [PMID: 29495629 PMCID: PMC5867852 DOI: 10.3390/genes9030131] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 02/16/2018] [Accepted: 02/20/2018] [Indexed: 01/01/2023] Open
Abstract
Extremely halophilic Archaea are the only known hosts for pleolipoviruses which are pleomorphic non-lytic viruses resembling cellular membrane vesicles. Recently, pleolipoviruses have been acknowledged by the International Committee on Taxonomy of Viruses (ICTV) as the first virus family that contains related viruses with different DNA genomes. Genomic diversity of pleolipoviruses includes single-stranded and double-stranded DNA molecules and their combinations as linear or circular molecules. To date, only eight viruses belong to the family Pleolipoviridae. In order to obtain more information about the diversity of pleolipoviruses, further isolates are needed. Here we describe the characterization of a new halophilic virus isolate, Haloarcula hispanica pleomorphic virus 4 (HHPV4). All pleolipoviruses and related proviruses contain a conserved core of approximately five genes designating this virus family, but the sequence similarity among different isolates is low. We demonstrate that over half of HHPV4 genome is identical to the genome of pleomorphic virus HHPV3. The genomic regions encoding known virion components are identical between the two viruses, but HHPV4 includes unique genetic elements, e.g., a putative integrase gene. The co-evolution of these two viruses demonstrates the presence of high recombination frequency in halophilic microbiota and can provide new insights considering links between viruses, membrane vesicles, and plasmids.
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Affiliation(s)
- Nina S Atanasova
- Research Programme on Molecular and Integrative Biosciences, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 9, FI-00014 Helsinki, Finland.
- Finnish Meteorological Institute; Erik Palménin aukio 1, FI-00101 Helsinki, Finland.
| | - Camilla H Heiniö
- Research Programme on Molecular and Integrative Biosciences, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 9, FI-00014 Helsinki, Finland.
| | - Tatiana A Demina
- Research Programme on Molecular and Integrative Biosciences, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 9, FI-00014 Helsinki, Finland.
| | - Dennis H Bamford
- Research Programme on Molecular and Integrative Biosciences, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 9, FI-00014 Helsinki, Finland.
| | - Hanna M Oksanen
- Research Programme on Molecular and Integrative Biosciences, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 9, FI-00014 Helsinki, Finland.
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23
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Bhatt HB, Gohel SD, Singh SP. Phylogeny, novel bacterial lineage and enzymatic potential of haloalkaliphilic bacteria from the saline coastal desert of Little Rann of Kutch, Gujarat, India. 3 Biotech 2018; 8:53. [PMID: 29354364 DOI: 10.1007/s13205-017-1075-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Accepted: 12/26/2017] [Indexed: 12/28/2022] Open
Abstract
This report describes cultivation-dependent diversity, phylogeny and enzymatic potential of the haloalkaliphilic bacteria isolated from the unvegetated desert soil of yet unexplored, saline desert of Little Rann of Kutch (LRK), India. The LRK is a unique ecosystem displaying a combination of Dry Rann and Wet Rann. A total of 25 bacteria were isolated and characterized on the basis of colony morphology, biochemical profile, sugar utilization, secretion of the extracellular enzymes and antibiotic sensitivity. Further, the identification and phylogenetic relatedness of 23 bacteria were established by the analysis of 16S rRNA gene sequences. The phylogenetic analysis indicated that the isolates belong to the phylum Firmicutes, comprising low G + C, Gram-positive bacteria, with different genera: Bacillus (~ 39%), Staphylococcus (~ 30%), Halobacillus (~ 13%), Virgibacillus (~ 13%), Oceanobacillus (~ 4%). Majority of the bacterial isolates produced proteases (30% isolates) followed by cellulases (24% isolates), CMCases (24% isolates) and amylases (20% isolates). Halobacillus, Virgibacillus and Bacillus predominantly produced hydrolases, while many produced multiple enzymes at high salinity and alkaline pH. Highest antibiotic resistance was observed against Ampicillin and Penicillin (32%) followed by Cefaclor (20%); Colistin, Cefoperazone and Cefotaxime (16%); Cefuroxime (12%); Gentamycin and Cefixime (8%); Erythromycin, Cefadroxil, Azithromycin, Co-trimoxazole, Amoxycillin, Norfloxacin, Cefpodoxime, Amikacin and Augmentin (4%). KJ1-10-99 and KJ1-10-93 representing < 97% of 16S rRNA gene sequence similarity belong to a novel lineage within the family Bacillaceae. Comparison of the phenogram and phylogram revealed the contradiction of the phenogram pattern and the phylogenetic placement of the isolates. The isolates belonging to same species have shown considerable phenotypic variation. The study on the cultivable haloalkaliphilic bacteria of an unexplored enigmatic niche reflects ecological and biotechnological significance.
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Affiliation(s)
- Hitarth B Bhatt
- UGC-CAS Department of Biosciences, Saurashtra University, Rajkot, Gujarat 360005 India
| | - Sangeeta D Gohel
- UGC-CAS Department of Biosciences, Saurashtra University, Rajkot, Gujarat 360005 India
| | - Satya P Singh
- UGC-CAS Department of Biosciences, Saurashtra University, Rajkot, Gujarat 360005 India
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24
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Microbial Diversity in Extreme Marine Habitats and Their Biomolecules. Microorganisms 2017; 5:microorganisms5020025. [PMID: 28509857 PMCID: PMC5488096 DOI: 10.3390/microorganisms5020025] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 05/02/2017] [Accepted: 05/11/2017] [Indexed: 11/17/2022] Open
Abstract
Extreme marine environments have been the subject of many studies and scientific publications. For many years, these environmental niches, which are characterized by high or low temperatures, high-pressure, low pH, high salt concentrations and also two or more extreme parameters in combination, have been thought to be incompatible to any life forms. Thanks to new technologies such as metagenomics, it is now possible to detect life in most extreme environments. Starting from the discovery of deep sea hydrothermal vents up to the study of marine biodiversity, new microorganisms have been identified, and their potential uses in several applied fields have been outlined. Thermophile, halophile, alkalophile, psychrophile, piezophile and polyextremophile microorganisms have been isolated from these marine environments; they proliferate thanks to adaptation strategies involving diverse cellular metabolic mechanisms. Therefore, a vast number of new biomolecules such as enzymes, polymers and osmolytes from the inhabitant microbial community of the sea have been studied, and there is a growing interest in the potential returns of several industrial production processes concerning the pharmaceutical, medical, environmental and food fields.
