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León MJ, Sánchez-Porro C, de la Haba RR, Pfeiffer F, Dyall-Smith M, Oksanen HM, Ventosa A. Halobacterium hubeiense sp. nov., a haloarchaeal species isolated from a bore core drilled in Hubei Province, PR China. Int J Syst Evol Microbiol 2024; 74:006296. [PMID: 38512754 PMCID: PMC11004503 DOI: 10.1099/ijsem.0.006296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 03/05/2024] [Indexed: 03/23/2024] Open
Abstract
Eight colonies of live microbes were isolated from an extensively surface-sterilized halite sample which had been retrieved from a depth of 2000 m from a salt mine in the Qianjiang Depression, Hubei Province, PR China. The eight colonies, obtained after 4 weeks of incubation, were named JI20-1T-JI20-8 and JI20-1T was selected as the type strain. The strains have been previously described, including a genomic analysis based on the complete genome for strain JI20-1T and draft genomes for the other strains. In that study, the name Halobacterium hubeiense was suggested, based on the location of the drilling site. Previous phylogenomic analysis showed that strain JI20-1T is most closely related to the Permian isolate Halobacterium noricense from Alpine rock salt. The orthologous average nucleotide identity (orthoANI) and digital DNA-DNA hybridization (dDDH) percentages between the eight strains are 100-99.6 % and 99.8-96.4 %, respectively. The orthoANI and dDDH values of these strains with respect to the type strains of species of the genus Halobacterium are 89.9-78.2 % and 37.3-21.6 %, respectively, supporting their placement in a novel extremely halophilic archaeal species. The phylogenomic tree based on the comparison of sequences of 632 core-orthologous proteins confirmed the novel species status for these haloarchaea. The polar lipid profile includes phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate, and sulfated galactosyl mannosyl galactosyl glucosyl diether, a profile compatible with that of Halobacterium noricense. Based on genomic, phenotypic, and chemotaxonomic characterization, we propose strain JI20-1T (=DSM 114402T = HAMBI 3616T) as the type strain of a novel species in the genus Halobacterium, with the name Halobacterium hubeiense sp. nov.
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Affiliation(s)
- María José León
- 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
| | - Rafael R. de la Haba
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
| | - Friedhelm Pfeiffer
- Computational Biology Group, Max-Planck-Institute of Biochemistry, Martinsried, Germany
- Biology II, Ulm University, 89069 Ulm, Germany
| | - Mike Dyall-Smith
- Computational Biology Group, Max-Planck-Institute of Biochemistry, Martinsried, Germany
- Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, VIC 3052, Australia
| | - Hanna M. Oksanen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
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Kothe CI, Monnet C, Irlinger F, Virsolvy M, Frühling A, Neumann-Schaal M, Wolf J, Renault P. Halomonas citrativorans sp. nov., Halomonas casei sp. nov. and Halomonas colorata sp. nov., isolated from French cheese rinds. Int J Syst Evol Microbiol 2024; 74. [PMID: 38265421 DOI: 10.1099/ijsem.0.006234] [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: 01/25/2024] Open
Abstract
Eight Gram-stain-negative bacterial strains were isolated from cheese rinds sampled in France. On the basis of 16S rRNA gene sequence analysis, all isolates were assigned to the genus Halomonas. Phylogenetic investigations, including 16S rRNA gene studies, multilocus sequence analysis, reconstruction of a pan-genome phylogenetic tree with the concatenated core-genome content and average nucleotide identity (ANI) calculations, revealed that they constituted three novel and well-supported clusters. The closest relative species, determined using the whole-genome sequences of the strains, were Halomonas zhanjiangensis for two groups of cheese strains, sharing 82.4 and 93.1 % ANI, and another cluster sharing 92.2 % ANI with the Halomonas profundi type strain. The strains isolated herein differed from the previously described species by ANI values <95 % and several biochemical, enzymatic and colony characteristics. The results of phenotypic, phylogenetic and chemotaxonomic analyses indicated that the isolates belonged to three novel Halomonas species, for which the names Halomonas citrativorans sp. nov., Halomonas casei sp. nov. and Halomonas colorata sp. nov. are proposed, with isolates FME63T (=DSM 113315T=CIRM-BIA2430T=CIP 111880T=LMG 32013T), FME64T (=DSM 113316T=CIRM-BIA2431T=CIP 111877T=LMG 32015T) and FME66T (=DSM 113318T=CIRM-BIA2433T=CIP 111876T=LMG 32014T) as type strains, respectively.
