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Sato Y, Mino S, Thompson F, Sawabe T. Core Transcriptome of Hydrogen Producing Marine Vibrios Reveals Contribution of Glycolysis in Their Efficient Hydrogen Production. Curr Microbiol 2024; 81:230. [PMID: 38896159 DOI: 10.1007/s00284-024-03764-z] [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: 04/11/2024] [Accepted: 05/29/2024] [Indexed: 06/21/2024]
Abstract
Pyruvate (Pyr) is the end product of the glycolysis pathway. Pyr is also renewable and is further metabolized to produce formate, which is the precursor of H2, via pyruvate formate lyase (PFL) under anaerobic conditions. The formate is excluded and re-imported via the formate channel and is then converted to H2 via the formate hydrogenlyase (FHL) complex. In H2 producing marine vibrios, such as Vibrio tritonius and Vibrio porteresiae in the Porteresiae clade of the family Vibrionaceae, apparent but inefficient H2 production from Pyr has been observed. To elucidate the molecular mechanism of why this inefficient H2 production is observed in Pry-metabolized marine vibrio cells and how glycolysis affects those H2 productions of marine vibrios, the "Core Transcriptome" approach to find common gene expressions of those two major H2 producing Vibrio species in Pyr metabolism was first applied. In the Pyr-metabolized vibrio cells, genes for the "Phosphoenolpyruvate (PEP)-Pyruvate-Oxalate (PPO)" node, due to energy saving, and PhoB-, RhaR-, and DeoR-regulons were regulated. Interestingly, a gene responsible for oxalate/formate family antiporter was up-regulated in Pyr-metabolized cells compared to those of Glc-metabolized cells, which provides new insights into the uses of alternative formate exclusion mechanics due to energy deficiencies in Pyr-metabolized marine vibrios cells. We further discuss the contribution of the Embden-Meyerhof-Parnas (EMP) pathway to efficient H2 production in marine vibrios.
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Affiliation(s)
- Yoshihiro Sato
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
| | - Sayaka Mino
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan.
| | - Fabiano Thompson
- Laboratory of Microbiology, Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Tomoo Sawabe
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan.
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Enciso-Ibarra J, Roque A, Bolán-Mejia C, Enciso-Ibarra K, González-Castillo A, Gomez-Gil B. Vibrio eleionomae sp. nov., isolated from shrimp ( Penaeus vannamei) pond water. Int J Syst Evol Microbiol 2023; 73. [PMID: 37167075 DOI: 10.1099/ijsem.0.005866] [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: 05/13/2023] Open
Abstract
A novel Vibrio strain (CAIM 722T=SW9T=DSM 24596T) was isolated in 2003 from water of a shrimp (Penaeus vannamei) culture pond located in Los Mochis, Sinaloa, Mexico, and taxonomically characterized using a polyphasic approach. The 16S rRNA gene sequence clustered within those of the genus Vibrio, showing high similarity to the type strains of the Porteresiae clade. Multilocus sequence analysis using eight housekeeping genes (ftsZ, gapA, gyrB, mreB, pyrH, recA, rpoA, topA and 16S rRNA) and phylogenetic analysis with 139 single-copy genes showed that the strain forms an independent branch. Whole genome sequencing and genomic analyses (average nucleotide identity, OrthoANI, average amino acid identity and in silico DNA-DNA hybridization) produced values well below the thresholds for species delineation with all methods tested. In addition, a phenotypic characterization was performed to support the description and differentiation of the novel strain from related taxa. The results obtained demonstrate that the strain represent a novel species, for which the name Vibrio eleionomae sp. nov. is proposed.
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Affiliation(s)
| | - Ana Roque
- Institut de Recerca i Tecnologia Agroalimentaries, Centre d'Aquicultura, Crta: Poble Nou, Km 5,5. La Ràpita, 43540, Spain
| | - Carmen Bolán-Mejia
- CIAD, A.C., Mazatlán Unit for Aquaculture, AP. 711 Mazatlán, Sinaloa 82000, Mexico
| | - Karen Enciso-Ibarra
- CIAD, A.C., Mazatlán Unit for Aquaculture, AP. 711 Mazatlán, Sinaloa 82000, Mexico
| | - Adrián González-Castillo
- Universidad Politécnica de Sinaloa, Programa Académico de Ingeniería en Biotecnología, Carretera Municipal Libre Km.3 Mazatlán-Higueras, Mazatlán, Sinaloa 82199, Mexico
| | - Bruno Gomez-Gil
- CIAD, A.C., Mazatlán Unit for Aquaculture, AP. 711 Mazatlán, Sinaloa 82000, Mexico
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Comparative Physiology and Genomics of Hydrogen-Producing Vibrios. Curr Microbiol 2022; 79:360. [PMID: 36253650 DOI: 10.1007/s00284-022-03065-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 09/27/2022] [Indexed: 11/03/2022]
Abstract
The Hyf-type formate hydrogen lyase (FHL) complex was first proposed based on sequence comparisons in Escherichia coli in 1997 (Andrews et al. in Microbiology 143:3633-3647, 1997). The hydrogenase in the Hyf-type FHL was estimated to be a proton-translocating energy-conserving [NiFe]-hydrogenase. Although the structure of FHL is similar to that of complex I, silent gene expression in E. coli has caused delays in unveiling the genetic and biochemical features of the FHL. The entire set of genes required for Hyf-type FHL synthesis has also been found in the genome sequences of Vibrio tritonius in 2015 (Matsumura et al. in Int J Hydrog Energy 40:9137-9146, 2015), which produces more hydrogen (H2) than E. coli. Here we investigate the physiological characteristics, genome comparisons, and gene expressions to elucidate the genetic backgrounds of Hyf-type FHL, and how Hyf-type FHL correlates with the higher H2 production of V. tritonius. Physiological comparisons among the seven H2-producing vibrios reveal that V. porteresiae and V. tritonius, grouped in the Porteresiae clade, show greater capacity for H2 production than the other species. The structures of FHL-Hyp gene clusters were closely related in both Porteresiae species, but differed from those of the other species with the presence of hupE, a possible nickel permease gene. Interestingly, deeper genome comparisons revealed the co-presence of nickel ABC transporter genes (nik) with the Hyf-type FHL gene only on the genome of the Porteresiae clade species. Therefore, active primary Ni transport might be one of the key factors characterizing higher H2 production in V. tritonius. Furthermore, the expression of FHL gene cluster was significantly up-regulated in V. tritonius cells stimulated with formate, indicating that formate is likely to be a control factor for the gene expression of V. tritonius FHL in a similar way to the formate regulon encoding the E. coli FHL.
