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Baseggio L, Silayeva O, Buller N, Landos M, Englestädter J, Barnes AC. Complete, closed and curated genome sequences of Photobacterium damselae subsp. piscicida isolates from Australia indicate mobilome-driven localized evolution and novel pathogenicity determinants. Microb Genom 2021; 7:000562. [PMID: 33885359 PMCID: PMC8208687 DOI: 10.1099/mgen.0.000562] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Despite the recent advances in sequencing technologies, the complete assembly of multi-chromosome genomes of the Vibrionaceae, often containing several plasmids, remains challenging. Using a combination of Oxford Nanopore MinION long reads and short Illumina reads, we fully sequenced, closed and curated the genomes of two strains of a primary aquatic pathogen Photobacterium damselae subsp. piscicida isolated in Australia. These are also the first genome sequences of P. damselae subsp. piscicida isolated in Oceania and, to our knowledge, in the Southern hemisphere. We also investigated the phylogenetic relationships between Australian and overseas isolates, revealing that Australian P. damselae subsp. piscicida are more closely related to the Asian and American strains rather than to the European ones. We investigated the mobilome and present new evidence showing that a host specialization process and progressive adaptive evolution to fish are ongoing in P. damselae subsp. piscicida, and are largely mediated by transposable elements, predominantly in chromosome 2, and by plasmids. Finally, we identified two novel potential virulence determinants in P. damselae subsp. piscicida - a chorismate mutase gene, which is ubiquitously retained and co-localized with the AIP56 apoptogenic toxin-encoding gene on the pPHDP10 plasmid, and transfer-messenger RNA gene ssrA located on the main chromosome, homologous to a critical-to-virulence determinant in Yersinia pseudotuberculosis. Our study describes, to our knowledge, the only fully closed and manually curated genomes of P. damselae subsp. piscicida available to date, offering new insights into this important fish pathogen and its evolution.
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Affiliation(s)
- Laura Baseggio
- School of Biological Sciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Oleksandra Silayeva
- School of Biological Sciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Nicky Buller
- Diagnostic and Laboratory Services (DDLS), Department of Primary Industries and Regional Development (DPIRD), 3 Baron-Hay Court, South Perth, Western Australia 6151, Australia
| | - Matt Landos
- Future Fisheries Veterinary Services, East Ballina, New South Wales 2478, Australia
| | - Jan Englestädter
- School of Biological Sciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Andrew C. Barnes
- School of Biological Sciences, University of Queensland, Brisbane, Queensland 4072, Australia
- *Correspondence: Andrew C. Barnes,
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Lascu I, Mereuță I, Chiciudean I, Hansen H, Avramescu SM, Tănase A, Stoica I. Complete genome sequence of Photobacterium ganghwense C2.2: A new polyhydroxyalkanoate production candidate. Microbiologyopen 2021; 10:e1182. [PMID: 33970538 PMCID: PMC8087987 DOI: 10.1002/mbo3.1182] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/12/2021] [Accepted: 03/15/2021] [Indexed: 12/30/2022] Open
Abstract
Polyhydroxyalkanoates (PHAs) are biodegradable bioplastics that can be manufactured sustainably and represent a promising green alternative to petrochemical-based plastics. Here, we describe the complete genome of a new marine PHA-producing bacterium-Photobacterium ganghwense (strain C2.2), which we have isolated from the Black Sea seashore. This new isolate is psychrotolerant and accumulates PHA when glycerol is provided as the main carbon source. Transmission electron microscopy, specific staining with Nile Red visualized via epifluorescence microscopy and gas chromatography analysis confirmed the accumulation of PHA. This is the only PHA-producing Photobacterium for which we now have a complete genome sequence, allowing us to investigate the pathways for PHA production and other secondary metabolite synthesis pathways. The de novo assembly genome, obtained using open-source tools, comprises two chromosomes (3.5, 2 Mbp) and a megaplasmid (202 kbp). We identify the entire PHA synthesis gene cluster that encodes a class I PHA synthase, a phasin, a 3-ketothiolase, and an acetoacetyl-CoA reductase. No conventional PHA depolymerase was identified in strain C2.2, but a putative lipase with extracellular amorphous PHA depolymerase activity was annotated, suggesting that C2.2 is unable to degrade intracellular PHA. A complete pathway for the conversion of glycerol to acetyl-CoA was annotated, in accordance with its ability to convert glycerol to PHA. Several secondary metabolite biosynthetic gene clusters and a low number of genes involved in antibiotic resistance and virulence were also identified, indicating the strain's suitability for biotechnological applications.