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Affiliation(s)
- Caroline Isabel Kothe
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France
- Sustainable Food Innovation Group, The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Christophe Monnet
- Université Paris-Saclay, INRAE, AgroParisTech, UMR SayFood, 91120 Palaiseau, France
| | - Françoise Irlinger
- Université Paris-Saclay, INRAE, AgroParisTech, UMR SayFood, 91120 Palaiseau, France
| | - Mathieu Virsolvy
- Sustainable Food Innovation Group, The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Anja Frühling
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, D-38124 Braunschweig, Germany
| | - Meina Neumann-Schaal
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, D-38124 Braunschweig, Germany
| | - Jacqueline Wolf
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, D-38124 Braunschweig, Germany
| | - Pierre Renault
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France
- Sustainable Food Innovation Group, The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
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Lee SD, Kim IS. Larsenimonas rhizosphaerae sp. nov., isolated from a tidal mudflat. Int J Syst Evol Microbiol 2023; 73. [PMID: 37339061 DOI: 10.1099/ijsem.0.005930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2023] Open
Abstract
A Gram-reaction-negative, aerobic, motile, rod-shaped bacterium, designated GH3-8T, was isolated from rhizosphere mudflats of halophytes on the seashore of Gangwha Island, Republic of Korea. Growth was observed at pH 4-10 (optimum, pH 7-8), at 4-40 °C (optimum, 37 °C) and in the presence of 0.5-20 % (w/v) NaCl (optimum, 4 %). The predominant respiratory quinone was Q-9. The major fatty acids were C18 : 1 ω7c, C16 : 0, summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c) and C12 : 0 3OH. The polar lipids contained phosphatidylethanolamine, phosphatidylglycerol, an unidentified phosphoglycolipid, an unidentified phosphoglycoaminolipid, an unidentified glycoaminolipid, two unidentified phospholipids and two unidentified lipids. Phylogenetic analysis based on 16S rRNA gene sequences exhibited that the isolate belonged to the family Halomonadaceae, with the most closely related species, Larsenimonas suaedae (98.1 % sequence similarity) and Larsenimonas salina (97.9 %). Sequence similarity values between the isolate and other representatives of the family Halomonadaceae were all below 95.3 %. The values of average nucleotide identity between strain GH3-8T and members of the genus Larsenimonas were 73.42 % with L. salina CCM 8464T and 72.38 % with L. suaedae DSM 22428T. Strain GH3-8T showed digital DNA-DNA hybridization values of 18.5-18.6 % with members of the genus Larsenimonas. Based on phenotypic and chemotaxonomic distinctiveness together with low overall genomic relatedness indices and phylogenetic data, the isolate is considered to represent a new species of the genus Larsenimonas, for which the name Larsenimonas rhizosphaerae sp. nov. is proposed, with the type strain GH3-8T (=KCTC 62127T=NBRC 113214T).
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Affiliation(s)
- Soon Dong Lee
- Institute of Jeju Microbial Resources, BioPS Co., Ltd., Jeju 63243, Republic of Korea
| | - In Seop Kim
- Department of Biological Sciences and Biotechnology, Hannam University, Daejon 34054, Republic of Korea
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Pandiyan K, Kushwaha P, Bagul SY, Chakdar H, Madhaiyan M, Krishnamurthi S, Kumar P, Karthikeyan N, Singh A, Kumar M, Singh UB, Saxena AK. Halomonas icarae sp. nov., a moderately halophilic bacterium isolated from beach soil in India. Int J Syst Evol Microbiol 2020; 71. [PMID: 33351740 DOI: 10.1099/ijsem.0.004611] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A moderately halophilic, Gram-stain-negative, aerobic bacterium, strain D1-1T, belonging to the genus Halomonas, was isolated from soil sampled at Pentha beach, Odisha, India. Phylogenetic trees reconstructed based on 16S rRNA genes and multilocus sequence analysis of gyrB and rpoD genes revealed that strain D1-1T belonged to the genus Halomonas and was most closely related to Halomonas alimentaria YKJ-16T (98.1 %) followed by Halomonas ventosae Al12T (97.5 %), Halomonas sediminicola CPS11T (97.5 %), Halomonas fontilapidosi 5CRT (97.4 %) and Halomonas halodenitrificans DSM 735T (97.2 %) on the basis of 16S rRNA gene sequence similarity. Sequence identities with other species within the genus were lower than 97.0 %. The digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values of 22.4-30 % and 79.5-85.4 % with close relatives of H. halodenitrificans DSM 735T, H. alimentaria YKJ-16T, H. ventosae Al12T and H. fontilapidosi 5CRT were lower than the threshold recommended for species delineation (70 % and 95-96 % for dDDH and ANI, respectively). Further, strain D1-1T formed yellow-coloured colonies; cells were rod-shaped, motile with optimum growth at 30 °C (range, 4-45 °C) and 2-8 % NaCl (w/v; grew up to 24 % NaCl). The major fatty acids were summed feature 8 (C18 : 1 ω7c/C18 : 1 ω6c), summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c) and C16 : 0 and the main respiratory quinone was ubiquinone Q-9 in line with description of the genus. Based on its chemotaxonomic and phylogenetic characteristics and genome uniqueness, strain D1-1T represents a novel species in the genus Halomonas, for which we propose the name Halomonas icarae sp. nov., within the family Halomonadaceae. The type strain is D1-1T (=JCM 33602T=KACC 21317T=NAIMCC-B-2254T).