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25
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Sato Y, Fujiwara T, Kimura H. Expression and Function of Different Guanine-Plus-Cytosine Content 16S rRNA Genes in Haloarcula hispanica at Different Temperatures. Front Microbiol 2017; 8:482. [PMID: 28400752 PMCID: PMC5368182 DOI: 10.3389/fmicb.2017.00482] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 03/08/2017] [Indexed: 11/13/2022] Open
Abstract
The halophilic archaeon Haloarcula hispanica harbors three ribosomal RNA (rRNA) operons (rrnA, rrnB, and rrnC) that contain the 16S rRNA genes rrsA, rrsB, and rrsC, respectively. Although rrsB and rrsC (rrsBC) have almost identical sequences, the rrsA and rrsBC sequences differ by 5.4%, and they differ by 2.5% with respect to guanine-plus-cytosine content (PGC). The strong correlation between the typical growth temperatures of archaea and PGC of their 16S rRNA genes suggests that H. hispanica may harbor different 16S rRNA genes having different PGC to maintain rapid growth in a wide range of temperatures. We therefore performed reverse transcription-coupled quantitative PCR to assess expression levels of rrsA (PGC, 58.9%) and rrsBC (PGC, 56.4-56.5%) at various temperatures. The expression ratio of rrsA to rrsBC increased with culture temperature. Mutants with complete deletions of one or two of the three rRNA operons were constructed and their growth rates at different temperatures compared to that of the wild-type. The growth characteristics of the rRNA operon single-mutant strains were indistinguishable from the wild-type. The rRNA operon double-mutant strains maintained the same temperature range as wild-type but displayed reduced growth rates. In particular, the double-mutant strains grew much slower than wild-type at low temperature related to minimum growth temperature of the wild-type. On the other hand, at physiologically high temperatures the wild-type and the double-mutant strain which harbors only rrnA with high-PGCrrsA grew significantly faster than the double-mutant strain which harbors only rrnC with low-PGCrrsC. These findings suggest the importance of 16S rRNAs transcribed from rrsA with high-PGC in maintaining rapid growth of this halophilic archaeon at raised growth temperatures.
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Affiliation(s)
- Yu Sato
- Department of Environment and Energy Systems, Graduate School of Science and Technology, Shizuoka University Shizuoka, Japan
| | - Taketomo Fujiwara
- Department of Environment and Energy Systems, Graduate School of Science and Technology, Shizuoka UniversityShizuoka, Japan; Department of Biological Science, Faculty of Science, Shizuoka UniversityShizuoka, Japan
| | - Hiroyuki Kimura
- Department of Environment and Energy Systems, Graduate School of Science and Technology, Shizuoka UniversityShizuoka, Japan; Department of Geosciences, Faculty of Science, Shizuoka UniversityShizuoka, Japan; Research Institute of Green Science and Technology, Shizuoka UniversityShizuoka, Japan
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26
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Huang HH, Yu C. Clustering DNA sequences using the out-of-place measure with reduced n-grams. J Theor Biol 2016; 406:61-72. [PMID: 27375217 DOI: 10.1016/j.jtbi.2016.06.029] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Revised: 05/18/2016] [Accepted: 06/21/2016] [Indexed: 11/25/2022]
Abstract
The alignment-free n-gram based method with the out-of-place measures as the distance has been successfully applied to automatic text or natural languages categorization in real time. However, it is not clear about its performance and the selection of n for comparing genome sequences. Here we propose a symmetric version of the out-of-place measure and a new approach for finding the optimal range of n to construct a phylogenetic tree with the symmetric out-of-place measures. Our method is then applied to real genome sequence datasets. The resulting phylogenetic trees are matching with the standard biological classification. It shows that our proposed method is a very powerful tool for phylogenetic analysis in terms of both classification accuracy and computation efficiency.
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Affiliation(s)
- Hsin-Hsiung Huang
- Department of Statistics, University of Central Florida, Orlando, FL 32816, USA.
| | - Chenglong Yu
- Mind and Brain Theme, South Australian Health and Medical Research Institute, North Terrace, Adelaide, SA 5000, Australia; School of Medicine, Flinders University, Adelaide, SA 5001, Australia
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Antagonistic interactions and production of halocin antimicrobial peptides among extremely halophilic prokaryotes isolated from the solar saltern of Sfax, Tunisia. Extremophiles 2016; 20:363-74. [PMID: 27074936 DOI: 10.1007/s00792-016-0827-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 03/24/2016] [Indexed: 10/22/2022]
Abstract
Thirty-five extremely halophilic microbial strains isolated from crystallizer (TS18) and non-crystallizer (M1) ponds in the Sfax solar saltern in Tunisia were examined for their ability to exert antimicrobial activity. Antagonistic assays resulted in the selection of eleven strains that displayed such antimicrobial activity and they were further characterized. Three cases of cross-domain inhibition (archaea/bacteria or bacteria/archaea) were observed. Four archaeal strains exerted antimicrobial activity against several other strains. Three strains, for which several lines of evidence suggested the antimicrobial activity was, at least in part, due to peptide/protein agents (Halobacterium salinarum ETD5, Hbt. salinarum ETD8, and Haloterrigena thermotolerans SS1R12), were studied further. Optimal culture conditions for growth and antimicrobial production were determined. Using DNA amplification with specific primers, sequencing and RT-PCR analysis, Hbt. salinarum ETD5 and Hbt. salinarum ETD8 were shown to encode and express halocin S8, a hydrophobic antimicrobial peptide targeting halophilic archaea. Although the gene encoding halocin H4 was amplified from the genome of Htg. thermotolerans SS1R12, no transcript could be detected and the antimicrobial activity was most likely due to multiple antimicrobial compounds. This is also the first report that points to four different strains isolated from different geographical locations with the capacity to produce identical halocin S8 proteins.
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Finore I, Orlando P, Di Donato P, Leone L, Nicolaus B, Poli A. Nesterenkonia aurantiaca sp. nov., an alkaliphilic actinobacterium isolated from Antarctica. Int J Syst Evol Microbiol 2016; 66:1554-1560. [PMID: 26813578 DOI: 10.1099/ijsem.0.000917] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive, non-endospore-forming, haloalkaliphilic actinobacterium, strain CK5T, was isolated from a soil sample, collected at Cape King (Antarctica), and its taxonomic position was investigated by using a polyphasic approach. Cells were cocci with orange pigmentation, non-motile and grew optimally at 25 °C and pH 9.0-9.5 in the presence of 2 % (w/v) NaCl. Cellular membrane contained MK-7 (72 %) and MK-8 (28 %), and anteiso-C15 : 0 (64.8 %), iso-C16 : 0 (13.3 %), n-C17 : 0 (9.9 %), n-C16 : 0 (4.0 %), n-C14 : 0 (3.7 %) as major cellular fatty acids. The DNA G+C content was 64.8 mol%. Strain CK5T, based on the 16S rRNA gene sequence similarity, was most closely related to Nesterenkonia jeotgali JG-241T (99.5 %), Nesterenkonia sandarakina YIM 70009T (99.4 %), Nesterenkonia lutea YIM 70081T (99.4 %), Nesterenkonia halotolerans YIM 70084T (99.3 %), Nesterenkonia xinjiangensis YIM 70097T (97.2 %), Nesterenkonia flava CAAS 251T (97.1 %) and Nesterekonia aethiopica CCUG 48939T (97.1 %). Strain CK5T revealed 31 % DNA-DNA relatedness with respect to N. sandarakina DSM 15664T, 29 % with respect to N. jeotgali DSM 19081T, 10 % with respect to N. lutea DSM 15666T and 1 % with respect to N. halotolerans, DSM 15474T, N. xinjiangensis DSM 15475T, N. aethiopica DSM 17733T and N. flava DSM 19422T. On the basis of 16S rRNA gene sequences, DNA-DNA hybridization and chemotaxonomic characteristics, strain CK5T represents a novel species of the genus Nesterenkonia, for which the name Nesterenkonia aurantiaca sp. nov. is proposed. The type strain is CK5T ( = DSM 27373T = JCM 19723T).
