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Hyper production of polyhydroxyalkanoates by a novel bacterium Salinivibrio sp. TGB11. Biochem Eng J 2022. [DOI: 10.1016/j.bej.2022.108538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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2
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Wang Y, Wang Z, Han Q, Xie Y, Zhou H, Zhou K, Li X, Xu B. Comprehensive insights into the evolution of microbiological and metabolic characteristics of the fat portion during the processing of traditional Chinese bacon. Food Res Int 2022; 155:110987. [DOI: 10.1016/j.foodres.2022.110987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 01/13/2022] [Accepted: 01/29/2022] [Indexed: 11/04/2022]
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3
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Sigida EN, Ibrahim IM, Kokoulin MS, Abulreesh HH, Elbanna K, Konnova SA, Fedonenko YP. Structure of the 4-O-[1-Carboxyethyl]-d-Mannose-Containing O-Specific Polysaccharide of a Halophilic Bacterium Salinivibrio sp. EG9S8QL. Mar Drugs 2021; 19:md19090508. [PMID: 34564170 PMCID: PMC8466920 DOI: 10.3390/md19090508] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/01/2021] [Accepted: 09/02/2021] [Indexed: 01/26/2023] Open
Abstract
The moderately halophilic strain Salinivibrio sp. EG9S8QL was isolated among 11 halophilic strains from saline mud (Emisal Salt Company, Lake Qarun, Fayoum, Egypt). The lipopolysaccharide was extracted from dried cells of Salinivibrio sp. EG9S8QL by the phenol–water procedure. The OPS was obtained by mild acid hydrolysis of the lipopolysaccharide and was studied by sugar analysis along with 1H and 13C NMR spectroscopy, including 1H,1H COSY, TOCSY, ROESY, 1H,13C HSQC, and HMBC experiments. The OPS was found to be composed of linear tetrasaccharide repeating units of the following structure: →2)-β-Manp4Lac-(1→3)-α-ManpNAc-(1→3)-β-Rhap-(1→4)-α-GlcpNAc-(1→, where Manp4Lac is 4-O-[1-carboxyethyl]mannose.
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Affiliation(s)
- Elena N. Sigida
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences, 13 Prospekt Entuziastov, 410049 Saratov, Russia; (S.A.K.); (Y.P.F.)
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 47 Leninsky Prospekt, 119991 Moscow, Russia
- Correspondence: ; Tel.: +7-8452-970044
| | - Ibrahim M. Ibrahim
- N. G. Chernyshevsky Saratov State University, 83 Ulitsa Astrakhanskaya, 410012 Saratov, Russia;
- Department of Agricultural Microbiology, Faculty of Agriculture, Fayoum University, Fayoum 63514, Egypt;
| | - Maxim S. Kokoulin
- G. B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of Russian Academy of Sciences, 159 Prospekt 100 let Vladivostoku, 690022 Vladivostok, Russia;
| | - Hussein H. Abulreesh
- Department of Biology, Faculty of Applied Science, Umm Al-Qura University, Makkah 21955, Saudi Arabia;
- Research Laboratories Unit, Faculty of Applied Science, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Khaled Elbanna
- Department of Agricultural Microbiology, Faculty of Agriculture, Fayoum University, Fayoum 63514, Egypt;
- Department of Biology, Faculty of Applied Science, Umm Al-Qura University, Makkah 21955, Saudi Arabia;
- Research Laboratories Unit, Faculty of Applied Science, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Svetlana A. Konnova
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences, 13 Prospekt Entuziastov, 410049 Saratov, Russia; (S.A.K.); (Y.P.F.)
- N. G. Chernyshevsky Saratov State University, 83 Ulitsa Astrakhanskaya, 410012 Saratov, Russia;
| | - Yulia P. Fedonenko
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences, 13 Prospekt Entuziastov, 410049 Saratov, Russia; (S.A.K.); (Y.P.F.)