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Affiliation(s)
- Kuppusamy Pandiyan
- ICAR - National Bureau of Agriculturally Important Microorganisms (NBAIM), Mau, Uttar Pradesh- 275103, India.,Ginning Training Centre, ICAR - Central Institute for Research on Cotton Technology (CIRCOT), Nagpur, Maharashtra - 440023, India
| | - Prity Kushwaha
- ICAR - National Bureau of Agriculturally Important Microorganisms (NBAIM), Mau, Uttar Pradesh- 275103, India
| | - Samadhan Y Bagul
- ICAR - National Bureau of Agriculturally Important Microorganisms (NBAIM), Mau, Uttar Pradesh- 275103, India
| | - Hillol Chakdar
- ICAR - National Bureau of Agriculturally Important Microorganisms (NBAIM), Mau, Uttar Pradesh- 275103, India
| | - Munusamy Madhaiyan
- Biomaterials and Biocatalysts, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Singapore
| | - Srinivasan Krishnamurthi
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology (IMTECH), Sector 39A, Chandigarh-160036, India
| | - Pravin Kumar
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology (IMTECH), Sector 39A, Chandigarh-160036, India
| | - Nanjappan Karthikeyan
- School of Water Stress Management, ICAR-National Institute for Abiotic Stress Management (NIASM), Baramati, Maharashtra - 413115, India.,ICAR - National Bureau of Agriculturally Important Microorganisms (NBAIM), Mau, Uttar Pradesh- 275103, India
| | - Arjun Singh
- Regional Research Station, ICAR - Central Soil Salinity Research Institute (CSSRI), Lucknow, Uttar Pradesh - 226002, India.,ICAR - National Bureau of Agriculturally Important Microorganisms (NBAIM), Mau, Uttar Pradesh- 275103, India
| | - Murugan Kumar
- ICAR - National Bureau of Agriculturally Important Microorganisms (NBAIM), Mau, Uttar Pradesh- 275103, India
| | - Udai Bhan Singh
- ICAR - National Bureau of Agriculturally Important Microorganisms (NBAIM), Mau, Uttar Pradesh- 275103, India
| | - Anil Kumar Saxena
- ICAR - National Bureau of Agriculturally Important Microorganisms (NBAIM), Mau, Uttar Pradesh- 275103, India
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5
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Fidalgo C, Proença DN, Morais PV, Henriques I, Alves A. The endosphere of the salt marsh plant Halimione portulacoides is a diversity hotspot for the genus Salinicola: description of five novel species Salinicola halimionae sp. nov., Salinicola aestuarinus sp. nov., Salinicola endophyticus sp. nov., Salinicola halophyticus sp. nov. and Salinicola lusitanus sp. nov. Int J Syst Evol Microbiol 2018; 69:46-62. [PMID: 30418109 DOI: 10.1099/ijsem.0.003061] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Seven endophytic strains were isolated from the halophyte Halimione portulacoides, collected from Ria de Aveiro, Portugal. To determine their exact taxonomic position, comparative analyses were performed with these strains and closely related type strains of Salinicola species. Genome sequencing and comparison indicated that five of the seven isolated strains comprised distinct and novel species (average nucleotide identity <0.95; in silico DNA-DNA hybridization <70 %; G+C difference >1 %). Multilocus sequence analysis was performed using gyrB, rpoD and 16S rRNA gene sequences from the novel and type strains to determine their phylogenetic positions. The novel strains are facultative anaerobes, mesophilic, facultative alkaliphic and halophilic, test positive for catalase and oxidase