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Affiliation(s)
- Irina Lascu
- Department of GeneticsFaculty of BiologyUniversity of BucharestBucharestRomania
| | - Ioana Mereuță
- Department of GeneticsFaculty of BiologyUniversity of BucharestBucharestRomania
| | - Iulia Chiciudean
- Department of GeneticsFaculty of BiologyUniversity of BucharestBucharestRomania
| | - Hilde Hansen
- Department of ChemistryFaculty of Science and TechnologyUiT The Arctic University of NorwayTromsøNorway
| | - Sorin Marius Avramescu
- Department of Organic Chemistry, Biochemistry and CatalysisFaculty of ChemistryUniversity of BucharestBucharestRomania
| | - Ana‐Maria Tănase
- Department of GeneticsFaculty of BiologyUniversity of BucharestBucharestRomania
| | - Ileana Stoica
- Department of GeneticsFaculty of BiologyUniversity of BucharestBucharestRomania
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Roslan NN, Ngalimat MS, Leow ATC, Oslan SN, Baharum SN, Sabri S. Genomic and phenomic analysis of a marine bacterium, Photobacterium marinum J15. Microbiol Res 2020; 233:126410. [PMID: 31945517 DOI: 10.1016/j.micres.2020.126410] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 11/29/2019] [Accepted: 01/09/2020] [Indexed: 11/18/2022]
Abstract
Photobacterium species are widely distributed in the marine environment. The overall metabolism of this genus remains largely unknown. In order to improve our knowledge on this bacterium, the relationship between the genome and phenome of the Photobacterium isolate was analyzed. The cream colored, Gram-negative, rod-shaped and motile bacterial strain, J15, was isolated from marine water of Tanjung Pelepas, Johor, Malaysia. The 5,684,538 bp genome of strain J15 comprised 3 contigs (2 chromosomes and 1 plasmid) with G + C content of 46.39 % and contained 4924 protein-coding genes including 180 tRNAs and 40 rRNAs. The phenotypic microarray (PM) as analyzed using BIOLOG showed the utilization of; i) 93 of the 190 carbon sources tested, where 61 compounds were used efficiently; ii) 41 of the 95 nitrogen sources tested, where 22 compounds were used efficiently; and iii) 3 of the 94 phosphorous and sulphur sources tested. Furthermore, high tolerance to osmotic stress, basic pH and toxic compounds as well as resistance to antibiotics of strain J15 were determined by BIOLOG PM. The ANI and kSNP analyses revealed that strain J15 to be the same species with Photobacterium marinum AK15 with ANI value of 96.93 % and bootstrapping value of 100 in kSNP. Based on the ANI and kSNP analyses, strain J15 was identified as P. marinum J15.
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Affiliation(s)
- Noordiyanah Nadhirah Roslan
- Enzyme and Microbial Technology Research Center, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Mohamad Syazwan Ngalimat
- Enzyme and Microbial Technology Research Center, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Adam Thean Chor Leow
- Enzyme and Microbial Technology Research Center, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Department of Cell and Molecular Biology, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Siti Nurbaya Oslan
- Enzyme and Microbial Technology Research Center, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Department of Biochemistry, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Syarul Nataqain Baharum
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, 43600 UKM, Bangi, Selangor, Malaysia
| | - Suriana Sabri
- Enzyme and Microbial Technology Research Center, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
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Li M, Kong D, Wang Y, Ma Q, Han X, Zhou Y, Jiang X, Zhang Y, Ruan Z, Zhang Q. Photobacterium salinisoli sp. nov., isolated from a sulfonylurea herbicide-degrading consortium enriched with saline soil. Int J Syst Evol Microbiol 2019; 69:3910-3916. [PMID: 31693472 DOI: 10.1099/ijsem.0.003705] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, aerobic, motile, rod-shaped bacterium, designated strain LAM9072T, was isolated from a sample of a sulfonylurea herbicide-degrading consortium enriched with saline soil. The optimal temperature and pH for the growth of strain LAM9072T were 35 °C and 7.0, respectively. Strain LAM9072T could grow in the presence of NaCl up to 9 % (w/v). Comparative analysis of the 16S rRNA gene sequences revealed that strain LAM9072T was closely related to members of the family Vibrionaceae, with the highest similarities to Photobacterium halotolerans MACL01T (97.7 %) and Photobacterium galatheae S2753T (97.7 %). Strain LAM9072T formed a distinct phylogenetic subclade within the genus Photobacterium in the 16S rRNA gene phylogenetic trees. The results of multi-locus sequence analysis revealed a distinct lineage with P. halotolerans MACL01T as its closest relative. The genomic G+C content was 50.2 mol%. The DNA-DNA hybridization values between strain LAM9072T and P. halotolerans LMG 22194T and P. galatheae LMG 28894T were 41.6 and 22.2 %, respectively. The average nucleotide identity values were 90.9 and 78.8 %, respectively, by comparing the draft genome sequences of strain LAM9072T and P. halotolerans LMG 22194T and P. galatheae LMG 28894T. The major fatty acids were summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c), C16 : 0 and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). Ubiquinone 8 was detected as the predominant respiratory quinone. The main polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, aminophospholipid and four unidentified lipids. Based on its phenotypic characteristics and the results of genotypic analyses, we propose that strain LAM9072T represents a novel species, for which the name Photobacteriumsalinisoli sp. nov. is proposed. The type strain is LAM9072T (=ACCC 19961T=JCM 30852T).