- N. G. Chernyshevsky Saratov State University, 83 Ulitsa Astrakhanskaya, 410012 Saratov, Russia;
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Van Thuoc D, Loan TT, Trung TA, Van Quyen N, Tung QN, Tien PQ, Sudesh K. Genome Mining Reveals the Biosynthetic Pathways of Polyhydroxyalkanoate and Ectoines of the Halophilic Strain Salinivibrio proteolyticus M318 Isolated from Fermented Shrimp Paste. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2020; 22:651-660. [PMID: 32827070 DOI: 10.1007/s10126-020-09986-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 08/03/2020] [Indexed: 06/11/2023]
Abstract
Salinivibrio proteolyticus M318, a halophilic bacterium isolated from fermented shrimp paste, is able to produce polyhydroxyalkanoate (PHA) from different carbon sources. In this study, we report the whole-genome sequence of strain M138, which comprises 2 separated chromosomes and 2 plasmids, and the complete genome contains 3,605,935 bp with an average GC content of 49.9%. The genome of strain M318 contains 3341 genes, 98 tRNA genes, and 28 rRNA genes. The 16S rRNA gene sequence and average nucleotide identity analysis associated with morphological and biochemical tests showed that this strain has high homology to the reference strain Salinivibrio proteolyticus DSM 8285. The genes encoding key enzymes for PHA and ectoine synthesis were identified from the bacterial genome. In addition, the TeaABC transporter responsible for ectoine uptake from the environment and the operon doeABXCD responsible for the degradation of ectoine were also detected. Strain M318 was able to produce poly(3-hydroxybutyrate) [P(3HB)] from different carbon sources such as glycerol, maltose, glucose, fructose, and starch. The ability to produce ectoines at different NaCl concentrations was investigated. High ectoine content of 26.2% of cell dry weight was obtained by this strain at 18% NaCl. This report provides genetic information regarding adaptive mechanisms of strain M318 to stress conditions, as well as new knowledge to facilitate the application of this strain as a bacterial cell factory for the production of PHA and ectoine.
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Affiliation(s)
- Doan Van Thuoc
- Faculty of Biology, Hanoi National University of Education, 136 Xuan Thuy, Cau Giay, Hanoi, Vietnam.
| | - Tran Thi Loan
- Faculty of Biology, Hanoi National University of Education, 136 Xuan Thuy, Cau Giay, Hanoi, Vietnam
| | - Trieu Anh Trung
- Faculty of Biology, Hanoi National University of Education, 136 Xuan Thuy, Cau Giay, Hanoi, Vietnam
| | - Nguyen Van Quyen
- Faculty of Biology, Hanoi National University of Education, 136 Xuan Thuy, Cau Giay, Hanoi, Vietnam
| | - Quach Ngoc Tung
- Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Caugiay, Hanoi, Vietnam
| | - Phi Quyet Tien
- Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Caugiay, Hanoi, Vietnam
| | - Kumar Sudesh
- School of Biological Sciences, Universiti Sains Malaysia, 11800, Penang, Malaysia
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5
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Life in High Salt Concentrations with Changing Environmental Conditions: Insights from Genomic and Phenotypic Analysis of Salinivibrio sp. Microorganisms 2019; 7:microorganisms7110577. [PMID: 31752335 PMCID: PMC6920786 DOI: 10.3390/microorganisms7110577] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 11/05/2019] [Accepted: 11/15/2019] [Indexed: 12/17/2022] Open
Abstract
Life in salt pans with varying chemical compositions require special adaptation strategies at both the physiological and molecular level. The Marakkanam salt pan in South India is characterized with a high fluctuation in salinity (19–490 ppt), Ultravioletradiation, and heavy metal concentrations. Several bacterial species have been isolated and identified in the view of phylogenetic analysis and for the subsequent production of industrially important enzymes. However, limited information exists on the genomic basis of their survival under variable environmental conditions. To this extent, we sequenced the whole genome of the Salinivibrio sp. HTSP, a moderately halophilic bacterium. We analysed the physiological and genomic attributes of Salinivibrio sp. HTSP to elucidate the strategies of adaptation under various abiotic stresses. The genome size is estimated to be 3.39 Mbp with a mean G + C content of 50.6%, including 3150 coding sequences. The genome possessed osmotic stress-related coding sequences, and genes involved in different pathways of DNA repair mechanisms and genes related to the resistance to toxic metals were identified. The periplasmic stress response genes and genes of different oxidative stress mechanisms were also identified. The tolerance capacity of the bacterial isolates to heavy metals, UV-radiation, and salinity was also confirmed through appropriate laboratory experiments under controlled conditions.