activities, for hydrolysis of Tween 20 and phosphate, for production of indole-3-acetic acid, but do not produce H2S. Ubiquinone UQ-9 is present in major amounts in all strains. The major fatty acids include C16 : 0 and the summed feature containing C18 : 1ω7c and/or C18 : 1ω6c. The DNA G+C content ranges from 60.6 to 65.8 mol%. Five strains were confirmed as new species belonging to the genus Salinicola, for which the names Salinicolahalimionae sp. nov. (type strain CPA60T=CECT 9338T=LMG 30107T), Salinicolaaestuarinus sp. nov. (type strain CPA62T=CECT 9339T=LMG 30108T), Salinicolaendophyticus sp. nov. (type strain CPA92T=CECT 9340T=LMG 30109T), Salinicolahalophyticus sp. nov. (type strain CR45T=CECT 9341T=LMG 30105T) and Salinicola lusitanus sp. nov. (type strain CR50T=CECT 9342T=LMG 30106T) are proposed.
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Affiliation(s)
- Cátia Fidalgo
- 1Department of Biology & CESAM, Universidade de Aveiro, 3810-193 Aveiro, Portugal
| | | | - Paula V Morais
- 2CEMMPRE, University of Coimbra, 3030-788 Coimbra, Portugal
- 3Department of Life Sciences, FCTUC, University of Coimbra, 3000-456 Coimbra, Portugal
| | - Isabel Henriques
- 1Department of Biology & CESAM, Universidade de Aveiro, 3810-193 Aveiro, Portugal
| | - Artur Alves
- 1Department of Biology & CESAM, Universidade de Aveiro, 3810-193 Aveiro, Portugal
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6
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de Carvalho CCCR, Caramujo MJ. The Various Roles of Fatty Acids. Molecules 2018; 23:molecules23102583. [PMID: 30304860 PMCID: PMC6222795 DOI: 10.3390/molecules23102583] [Citation(s) in RCA: 290] [Impact Index Per Article: 48.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 10/01/2018] [Accepted: 10/06/2018] [Indexed: 12/31/2022] Open
Abstract
Lipids comprise a large group of chemically heterogeneous compounds. The majority have fatty acids (FA) as part of their structure, making these compounds suitable tools to examine processes raging from cellular to macroscopic levels of organization. Among the multiple roles of FA, they have structural functions as constituents of phospholipids which are the "building blocks" of cell membranes; as part of neutral lipids FA serve as storage materials in cells; and FA derivatives are involved in cell signalling. Studies on FA and their metabolism are important in numerous research fields, including biology, bacteriology, ecology, human nutrition and health. Specific FA and their ratios in cellular membranes may be used as biomarkers to enable the identification of organisms, to study adaptation of bacterial cells to toxic compounds and environmental conditions and to disclose food web connections. In this review, we discuss the various roles of FA in prokaryotes and eukaryotes and highlight the application of FA analysis to elucidate ecological mechanisms. We briefly describe FA synthesis; analyse the role of FA as modulators of cell membrane properties and FA ability to store and supply energy to cells; and inspect the role of polyunsaturated FA (PUFA) and the suitability of using FA as biomarkers of organisms.
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Affiliation(s)
- Carla C C R de Carvalho
- Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal.
| | - Maria José Caramujo
- Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Edifício C2-5º Piso, 1749-016 Lisboa, Portugal.