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Affiliation(s)
- Miaomiao Li
- Key Laboratory of Microbial Resources (Ministry of Agriculture, China), Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang 330045, PR China
| | - Delong Kong
- Key Laboratory of Microbial Resources (Ministry of Agriculture, China), Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China
| | - Yani Wang
- Key Laboratory of Microbial Resources (Ministry of Agriculture, China), Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China
| | - Qingyun Ma
- Key Laboratory of Microbial Resources (Ministry of Agriculture, China), Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China
| | - Xiaoyan Han
- Key Laboratory of Microbial Resources (Ministry of Agriculture, China), Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang 330045, PR China
| | - Yiqing Zhou
- Key Laboratory of Microbial Resources (Ministry of Agriculture, China), Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China
| | - Xu Jiang
- Key Laboratory of Microbial Resources (Ministry of Agriculture, China), Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China
| | - Yuqin Zhang
- Chinese Academy of Medical Sciences and Peking Union Medical College, Institute of Medicinal Biotechnology, Beijing 100050, PR China
| | - Zhiyong Ruan
- Key Laboratory of Microbial Resources (Ministry of Agriculture, China), Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China
| | - Qinghua Zhang
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang 330045, PR China
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Le Doujet T, De Santi C, Klemetsen T, Hjerde E, Willassen NP, Haugen P. Closely-related Photobacterium strains comprise the majority of bacteria in the gut of migrating Atlantic cod (Gadus morhua). Microbiome 2019; 7:64. [PMID: 30995938 PMCID: PMC6471968 DOI: 10.1186/s40168-019-0681-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 04/05/2019] [Indexed: 05/23/2023]
Abstract
BACKGROUND The population of Atlantic cod (Gadus morhua), also known as Northeast Arctic cod, migrating Atlantic cod, or simply "skrei," lives mainly in the Barents Sea and Svalbard waters and migrates in annual cycles to the Norwegian coast in order to spawn eggs during late winter. It is the world's largest population of Atlantic cod, and the population is distinct from the Norwegian coastal cod (or "fjord" cod). Despite the biological, economic, and cultural importance of migrating Atlantic cod, current knowledge on the associated microbiota is very limited. Using shotgun metagenomics and metaproteomics approaches, we present here the gut microbiota, metagenome-assembled genomes (MAGs) of the most abundant bacterial species, DNA-based functional profile, and the metaproteome of Atlantic cod specimens caught at a spawning area in an open ocean outside of Tromsø, Norway. RESULTS Our analyses identified 268 bacterial families in DNA isolated from feces of 6 individual migrating Atlantic cod. The most abundant family was Vibrionaceae (52%; 83% if unclassified reads are excluded), with Photobacterium (genus) representing the vast majority. The recovery of metagenome-assembled genomes provided further details and suggests that several closely related Photobacterium strains from the Photobacterium phosphoreum clade are the most abundant. A genomic-based functional profiling showed that the most abundant functional subsystems are "Carbohydrates"; "Amino Acids and Derivatives"; "Protein Metabolism"; "Cofactors, Vitamins, Prosthetic, Groups, and Pigments"; and "DNA Metabolism," which is in agreement with other studies of gut microbiomes of marine organisms. Finally, the MS-based metaproteomic dataset revealed that the functional category "Protein Metabolism" is highly overrepresented (3×) when compared to the genome-based functional profile, which shows that ribosomal proteins are rich in the bacterial cytosol. CONCLUSION We present here the first study of bacterial diversity of the gut of migrating Atlantic cod using shotgun sequencing and metagenome-assembled genomes (MAGs). The most abundant bacteria belong to the Photobacterium genus (Vibrionaceae family). We also constructed functional profiles of the gut microbiome. These may be used in future studies as a platform for mining of commercially interesting cold-active enzymes.