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Huang WS, Wang LT, Chen JS, Chen YT, Wei STS, Chiang YR, Wang PL, Lee TH, Lin ST, Huang L, Shieh WY. Vibrio nitrifigilis sp. nov., a marine nitrogen-fixing bacterium isolated from the lagoon sediment of an islet inside an atoll. Antonie van Leeuwenhoek 2021; 114:933-945. [PMID: 33864545 DOI: 10.1007/s10482-021-01567-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 04/01/2021] [Indexed: 10/21/2022]
Abstract
A nitrogen-fixing isolate of facultatively anaerobic, marine bacterium, designated strain NFV-1T, was recovered from the lagoon sediment of Dongsha Island, Taiwan. It was a Gram-negative rod which exhibited motility with monotrichous flagellation in broth cultures. The strain required NaCl for growth and grew optimally at about 25-35 °C, 3% NaCl and pH 7-8. It grew aerobically and could achieve anaerobic growth by fermenting D-glucose or other carbohydrates as substrates. NH4Cl could serve as a sole nitrogen source for growth aerobically and anaerobically, whereas growth with N2 as the sole nitrogen source was observed only under anaerobic conditions. Cellular fatty acids were predominated by C16:1 ω7c, C16:0, and C18:1 ω7c. The major polar lipids consisted of phosphatidylethanolamine and phosphatidylserine. Strain NFV-1T had a DNA G + C content of 42.5 mol%, as evaluated according to the chromosomal DNA sequencing data. Analyses of sequence similarities and phylogeny based on the 16S rRNA genes, together with the housekeeping genes, gyrB, ftsZ, mreB, topA and gapA, indicated that the strain formed a distinct species-level lineage in the genus Vibrio of the family Vibrionaceae. These phylogenetic data and those from genomic and phenotypic characterisations support the establishment of a novel Vibrio species, for which the name Vibrio nitrifigilis sp. nov. (type strain NFV-1T = BCRC 81211T = JCM 33628T) is proposed.
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Affiliation(s)
- Wei-Sheng Huang
- Institute of Oceanography, National Taiwan University, P.O. Box 23-13, Taipei, 10617, Taiwan
| | - Li-Ting Wang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Rd., Hsinchu, 30062, Taiwan
| | - Jwo-Sheng Chen
- College of Health Care, China Medical University, No. 91, Shyue-Shyh Rd, Taichung, Taiwan
| | - Yen-Ting Chen
- Institute of Oceanography, National Taiwan University, P.O. Box 23-13, Taipei, 10617, Taiwan
| | | | - Yin-Ru Chiang
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Pei-Ling Wang
- Institute of Oceanography, National Taiwan University, P.O. Box 23-13, Taipei, 10617, Taiwan
| | - Tzong-Huei Lee
- Institute of Fisheries Science, National Taiwan University, Taipei, 10617, Taiwan
| | - Shih-Ting Lin
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Rd., Hsinchu, 30062, Taiwan
| | - Lina Huang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Rd., Hsinchu, 30062, Taiwan
| | - Wung Yang Shieh
- Institute of Oceanography, National Taiwan University, P.O. Box 23-13, Taipei, 10617, Taiwan.
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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 XF, Liu YJ, Dong JD, Qu LY, Zhang YY, Wang FZ, Tian XP, Zhang S. Mangrovibacterium diazotrophicum gen. nov., sp. nov., a nitrogen-fixing bacterium isolated from a mangrove sediment, and proposal of Prolixibacteraceae fam. nov. Int J Syst Evol Microbiol 2014; 64:875-881. [DOI: 10.1099/ijs.0.052779-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A nitrogen-fixing bacterium, designated strain SCSIO N0430T, was isolated from a mangrove sediment sample. Analysis of the sequence of the nifH gene responsible for nitrogen fixation in this strain indicated a close relationship to an uncultured bacterium ZNZ-D11 (GenBank accession no. JF896696). 16S rRNA gene sequence analysis revealed that this isolate had less than 93 % similarity to its closest relative,
Sunxiuqinia elliptica
DQHS4T. A phylogenetic tree reconstructed based on 16S rRNA gene sequences revealed that strain SCSIO N0430T was a member of the phylum
Bacteroidetes
. Chemotaxonomic and physiological characteristics, including phospholipids and major fatty acids, readily distinguished the isolate from established members of the phylum
Bacteroidetes
. It is concluded that strain SCSIO N0430T represents a novel genus and species, for which the name Mangrovibacterium diazotrophicum gen. nov., sp. nov. is proposed, with the type strain of the species SCSIO N0430T ( = KCTC 32129T = DSM 27148T = JCM 19152T). Based on phylogenetic characteristics and 16S rRNA gene signature nucleotide patterns, the three genera
Sunxiuqinia
,
Prolixibacter
and Mangrovibacterium are proposed to make up a novel family, Prolixibacteraceae fam. nov., in the order
Bacteroidales
.