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Du GX, Qu LY, Shang K, Gao P, Ding DW, Sun CJ. Complete Genome Sequence of Strain YCSC6, a Marine Bacterium Isolated from Saturated Saltpan with Activity Against Uronema marinum. Curr Microbiol 2019; 77:129-135. [PMID: 31691022 DOI: 10.1007/s00284-019-01796-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 10/18/2019] [Indexed: 11/30/2022]
Abstract
Salinivibrio proteolyticus strain YCSC6 was isolated from a saturated saltpan and demonstrated to have strong insecticidal activity against turbot's pathogenic ciliate-Uronema marinum. In this study, we sequenced its complete genome. Results showed that it consists of two circular chromosomes: 2.49 Mbps and 0.74 Mbps, respectively. It encodes 3429 protein-coding sequences. Biosynthetic gene clusters predicted to synthesize bacteriocins and antimicrobial peptides were discovered, which might be the key factors to lyse and kill U. marinum. The complete genome sequence of strain YCSC6 provides insights into the fundamental genetic potential for elucidating its insecticidal mechanism against U. marinum.
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Affiliation(s)
- Guang Xun Du
- School of Marine Sciences, Ningbo University, Ningbo, 315823, People's Republic of China.,First Institute of Oceanography, MNR, Qingdao, 266061, People's Republic of China
| | - Ling Yun Qu
- First Institute of Oceanography, MNR, Qingdao, 266061, People's Republic of China. .,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, People's Republic of China.
| | - Kun Shang
- First Institute of Oceanography, MNR, Qingdao, 266061, People's Republic of China.,College of Fisheries and Life Science, Dalian Ocean University, Dalian, 116023, People's Republic of China
| | - Ping Gao
- First Institute of Oceanography, MNR, Qingdao, 266061, People's Republic of China
| | - De Wen Ding
- School of Marine Sciences, Ningbo University, Ningbo, 315823, People's Republic of China.,First Institute of Oceanography, MNR, Qingdao, 266061, People's Republic of China
| | - Cheng Jun Sun
- First Institute of Oceanography, MNR, Qingdao, 266061, People's Republic of China
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de la Haba RR, López-Hermoso C, Sánchez-Porro C, Konstantinidis KT, Ventosa A. Comparative Genomics and Phylogenomic Analysis of the Genus Salinivibrio. Front Microbiol 2019; 10:2104. [PMID: 31572321 PMCID: PMC6749099 DOI: 10.3389/fmicb.2019.02104] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 08/27/2019] [Indexed: 12/02/2022] Open
Abstract
In the genomic era phylogenetic relationship among prokaryotes can be inferred from the core orthologous genes (OGs) or proteins in order to elucidate their evolutionary history and current taxonomy should benefits of that. The genus Salinivibrio belongs to the family Vibrionaceae and currently includes only five halophilic species, in spite the fact that new strains are very frequently isolated from hypersaline environments. Species belonging to this genus have undergone several reclassifications and, moreover, there are many strains of Salinivibrio with available genomes which have not been affiliated to the existing species or have been wrongly designated. Therefore, a phylogenetic study using the available genomic information is necessary to clarify the relationships of existing strains within this genus and to review their taxonomic affiliation. For that purpose, we have also sequenced the first complete genome of a Salinivibrio species, Salinivibrio kushneri AL184T, which was employed as a reference to order the contigs of the draft genomes of the type strains of the current species of this genus, as well as to perform a comparative analysis with all the other available Salinivibrio sp. genomes. The genome of S. kushneri AL184T was assembled in two circular chromosomes (with sizes of 2.84 Mb and 0.60 Mb, respectively), as typically occurs in members of the family Vibrionaceae, with nine complete ribosomal operons, which might explain the fast growing rate of salinivibrios cultured under laboratory conditions. Synteny analysis among the type strains of the genus revealed a high level of genomic conservation in both chromosomes, which allow us to hypothesize a slow speciation process or homogenization events taking place in this group of microorganisms to be tested experimentally in the future. Phylogenomic and orthologous average nucleotide identity (OrthoANI)/average amino acid identity (AAI) analyses also evidenced the elevated level of genetic relatedness within members of this genus and allowed to group all the Salinivibrio strains with available genomes in seven separated species. Genome-scale attribute study of the salinivibrios identified traits related to polar flagellum, facultatively anaerobic growth and osmotic response, in accordance to the phenotypic features described for species of this genus.