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Affiliation(s)
- Ilaria Finore
- Consiglio Nazionale delle Ricerche (C.N.R.), Istituto di Chimica Biomolecolare (I.C.B.), Via Campi Flegrei 34, 80078 Pozzuoli, Naples, Italy
| | - Pierangelo Orlando
- Consiglio Nazionale delle Ricerche (C.N.R.), Istituto di Biochimica delle Proteine (I.B.P.), Via P. Castellino 111, 80124, Naples, Italy
| | - Paola Di Donato
- Consiglio Nazionale delle Ricerche (C.N.R.), Istituto di Chimica Biomolecolare (I.C.B.), Via Campi Flegrei 34, 80078 Pozzuoli, Naples, Italy.,University of Naples 'Parthenope', Department of Sciences and Technologies, Centro Direzionale, Naples, Italy
| | - Luigi Leone
- Consiglio Nazionale delle Ricerche (C.N.R.), Istituto di Chimica Biomolecolare (I.C.B.), Via Campi Flegrei 34, 80078 Pozzuoli, Naples, Italy
| | - Barbara Nicolaus
- Consiglio Nazionale delle Ricerche (C.N.R.), Istituto di Chimica Biomolecolare (I.C.B.), Via Campi Flegrei 34, 80078 Pozzuoli, Naples, Italy
| | - Annarita Poli
- Consiglio Nazionale delle Ricerche (C.N.R.), Istituto di Chimica Biomolecolare (I.C.B.), Via Campi Flegrei 34, 80078 Pozzuoli, Naples, Italy
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Corral P, de la Haba RR, Sánchez-Porro C, Ali Amoozegar M, Thane Papke R, Ventosa A. Halorubrum halodurans sp. nov., an extremely halophilic archaeon isolated from a hypersaline lake. Int J Syst Evol Microbiol 2015; 66:435-444. [PMID: 26537912 DOI: 10.1099/ijsem.0.000738] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two extremely halophilic archaea, strains Cb34T and C170, belonging to the genus Halorubrum, were isolated from the brine of the hypersaline lake Aran-Bidgol in Iran. Cells of the two strains were motile, pleomorphic rods, stained Gram-variable and produced red-pigmented colonies. Strains Cb34T and C170 required 25 % (w/v) salts, pH 7.0 and 37 °C for optimal growth under aerobic conditions; 0.3 M Mg2+ was required. Cells of both isolates were lysed in distilled water and hypotonic treatment with < 10 % NaCl provoked cell lysis. Phylogenetic analysis based on 16S rRNA gene sequence similarities showed that these two strains were closely related to Halorubrum cibi B31T (98.8 %) and other members of the genus Halorubrum. In addition, studies based on the rpoB' gene revealed that strains Cb34T and C170 are placed among the species of Halorubrum and are closely related to Halorubrum cibi B31T, with rpoB' gene sequence similarity less than or equal to 95.7 %. The polar lipid patterns of both strains consisted of phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate and sulfated mannosyl glucosyl diether. The DNA G+C content was 62.1-62.4 mol%. DNA-DNA hybridization studies confirmed that strains Cb34T and C170 constitute a distinct species. Data obtained in this study show that the two strains represent a novel species, for which the name Halorubrum halodurans sp. nov. is proposed. The type strain is Cb34T ( = CECT 8745T = IBRC-M 10233T).
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Affiliation(s)
- Paulina Corral
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
| | - Rafael R de la Haba
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
| | - Cristina Sánchez-Porro
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
| | - Mohammad Ali Amoozegar
- Department of Microbiology, Faculty of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
| | - R Thane Papke
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
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A diverse group of halophilic bacteria exist in Lunsu, a natural salt water body of Himachal Pradesh, India. SPRINGERPLUS 2015; 4:274. [PMID: 26090321 PMCID: PMC4469599 DOI: 10.1186/s40064-015-1028-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 05/12/2015] [Indexed: 11/10/2022]
Abstract
Five halophilic bacterial isolates namely SS1, SS2, SS3, SS5 and SS8 were isolated from soil sediments of Lunsu, a salty water body. All the bacterial isolates showed growth in LB medium containing up to 8.7% NaCl, pH 7-8 and at temperature range of 30-37°C. The bacterial isolates SS1 and SS3 require at least 3.8% NaCl for their growth, indicating their strict halophilic nature. Interestingly, bacterial isolates SS2, SS5 and SS8 but not SS1 and SS3 exhibited growth in medium supplemented with KCl. Accordingly, Na(+) and K(+) ions were detected at 1.39 and 0.0035%, respectively in Lunsu water. All the bacterial isolates were analyzed by random amplification of polymorphic DNA (RAPD) using four different random primers and produced PCR fragments ranging from 0.1 to 5 kb in size. Phylogenetic tree based on RAPD finger prints showed that SS1 and SS3 formed one group, while SS2 and SS5 formed the second group, whereas SS8 was out group. Sequence analysis of 16S rDNA identified SS1 and SS3 as Halobacillus trueperi, SS2 as Shewanella algae, SS5 as Halomonas venusta, and SS8 as Marinomonas sp. were deposited in GenBank with accession numbers of KM260166, KF751761, KF751760, KF751762 and KF751763, respectively. This is the first report on the presence of diverse halophilic bacteria in the foot hills of Himalayas.
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Archaeal viruses multiply: temporal screening in a solar saltern. Viruses 2015; 7:1902-26. [PMID: 25866903 PMCID: PMC4411682 DOI: 10.3390/v7041902] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Revised: 03/16/2015] [Accepted: 03/31/2015] [Indexed: 11/16/2022] Open
Abstract
Hypersaline environments around the world are dominated by archaea and their viruses. To date, very little is known about these viruses and their interaction with the host strains when compared to bacterial and eukaryotic viruses. We performed the first culture-dependent temporal screening of haloarchaeal viruses and their hosts in the saltern of Samut Sakhon, Thailand, during two subsequent years (2009, 2010). Altogether we obtained 36 haloarchaeal virus isolates and 36 archaeal strains, significantly increasing the number of known archaeal virus isolates. Interestingly, the morphological distribution of our temporal isolates (head-tailed, pleomorphic, and icosahedral membrane-containing viruses) was similar to the outcome of our previous spatial survey supporting the observations of a global resemblance of halophilic microorganisms and their viruses. Myoviruses represented the most abundant virus morphotype with strikingly broad host ranges. The other viral morphotypes (siphoviruses, as well as pleomorphic and icosahedral internal membrane-containing viruses) were more host-specific. We also identified a group of Halorubrum strains highly susceptible to numerous different viruses (up to 26). This high virus sensitivity, the abundance of broad host range viruses, and the maintenance of infectivity over a period of one year suggest constant interplay of halophilic microorganisms and their viruses within an extreme environment.