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Affiliation(s)
- Xiao-Fang Huang
- Graduate University of the Chinese Academy of Sciences, Beijing 100049, PR China
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, CAS; RNAM Center for Marine Microbiology, CAS; Guangdong Key Laboratory of Marine Materia Medica; and South China Sea Institute of Oceanology, CAS, Guangzhou 510301, PR China
| | - Yu Juan Liu
- Graduate University of the Chinese Academy of Sciences, Beijing 100049, PR China
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, CAS; RNAM Center for Marine Microbiology, CAS; Guangdong Key Laboratory of Marine Materia Medica; and South China Sea Institute of Oceanology, CAS, Guangzhou 510301, PR China
| | - Jun-De Dong
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, CAS; RNAM Center for Marine Microbiology, CAS; Guangdong Key Laboratory of Marine Materia Medica; and South China Sea Institute of Oceanology, CAS, Guangzhou 510301, PR China
| | - Ling-Yun Qu
- First Institute of Oceanography, State Oceanic Administration, Qingdao 266061, PR China
| | - Yan-Ying Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, CAS; RNAM Center for Marine Microbiology, CAS; Guangdong Key Laboratory of Marine Materia Medica; and South China Sea Institute of Oceanology, CAS, Guangzhou 510301, PR China
| | - Fa-Zuo Wang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, CAS; RNAM Center for Marine Microbiology, CAS; Guangdong Key Laboratory of Marine Materia Medica; and South China Sea Institute of Oceanology, CAS, Guangzhou 510301, PR China
| | - Xin-Peng Tian
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, CAS; RNAM Center for Marine Microbiology, CAS; Guangdong Key Laboratory of Marine Materia Medica; and South China Sea Institute of Oceanology, CAS, Guangzhou 510301, PR China
| | - Si Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, CAS; RNAM Center for Marine Microbiology, CAS; Guangdong Key Laboratory of Marine Materia Medica; and South China Sea Institute of Oceanology, CAS, Guangzhou 510301, PR China
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Lee GH, Rhee MS, Chang DH, Kwon KK, Bae KS, Yang SH, Kim BC. Bacillus solimangrovi sp. nov., isolated from mangrove soil. Int J Syst Evol Microbiol 2014; 64:1622-1628. [PMID: 24488932 DOI: 10.1099/ijs.0.058230-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two novel bacterial strains, GH2-4T and GH2-5, were isolated from mangrove soil near the seashore of Weno island in Chuuk state, Micronesia, and were characterized by a polyphasic approach. The two strains were strictly aerobic, Gram-staining-positive, motile, endospore-forming rods that were catalase- and oxidase-positive. Colonies were circular, convex, stringy and transparent yellowish (GH2-4T) or opaque whitish (GH2-5). The 16S rRNA gene sequences of the two isolates were identical. The most closely related strains in terms of 16S rRNA gene sequence similarity were Bacillus kochii WCC 4582T, B. horneckiae DSM 23495T, B. azotoformans LMG 9581T, B. cohnii DSM 6307T and B. halmapalus DSM 8723T (95.6, 95.4, 95.4, 95.2 and 95.2% similarity, respectively). The partial groEL sequence of strain GH2-4T was identical to that of strain GH2-5 and showed <85% similarity to those of the most closely related strains. The isolates grew at pH 5-12 (optimal growth at pH 9), at 10-40 °C (optimum 30-35 °C) and at 0-9% (w/v) NaCl (optimum 1-3% NaCl). The cell-wall peptidoglycan of strains GH2-4T and GH2-5 contained meso-diaminopimelic acid and cell-wall hydrolysates contained ribose as a major sugar. The DNA G+C content was 36 mol%, and DNA-DNA relatedness between the isolates and five related reference strains was 20-24%. Strain GH2-4T exhibited 81% DNA-DNA relatedness with strain GH2-5. The major cellular fatty acids of both strains were iso-C15:0, iso-C16:0, iso-C14:0 and anteiso-C15:0 and the predominant menaquinone was MK-7. On the basis of the evidence from this polyphasic study, strains GH2-4T and GH2-5 (=KCTC 33143=JCM 18995=DSM 27084) represent a novel species of the genus Bacillus, for which the name Bacillus solimangrovi sp. nov. is proposed; the type strain is GH2-4T (=KCTC 33142T=JCM 18994T=DSM 27083T).
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Affiliation(s)
- Geun-Hye Lee
- Korean Collection for Type Cultures (KCTC), Biological Resource Center (BRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahangno, Yuseong-gu, Daejeon 305-806, Republic of Korea
| | - Moon-Soo Rhee
- Korean Collection for Type Cultures (KCTC), Biological Resource Center (BRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahangno, Yuseong-gu, Daejeon 305-806, Republic of Korea
| | - Dong-Ho Chang
- Korean Collection for Type Cultures (KCTC), Biological Resource Center (BRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahangno, Yuseong-gu, Daejeon 305-806, Republic of Korea
| | - Kae Kyoung Kwon
- Marine Biotechnology Research Division, Korea Institute of Ocean Science & Technology, PO Box 29, Ansan 425-600, Republic of Korea
| | - Kyung Sook Bae
- Korean Collection for Type Cultures (KCTC), Biological Resource Center (BRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahangno, Yuseong-gu, Daejeon 305-806, Republic of Korea
| | - Seong-Hyun Yang
- Marine Biotechnology Research Division, Korea Institute of Ocean Science & Technology, PO Box 29, Ansan 425-600, Republic of Korea
| | - Byoung-Chan Kim
- Korean Collection for Type Cultures (KCTC), Biological Resource Center (BRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahangno, Yuseong-gu, Daejeon 305-806, Republic of Korea
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Sawabe T, Ogura Y, Matsumura Y, Feng G, Amin AR, Mino S, Nakagawa S, Sawabe T, Kumar R, Fukui Y, Satomi M, Matsushima R, Thompson FL, Gomez-Gil B, Christen R, Maruyama F, Kurokawa K, Hayashi T. Updating the Vibrio clades defined by multilocus sequence phylogeny: proposal of eight new clades, and the description of Vibrio tritonius sp. nov. Front Microbiol 2013; 4:414. [PMID: 24409173 PMCID: PMC3873509 DOI: 10.3389/fmicb.2013.00414] [Citation(s) in RCA: 183] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Accepted: 12/16/2013] [Indexed: 12/13/2022] Open