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7
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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: 17] [Impact Index Per Article: 2.8] [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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Torregrosa-Crespo J, González-Torres P, Bautista V, Esclapez JM, Pire C, Camacho M, Bonete MJ, Richardson DJ, Watmough NJ, Martínez-Espinosa RM. Analysis of multiple haloarchaeal genomes suggests that the quinone-dependent respiratory nitric oxide reductase is an important source of nitrous oxide in hypersaline environments. ENVIRONMENTAL MICROBIOLOGY REPORTS 2017; 9:788-796. [PMID: 28925557 DOI: 10.1111/1758-2229.12596] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Microorganisms, including Bacteria and Archaea, play a key role in denitrification, which is the major mechanism by which fixed nitrogen returns to the atmosphere from soil and water. While the enzymology of denitrification is well understood in Bacteria, the details of the last two reactions in this pathway, which catalyse the reduction of nitric oxide (NO) via nitrous oxide (N2 O) to nitrogen (N2 ), are little studied in Archaea, and hardly at all in haloarchaea. This work describes an extensive interspecies analysis of both complete and draft haloarchaeal genomes aimed at identifying the genes that encode respiratory nitric oxide reductases (Nors). The study revealed that the only nor gene found in haloarchaea is one that encodes a single subunit quinone dependent Nor homologous to the qNor found in bacteria. This surprising discovery is considered in terms of our emerging understanding of haloarchaeal bioenergetics and NO management.
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Affiliation(s)
- Javier Torregrosa-Crespo
- Department of Agrochemistry and Biochemistry. Faculty of Science, University of Alicante, Ap. 99, E-03080 Alicante, Spain
| | - Pedro González-Torres
- Bioinformatics and Genomics Program, Centre for Genomic Regulation (CRG), Dr. Aiguader, 88. 08003 Barcelona, Spain
| | - Vanesa Bautista
- Department of Agrochemistry and Biochemistry. Faculty of Science, University of Alicante, Ap. 99, E-03080 Alicante, Spain
| | - Julia M Esclapez
- Department of Agrochemistry and Biochemistry. Faculty of Science, University of Alicante, Ap. 99, E-03080 Alicante, Spain
| | - Carmen Pire
- Department of Agrochemistry and Biochemistry. Faculty of Science, University of Alicante, Ap. 99, E-03080 Alicante, Spain
| | - Mónica Camacho
- Department of Agrochemistry and Biochemistry. Faculty of Science, University of Alicante, Ap. 99, E-03080 Alicante, Spain
| | - María José Bonete
- Department of Agrochemistry and Biochemistry. Faculty of Science, University of Alicante, Ap. 99, E-03080 Alicante, Spain
| | - David J Richardson
- Centre for Molecular Structure and Biochemistry, School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Nicholas J Watmough
- Centre for Molecular Structure and Biochemistry, School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Rosa María Martínez-Espinosa
- Department of Agrochemistry and Biochemistry. Faculty of Science, University of Alicante, Ap. 99, E-03080 Alicante, Spain
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Xia ZJ, Wu HZ, Cui CX, Chen Q, Zhao GY, Wang HX, Dai MX. Larsenimonas suaedae sp. nov., a moderately halophilic, endophytic bacterium isolated from the halophyte Suaeda salsa. Int J Syst Evol Microbiol 2016; 66:2952-2958. [PMID: 27129697 DOI: 10.1099/ijsem.0.001126] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A moderately halophilic, Gram-stain-negative, non-endospore-forming endophytic bacterium designated strain ST307T was isolated from the euhalophyte Suaeda salsa in Dongying, China. Strain ST307T was aerobic, rod-shaped, motile and orange-yellow-pigmented. The organism grew at NaCl concentrations of 0.6-20 % (w/v) (optimum 5-6 %, w/v), at temperatures of 5-45 °C (optimum 35 °C) and at pH 5-9 (optimum pH 7-8). It accumulated poly-β-hydroxybutyric acid and produced exopolysaccharides. The major fatty acids were C18 : 1ω7c/C18 : 1ω6c, C16 : 0 and C16 : 1ω7c/C16 : 1ω6c. The predominant lipoquinone was ubiquinone Q-9. The polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, a glycoaminolipid and a phosphoglycoaminolipid. The DNA G+C content was 60.5 mol%. Phylogenetic analyses of 16S rRNA gene sequences and concatenated atpA, rpoD and secA gene sequences revealed that the strain represents a member of the genus Larsenimonas. The closest related type strain was Larsenimonas salina M1-18T. Mean DNA-DNA relatedness values between strain ST307T and the related species L. salina M1-18T, Chromohalobacter beijerinckii DSM 7218T, C. canadensis DSM 6769T, C. israelensis DSM 6768T, C. marismortui CGMCC 1.2321T, C. nigrandesensis DSM 14323T, C. salexigens DSM 3043T and C. sarecensis DSM 15547T were 15±2-45±1 %. On the basis of phenotypic, chemotaxonomic and molecular features, strain ST307T clearly represents a novel species of the genus Larsenimonas. The name Larsenimonassuaedae sp. nov. is proposed, with ST307T (=CGMCC 1.8902T=DSM 22428T) as the type strain.