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Corral P, de la Haba RR, Sánchez-Porro C, Amoozegar MA, Papke RT, Ventosa A. Halorubrum persicum sp. nov., an extremely halophilic archaeon isolated from sediment of a hypersaline lake. Int J Syst Evol Microbiol 2015; 65:1770-1778. [PMID: 25744586 DOI: 10.1099/ijs.0.000175] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An extremely halophilic archaeon belonging to the genus Halorubrum, strain C49T, was isolated from sediment of the hypersaline lake Aran-Bidgol in Iran. Phylogenetic analysis based on 16S rRNA gene sequence similarities showed that strain C49T was closely related to Halorubrum saccharovorum JCM 8865T (99.5 %) and other species of the genus Halorubrum. Studies based on multilocus sequence analysis revealed that strain C49T is placed among the species of Halorubrum; the strain constituted a defined branch in comparison with the type strains of species of Halorubrum, while the 16S rRNA gene sequence divergence could not define the status of the newly isolated strain. For optimum growth, strain C49T required 20 % (w/v) salts at pH 7.0 and 37 °C under aerobic conditions. Mg2+ was not required. The cells were pleomorphic rods, motile and stained Gram-variable. Colonies of the strain were pink. Hypotonic treatment with <12 % NaCl provoked cell lysis. The polar lipid pattern of strain C49T consisted of phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester derived from both C20C20 and C20C25 archaeol, phosphatidylglycerol sulfate and sulfated mannosyl glucosyl diether. The DNA G+C content was 64.2 mol%. DNA-DNA hybridization studies and average nucleotide identity confirmed that strain C49T constitutes a distinct genospecies. Data obtained in this study show that strain C49T represents a novel species, for which the name Halorubrum persicum sp. nov. is proposed. The type strain is C49T ( = IBRC-M 10232T = JCM 30541T).
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Affiliation(s)
- Paulina Corral
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
| | - Rafael R de la Haba
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
| | - Cristina Sánchez-Porro
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
| | - Mohammad Ali Amoozegar
- Department of Microbiology, Faculty of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
| | - R Thane Papke
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
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Danis O, Ogan A, Tatlican P, Attar A, Cakmakci E, Mertoglu B, Birbir M. Preparation of poly(3-hydroxybutyrate-co-hydroxyvalerate) films from halophilic archaea and their potential use in drug delivery. Extremophiles 2015; 19:515-24. [PMID: 25663452 DOI: 10.1007/s00792-015-0735-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Accepted: 01/23/2015] [Indexed: 02/04/2023]
Abstract
Halophilic archaea offer a potential source for production of polyhydroxyalkanoates (PHAs). Hence, the experiments were carried out with five extremely halophilic archaeal isolates to determine the highest PHA-producing strain. PHA production of each isolates was separately examined in cheap carbon sources such as corn starch, sucrose, whey, apple, melon and tomato wastes. Corn starch was found to be a fairly effective substrate for PHA production. Among the strains studied here, the strain with the highest capability for PHA biosynthesis was found to be 1KYS1. Phylogenetic analysis based on 16S rRNA gene sequence comparison showed that 1KYS1 closely related to species of the genus Natrinema. The closest phylogenetic similarity was with the strain of Natrinema pallidum JCM 8980 (99 %). PHA content of 1KYS1 was about 53.14 % of the cell dry weight when starch was used as a carbon source. The formation of large and uniform PHA granules was confirmed by transmission electron microscopy and the biopolymer was identified as poly(3-hydroxybutyrate-co-hydroxyvalerate) (PHBV). PHBV produced by 1KYS1 was blended with low molar mass polyethylene glycol (PEG 300) to prepare biocompatible films for drug delivery. Rifampicin was used as a model drug and its release from PHBV films was investigated at pH 7.4, 37 °C. It was found that PHBV films obtained from 1KYS1 were very effective for drug delivery. In conclusion, PHBV of 1KYS1 may have a potential usage in drug delivery applications.
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Affiliation(s)
- Ozkan Danis
- Faculty of Arts and Sciences, Mamara University, 34722, Istanbul, Turkey,
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34
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Corral P, Corcelli A, Ventosa A. Halostagnicola bangensis sp. nov., an alkaliphilic haloarchaeon from a soda lake. Int J Syst Evol Microbiol 2014; 65:754-759. [PMID: 25479949 DOI: 10.1099/ijs.0.000006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An extremely haloalkaphilic archaeon, strain T26(T), belonging to the genus Halostagnicola, was isolated from sediment of the soda lake Bange in the region of Tibet, China. Phylogenetic analysis based on 16S rRNA gene sequence similarities showed that strain T26(T) was closely related to Halostagnicola alkaliphila 167-74(T) (98.4 %), Halostagnicola larsenii XH-48(T) (97.5 %) and Halostagnicola kamekurae 194-10(T) (96.8 %). Strain T26(T) grew optimally in media containing 25 % (w/v) salts, at pH 9.0 and 37 °C in aerobic conditions. Mg(2+) was not required for growth. The cells were motile, pleomorphic and Gram-stain-variable. Colonies of this strain were pink pigmented. Hypotonic treatment caused cell lysis. The polar lipids of the isolate consisted of C20C20 and C20C25 derivatives of phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and minor phospholipids components. Glycolipids were not detected, in contrast to the two neutrophilic species of this genus. The genomic DNA G+C content of strain T26(T) was 60.1 mol% and DNA-DNA hybridization showed a relatedness of 19 and 17 % with Halostagnicola alkaliphila CECT 7631(T) and Halostagnicola larsenii CECT 7116(T), respectively. The comparison of 16S rRNA gene sequences, detailed phenotypic characterization, polar lipid profile and DNA-DNA hybridization studies revealed that strain T26(T) belongs to the genus Halostagnicola, and represents a novel species for which the name Halostagnicola bangensis sp. nov. is proposed. The type strain is T26(T) ( = CECT 8219(T) = IBRC-M 10759(T) = JCM 18750(T)).