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Affiliation(s)
- Rafael R. de la Haba
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Seville, Seville, Spain
| | - Clara López-Hermoso
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Seville, Seville, Spain
| | - 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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Galisteo C, Sánchez-Porro C, de la Haba RR, López-Hermoso C, Fernández AB, Farias ME, Ventosa A. Characterization of Salinivibrio socompensis sp. nov., A New Halophilic Bacterium Isolated from the High-Altitude Hypersaline Lake Socompa, Argentina. Microorganisms 2019; 7:microorganisms7080241. [PMID: 31387286 PMCID: PMC6723482 DOI: 10.3390/microorganisms7080241] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 08/01/2019] [Accepted: 08/02/2019] [Indexed: 11/16/2022] Open
Abstract
The genus Salinivibrio belongs to the family Vibrionaceae and includes Gram-stain-negative, motile by a polar flagellum, and facultatively anaerobic curved rods. They are halophilic bacteria commonly found in hypersaline aquatic habitats and salted foods. This genus includes five species and two subspecies. A presumed novel species, strain S35T, was previously isolated from the high-altitude volcanic, alkaline, and saline lake Socompa (Argentinean Andes). In this study we carried out a complete taxonomic characterization of strain S35T, including the 16S rRNA gene sequence and core-genome analysis, the average nucleotide identity (ANIb, ANIm, and orthoANI), and in silico DNA-DNA hybridization (GGDC), as well as the phenotypic and chemotaxonomic characterization. It grew at 3%-20% (w/v) NaCl, pH 6-10, and 10-42 °C, with optimum growth at 7.0%-7.5% (w/v) NaCl, pH 8.0, and 37 °C, respectively. Strain S35T was oxidase- and catalase-positive, able to produce acid from D-glucose and other carbohydrates. Hydrolysis of DNA, methyl red test, and nitrate and nitrite reduction were positive. Its main fatty acids were C16:0, C16:1 ω7c and C16:1 ω6c, and C18:1 ω7c and/or C18:1 ω6c. ANI, GGDC, and core-genome analysis determined that strain S35T constitutes a novel species of the genus Salinivibrio, for which the name Salinivibrio socompensis sp. nov. is proposed. The type strain is S35T (= CECT 9634T = BNM 0535T).
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Affiliation(s)
- Cristina Galisteo
- 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
| | - Clara López-Hermoso
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
| | - Ana B Fernández
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas, Planta Piloto de Procesos Industriales Microbiológicos, Centro Científico Tecnológico, CONICET Tucumán T4000, Argentina
| | - María E Farias
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas, Planta Piloto de Procesos Industriales Microbiológicos, Centro Científico Tecnológico, CONICET Tucumán T4000, Argentina
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain.
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López-Hermoso C, de la Haba RR, Sánchez-Porro C, Ventosa A. Emended description of Salinivibrio proteolyticus, including Salinivibrio costicola subsp. vallismortis and five new isolates. Int J Syst Evol Microbiol 2018; 68:1599-1607. [PMID: 29580324 DOI: 10.1099/ijsem.0.002716] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We carried out a comparative taxonomic study of Salinivibrio proteolyticus and Salinivibrio costicola subsp. vallismortis, as well as of five halophilic strains (IB574, IB872, PR5, PR919 and PR932), isolated from salterns in Spain and Puerto Rico that were closely related to these bacteria. Multilocus sequence analysis of concatenated gyrB, recA, rpoA and rpoD housekeeping genes showed that they constituted a single cluster separate from the other species and subspecies of Salinivibrio. Experimental and in silico DNA-DNA hybridization studies indicated that they are members of the same species, with relatedness of 100-74 % and 97.8-70.0 %, respectively. The average nucleotide identity (ANI) determined for these strains was 99.7-95.6 % for ANIb and 99.7-95.7 % for OrthoANI. However, the ANI values for S. costicolasubsp.vallismortis DSM 8285T with respect to S. costicolasubsp.costicola DSM 11403T and S. costicolasubsp.alcaliphilus DSM 16359T were 78.7 and 78.9 % (ANIb) and 79.4 and 79.4 % (OrthoANI), respectively. The phylogenomic tree based on 1072 concatenated orthologous single-copy core genes confirmed that S. proteolyticus, S. costicolasubsp.vallismortis and the five new isolates constitute a coherent single phylogroup, separated from the other species and subspecies of Salinivibrio. All these data indicate that S. costicolasubsp.vallismortis is a heterotypic synonym of S. proteolyticus and we propose an emended description of this species.