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Affiliation(s)
- Zhi-Jie Xia
- College of Life Science, Shandong Normal University, Jinan 250014, PR China
| | - Hong-Zhen Wu
- College of Life Science, Shandong Normal University, Jinan 250014, PR China
| | - Chun-Xiao Cui
- Medical College, Shandong Xiehe University, Jinan 250107, PR China
| | - Qi Chen
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
| | - Guo-Yan Zhao
- College of Life Science, Shandong Normal University, Jinan 250014, PR China
| | - Hai-Xia Wang
- College of Life Science, Shandong Normal University, Jinan 250014, PR China
| | - Mei-Xue Dai
- College of Life Science, Shandong Normal University, Jinan 250014, PR China
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Infante-Domínguez C, Corral P, Sánchez-Porro C, Ventosa A. Halovenus salina sp. nov., an extremely halophilic archaeon isolated from a saltern. Int J Syst Evol Microbiol 2015; 65:3016-3023. [PMID: 26040580 DOI: 10.1099/ijs.0.000370] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An extremely halophilic archaeon was isolated from a water sample of Isla Bacuta saltern in Huelva, Spain. Strain ASP54(T) is a novel red-pigmented, motile, rod-shaped, Gram-stain-negative and strictly aerobic haloarchaeon. Strain ASP54(T) grew in media containing 15-30% (w/v) salts and optimally with 25% (w/v) salts. It grew between pH 5.0 and 9.0 (optimally at pH 7.5) and at 20-40 °C (optimally at 37 °C). Phylogenetic analysis based on multi-locus sequence analysis (MLSA) and the comparison of 16S rRNA gene sequences revealed that strain ASP54(T) is most closely related to the genus Halovenus. The closest relatives were Halovenus aranensis EB27(T) (92.1% 16S rRNA gene sequence similarity), Halorientalis regularis TNN28(T) (92.1%), and Halorientalis persicus D108(T) (92.0%). The polar lipid pattern of strain ASP54(T) consisted of biphosphatidylglycerol, phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate, sulfated mannosyl glucosyl diether and a minor-phospholipid. The predominant respiratory quinone was menaquinone-8 (MK-8) (83%), and a minor amount of MK-8(VIII-H2) (17%) was also detected. The G+C content of the genomic DNA of this strain was 63.1 mol%. Based on the phenotypic, chemotaxonomic and phylogenetic data presented in this study, strain ASP54(T) represents a novel species of the genus Halovenus, for which the name Halovenus salina sp. nov. is proposed. The type strain is ASP54(T) ( = CEC(T) 8749(T) = IBRC-M 10946(T) = JCM 30072(T)).
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Affiliation(s)
- Carmen Infante-Domínguez
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
| | - Paulina Corral
- 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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Gupta RS, Naushad S, Baker S. Phylogenomic analyses and molecular signatures for the class Halobacteria and its two major clades: a proposal for division of the class Halobacteria into an emended order Halobacteriales and two new orders, Haloferacales ord. nov. and Natrialbales ord. nov., containing the novel families Haloferacaceae fam. nov. and Natrialbaceae fam. nov. Int J Syst Evol Microbiol 2014; 65:1050-1069. [PMID: 25428416 DOI: 10.1099/ijs.0.070136-0] [Citation(s) in RCA: 235] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Halobacteria constitute one of the largest groups within the Archaea. The hierarchical relationship among members of this large class, which comprises a single order and a single family, has proven difficult to determine based upon 16S rRNA gene trees and morphological and physiological characteristics. This work reports detailed phylogenetic and comparative genomic studies on >100 halobacterial (haloarchaeal) genomes containing representatives from 30 genera to investigate their evolutionary relationships. In phylogenetic trees reconstructed on the basis of 32 conserved proteins, using both neighbour-joining and maximum-likelihood methods, two major clades (clades A and B) encompassing nearly two-thirds of the sequenced haloarchaeal species were strongly supported. Clades grouping the same species/genera were also supported by the 16S rRNA gene trees and trees for several individual highly conserved proteins (RpoC, EF-Tu, UvrD, GyrA, EF-2/EF-G). In parallel, our comparative analyses of protein sequences from haloarchaeal genomes have identified numerous discrete molecular markers in the form of conserved signature indels (CSI) in protein sequences and conserved signature proteins (CSPs) that are found uniquely in specific groups of haloarchaea. Thirteen CSIs in proteins involved in diverse functions and 68 CSPs that are uniquely present in all or most genome-sequenced haloarchaea provide novel molecular means for distinguishing members of the class Halobacteria from all other prokaryotes. The members of clade A are distinguished from all other haloarchaea by the unique shared presence of two CSIs in the ribose operon protein and small GTP-binding protein and eight CSPs that are found specifically in members of this clade. Likewise, four CSIs in different proteins and five other CSPs are present uniquely in members of clade B and distinguish them from all other haloarchaea. Based upon their specific clustering in phylogenetic trees for different gene/protein sequences and the unique shared presence of large numbers of molecular signatures, members of clades A and B are indicated to be distinct from all other haloarchaea because of their uniquely shared evolutionary histories. Based upon these results, it is proposed that clades A and B be recognized as two new orders, Natrialbales ord. nov. and Haloferacales ord. nov., within the class Halobacteria, containing the novel families Natrialbaceae fam. nov. and Haloferacaceae fam. nov. Other members of the class Halobacteria that are not members of these two orders will remain part of the emended order Halobacteriales in an emended family Halobacteriaceae.