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Affiliation(s)
- Paulina Corral
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
| | - Angela Corcelli
- Department of Basic Medical Sciences, Neurosciences and Sensory Organs, University of Bari Aldo Moro, 70124 Bari, Italy
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
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Jaakkola ST, Zerulla K, Guo Q, Liu Y, Ma H, Yang C, Bamford DH, Chen X, Soppa J, Oksanen HM. Halophilic archaea cultivated from surface sterilized middle-late eocene rock salt are polyploid. PLoS One 2014; 9:e110533. [PMID: 25338080 PMCID: PMC4206341 DOI: 10.1371/journal.pone.0110533] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Accepted: 09/11/2014] [Indexed: 11/24/2022] Open
Abstract
Live bacteria and archaea have been isolated from several rock salt deposits of up to hundreds of millions of years of age from all around the world. A key factor affecting their longevity is the ability to keep their genomic DNA intact, for which efficient repair mechanisms are needed. Polyploid microbes are known to have an increased resistance towards mutations and DNA damage, and it has been suggested that microbes from deeply buried rock salt would carry several copies of their genomes. Here, cultivable halophilic microbes were isolated from a surface sterilized middle-late Eocene (38–41 million years ago) rock salt sample, drilled from the depth of 800 m at Yunying salt mine, China. Eight unique isolates were obtained, which represented two haloarchaeal genera, Halobacterium and Halolamina. We used real-time PCR to show that our isolates are polyploid, with genome copy numbers of 11–14 genomes per cell in exponential growth phase. The ploidy level was slightly downregulated in stationary growth phase, but the cells still had an average genome copy number of 6–8. The polyploidy of halophilic archaea living in ancient rock salt might be a factor explaining how these organisms are able to overcome the challenge of prolonged survival during their entombment.
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Affiliation(s)
- Salla T. Jaakkola
- Institute of Biotechnology and Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Karolin Zerulla
- Institute for Molecular Biology, Goethe-University Frankfurt am Main, Frankfurt am Main, Germany
| | - Qinggong Guo
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, Hubei, People's Republic of China
| | - Ying Liu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, Hubei, People's Republic of China
| | - Hongling Ma
- Institute of Rock and Soil Mechanics, The Chinese Academy of Sciences, Wuhan, Hubei, People's Republic of China
| | - Chunhe Yang
- Institute of Rock and Soil Mechanics, The Chinese Academy of Sciences, Wuhan, Hubei, People's Republic of China
| | - Dennis H. Bamford
- Institute of Biotechnology and Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Xiangdong Chen
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, Hubei, People's Republic of China
- * E-mail: (HMO); (JS); (XC)
| | - Jörg Soppa
- Institute for Molecular Biology, Goethe-University Frankfurt am Main, Frankfurt am Main, Germany
- * E-mail: (HMO); (JS); (XC)
| | - Hanna M. Oksanen
- Institute of Biotechnology and Department of Biosciences, University of Helsinki, Helsinki, Finland
- * E-mail: (HMO); (JS); (XC)
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Piubeli F, Grossman MJ, Fantinatti-Garboggini F, Durrant LR. Phylogenetic analysis of the microbial community in hypersaline petroleum produced water from the Campos Basin. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2014; 21:12006-12016. [PMID: 24920265 DOI: 10.1007/s11356-014-3155-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Accepted: 06/04/2014] [Indexed: 06/03/2023]
Abstract
In this work the archaea and eubacteria community of a hypersaline produced water from the Campos Basin that had been transported and discharged to an onshore storage facility was evaluated by 16S recombinant RNA (rRNA) gene sequence analysis. The produced water had a hypersaline salt content of 10 (w/v), had a carbon oxygen demand (COD) of 4,300 mg/l and contains phenol and other aromatic compounds. The high salt and COD content and the presence of toxic phenolic compounds present a problem for conventional discharge to open seawater. In previous studies, we demonstrated that the COD and phenolic content could be largely removed under aerobic conditions, without dilution, by either addition of phenol degrading Haloarchaea or the addition of nutrients alone. In this study our goal was to characterize the microbial community to gain further insight into the persistence of reservoir community members in the produced water and the potential for bioremediation of COD and toxic contaminants. Members of the archaea community were consistent with previously identified communities from mesothermic reservoirs. All identified archaea were located within the phylum Euryarchaeota, with 98 % being identified as methanogens while 2 % could not be affiliated with any known genus. Of the identified archaea, 37 % were identified as members of the strictly carbon-dioxide-reducing genus Methanoplanus and 59 % as members of the acetoclastic genus Methanosaeta. No Haloarchaea were detected, consistent with the need to add these organisms for COD and aromatic removal. Marinobacter and Halomonas dominated the eubacterial community. The presence of these genera is consistent with the ability to stimulate COD and aromatic removal with nutrient addition. In addition, anaerobic members of the phyla Thermotogae, Firmicutes, and unclassified eubacteria were identified and may represent reservoir organisms associated with the conversion hydrocarbons to methane.
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Affiliation(s)
- Francine Piubeli
- Department of Food Science (DCA), Food Engineering Faculty (FEA), University of Campinas (UNICAMP), Rua Monteiro Lobato, 80, Campinas, SP, CEP 13083-862, Brazil
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Halomonas smyrnensis sp. nov., a moderately halophilic, exopolysaccharide-producing bacterium. Int J Syst Evol Microbiol 2013; 63:10-18. [DOI: 10.1099/ijs.0.037036-0] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Four Gram-negative, moderately halophilic, exopolysaccharide-producing strains, designated AAD6T, AAD4, AAD17 and AAD21, were isolated from Çamaltı Saltern Area, a wildlife reserve in Sasalı, İzmir province located in the Aegean Region of Turkey. The isolates grew at an optimum NaCl concentration of 10 % (w/v). The major cellular fatty acids were C16 : 0, C18 : 1ω7c, C16 : 1ω7c and C12 : 0 3OH, respectively and the predominant lipoquinone was ubiquinone Q-9. The G+C content of the genomic DNA of strains AAD6T, AAD4, AAD17 and AAD21 was 63.0, 63.3, 62.8 and 62.6 mol%, respectively. Comparative 16S rRNA gene sequence studies showed that the isolates belonged to the genus
Halomonas
. The DNA–DNA hybridization mean values between the representative strain AAD6T and the closely related species
Halomonas salina
DSM 5928T,
Halomonas halophila
DSM 4770T,
Halomonas maura
DSM 13445T,
Halomonas organivorans
DSM 16226T,
Halomonas elongata
DSM 2581T,
Halomonas koreensis
JCM 12237T and
Halomonas nitroreducens
LMG 24185, were 40.8, 39.6, 24.2, 23.3, 12.6, 14.5 and 12.2 %, respectively. Based on these data the strains represent a novel species of the genus
Halomonas
for which the name Halomonas smyrnensis sp. nov. is proposed. The type strain is AAD6T ( = DSM 21644T = JCM 15723T).