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Affiliation(s)
- Typhaine Le Doujet
- Department of Chemistry and the Center for Bioinformatics (SfB), Faculty of Science and Technology, UiT The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Concetta De Santi
- Department of Chemistry and the Center for Bioinformatics (SfB), Faculty of Science and Technology, UiT The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Terje Klemetsen
- Department of Chemistry and the Center for Bioinformatics (SfB), Faculty of Science and Technology, UiT The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Erik Hjerde
- Department of Chemistry and the Center for Bioinformatics (SfB), Faculty of Science and Technology, UiT The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Nils-Peder Willassen
- Department of Chemistry and the Center for Bioinformatics (SfB), Faculty of Science and Technology, UiT The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Peik Haugen
- Department of Chemistry and the Center for Bioinformatics (SfB), Faculty of Science and Technology, UiT The Arctic University of Norway, N-9037 Tromsø, Norway
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Bjornsdottir-Butler K, McCarthy SA, Dunlap PV, Benner RA. Photobacterium angustum and Photobacterium kishitanii, Psychrotrophic High-Level Histamine-Producing Bacteria Indigenous to Tuna. Appl Environ Microbiol 2016; 82:2167-2176. [PMID: 26826233 PMCID: PMC4807525 DOI: 10.1128/aem.02833-15] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 01/26/2016] [Indexed: 11/20/2022] Open
Abstract
Scombrotoxin fish poisoning (SFP) remains the main contributor of fish poisoning incidents in the United States, despite efforts to control its spread. Psychrotrophic histamine-producing bacteria (HPB) indigenous to scombrotoxin-forming fish may contribute to the incidence of SFP. We examined the gills, skin, and anal vents of yellowfin (n = 3), skipjack (n = 1), and albacore (n = 6) tuna for the presence of indigenous HPB. Thirteen HPB strains were isolated from the anal vent samples from albacore (n = 3) and yellowfin (n = 2) tuna. Four of these isolates were identified as Photobacterium kishitanii and nine isolates as Photobacterium angustum; these isolates produced 560 to 603 and 1,582 to 2,338 ppm histamine in marine broth containing 1% histidine (25°C for 48 h), respectively. The optimum growth temperatures and salt concentrations were 26 to 27°C and 1% salt for P. kishitanii and 30 to 32°C and 2% salt for P. angustum in Luria 70% seawater (LSW-70). The optimum activity of the HDC enzyme was at 15 to 30°C for both species. At 5°C, P. kishitanii and P. angustum had growth rates of 0.1 and 0.2 h(-1), respectively, and the activities of histidine decarboxylase (HDC) enzymes were 71% and 63%, respectively. These results show that indigenous HPB in tuna are capable of growing at elevated and refrigeration temperatures. These findings demonstrate the need to examine the relationships between the rate of histamine production at refrigeration temperatures, seafood shelf life, and regulatory limits.
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Affiliation(s)
- K Bjornsdottir-Butler
- FDA, Division of Seafood Science and Technology, Gulf Coast Seafood Laboratory, Dauphin Island, Alabama, USA
| | - S A McCarthy
- FDA, Division of Seafood Science and Technology, Gulf Coast Seafood Laboratory, Dauphin Island, Alabama, USA
| | - P V Dunlap
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - R A Benner
- FDA, Division of Seafood Science and Technology, Gulf Coast Seafood Laboratory, Dauphin Island, Alabama, USA
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Machado H, Giubergia S, Mateiu RV, Gram L. Photobacterium galatheae sp. nov., a bioactive bacterium isolated from a mussel in the Solomon Sea. Int J Syst Evol Microbiol 2015; 65:4503-4507. [PMID: 26374506 DOI: 10.1099/ijsem.0.000603] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
A novel, Gram-negative marine bacterium, S2753T, was isolated from a mussel of the Solomon Sea, Solomon Islands. Analysis of the 16S rRNA gene sequence and whole genome sequence data placed strain S2753T in the genus Photobacterium with the closest relative being Photobacterium halotolerans DSM 18316T (97.7 % 16S rRNA gene similarity). Strain S2753T was able to grow from 15 to 40 °C and in NaCl concentrations of 0.5 to 9 % (w/v). The predominant fatty acids were 16 : 1ω7c/16 : 1ω6c (27.9 %), 16 : 0 (22.1 %) and 18 : 1ω7c/8 : 1ω6c (21.4 %). The genomic DNA G+C mol content was 49.5 mol%. Based on the phylogenetic, chemotaxonomic and phenotypic differences, strain S2753T is considered to represent a novel species of the genus Photobacterium. Furthermore, whole genome sequence analysis comparing S2753T and type-strains of closely related species of the genus Photobacterium also demonstrated that the strain is genomically distinct enough to be considered a novel species. The name Photobacterium galatheae is proposed and the type-strain is S2753T( = LMG 28894T = DSM 100496T).