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Affiliation(s)
- Radhey S Gupta
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada L8N 3Z5
| | - Sohail Naushad
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada L8N 3Z5
| | - Sheridan Baker
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada L8N 3Z5
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Larsenia salina gen. nov., sp. nov., a new member of the family Halomonadaceae based on multilocus sequence analysis. Syst Appl Microbiol 2014; 37:480-7. [DOI: 10.1016/j.syapm.2014.07.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 07/22/2014] [Accepted: 07/31/2014] [Indexed: 11/24/2022]
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Das D, Salgaonkar BB, Mani K, Braganca JM. Cadmium resistance in extremely halophilic archaeon Haloferax strain BBK2. CHEMOSPHERE 2014; 112:385-392. [PMID: 25048931 DOI: 10.1016/j.chemosphere.2014.04.058] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Revised: 03/26/2014] [Accepted: 04/22/2014] [Indexed: 06/03/2023]
Abstract
Halophilic archaea are prevalent in highly saline habitats. Haloferax strain BBK2 is an orange pigmented, exopolysaccharide (EPS) producing extremely halophilic archaeon, isolated from solar salterns of Ribandar, Goa, India. It grew in varying pH (5-10) and NaCl concentration (10-30%). The isolate grew well in complex (NTYE) and minimal media (NGSM) in presence of heavy metal cadmium (Cd) up to 4.0 mM (805.28 mg L(-1)) concentration. The optimum growth in the presence and absence of Cd was seen at a pH range of 7-9 and salinity of 15-25%. The growth kinetics of the isolate in NTYE showed a specific growth rate (μmax) of 0.352 with generation time of 1.968 days. In presence of 1mM Cd, the μmax was 0.325 day(-1) and generation time was 2.132 days. In NGSM, the μmax decreased from 0.517 day(-1) (in control) to 0.265 day(-1) in 1mM Cd while, the doubling time increased from 1.34 days in control to 2.615 days in presence of 1 mM Cd. SDS PAGE of the whole cell protein extracts showed overexpressed proteins of 74.14 and 40 kDa. The scanning electron microscopy, energy dispersive X-ray spectroscopy (SEM-EDX) analysis of the intact cells and cells disrupted by dialysis revealed that Cd was bound onto the cells, which was further confirmed by AAS, FTIR and XRD analysis.
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Affiliation(s)
- Deepthi Das
- Department of Biological Sciences, Birla Institute of Technology and Science Pilani, KK Birla Goa Campus, NH 17B Zuarinagar, Goa 403 726, India
| | - Bhakti B Salgaonkar
- Department of Biological Sciences, Birla Institute of Technology and Science Pilani, KK Birla Goa Campus, NH 17B Zuarinagar, Goa 403 726, India
| | - Kabilan Mani
- Department of Biological Sciences, Birla Institute of Technology and Science Pilani, KK Birla Goa Campus, NH 17B Zuarinagar, Goa 403 726, India
| | - Judith M Braganca
- Department of Biological Sciences, Birla Institute of Technology and Science Pilani, KK Birla Goa Campus, NH 17B Zuarinagar, Goa 403 726, India.