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Affiliation(s)
- Clara López-Hermoso
- 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
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
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López-Hermoso C, de la Haba RR, Sánchez-Porro C, Ventosa A. Salinivibrio kushneri sp. nov., a moderately halophilic bacterium isolated from salterns. Syst Appl Microbiol 2017; 41:159-166. [PMID: 29331569 DOI: 10.1016/j.syapm.2017.12.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2017] [Revised: 11/26/2017] [Accepted: 12/01/2017] [Indexed: 11/26/2022]
Abstract
Ten Gram-strain-negative, facultatively anaerobic, moderately halophilic bacterial strains, designated AL184T, IB560, IB563, IC202, IC317, MA421, ML277, ML318, ML328A and ML331, were isolated from water ponds of five salterns located in Spain. The cells were motile, curved rods and oxidase and catalase positive. All of them grew optimally at 37°C, at pH 7.2-7.4 and in the presence of 7.5% (w/v) NaCl. Based on phylogenetic analyses of the 16S rRNA, the isolates were most closely related to Salinivibrio sharmensis BAGT (99.6-98.2% 16S rRNA gene sequence similarity) and Salinivibrio costicola subsp. costicola ATCC 35508T (99.0-98.1%). According to the MLSA analyses based on four (gyrB, recA, rpoA and rpoD) and eight (ftsZ, gapA, gyrB, mreB, pyrH, recA, rpoA and topA) concatenated gene sequences, the most closely relatives were S. siamensis JCM 14472T (96.8-95.4% and 94.9-94.7%, respectively) and S. sharmensis DSM 18182T (94.0-92.6% and 92.9-92.7%, respectively). In silico DNA-DNA hybridization (GGDC) and average nucleotide identity (ANI) showed values of 23.3-44.8% and 80.2-91.8%, respectively with the related species demonstrating that the ten isolates constituted a single novel species of the genus Salinivibrio. Its pangenome and core genome consist of 6041 and 1230 genes, respectively. The phylogeny based on the concatenated orthologous core genes revealed that the ten strains form a coherent phylogroup well separated from the rest of the species of the genus Salinivibrio. The major cellular fatty acids of strain AL184T were C16:0 and C18:1. The DNA G+C content range was 51.9-52.5mol% (Tm) and 50.2-50.9mol% (genome). Based on the phylogenetic-phylogenomic, phenotypic and chemotaxonomic data, the ten isolates represent a novel species of the genus Salinivibrio, for which the name Salinivibrio kushneri sp. nov. is proposed. The type strain is AL184T (=CECT 9177T=LMG 29817T).
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Affiliation(s)
- Clara López-Hermoso
- 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
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain.
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11
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López-Hermoso C, de la Haba RR, Sánchez-Porro C, Bayliss SC, Feil EJ, Ventosa A. Draft Genome Sequences of Salinivibrio proteolyticus, Salinivibrio sharmensis, Salinivibrio siamensis, Salinivibrio costicola subsp. alcaliphilus, Salinivibrio costicola subsp. vallismortis, and 29 New Isolates Belonging to the Genus Salinivibrio. GENOME ANNOUNCEMENTS 2017; 5:e00244-17. [PMID: 28684561 PMCID: PMC5502842 DOI: 10.1128/genomea.00244-17] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 03/20/2017] [Indexed: 11/20/2022]
Abstract
The draft genome sequences of 5 type strains of species of the halophilic genus Salinivibrio and 29 new isolates from different hypersaline habitats belonging to the genus Salinivibrio have been determined. The genomes have 3,123,148 to 3,641,359 bp, a G+C content of 49.2 to 50.9%, and 2,898 to 3,404 open reading frames (ORFs).