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Affiliation(s)
- Henrique Machado
- Department of Systems Biology, Technical University of Denmark, Matematiktorvet, bldg 301, DK-2800 Kgs . Lyngby, Denmark
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Allé 6, DK-2970 Hørsholm, Denmark
| | - Sonia Giubergia
- Department of Systems Biology, Technical University of Denmark, Matematiktorvet, bldg 301, DK-2800 Kgs . Lyngby, Denmark
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Allé 6, DK-2970 Hørsholm, Denmark
| | - Ramona Valentina Mateiu
- Center for Electron Nanoscopy, Danchip, Technical University of Denmark, DK-2800 Kgs . Lyngby, Denmark
| | - Lone Gram
- Department of Systems Biology, Technical University of Denmark, Matematiktorvet, bldg 301, DK-2800 Kgs . Lyngby, Denmark
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Figge MJ, Cleenwerck I, van Uijen A, De Vos P, Huys G, Robertson L. Photobacterium piscicola sp. nov., isolated from marine fish and spoiled packed cod. Syst Appl Microbiol 2014; 37:329-35. [PMID: 24951451 DOI: 10.1016/j.syapm.2014.05.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Revised: 05/12/2014] [Accepted: 05/16/2014] [Indexed: 11/17/2022]
Abstract
Five isolates from marine fish (W3(T), WM, W1S, S2 and S3) and three isolates misclassified as Photobacterium phosphoreum, originating from spoiled modified atmosphere packed stored cod (NCIMB 13482 and NCIMB 13483) and the intestine of skate (NCIMB 192), were subjected to a polyphasic taxonomic study. Phylogenetic analysis of 16S rRNA gene sequences showed that the isolates were members of the genus Photobacterium. Sequence analysis using the gapA, gyrB, pyrH, recA and rpoA loci showed that these isolates formed a distinct branch in the genus Photobacterium, and were most closely related to Photobacterium aquimaris, Photobacterium kishitanii, Photobacterium phosphoreum and Photobacterium iliopiscarium. The luxA gene was present in isolates W3(T), WM, W1S, S2 and S3 but not in NCIMB 13482, NCIMB 13483 and NCIMB 192. AFLP and (GTG)5-PCR fingerprinting indicated that the eight isolates represented at least five distinct genotypes. DNA-DNA hybridizations revealed 89% relatedness between isolate W3(T) and NCIMB 192, and values below 70% with the type strains of the phylogenetically closest species, P. iliopiscarium LMG 19543(T), P. kishitanii LMG 23890(T), P. aquimaris LMG 26951(T) and P. phosphoreum LMG4233(T). The strains of this new taxon could also be distinguished from the latter species by phenotypic characteristics. Therefore, we propose to classify this new taxon as Photobacterium piscicola sp. nov., with W3(T) (=NCCB 100098(T)=LMG 27681(T)) as the type strain.
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Affiliation(s)
- Marian J Figge
- Netherlands Culture Collection of Bacteria, Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands.
| | - Ilse Cleenwerck
- BCCM/LMG Bacteria Collection, Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Astrid van Uijen
- Department of Biotechnology, Delft University of Biotechnology, Delft, The Netherlands
| | - Paul De Vos
- BCCM/LMG Bacteria Collection, Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium; Laboratory of Microbiology, Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Geert Huys
- BCCM/LMG Bacteria Collection, Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium; Laboratory of Microbiology, Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Lesley Robertson
- Department of Biotechnology, Delft University of Biotechnology, Delft, The Netherlands
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Abstract
Understanding of processes driving bacterial speciation requires examination of closely related, recently diversified lineages. To gain an insight into diversification of bacteria, we conducted comparative genomic analysis of two lineages of bioluminescent symbionts, Photobacterium leiognathi and 'P. mandapamensis'. The two lineages are evolutionary and ecologically closely related. Based on the methods used in bacterial taxonomy for classification of new species (DNA-DNA hybridization and ANI), genetic relatedness of the two lineages is at a cut-off point for species delineation. In this study, we obtained the whole genome sequence of a representative P. leiognathi strain lrivu.4.1, and compared it to the whole genome sequence of 'P. mandapamensis' svers.1.1. Results of the comparative genomic analysis suggest that P. leiognathi has a more plastic genome and acquired genes horizontally more frequently than 'P. mandapamensis'. We predict that different rates of recombination and gene acquisition contributed to diversification of the two lineages. Analysis of lineage-specific sequences in 25 strains of P. leiognathi and 'P. mandapamensis' found no evidence that bioluminescent symbioses with specific host animals have played a role in diversification of the two lineages.