Abstract
To date 142 species have been described in the Vibrionaceae family of bacteria, classified into seven genera; Aliivibrio, Echinimonas, Enterovibrio, Grimontia, Photobacterium, Salinivibrio and Vibrio. As vibrios are widespread in marine environments and show versatile metabolisms and ecologies, these bacteria are recognized as one of the most diverse and important marine heterotrophic bacterial groups for elucidating the correlation between genome evolution and ecological adaptation. However, on the basis of 16S rRNA gene phylogeny, we could not find any robust monophyletic lineages in any of the known genera. We needed further attempts to reconstruct their evolutionary history based on multilocus sequence analysis (MLSA) and/or genome wide taxonomy of all the recognized species groups. In our previous report in 2007, we conducted the first broad multilocus sequence analysis (MLSA) to infer the evolutionary history of vibrios using nine housekeeping genes (the 16S rRNA gene, gapA, gyrB, ftsZ, mreB, pyrH, recA, rpoA, and topA), and we proposed 14 distinct clades in 58 species of Vibrionaceae. Due to the difficulty of designing universal primers that can amplify the genes for MLSA in every Vibrionaceae species, some clades had yet to be defined. In this study, we present a better picture of an updated molecular phylogeny for 86 described vibrio species and 10 genome sequenced Vibrionaceae strains, using 8 housekeeping gene sequences. This new study places special emphasis on (1) eight newly identified clades (Damselae, Mediterranei, Pectenicida, Phosphoreum, Profundum, Porteresiae, Rosenbergii, and Rumoiensis); (2) clades amended since the 2007 proposal with recently described new species; (3) orphan clades of genomospecies F6 and F10; (4) phylogenetic positions defined in 3 genome-sequenced strains (N418, EX25, and EJY3); and (5) description of V. tritonius sp. nov., which is a member of the “Porteresiae” clade.
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Affiliation(s)
- Tomoo Sawabe
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University Hakodate, Japan
| | - Yoshitoshi Ogura
- Division of Genomics and Bioenvironmental Science, Frontier Science Research Center, University of Miyazaki Miyazaki, Japan
| | - Yuta Matsumura
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University Hakodate, Japan
| | - Gao Feng
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University Hakodate, Japan
| | - Akm Rohul Amin
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University Hakodate, Japan
| | - Sayaka Mino
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University Hakodate, Japan
| | - Satoshi Nakagawa
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University Hakodate, Japan
| | - Toko Sawabe
- Department of Food and Nutrition, Hakodate Junior College Hakodate, Japan
| | - Ramesh Kumar
- National Institute for Interdisciplinary Science and Technology (CSIR) Kerala, India
| | - Yohei Fukui
- National Research Institute of Fisheries Science, Fisheries Research Agency Yokohama, Japan
| | - Masataka Satomi
- National Research Institute of Fisheries Science, Fisheries Research Agency Yokohama, Japan
| | - Ryoji Matsushima
- National Research Institute of Fisheries Science, Fisheries Research Agency Yokohama, Japan
| | - Fabiano L Thompson
- Department of Genetics, Center of Health Sciences, Federal University of Rio de Janeiro (UFRS) Rio de Janeiro, Brazil
| | | | - Richard Christen
- CNRS UMR 7138, Systématique-Adaptation-Evolution Nice, France ; Systématique-Adaptation-Evolution, Université de Nice-Sophia Antipolis Nice, France
| | - Fumito Maruyama
- Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University Tokyo, Japan
| | - Ken Kurokawa
- Earth-Life Science Institute, Tokyo Institute of Technology Tokyo, Japan
| | - Tetsuya Hayashi
- Division of Genomics and Bioenvironmental Science, Frontier Science Research Center, University of Miyazaki Miyazaki, Japan
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9
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Gomez-Gil B, Roque A, Chimetto L, Moreira APB, Lang E, Thompson FL. Vibrio alfacsensis sp. nov., isolated from marine organisms. Int J Syst Evol Microbiol 2012; 62:2955-2961. [PMID: 22286904 DOI: 10.1099/ijs.0.033191-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Five strains (CAIM 1831(T), CAIM 1832, CAIM 1833, CAIM 1834 and CAIM 1836) were isolated from cultured sole (Solea senegalensis) in two regions of Spain, two strains (CAIM 404 and CAIM 1294) from wild-caught spotted rose snapper (Lutjanus guttatus) in Mexico, and one strain (CAIM 1835) from corals in Brazil. The 16S rRNA gene sequences of the novel isolates showed similarity to Vibrio ponticus (98.2-98.3%, GenBank accession no. AJ630103) and to a lesser degree to Vibrio furnissii (97.2-97.3%, X76336) and to Vibrio fluvialis (96.9-97.1%, X74703). Multilocus sequence analysis clustered these strains closely together and clearly separated them from phylogenetically related species of the genus Vibrio. Genomic fingerprinting by rep-PCR clustered the novel strains according to their geographical origin. Phenotypic analyses showed a large variation among the new strains, but many tests enabled them to be differentiated from other species of the genus Vibrio. The mean ΔT(m) values between the strains analysed here and closely related type strains were above 6.79 °C. The values between the novel isolates were below 2.35 °C, well outside the limit suggested for the delineation of a bacterial species. The phenotypic and genotypic data presented here clearly place these new strains as a coherent group within the genus Vibrio, for which we propose the name Vibrio alfacsensis sp. nov. with CAIM 1831(T) ( = DSM 24595(T) = S277(T)) as the type strain.