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Affiliation(s)
- Clara López-Hermoso
- 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
| | - Cristina Sánchez-Porro
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, Spain
| | - Sion C Bayliss
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, Spain
| | - Edward J Feil
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, Spain
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12
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López-Hermoso C, de la Haba RR, Sánchez-Porro C, Papke RT, Ventosa A. Assessment of MultiLocus Sequence Analysis As a Valuable Tool for the Classification of the Genus Salinivibrio. Front Microbiol 2017; 8:1107. [PMID: 28690592 PMCID: PMC5479898 DOI: 10.3389/fmicb.2017.01107] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 05/31/2017] [Indexed: 01/15/2023] Open
Abstract
The genus Salinivibrio includes obligatory halophilic bacteria and is commonly isolated from hypersaline habitats and salted food products. They grow optimally between 7.5 and 10% salts and are facultative anaerobes. Currently, this genus comprises four species, one of them, S. costicola, with three subspecies. In this study we isolated and characterized an additional 70 strains from solar salterns located in different locations. Comparative 16S rRNA gene sequence analysis identified these strains as belonging to the genus Salinivibrio but could not differentiate strains into species-like groups. To achieve finer phylogenetic resolution, we carried out a MultiLocus Sequence Analysis (MLSA) of the new isolates and the type strains of the species of Salinivibrio based on the individual as well as concatenated sequences of four housekeeping genes: gyrB, recA, rpoA, and rpoD. The strains formed four clearly differentiated species-like clusters called phylogroups. All of the known type and subspecies strains were associated with one of these clusters except S. sharmensis. One phylogroup had no previously described species coupled to it. Further DNA–DNA hybridization (DDH) experiments with selected representative strains from these phylogroups permitted us to validate the MLSA study, correlating the species level defined by the DDH (70%) with a 97% cut-off for the concatenated MLSA gene sequences. Based on these criteria, the novel strains forming phylogroup 1 could constitute a new species while strains constructing the other three phylogroups are members of previously recognized Salinivibrio species. S. costicola subsp. vallismortis co-occurs with S. proteolyticus in phylogroup 4, and separately from other S. costicola strains, indicating its need for reclassification. On the other hand, genome fingerprinting analysis showed that the environmental strains do not form clonal populations and did not cluster according to their site of cultivation. In future studies regarding the classification and identification of new Salinivibrio strains we recommend the following strategy: (i) initial partial sequencing of the 16S rRNA gene for genus-level identification; (ii) sequencing and concatenation of the four before mentioned housekeeping genes for species-level discrimination; (iii) DDH experiments, only required when the concatenated MLSA similarity values among a new isolate and other Salinivibrio strains are above the 97% cut-off.
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Affiliation(s)
- Clara López-Hermoso
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of SevillaSevilla, Spain
| | - Rafael R de la Haba
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of SevillaSevilla, Spain
| | - Cristina Sánchez-Porro
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of SevillaSevilla, Spain
| | - R Thane Papke
- Department of Molecular and Cell Biology, University of Connecticut, StorrsCT, United States
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of SevillaSevilla, Spain
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Huang Z, Dong C, Shao Z. Paraphotobacterium marinum gen. nov., sp. nov., a member of the family Vibrionaceae, isolated from surface seawater. Int J Syst Evol Microbiol 2016; 66:3050-3056. [DOI: 10.1099/ijsem.0.001142] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Affiliation(s)
- Zhaobin Huang
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen 361005, PR China
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA, Xiamen 361005, PR China
- Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, P. R. China
| | - Chunming Dong
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen 361005, PR China
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA, Xiamen 361005, PR China
- Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, P. R. China
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, P. R. China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen 361005, PR China
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA, Xiamen 361005, PR China
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Speranza B, Racioppo A, Bevilacqua A, Beneduce L, Sinigaglia M, Corbo MR. Selection of Autochthonous Strains as Starter Cultures for Fermented Fish Products. J Food Sci 2014; 80:M151-60. [DOI: 10.1111/1750-3841.12721] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 10/22/2014] [Indexed: 11/27/2022]