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Affiliation(s)
- Henryk Urbanczyk
- Interdisciplinary Research Organization, University of Miyazaki, Miyazaki, Japan
| | - Yoshiko Urbanczyk
- Interdisciplinary Research Organization, University of Miyazaki, Miyazaki, Japan
| | - Tetsuya Hayashi
- Division of Bioenvironmental Science, Frontier Science Research Center, University of Miyazaki, Miyazaki, Japan
- Division of Microbiology, Department of Infectious Diseases, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Yoshitoshi Ogura
- Division of Bioenvironmental Science, Frontier Science Research Center, University of Miyazaki, Miyazaki, Japan
- Division of Microbiology, Department of Infectious Diseases, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
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Guerrero-Ferreira R, Gorman C, Chavez AA, Willie S, Nishiguchi MK. Characterization of the bacterial diversity in Indo-West Pacific loliginid and sepiolid squid light organs. Microb Ecol 2013; 65:214-26. [PMID: 22885637 PMCID: PMC3557516 DOI: 10.1007/s00248-012-0099-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Accepted: 04/07/2012] [Indexed: 06/01/2023]
Abstract
Loliginid and sepiolid squid light organs are known to host a variety of bacterial species from the family Vibrionaceae, yet little is known about the species diversity and characteristics among different host squids. Here we present a broad-ranging molecular and physiological analysis of the bacteria colonizing light organs in loliginid and sepiolid squids from various field locations of the Indo-West Pacific (Australia and Thailand). Our PCR-RFLP analysis, physiological characterization, carbon utilization profiling, and electron microscopy data indicate that loliginid squid in the Indo-West Pacific carry a consortium of bacterial species from the families Vibrionaceae and Photobacteriaceae. This research also confirms our previous report of the presence of Vibrio harveyi as a member of the bacterial population colonizing light organs in loliginid squid. pyrH sequence data were used to confirm isolate identity, and indicates that Vibrio and Photobacterium comprise most of the light organ colonizers of squids from Australia, confirming previous reports for Australian loliginid and sepiolid squids. In addition, combined phylogenetic analysis of PCR-RFLP and 16S rDNA data from Australian and Thai isolates associated both Photobacterium and Vibrio clades with both loliginid and sepiolid strains, providing support that geographical origin does not correlate with their relatedness. These results indicate that both loliginid and sepiolid squids demonstrate symbiont specificity (Vibrionaceae), but their distribution is more likely due to environmental factors that are present during the infection process. This study adds significantly to the growing evidence for complex and dynamic associations in nature and highlights the importance of exploring symbiotic relationships in which non-virulent strains of pathogenic Vibrio species could establish associations with marine invertebrates.
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Affiliation(s)
- Ricardo Guerrero-Ferreira
- Department of Pediatrics, Division of Pediatric Infectious Diseases, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Clayton Gorman
- Department of Biology, New Mexico State University, Las Cruces, NM 88003-8001, USA
| | - Alba A. Chavez
- Department of Biology, New Mexico State University, Las Cruces, NM 88003-8001, USA
| | - Shantell Willie
- Department of Biology, New Mexico State University, Las Cruces, NM 88003-8001, USA
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11
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Kim BC, Poo H, Kim MN, Lee KH, Lee J, Rhee MS, Shin KS. Photobacterium atrarenae sp. nov. a novel bacterium isolated from sea sand. Curr Microbiol 2011; 63:433-8. [PMID: 21861148 DOI: 10.1007/s00284-011-9994-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2011] [Accepted: 08/07/2011] [Indexed: 11/26/2022]
Abstract
The gram-reaction-negative, motile, facultatively anaerobic, catalase-positive, oxidase-positive bacterial strain M3-4(T) was isolated from black sea sand and subjected to a taxonomic study. Cells of strain M3-4(T) have monotrichous flagella, grow optimally at 37°C and at pH 7-8 in the presence of 1-4% (w/v) NaCl and hydrolyze casein, starch and L: -tyrosine. According to phylogenetic analyses using 16S rRNA gene sequences, strain M3-4(T) belongs to the genus Photobacterium and is most closely related to Photobacterium rosenbergii LMG 22223(T) (97.4%) and P. gaetbulicola KCTC 22804(T) (96.6%). The DNA-DNA relatedness value between M3-4(T) and P. rosenbergii LMG 22223(T) was 21.5%. The DNA G+C mol% of strain M3-4(T) was 53.6. The major cellular fatty acid of strain M3-4(T) was a summed feature 3 consisting of C(16:1) ω7c and/or iso-C(15:0) 2-OH (35.0%), followed by C(16:0) (25.4%) and C(18:1)ω7c (16.8%). These data suggest that strain M3-4(T) represents a novel species in genus Photobacterium, for which the name P. atrarenae sp. nov. is proposed. The type strain is M3-4(T) (= KCTC 23265(T) = NCAIM B 02414(T)).