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Affiliation(s)
- Bruno Gomez-Gil
- CIAD, A.C. Mazatlán Unit for Aquaculture and Environmental Management, AP. 711 Mazatlán, CP 82000 Sinaloa, México
| | - Ana Roque
- Institut de Reçerca i Tecnologia Agroalimentaries, Centre d'Aquicultura, Sant Carles de la Rapita, Spain
| | - Luciane Chimetto
- Universidade Federal de Rio de Janeiro, Ilh Cidade Universitária, Rio de Janeiro 21941-970, Brazil
| | - Ana Paula B Moreira
- Universidade Federal de Rio de Janeiro, Ilh Cidade Universitária, Rio de Janeiro 21941-970, Brazil
| | - Elke Lang
- DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstr. 7B, 38124 Braunschweig, Germany
| | - Fabiano L Thompson
- Universidade Federal de Rio de Janeiro, Ilh Cidade Universitária, Rio de Janeiro 21941-970, Brazil
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10
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Gao ZM, Xiao J, Wang XN, Ruan LW, Chen XL, Zhang YZ. Vibrio xiamenensis sp. nov., a cellulase-producing bacterium isolated from mangrove soil. Int J Syst Evol Microbiol 2011; 62:1958-1962. [PMID: 22039001 DOI: 10.1099/ijs.0.033597-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A taxonomic study was carried out on a cellulase-producing bacterium, strain G21(T), isolated from mangrove soil in Xiamen, Fujian province, China. Cells were Gram-negative, slightly curved rods, motile with a single polar flagellum. The strain grew at 15-40 °C and in 0.5-10% (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain G21(T) belonged to the genus Vibrio and formed a clade with Vibrio furnissii ATCC 350116(T) (97.4% sequence similarity), V. fluvialis LMG 7894(T) (97.1%) and V. ponticus CECT 5869(T) (96.1%). However, multilocus sequence analysis (using rpoA, recA, mreB, gapA, gyrB and pyrH sequences) and DNA-DNA hybridization experiments indicated that the strain was distinct from the closest related Vibrio species. Additionally, strain G21(T) could be differentiated from them phenotypically by the ability to grow in 10% NaCl but not on TCBS plates, its enzyme activity spectrum, citrate utilization, oxidization of various carbon sources, hydrolysis of several substrates and its cellular fatty acid profile. The G+C content of the genomic DNA was 46.0 mol%. The major cellular fatty acids were summed feature 3 (C(16:1)ω7c and/or iso-C(15:0) 2-OH), C(16:0) and C(18:1)ω7c. The major polar lipids were phosphatidylethanolamine and phosphatidylglycerol, with trace amounts of diphosphatidylglycerol. The predominant quinones were Q-8 and Q-7. Based on phylogenetic, phenotypic and chemotaxonomic characteristics and DNA-DNA hybridization analysis, it is concluded that strain G21(T) represents a novel species of the genus Vibrio, for which the name Vibrio xiamenensis sp. nov. is proposed. The type strain is G21(T) ( = DSM 22851(T) = CGMCC 1.10228(T)).
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Affiliation(s)
- Zhao-Ming Gao
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration (SOA), Xiamen 361005, PR China.,The State Key Lab of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Jinan 250100, PR China
| | - Jing Xiao
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration (SOA), Xiamen 361005, PR China
| | - Xing-Na Wang
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration (SOA), Xiamen 361005, PR China
| | - Ling-Wei Ruan
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration (SOA), Xiamen 361005, PR China
| | - Xiu-Lan Chen
- The State Key Lab of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Jinan 250100, PR China
| | - Yu-Zhong Zhang
- The State Key Lab of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Jinan 250100, PR China
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11
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Rameshkumar N, Gomez-Gil B, Spröer C, Lang E, Dinesh Kumar N, Krishnamurthi S, Nair S, Roque A. Vibrio plantisponsor sp. nov., a diazotrophic bacterium isolated from a mangrove associated wild rice (Porteresia coarctata Tateoka). Syst Appl Microbiol 2011; 34:487-93. [PMID: 21596509 DOI: 10.1016/j.syapm.2011.02.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2010] [Revised: 01/30/2011] [Accepted: 02/02/2011] [Indexed: 12/14/2022]
Abstract
Two Gram negative, facultatively anaerobic, halophilic, motile, slightly curved rod-shaped bacterial strains MSSRF60(T) and MSSRF64 were isolated from the roots of a mangrove-associated wild rice collected in the Pichavaram mangroves, India. These strains possess the key functional nitrogenase gene nifH. Phylogenetic analysis based on the 16S rRNA, recA, gapA, mreB, gyrB and pyrH, gene sequences revealed that strains MSSRF60(T) and MSSRF64 belong to the genus Vibrio, and had the highest sequence similarity with the type strains of Vibrio diazotrophicus LMG 7893(T) (99.7, 94.8, 98.5, 97.9, 94.0 and 90.7%, respectively), Vibrio areninigrae J74(T) (98.2, 87.5, 91.5, 88.9, 86.5 and 84.6% respectively) and Vibrio hispanicus LMG 13240(T) (97.8, 87.1, 91.7, 89.8, 84.1 and 81.9%, respectively). The fatty acid composition too confirmed the affiliation of strains MSSRF60(T) and MSSRF64 to the genus Vibrio. These strains can be differentiated from the most closely related Vibrio species by several phenotypic traits. The DNA G+C content of strain MSSRF60(T) was 41.8mol%. Based on phenotypic, chemotaxonomic, genotypic (multilocus sequence analysis using five genes and genomic fingerprinting using BOX-PCR) and DNA-DNA hybridization analyses, strains MSSRF60(T) and MSSRF64 represent a novel species of the genus Vibrio, for which the name Vibrio plantipsonsor sp. nov. is proposed. The type strain is MSSRF60(T) (=DSM 21026(T)=LMG 24470(T)=CAIM 1392(T)).
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Affiliation(s)
- N Rameshkumar
- Microbiology Department, M.S. Swaminathan Research Foundation, 3rd Cross Street, Taramani Institutional Area, Chennai 600 113, India.