Affiliation(s)
- Barbara Speranza
- Dept. of the Science of Agriculture; Food and Environment (SAFE); Univ. of Foggia; Via Napoli 25 71122 Foggia Italy
| | - Angela Racioppo
- Dept. of the Science of Agriculture; Food and Environment (SAFE); Univ. of Foggia; Via Napoli 25 71122 Foggia Italy
| | - Antonio Bevilacqua
- Dept. of the Science of Agriculture; Food and Environment (SAFE); Univ. of Foggia; Via Napoli 25 71122 Foggia Italy
| | - Luciano Beneduce
- Dept. of the Science of Agriculture; Food and Environment (SAFE); Univ. of Foggia; Via Napoli 25 71122 Foggia Italy
| | - Milena Sinigaglia
- Dept. of the Science of Agriculture; Food and Environment (SAFE); Univ. of Foggia; Via Napoli 25 71122 Foggia Italy
| | - Maria Rosaria Corbo
- Dept. of the Science of Agriculture; Food and Environment (SAFE); Univ. of Foggia; Via Napoli 25 71122 Foggia Italy
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Gorriti MF, Dias GM, Chimetto LA, Trindade-Silva AE, Silva BS, Mesquita MMA, Gregoracci GB, Farias ME, Thompson CC, Thompson FL. Genomic and phenotypic attributes of novel salinivibrios from stromatolites, sediment and water from a high altitude lake. BMC Genomics 2014; 15:473. [PMID: 24927949 PMCID: PMC4094778 DOI: 10.1186/1471-2164-15-473] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Accepted: 06/06/2014] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Salinivibrios are moderately halophilic bacteria found in salted meats, brines and hypersaline environments. We obtained three novel conspecific Salinivibrio strains closely related to S. costicola, from Socompa Lake, a high altitude hypersaline Andean lake (approx. 3,570 meters above the sea level). RESULTS The three novel Salinivibrio spp. were extremely resistant to arsenic (up to 200 mM HAsO42-), NaCl (up to 15%), and UV-B radiation (19 KJ/m2, corresponding to 240 minutes of exposure) by means of phenotypic tests. Our subsequent draft genome ionsequencing and RAST-based genome annotation revealed the presence of genes related to arsenic, NaCl, and UV radiation resistance. The three novel Salinivibrio genomes also had the xanthorhodopsin gene cluster phylogenetically related to Marinobacter and Spiribacter. The genomic taxonomy analysis, including multilocus sequence analysis, average amino acid identity, and genome-to-genome distance revealed that the three novel strains belong to a new Salinivibrio species. CONCLUSIONS Arsenic resistance genes, genes involved in DNA repair, resistance to extreme environmental conditions and the possible light-based energy production, may represent important attributes of the novel salinivibrios, allowing these microbes to thrive in the Socompa Lake.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Fabiano L Thompson
- Laboratório de Microbiologia, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brasil.
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Salinivibrio sharmensis sp. nov., a novel haloalkaliphilic bacterium from a saline lake in Ras Mohammed Park (Egypt). Extremophiles 2011; 15:213-20. [DOI: 10.1007/s00792-010-0349-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2010] [Accepted: 12/08/2010] [Indexed: 10/18/2022]
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Tanasupawat S, Chamroensaksri N, Kudo T, Itoh T. Identification of moderately halophilic bacteria from Thai fermented fish ( pla-ra ) and proposal of Virgibacillus siamensis sp. nov. J GEN APPL MICROBIOL 2011; 56:369-79. [PMID: 21099133 DOI: 10.2323/jgam.56.369] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Forty-one isolates of moderately halophilic bacteria were isolated from fermented fish (pla-ra) in Thailand. On the basis of their phenotypic and chemotaxonomic characteristics, DNA-DNA relatedness and 16S rRNA gene sequences analyses, they were divided into six groups. The isolates in Group I to V were Gram-positive rod-shaped bacteria. They contained meso-diaminopimelic acid in the cell-wall peptidoglycan and menaquinone with seven isoprene units (MK-7). An isolate in Group VI was a Gram-negative rod-shaped bacterium. The DNA G+C contents of tested strains ranged from 36.5-63 mol%. Ten strains (Group I) were identified as Virgibacillus dokdonensis, 13 isolates (Group II) as V. halodenitrificans, 14 isolates (Group III) as V. marismortui, 1 isolate (Group IV) as Virgibacillus sp., 2 isolates (Group V) as Bacillus vietnamnensis, and 1 isolate (Group VI) as Chromohalobacter salexigens. Isolate MS3-4 in Group IV was closely related to V. carmonensis KCTC 3819(T) (95.9%). This strain contained anteiso-C(15:0) (55.8%) and anteiso-C(17:0) (17.7%) as major cellular fatty acids and had phosphatidylglycerol, diphosphatidylglycerol and an unidentified glycolipid as polar lipids. The DNA G+C content of MS3-4 was 38.0 mol%. The strain from Group IV is proposed as Virgibacillus siamensis sp. nov. and MS3-4(T) is the type strain (JCM 15395(T) =PCU 312(T) =TISTR 1957(T)).
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Affiliation(s)
- Somboon Tanasupawat
- Department of Biochemistry and Microbiology, Chulalongkorn University, Bangkok, Thailand.
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