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Affiliation(s)
- Byung-Chun Kim
- Microbial Resource Center, KRIBB, Daejeon 305-806, Republic of Korea
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12
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Laganà P, Caruso G, Minutoli E, Zaccone R, Santi D. Susceptibility to antibiotics of Vibrio spp. and Photobacterium damsela ssp. piscicida strains isolated from Italian aquaculture farms. New Microbiol 2011; 34:53-63. [PMID: 21344147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 06/30/2010] [Accepted: 10/06/2010] [Indexed: 05/30/2023]
Abstract
The antibiotic resistance patterns of aetiological agents responsible for vibriosis and pasteurellosis were studied to contribute to control the spread of these two bacterial diseases in Mediterranean fish farming. Strains of Photobacterium damsela ssp. piscicida, Vibrio fluvialis, Vibrio alginolyticus, Vibrio parahaemolyticus, Vibrio metschnikovii, isolated from Italian aquaculture (fish, shellfish and crustaceans) sites, were assayed for their susceptibility to some antibacterial agents currently used in farming practices. Kirby Bauer and Minimum Inhibitory Concentration (M.I.C.) tests were performed. The bacterial strains showed resistance to ampicillin, carbenicillin, kanamycin, cefalothin, while they were sensitive to chloramphenicol, nitrofurantoin and tobramycin; the sulfadiazine-trimethoprim association was completely ineffective. Conversely, flumequine showed the lowest M.I.C. value (0.97 �g mL-1), suggesting its marked antibiotic effect. Considering that quinolone resistance can be transmitted only by selection of mutations and not by other genetic mechanisms, this study stresses the importance of a more responsible use of this antibacterial drug in aquaculture.
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Affiliation(s)
- Pasqualina Laganà
- Department of Hygiene, Preventive Medicine and Public Health R. De Blasi, University of Messina, Messina, Italy
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13
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Wietz M, Mansson M, Gotfredsen CH, Larsen TO, Gram L. Antibacterial compounds from marine Vibrionaceae isolated on a global expedition. Mar Drugs 2010; 8:2946-60. [PMID: 21339958 PMCID: PMC3039463 DOI: 10.3390/md8122946] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2010] [Revised: 12/01/2010] [Accepted: 12/09/2010] [Indexed: 12/19/2022] Open
Abstract
On a global research expedition, over 500 bacterial strains inhibitory towards pathogenic bacteria were isolated. Three hundred of the antibacterial strains were assigned to the Vibrionaceae family. The purpose of the present study was to investigate the phylogeny and bioactivity of five Vibrionaceae strains with pronounced antibacterial activity. These were identified as Vibrio coralliilyticus (two strains), V. neptunius (two strains), and Photobacterium halotolerans (one strain) on the basis of housekeeping gene sequences. The two related V. coralliilyticus and V. neptunius strains were isolated from distant oceanic regions. Chemotyping by LC-UV/MS underlined genetic relationships by showing highly similar metabolite profiles for each of the two V. coralliilyticus and V. neptunius strains, respectively, but a unique profile for P. halotolerans. Bioassay-guided fractionation identified two known antibiotics as being responsible for the antibacterial activity; andrimid (from V. coralliilyticus) and holomycin (from P. halotolerans). Despite the isolation of already known antibiotics, our findings show that marine Vibrionaceae are a resource of antibacterial compounds and may have potential for future natural product discovery.
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Affiliation(s)
- Matthias Wietz
- National Food Institute, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark; E-Mail:
| | - Maria Mansson
- Centre for Microbial Biotechnology, Department of Systems Biology, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark; E-Mails: (M.M.); (T.O.L.)
| | - Charlotte H. Gotfredsen
- Department of Chemistry, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark; E-Mail:
| | - Thomas O. Larsen
- Centre for Microbial Biotechnology, Department of Systems Biology, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark; E-Mails: (M.M.); (T.O.L.)
| | - Lone Gram
- National Food Institute, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark; E-Mail:
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +45-4525-2586; Fax: +45-4588-4774
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14
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Labella A, Sanchez-Montes N, Berbel C, Aparicio M, Castro D, Manchado M, Borrego JJ. Toxicity of Photobacterium damselae subsp. damselae strains isolated from new cultured marine fish. Dis Aquat Organ 2010; 92:31-40. [PMID: 21166312 DOI: 10.3354/dao02275] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The in vivo and in vitro toxicity of bacterial cells and their extracellular products (ECPs) from 16 strains of Photobacterium damselae subsp. damselae isolated from 7 epizootic outbreaks were evaluated. On the basis of their 50% lethal dose (LD50) values (about 1 x 10(50 CFU), these strains may be considered as moderately virulent. However, their ECPs were strongly lethal for redbanded seabream Pagrus auriga causing fish death within 2 h post-inoculation (protein concentration ranged between 2.1 and 6.41 microg g(-1) fish). The bacterial ECPs tested exhibited several enzymatic activities, such as amylase, lipase, phospholipase, alkaline phosphatase, esterase-lipase, acid phosphatase, and beta-glucosaminidase. These ECPs displayed a strong cytotoxic effect on 4 fish and 2 mammalian cell lines, although this activity disappeared when ECPs were heated at 100 degrees C. The virulence of the strains tested could not be related to the hemolytic activity or to the production of the toxin damselysin. Therefore, another unknown type of toxin could play an important role in the virulence mechanisms of this bacterial pathogen.