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12
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Wang H, Liu J, Wang Y, Zhang XH. Vibrio marisflavi sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2011; 61:568-573. [DOI: 10.1099/ijs.0.022285-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-reaction-negative, facultatively anaerobic bacterial strain, designated WH134T, was isolated from a seawater sample collected at a depth of 10 m near the Yellow Sea Cold Water Mass (YSCWM), 3 ° 59.970′ N 12 ° 0.157′ E, PR China. Cells of strain WH134T were slightly curved rods, motile by means of a polar flagellum and positive for poly-β-hydroxybutyrate (PHB) accumulation. The strain was able to grow in 1–6 % (w/v) NaCl, at pH 5–10 and 16–37 °C but not at 4 or 40 °C. The major cellular fatty acids were summed feature 3 C16
: 1
ω7c and/or iso-C15 : 0 2-OH, C16 : 0, C18 : 1
ω7c, C18 : 0 and C14 : 0. The DNA G+C content was 42.5 mol%. Phylogenetic analyses based on 16S rRNA, gyrB, topA, recA, ftsZ, mreB, gapA and rpoA gene sequences revealed that strain WH134T belongs to the genus Vibrio and showed gene sequence similarities of 96.6, 75.7, 74.6, 83.6, 78.9, 82.9, 86.0 and 89.4 % , respectively, to Vibrio rumoiensis S-1T. The possession of a flagellum, activity of arginine dihydrolase and lysine decarboxylase and inability to utilize citrate, however, differentiated strain WH134T from V. rumoiensis DSM 19141T. On the basis of the phenotypic, chemotaxonomic and phylogenetic evidence, strain WH134T represents a novel species of the genus Vibrio, for which the name Vibrio marisflavi sp. nov. is proposed. The type strain is WH134T (=CGMCC 1.8994T =LMG 25284T =DSM 23086T).
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Affiliation(s)
- Hong Wang
- Department of Marine Biology, Ocean University of China, 5 Yushan Road, Qingdao 266003, PR China
| | - Jiwen Liu
- Department of Marine Biology, Ocean University of China, 5 Yushan Road, Qingdao 266003, PR China
| | - Yan Wang
- Department of Marine Biology, Ocean University of China, 5 Yushan Road, Qingdao 266003, PR China
| | - Xiao-Hua Zhang
- Department of Marine Biology, Ocean University of China, 5 Yushan Road, Qingdao 266003, PR China
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13
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Chimetto LA, Cleenwerck I, Alves N, Silva BS, Brocchi M, Willems A, De Vos P, Thompson FL. Vibrio communis sp. nov., isolated from the marine animals Mussismilia hispida, Phyllogorgia dilatata, Palythoa caribaeorum, Palythoa variabilis and Litopenaeus vannamei. Int J Syst Evol Microbiol 2011; 61:362-368. [DOI: 10.1099/ijs.0.019729-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Eight Vibrio isolates originating from the marine corals Mussismilia hispida and Phyllogorgia dilatata and the zoanthids Palythoa caribaeorum and Palythoa variabilis in Brazil and the Pacific white shrimp (Litopenaeus vannamei) in Ecuador were studied by means of a polyphasic approach. The novel isolates formed a tight monophyletic group in the genus Vibrio and were closely related to species of the Vibrio harveyi group, to which they showed more than 99 % 16S rRNA gene sequence similarity. Analysis based on concatenated sequences of the following seven genes, 16S rRNA, gyrB, recA, rpoA, topA, pyrH and mreB (5633 bp in length), showed clear separation between the isolates and species of the V. harveyi group. Amplified fragment length polymorphism (AFLP) analysis, performed previously, revealed that a representative isolate of this group, LMG 20370, was clearly separate from known Vibrio species (it belonged to the so-called AFLP cluster A31). DNA–DNA hybridization (DDH) experiments with representative isolates and type strains of the V. harveyi species group revealed high DDH between the novel isolates (more than 74 %) and less than 70 % DDH towards type strains of related Vibrio species, proving the novel species status of the isolates. Phenotypically, the novel species belongs to the arginine dihydrolase (A)-negative, lysine decarboxylase (L)-positive and ornithine decarboxylase (O)-positive (A−/L+/O+) cluster reported previously. Most species of the V. harveyi group (i.e. Vibrio rotiferianus, V. harveyi, V. parahaemolyticus and V. alginolyticus) also belong to this A−/L+/O+ cluster. However, several phenotypic features can be used for the identification of the novel species. In contrast to its closest phylogenetic neighbours, the novel species exhibits esterase (C4) and N-acetyl-β-glucosaminidase activities, but it does not produce acetoin, does not use citrate, α-ketoglutaric acid or propionic acid and does not ferment melibiose. The novel species can also be differentiated on the basis of the presence of the fatty acids C17 : 0, C17 : 1
ω8c, iso-C17 : 0 and iso-C13 : 0 and the absence of the fatty acid C18 : 0. The name Vibrio communis sp. nov. is proposed for this taxon. Strain R-40496T (=LMG 25430T =CAIM 1816T) is the type strain.