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Kim JS, Makama M, Petito J, Park NH, Cohan FM, Dungan RS. Diversity of Bacteria and Archaea in hypersaline sediment from Death Valley National Park, California. Microbiologyopen 2012; 1:135-48. [PMID: 22950020 PMCID: PMC3426423 DOI: 10.1002/mbo3.20] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2012] [Revised: 02/21/2012] [Accepted: 02/23/2012] [Indexed: 02/01/2023] Open
Abstract
The objective of this study was to phylogenetically analyze microorganisms from the domains Bacteria and Archaea in hypersaline sediment from Death Valley National Park. Using domain-specific primers, a region of the 16S rRNA gene was amplified using polymerase chain reaction (PCR), and the product was subsequently used to create a clone library. A total of 243 bacterial clones, 99 archaeal clones, and 209 bacterial isolates were examined. The 243 clones from Bacteria were affiliated with the following groups: the Bacilli (59 clones) and Clostridia (1) of the Firmicutes, Bacteroidetes (90), Proteobacteria (27), Cyanobacteria (18), Gemmatimonadetes (41), candidate division OP1 (5), Actinobacteria (1), and the Deinococcus-Thermus division (1). Within the class Bacilli, 46 of 59 clones were tentatively identified as 10 unclassified species. The majority of bacterial isolates (130 of 209) were more closely related to the Bacillus subtilis–B. licheniformis clade than to any other recognized taxon, and an Ecotype Simulation analysis of B. subtilis relatives identified four previously unknown ecotypes. Several new genera were discovered within the Bacteroidetes (4) and the Gemmatimonadetes (2). Of the 99 archaeal clones, 94 were tentatively identified as belonging to 3 new genera within the Halobacteriaceae; other clones represented novel species within each of 4 established genera.
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Virion architecture unifies globally distributed pleolipoviruses infecting halophilic archaea. J Virol 2012; 86:5067-79. [PMID: 22357279 DOI: 10.1128/jvi.06915-11] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Our understanding of the third domain of life, Archaea, has greatly increased since its establishment some 20 years ago. The increasing information on archaea has also brought their viruses into the limelight. Today, about 100 archaeal viruses are known, which is a low number compared to the numbers of characterized bacterial or eukaryotic viruses. Here, we have performed a comparative biological and structural study of seven pleomorphic viruses infecting extremely halophilic archaea. The pleomorphic nature of this novel virion type was established by sedimentation analysis and cryo-electron microscopy. These nonlytic viruses form virions characterized by a lipid vesicle enclosing the genome, without any nucleoproteins. The viral lipids are unselectively acquired from host cell membranes. The virions contain two to three major structural proteins, which either are embedded in the membrane or form spikes distributed randomly on the external membrane surface. Thus, the most important step during virion assembly is most likely the interaction of the membrane proteins with the genome. The interaction can be driven by single-stranded or double-stranded DNA, resulting in the virions having similar architectures but different genome types. Based on our comparative study, these viruses probably form a novel group, which we define as pleolipoviruses.
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Corral P, Gutiérrez MC, Castillo AM, Domínguez M, Lopalco P, Corcelli A, Ventosa A. Natronococcus roseus sp. nov., a haloalkaliphilic archaeon from a hypersaline lake. Int J Syst Evol Microbiol 2012; 63:104-108. [PMID: 22345136 DOI: 10.1099/ijs.0.036558-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel halophilic archaeon, strain CG-1(T), belonging to the genus Natronococcus was isolated from sediment of the soda lake Chagannor in Inner Mongolia, China. The colonies of this strain were pink pigmented, the intensity of the colour decreased when the cells grew at salt saturation levels. The cells were non-motile cocci and strictly aerobic. Hypotonic treatment did not cause cell lysis, even in distilled water. Strain CG-1(T) grew at 15-30.0 % (w/v) NaCl and at 30-50 °C and pH 8.0-11.0, with optimal growth occurring at 25-30 % (w/v) NaCl, 37-45 °C and pH 9-9.5. MgCl(2) was not required for growth. Strain CG-1(T) was most closely related to the type strains of Natronococcus amylolyticus Ah-36(T), Natronococcus jeotgali B1(T) and Natronococcus occultus SP4(T), with which it shared 98.4 %, 96.2 and 95.7 % 16S rRNA gene sequence similarity, respectively. The polar lipids consisted of C(20)C(20) and C(20)C(25) derivatives of phosphatidylglycerol (PG), phosphatidylglycerol phosphate methyl ester (PGP-Me) and minor phospholipid components. No glycolipids were detected. The DNA G+C content of strain CG-1(T) was 62.1 mol%. DNA-DNA hybridization with N. amylolyticus DSM 10524(T), phylogenetically the most closely related species, was 39 %; this value showed that strain CG-1(T) constituted a different genospecies. The comparison of 16S rRNA gene sequences, detailed phenotypic characterization, polar lipid profile and DNA-DNA hybridization studies revealed that strain CG-1(T) belongs to the genus Natronococcus and constitutes a novel species for which the name Natronococcus roseus sp. nov. is proposed. The type strain is CG-1(T) (=CECT 7984(T)=IBRC-M 10656(T)=JCM 17958(T)).
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Affiliation(s)
- P Corral
- 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
| | - A M Castillo
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
| | - M Domínguez
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
| | - P Lopalco
- Institute for Microelectronics and Microsystems, National Research Council (IMM-CNR) and Sens&Micro LAB, 73100 Lecce, Italy
| | - A Corcelli
- Department of Medical Biochemistry, Medical Biology and Medical Physics, University of Bari, 70124 Bari, Italy
| | - A Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
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Chan RH, Chan TH, Yeung HM, Wang RW. Composition vector method based on maximum entropy principle for sequence comparison. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2012; 9:79-87. [PMID: 21383416 DOI: 10.1109/tcbb.2011.45] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The composition vector (CV) method is an alignment-free method for sequence comparison. Because of its simplicity when compared with multiple sequence alignment methods, the method has been widely discussed lately; and some formulas based on probabilistic models, like Hao’s and Yu’s formulas, have been proposed. In this paper, we improve these formulas by using the entropy principle which can quantify the nonrandomness occurrence of patterns in the sequences. More precisely, existing formulas are used to generate a set of possible formulas from which we choose the one that maximizes the entropy. We give the closed-form solution to the resulting optimization problem. Hence, from any given CV formula, we can find the corresponding one that maximizes the entropy. In particular, we show that Hao’s formula is itself maximizing the entropy and we derive a new entropy-maximizing formula from Yu’s formula. We illustrate the accuracy of our new formula by using both simulated and experimental data sets. For the simulated data sets, our new formula gives the best consensus and significant values for three different kinds of evolution models. For the data set of tetrapod 18S rRNA sequences, our new formula groups the clades of bird and reptile together correctly, where Hao’s and Yu’s formulas failed. Using real data sets with different sizes, we show that our formula is more accurate than Hao’s and Yu’s formulas even for small data sets.