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Taxonomy of halophilic Archaea: current status and future challenges. Extremophiles 2014; 18:825-34. [DOI: 10.1007/s00792-014-0654-9] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Accepted: 05/09/2014] [Indexed: 10/24/2022]
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Physiological features of Halomonas lionensis sp. nov., a novel bacterium isolated from a Mediterranean Sea sediment. Res Microbiol 2014; 165:490-500. [PMID: 25086262 DOI: 10.1016/j.resmic.2014.07.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 07/22/2014] [Indexed: 11/19/2022]
Abstract
A novel halophilic bacterium, strain RHS90(T), was isolated from marine sediments from the Gulf of Lions, in the Mediterranean Sea. Its metabolic and physiological characteristics were examined under various cultural conditions, including exposure to stressful ones (oligotrophy, high pressure and high concentrations of metals). Based on phylogenetic analysis of the 16S rRNA gene, the strain was found to belong to the genus Halomonas in the class Gammaproteobacteria. Its closest relatives are Halomonas axialensis and Halomonas meridiana (98% similarity). DNA-DNA hybridizations indicated that the novel isolate is genotypically distinct from these species. The DNA G + C content of the strain is 54.4 mol%. The main fatty acids (C18:1ω7c, 2-OH iso-C15:0, C16:0 and/or C19:0 cyclo ω8c), main polar lipids (diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and an unidentified phosphoglycolipid) and major respiratory quinone (ubiquinone Q9) were determined. The novel isolate is heterotrophic, mesophilic, euryhaline (growth optimum ranging from 2 to 8% w/v NaCl) and is able to grow under stressful conditions. The strain accumulates poly-β-hydroxyalkanoates granules and compatible solutes. Based on genotypic, chemotaxonomic and phenotypic distinctiveness, this isolate is likely to represent a novel species, for which the name Halomonas lionensis is proposed. The type strain of H. lionensis is RHS90(T) (DSM 25632(T) = CIP 110370(T) = UBOCC 3186(T)).
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Fullmer MS, Soucy SM, Swithers KS, Makkay AM, Wheeler R, Ventosa A, Gogarten JP, Papke RT. Population and genomic analysis of the genus Halorubrum. Front Microbiol 2014; 5:140. [PMID: 24782836 PMCID: PMC3990103 DOI: 10.3389/fmicb.2014.00140] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2014] [Accepted: 03/18/2014] [Indexed: 11/13/2022] Open
Abstract
The Halobacteria are known to engage in frequent gene transfer and homologous recombination. For stably diverged lineages to persist some checks on the rate of between lineage recombination must exist. We surveyed a group of isolates from the Aran-Bidgol endorheic lake in Iran and sequenced a selection of them. Multilocus Sequence Analysis (MLSA) and Average Nucleotide Identity (ANI) revealed multiple clusters (phylogroups) of organisms present in the lake. Patterns of intein and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) presence/absence and their sequence similarity, GC usage along with the ANI and the identities of the genes used in the MLSA revealed that two of these clusters share an exchange bias toward others in their phylogroup while showing reduced rates of exchange with other organisms in the environment. However, a third cluster, composed in part of named species from other areas of central Asia, displayed many indications of variability in exchange partners, from within the lake as well as outside the lake. We conclude that barriers to gene exchange exist between the two purely Aran-Bidgol phylogroups, and that the third cluster with members from other regions is not a single population and likely reflects an amalgamation of several populations.
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Affiliation(s)
- Matthew S. Fullmer
- Department of Molecular and Cell Biology, University of ConnecticutStorrs, CT, USA
| | - Shannon M. Soucy
- Department of Molecular and Cell Biology, University of ConnecticutStorrs, CT, USA
| | - Kristen S. Swithers
- Department of Molecular and Cell Biology, University of ConnecticutStorrs, CT, USA
- Department of Cell Biology, Yale School of Medicine, Yale UniversityNew Haven, CT, USA
| | - Andrea M. Makkay
- Department of Molecular and Cell Biology, University of ConnecticutStorrs, CT, USA
| | - Ryan Wheeler
- Department of Molecular and Cell Biology, University of ConnecticutStorrs, CT, USA
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, University of SevilleSeville, Spain
| | - J. Peter Gogarten
- Department of Molecular and Cell Biology, University of ConnecticutStorrs, CT, USA
| | - R. Thane Papke
- Department of Molecular and Cell Biology, University of ConnecticutStorrs, CT, USA
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