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Affiliation(s)
- Luciane A. Chimetto
- BCCM/LMG Bacteria Collection, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
- Department of Genetics, Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
- Department of Genetics, Evolution and Bioagents, Biology Institute, State University of Campinas (UNICAMP), Campinas, Brazil
| | - Ilse Cleenwerck
- BCCM/LMG Bacteria Collection, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Nelson Alves
- Department of Genetics, Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Bruno Sergio Silva
- Department of Genetics, Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Marcelo Brocchi
- Department of Genetics, Evolution and Bioagents, Biology Institute, State University of Campinas (UNICAMP), Campinas, Brazil
| | - Anne Willems
- Laboratory of Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Paul De Vos
- Laboratory of Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
- BCCM/LMG Bacteria Collection, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Fabiano L. Thompson
- Department of Genetics, Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
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14
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Dikow RB. Systematic relationships within the Vibrionaceae (Bacteria: Gammaproteobacteria): steps toward a phylogenetic taxonomy. Cladistics 2011; 27:9-28. [DOI: 10.1111/j.1096-0031.2010.00312.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
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15
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Sheu SY, Jiang SR, Chen CA, Wang JT, Chen WM. Vibrio stylophorae sp. nov., isolated from the reef-building coral Stylophora pistillata. Int J Syst Evol Microbiol 2010; 61:2180-2185. [PMID: 20935089 DOI: 10.1099/ijs.0.026666-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A bacterial strain designated KTW-12(T) was isolated from a reef-building coral in Kenting, Taiwan, and was characterized using a polyphasic taxonomic approach. Strain KTW-12(T) was Gram-negative, semi-transparent, slightly curved rod-shaped, and non-motile. Growth occurred at 15-35 °C (optimum, 30 °C), at pH 6.0-9.0 (optimum, pH 7.0-8.0), and with 0.5-6.0 % NaCl (optimum, 2 %). The major cellular fatty acids were summed feature 3 (C₁₆:₁ω7c and/or C₁₆:₁ω6c), C₁₄:₀ and C₁₆:₀. The DNA G+C content was 47.8 mol%. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain KTW-12(T) was most closely related to Vibrio porteresiae MSSRF30(T), with 94.8 % gene sequence similarity. Further multilocus sequence analysis using rpoA, recA and pyrH genes also revealed low levels of sequence similarity (74.6-85.0 %) with all species of the genus Vibrio with validly published names. A multigene phylogenetic tree using concatenated sequences of the four genes (16S rRNA, rpoA, recA and pyrH) elucidated that strain KTW-12(T) occupied a distinct phylogenetic position, forming a long branch that was not clustered with any other known species of the genus Vibrio. Strain KTW-12(T) differed from V. porteresiae MSSRF30(T) in the ability to reduce nitrate to nitrite, hydrolysis of chitin, fermentation of sorbitol and production of arginine dihydrolase, valine arylamidase, cystine arylamidase and N-acetyl-β-glucosaminidase. On the basis of phenotypic, chemotaxonomic and phylogenetic distinctiveness, strain KTW-12(T) should be classified as representing a novel species, for which the name Vibrio stylophorae sp. nov. is proposed. The type strain is KTW-12(T) ( = BCRC 80105(T) = LMG 25357(T)).
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Affiliation(s)
- Shih-Yi Sheu
- Department of Marine Biotechnology, National Kaohsiung Marine University, No. 142, Hai-Chuan Rd. Nan-Tzu, Kaohsiung City 811, Taiwan
| | - Sing-Rong Jiang
- Laboratory of Microbiology, Department of Seafood Science, National Kaohsiung Marine University, No. 142, Hai-Chuan Rd. Nan-Tzu, Kaohsiung City 811, Taiwan
| | - Chaolun Allen Chen
- Research Center for Biodiversity, Academia Sinica, Nangang 115, Taipei, Taiwan
| | - Jih-Terng Wang
- Institute of Biotechnology, Tajen University, Yanpu, Pingtung 907, Taiwan
| | - Wen-Ming Chen
- Laboratory of Microbiology, Department of Seafood Science, National Kaohsiung Marine University, No. 142, Hai-Chuan Rd. Nan-Tzu, Kaohsiung City 811, Taiwan
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Rameshkumar N, Sproer C, Lang E, Nair S. Vibrio mangrovi sp. nov., a diazotrophic bacterium isolated from mangrove-associated wild rice (Poteresia coarctata Tateoka). FEMS Microbiol Lett 2010; 307:35-40. [DOI: 10.1111/j.1574-6968.2010.01958.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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17
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Rameshkumar N, Lang E, Nair S. Mangrovibacter plantisponsor gen. nov., sp. nov., a nitrogen-fixing bacterium isolated from a mangrove-associated wild rice (Porteresia coarctata Tateoka). Int J Syst Evol Microbiol 2010; 60:179-186. [DOI: 10.1099/ijs.0.008292-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A facultatively anaerobic, nitrogen-fixing bacterium, strain MSSRF40T, was isolated from roots of mangrove-associated wild rice (Porteresia coarctata Tateoka). On the basis of 16S rRNA gene sequence similarities, strain MSSRF40T was shown to belong to the family Enterobacteriaceae, most closely related to Cronobacter muytjensii E603T (97.2 % sequence similarity), Enterobacter cloacae subsp. dissolvens LMG 2683T (97.1 %), E. radicincitans D5/23T (97.1 %) and E. ludwigii EN-119T (97.0 %). Sequence analysis of rpoB, gyrB and hsp60 genes showed that strain MSSRF40T had relatively low sequence similarity (<91, <84 and <90 %) to recognized species of different genera of the family Enterobacteriaceae and formed an independent phyletic lineage in all phylogenetic analyses using the 16S rRNA, rpoB, gyrB and hsp60 genes, clearly indicating that strain MSSRF40T could not be affiliated to any of the recognized genera within the family Enterobacteriaceae. The dominant cellular fatty acids were C16 : 0, C16 : 1
ω7c and/or iso-C15 : 0 2-OH and C18 : 1
ω7c, similar to those of other members of the Enterobacteriaceae. The DNA G+C content was 50.1 mol%. Phylogenetic distinctiveness and phenotypic differences from its phylogenetic neighbours indicated that strain MSSRF40T represents a novel species and genus within the family Enterobacteriaceae, for which the name Mangrovibacter plantisponsor gen. nov., sp. nov. is proposed. The type strain of Mangrovibacter plantisponsor is strain MSSRF40T (=LMG 24236T =DSM 19579T).