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Atanasova NS, Roine E, Oren A, Bamford DH, Oksanen HM. Global network of specific virus-host interactions in hypersaline environments. Environ Microbiol 2011; 14:426-40. [PMID: 22003883 DOI: 10.1111/j.1462-2920.2011.02603.x] [Citation(s) in RCA: 109] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Hypersaline environments are dominated by archaea and bacteria and are almost entirely devoid of eukaryotic organisms. In addition, hypersaline environments contain considerable numbers of viruses. Currently, there is only a limited amount of information about these haloviruses. The ones described in detail mostly resemble head-tail bacteriophages, whereas observations based on direct microscopy of the hypersaline environmental samples highlight the abundance of non-tailed virus-like particles. Here we studied nine spatially distant hypersaline environments for the isolation of new halophilic archaea (61 isolates), halophilic bacteria (24 isolates) and their viruses (49 isolates) using a culture-dependent approach. The obtained virus isolates approximately double the number of currently described archaeal viruses. The new isolates could be divided into three tailed and two non-tailed virus morphotypes, suggesting that both types of viruses are widely distributed and characteristic for haloarchaeal viruses. We determined the sensitivity of the hosts against all isolated viruses. It appeared that the host ranges of numerous viruses extend to hosts in distant locations, supporting the idea that there is a global exchange of microbes and their viruses. It suggests that hypersaline environments worldwide function like a single habitat.
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Affiliation(s)
- Nina S Atanasova
- Institute of Biotechnology and Department of Biosciences, University of Helsinki, Viikinkaari 5, Helsinki, Finland
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Boutaiba S, Hacene H, Bidle KA, Maupin-Furlow JA. Microbial Diversity of the Hypersaline Sidi Ameur and Himalatt Salt Lakes of the Algerian Sahara. JOURNAL OF ARID ENVIRONMENTS 2011; 75:909-916. [PMID: 21909172 PMCID: PMC3167213 DOI: 10.1016/j.jaridenv.2011.04.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Microbial populations within hypersaline lakes often exhibit high activities of photosynthesis, dissimilatory sulphate reduction and other processes and, thus, can have profound impacts on biogeochemical cycles of carbon, nitrogen, sulphur and other important elements within arid lands. To further understand these types of ecosystems, the physicochemical and biological properties of Sidi Ameur and Himalatt Salt Lakes in the Algerian Sahara were examined and compared. Both lakes were relatively neutral in pH (7.2 to 7.4) and high in salt, at 12% and 20 % (w/v) salinity for Himalatt and Sidi Ameur Lakes, respectively, with dominant ions of sodium and chloride. The community compositions of microbes from all three domains (Bacteria, Archaea and Eukarya) were surveyed through the use of 16S and 18S ribosomal gene amplification and clone library clustering using amplified ribosomal DNA restriction analysis (ARDRA) in conjunction with DNA sequencing and analysis. A high level of microbial diversity, particularly among the bacteria of the Himalatt Salt Lake and archaea of Sidi Ameur Lake, was found within these environments. Representatives from all known halophilic bacterial phyla as well as 6 different genera of halophilic archaea were identified. Moreover, several apparently novel phylotypes among both archaea and bacteria were revealed.
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Affiliation(s)
- Saad Boutaiba
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida 32611-0700
- Laboratory of Research on the Arid Area, FSB-Biologic Science Faculty, University of the Sciences and Technology H. Boumediene, BP no. 32, El-Alia, Algiers, Algeria
| | - Hocine Hacene
- Laboratory of Research on the Arid Area, FSB-Biologic Science Faculty, University of the Sciences and Technology H. Boumediene, BP no. 32, El-Alia, Algiers, Algeria
| | - Kelly A. Bidle
- Department of Biology, Rider University, Lawrenceville, New Jersey 08648
| | - Julie A. Maupin-Furlow
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida 32611-0700
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Trigui H, Masmoudi S, Brochier-Armanet C, Maalej S, Dukan S. Characterization of Halorubrum sfaxense sp. nov., a New Halophilic Archaeon Isolated from the Solar Saltern of Sfax in Tunisia. Int J Microbiol 2011; 2011:240191. [PMID: 21754938 PMCID: PMC3132631 DOI: 10.1155/2011/240191] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2010] [Revised: 03/02/2011] [Accepted: 03/31/2011] [Indexed: 11/18/2022] Open
Abstract
An extremely halophilic archaeon, strain ETD6, was isolated from a marine solar saltern in Sfax, Tunisia. Analysis of the 16S rRNA gene sequence showed that the isolate was phylogenetically related to species of the genus Halorubrum among the family Halobacteriaceae, with a close relationship to Hrr. xinjiangense (99.77% of identity). However, value for DNA-DNA hybridization between strain ETD6 and Hrr.xinjiangense were about 24.5%. The G+C content of the genomic DNA was 65.1 mol% (T(m)). Strain ETD6 grew in 15-35% (w/v) NaCl. The temperature and pH ranges for growth were 20-55°C and 6-9, respectively. Optimal growth occurred at 25% NaCl, 37°C, and pH 7.4. The results of the DNA hybridization against Hrr. xinjiangense and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain ETD6 from other Hrr. species. Therefore, strain ETD6 represents a novel species of the genus Halorubrum, for which the name Hrr. sfaxense sp. nov. is proposed. The Genbank EMBL-EBI accession number is GU724599.
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Affiliation(s)
- Hana Trigui
- Laboratoire de Chimie Bactérienne, Aix Marseille Université, UPR 9043-CNRS, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
- Laboratoire de Microbiologie, Faculté des Sciences de Sfax, BP802, Sfax 3000, Tunisia
| | - Salma Masmoudi
- Laboratoire de Microbiologie, Faculté des Sciences de Sfax, BP802, Sfax 3000, Tunisia
| | - Céline Brochier-Armanet
- Laboratoire de Chimie Bactérienne, Aix Marseille Université, UPR 9043-CNRS, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
| | - Sami Maalej
- Laboratoire de Microbiologie, Faculté des Sciences de Sfax, BP802, Sfax 3000, Tunisia
| | - Sam Dukan
- Laboratoire de Chimie Bactérienne, Aix Marseille Université, UPR 9043-CNRS, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
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Halorubrum aquaticum sp. nov., an archaeon isolated from hypersaline lakes. Int J Syst Evol Microbiol 2011; 61:1144-1148. [DOI: 10.1099/ijs.0.025015-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two halophilic archaea, strains EN-2T and SH-4, were isolated from the saline lakes Erliannor and Shangmatala, respectively, in Inner Mongolia, China. Cells were strictly aerobic, motile rods. Colonies were red. Strains EN-2T and SH-4 were able to grow at 25–50 °C (optimum 35–40 °C), with 2.5–5.0 M NaCl (optimum 3.4 M NaCl) and at pH 6.0–9.0 (optimum pH 7.5). MgCl2 was not required for growth. Cells lysed in distilled water and the lowest NaCl concentration that prevented cell lysis was 12 % (w/v). On the basis of 16S rRNA gene sequence analysis, strains EN-2T and SH-4 were closely related to Halorubrum cibi B31T (97.9 and 98.0 % similarity, respectively), Hrr. tibetense 8W8T (97.3 and 97.7 %), Hrr. alkaliphilum DZ-1T (96.8 and 97.1 %), Hrr. luteum CGSA15T (96.8 and 97.0 %) and Hrr. lipolyticum 9-3T (96.8 and 97.0 %). DNA–DNA hybridization showed that strains EN-2T and SH-4 did not belong to the same species as any of these strains (≤45 % DNA–DNA relatedness) but that they are members of the same species (>70 % DNA–DNA relatedness). Polar lipid analysis revealed that strains EN-2T and SH-4 contained phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, sulfated diglycosyl diethers and several unidentified glycolipids. The DNA G+C content of both isolates was 62.1 mol%. It was concluded that strains EN-2T and SH-4 represent a novel species of the genus Halorubrum, for which the name Halorubrum aquaticum sp. nov. is proposed. The type strain is EN-2T ( = CECT 7174T = CGMCC 1.6377T = JCM 14031T).