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Affiliation(s)
- N. Rameshkumar
- Microbiology Department, M. S. Swaminathan Research Foundation, 3rd Cross Street, Taramani Institutional Area, Chennai – 600 113, India
| | - Elke Lang
- DSMZ – Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstraße 7b, D-30124 Braunschweig, Germany
| | - Sudha Nair
- Microbiology Department, M. S. Swaminathan Research Foundation, 3rd Cross Street, Taramani Institutional Area, Chennai – 600 113, India
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18
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19
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Wang Y, Zhang XH, Yu M, Wang H, Austin B. Vibrio atypicus sp. nov., isolated from the digestive tract of the Chinese prawn (Penaeus chinensis O'sbeck). Int J Syst Evol Microbiol 2009; 60:2517-2523. [PMID: 19965995 DOI: 10.1099/ijs.0.016915-0] [Citation(s) in RCA: 25] [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 culture (designated strain HHS02(T)) was isolated from Chinese prawn (Penaeus chinensis, O'sbeck) and determined to be a member of the genus Vibrio. Strain HHS02(T) comprised slightly curved, rod-shaped, non-endospore-forming, Gram-negative, catalase-negative, oxidase-positive, O/129-sensitive and facultatively anaerobic cells that were motile by means of a single polar flagellum. Growth of strain HHS02(T) occurred in 0.5-7 % (w/v) NaCl [optimally in 1-3 % (w/v) NaCl] and between pH 7.0 and 10.0 (optimally at pH 8.0-9.0). The strain showed growth between 16 and 30 °C (optimum 20 °C). Analysis using the 16S rRNA, gapA, gyrB, mreB, pyrH, recA and topA gene sequences of the novel isolate revealed that the organism belonged to the genus Vibrio, with ∼98, 98, 90, 88, 92, 89 and 83 % sequence similarity, respectively, with representatives of the genus Vibrio. DNA-DNA hybridization experiments indicated that the novel strain was distinct from recognized species of the genus Vibrio. The major fatty acid components were summed feature 3 (C(16 : 1)ω7c and/or iso-C(15 : 0) 2-OH, 38.7 %), C(16 : 0) (22.9 %) and C(18 : 1)ω7c (12.5 %). The G+C content of the genomic DNA was 44.4 mol%. On the basis of the polyphasic taxonomic evidence presented in this study, it is concluded that strain HHS02(T) should be classified as a novel species of the genus Vibrio, for which the name Vibrio atypicus sp. nov. is proposed. The type strain is HHS02(T) (=CGMCC 1.8461(T)=LMG 24781(T)).
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Affiliation(s)
- Yan Wang
- Department of Marine Biology, Ocean University of China, Qingdao 266003, PR China
| | - Xiao-Hua Zhang
- Department of Marine Biology, Ocean University of China, Qingdao 266003, PR China
| | - Min Yu
- Department of Marine Biology, Ocean University of China, Qingdao 266003, PR China
| | - Hong Wang
- Department of Marine Biology, Ocean University of China, Qingdao 266003, PR China
| | - Brian Austin
- Institute of Aquaculture, University of Stirling, Stirling FK9 4LA, UK
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Pascual J, Macián MC, Arahal DR, Garay E, Pujalte MJ. Multilocus sequence analysis of the central clade of the genus Vibrio by using the 16S rRNA, recA, pyrH, rpoD, gyrB, rctB and toxR genes. Int J Syst Evol Microbiol 2009; 60:154-165. [PMID: 19648344 DOI: 10.1099/ijs.0.010702-0] [Citation(s) in RCA: 148] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
The central clade of the genus Vibrio, also called the Vibrio core group, comprises six species that are tightly related (DNA-DNA reassociation values are very close to 70 % for most species pairs). Identification of novel strains to the species level within this group is troublesome and results are quite often dependent on the methodology employed. Therefore, this group represents an excellent framework to test the robustness of multilocus sequence analysis (MLSA) not only for inferring phylogeny but also as an identification tool without the need for DNA-DNA hybridization assays. The genes selected, 16S rRNA, recA, pyrH, rpoD, gyrB, rctB and toxR, were amplified by direct PCR from 44 Vibrio core-group strains. Subsequent analysis allowed us to recognize toxR and rpoD as the most resolving individual genes and showed that concatenated sequences of rpoD, rctB and toxR were more useful than concatenated sequences of all seven genes. To validate our conclusions, MLSA similarities have been correlated with DNA-DNA relatedness values obtained in this study and values taken from the literature. Although the seven concatenated genes gave the best correlation, the concatenated sequences of rpoD, rctB and toxR have the practical advantage of showing a considerable gap between the maximal interspecies similarity and the minimal intraspecies similarity recorded, meaning that they can be used quite conveniently for species identification of vibrios.
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Affiliation(s)
- Javier Pascual
- Departamento de Microbiología y Ecología, Universidad de Valencia, Spain.,Instituto Cavanilles de Biodiversidad y Biología Evolutiva (ICBiBE), Universidad de Valencia, Spain
| | - M Carmen Macián
- Colección Española de Cultivos Tipo (CECT), Universidad de Valencia, Spain.,Departamento de Microbiología y Ecología, Universidad de Valencia, Spain
| | - David R Arahal
- Colección Española de Cultivos Tipo (CECT), Universidad de Valencia, Spain.,Departamento de Microbiología y Ecología, Universidad de Valencia, Spain
| | - Esperanza Garay
- Colección Española de Cultivos Tipo (CECT), Universidad de Valencia, Spain.,Departamento de Microbiología y Ecología, Universidad de Valencia, Spain
| | - María J Pujalte
- Colección Española de Cultivos Tipo (CECT), Universidad de Valencia, Spain.,Departamento de Microbiología y Ecología, Universidad de Valencia, Spain
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Rameshkumar N, Nair S. Isolation and molecular characterization of genetically diverse antagonistic, diazotrophic red-pigmented vibrios from different mangrove rhizospheres. FEMS Microbiol Ecol 2009; 67:455-67. [DOI: 10.1111/j.1574-6941.2008.00638.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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