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Jeyanathan J, Kirs M, Ronimus RS, Hoskin SO, Janssen PH. Methanogen community structure in the rumens of farmed sheep, cattle and red deer fed different diets. FEMS Microbiol Ecol 2011; 76:311-26. [DOI: 10.1111/j.1574-6941.2011.01056.x] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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Pasić L, Kovce B, Sket B, Herzog-Velikonja B. Diversity of microbial communities colonizing the walls of a Karstic cave in Slovenia. FEMS Microbiol Ecol 2010; 71:50-60. [PMID: 19817862 DOI: 10.1111/j.1574-6941.2009.00789.x] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Karstic cave systems in Slovenia receive substantial amounts of organic input from adjacent forest and freshwater systems. These caves host microbial communities that consist of distinct small colonies differing in colour and shape. Visible to the naked eye, the colonies cover cave walls and are strewn with light-reflecting water droplets. In this study, the diversity of prokaryotes constituting these unusual microbial communities in Pajsarjeva jama cave was examined. A molecular survey based on small subunit rRNA diversity showed a high diversity within the Bacteria, while members of Archaea were not recovered. A total of eight bacterial phyla were detected. The application of various species richness estimators confirmed the diverse nature of the microbial community sample. Members of Gammaproteobacteria were most abundant in the clone libraries constructed and were followed in abundance by members of Actinobacteria and Nitrospira. In addition, members of Alphaproteobacteria, Betaproteobacteria and Deltaproteobacteria as well as Acidobacteria, Verrucomicrobia, Planctomycetes, Chloroflexi and Gemmatimonadetes were identified in clone libraries. The high number of clones most closely related to environmental 16S rRNA gene clones showed the broad spectrum of unknown and yet to be cultivated microorganisms inhabiting these cave systems.
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Affiliation(s)
- Lejla Pasić
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia.
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49
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Namwong S, Tanasupawat S, Kudo T, Itoh T. Haloarcula salaria sp. nov. and Haloarcula tradensis sp. nov., isolated from salt in Thai fish sauce. Int J Syst Evol Microbiol 2010; 61:231-236. [PMID: 20207809 DOI: 10.1099/ijs.0.021790-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two red-pigmented, strictly aerobic, pleomorphic rod-shaped and extremely halophilic archaea, designated strains HST01-2R(T) and HST03(T), were isolated from salt in a fish sauce sample from Thailand. The novel strains grew optimally at 37 °C, pH 7.0, and in the presence of 20-25 % (w/v) NaCl. The DNA G+C contents of the isolates were 61.6-62.2 mol%. Phylogenetic analysis based on a comparison of 16S rRNA gene sequences revealed that strains HST01-2R(T) and HST03(T) were placed in the radiation of species of the genus Haloarcula. The chemotaxonomic properties of the two strains, i.e. the presence of MK-8 and MK-8(H(2)) as the major menaquinone components and C(20)C(20) derivatives of phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate and a triglycosyl diether as major polar lipids, supported the assignment of the two strains to the genus Haloarcula. Nevertheless, several phenotypic features and the low DNA-DNA relatedness between the two strains and related species of the genus Haloarcula (13.4-46.9 %) enabled the strains to be distinguished from each other and from recognized species. Therefore, strains HST01-2R(T) and HST03(T) represent two novel species in the genus Haloarcula, for which the names Haloarcula salaria sp. nov. and Haloarcula tradensis sp. nov. are proposed, respectively. The type strains are HST01-2R(T) (=BCC 40029(T)=JCM 15759(T)=PCU 313(T)) and HST03(T) (=BCC 40030(T)=JCM 15760(T)=PCU 314(T)).
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Affiliation(s)
- Sirilak Namwong
- Department of Biotechnology, Faculty of Science and Technology, Suan Sunandha Rajabhat University, Bangkok 10300, Thailand
| | - Somboon Tanasupawat
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Takuji Kudo
- Japan Collection of Microorganisms, RIKEN BioResource Center, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Takashi Itoh
- Japan Collection of Microorganisms, RIKEN BioResource Center, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
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Gutiérrez MC, Castillo AM, Corral P, Minegishi H, Ventosa A. Natronorubrum sediminis sp. nov., an archaeon isolated from a saline lake. Int J Syst Evol Microbiol 2009; 60:1802-1806. [PMID: 19767366 DOI: 10.1099/ijs.0.015602-0] [Citation(s) in RCA: 19] [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
Two novel haloalkaliphilic archaea, strains CG-6T and CG-4, were isolated from sediment of the hypersaline Lake Chagannor in Inner Mongolia, China. Cells of the two strains were pleomorphic, non-motile and strictly aerobic. They required at least 2.5 M NaCl for growth, with optimum growth at 3.4 M NaCl. They grew at pH 8.0-11.0, with optimum growth at pH 9.0. Hypotonic treatment with less than 1.5 M NaCl caused cell lysis. The two strains had similar polar lipid compositions, possessing C20C20 and C20C25 derivatives of phosphatidylglycerol and phosphatidylglycerol phosphate methyl ester. No glycolipids were detected. Comparison of 16S rRNA gene sequences and morphological features placed them in the genus Natronorubrum. 16S rRNA gene sequence similarities to strains of recognized species of the genus Natronorubrum were 96.2-93.8%. Detailed phenotypic characterization and DNA-DNA hybridization studies revealed that the two strains belong to a novel species in the genus Natronorubrum, for which the name Natronorubrum sediminis sp. nov. is proposed; the type strain is CG-6T (=CECT 7487T =CGMCC 1.8981T =JCM 15982T).
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Affiliation(s)
- M C Gutiérrez
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
| | - A M Castillo
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
| | - P Corral
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
| | - H Minegishi
- Bio-Nano Electronics Research Center, Toyo University, 2100 Kujirai, Kawagoe, Saitama 350-8585, Japan
| | - A Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
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