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Affiliation(s)
- Alejandro Labella
- Department of Microbiology, Faculty of Sciences, University of Malaga, 29071 Malaga, Spain
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15
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Pedersen K, Skall HF, Lassen-Nielsen AM, Bjerrum L, Olesen NJ. Photobacterium damselae subsp. damselae, an emerging pathogen in Danish rainbow trout, Oncorhynchus mykiss (Walbaum), mariculture. J Fish Dis 2009; 32:465-472. [PMID: 19364386 DOI: 10.1111/j.1365-2761.2009.01041.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
A selection of 16 field isolates of Photobacterium damselae from marine rainbow trout farms in Denmark was subjected to phenotypic and genotypic characterization and pathogenicity to fish. All isolates belonged to the subspecies damselae, being positive for haemolysis, motility and urease. There were considerable differences in haemolytic properties, some isolates presenting a broad zone of haemolysis and others only a narrow zone. Pulsed-field gel electrophoresis revealed a high diversity indicating that P. damselae subsp. damselae is an opportunistic, not clonal pathogen in Danish marine rainbow trout. Virulence of the strains to rainbow trout was highly variable with LD(50) values ranging from 3.9 x 10(3) to 1.5 x 10(8) cfu at 20 degrees C. The virulence was significantly higher at 20 degrees C than at 13 degrees C. The strains with the strongest haemolytic properties were the most virulent suggesting a strong involvement of haemolysin in the pathogenesis. The pathological changes were consistent with a bacterial septicaemia and the haemorrhages were more pronounced than for most other bacterial infections.
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Affiliation(s)
- K Pedersen
- National Veterinary Institute, Technical University of Denmark, Arhus N, Denmark.
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16
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Boiandin AN, Kalacheva GS, Rodicheva EK, Volova TG. [Synthesis of reserve polyhydroxyalkanoates by luminescent bacteria]. Mikrobiologiia 2008; 77:364-369. [PMID: 18683654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The ability of marine luminescent bacteria to synthesize polyesters of hydroxycarboxylic acids (polyhydroxyalkanoates, PHA) as reserve macromolecules was studied. Twenty strains from the collection of the luminescent bacteria CCIBSO (WDSM839) of the Institute of Biophysics, Siberian Branch, Russian Academy of Sciences, assigned to different taxa (Photobacterium leiognathi, Ph. phosphoreum, Vibrio harveyi, and V. fischeri) were analyzed. The most productive strains were identified, and the conditions ensuring high polymer yields in batch culture (40-70% of the cell dry mass weight) were determined. The capacity of synthesizing two- and three-component polymers containing hydroxybutyric acid as the main monomer and hydroxyvaleric and hydroxyhexanoic acids was revealed in Ph. leiognathi and V. harveyi strains. The results allow luminescent microorganisms to be regarded as new producers of multicomponent polyhydroxyalkanoates.
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17
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Süss J, Herrmann K, Seidel M, Cypionka H, Engelen B, Sass H. Two distinct Photobacterium populations thrive in ancient Mediterranean sapropels. Microb Ecol 2008; 55:371-83. [PMID: 17874305 DOI: 10.1007/s00248-007-9282-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2006] [Accepted: 05/22/2007] [Indexed: 05/17/2023]
Abstract
Eastern Mediterranean sediments are characterized by the periodic occurrence of conspicuous, organic matter-rich sapropel layers. Phylogenetic analysis of a large culture collection isolated from these sediments revealed that about one third of the isolates belonged to the genus Photobacterium. In the present study, 22 of these strains were examined with respect to their phylogenetic and metabolic diversity. The strains belonged to two distinct Photobacterium populations (Mediterranean cluster I and II). Strains of cluster I were isolated almost exclusively from organic-rich sapropel layers and were closely affiliated with P. aplysiae (based on their 16S rRNA gene sequences). They possessed almost identical Enterobacterial Repetitive Intergenic Consensus (ERIC) and substrate utilization patterns, even among strains from different sampling sites or from layers differing up to 100,000 years in age. Strains of cluster II originated from sapropels and from the surface and carbon-lean intermediate layers. They were related to Photobacterium frigidiphilum but differed significantly in their fingerprint patterns and substrate spectra, even when these strains were obtained from the same sampling site and layer. Temperature range for growth (4 to 33 degrees C), salinity tolerance (5 to 100 per thousand), pH requirements (5.5-9.3), and the composition of polar membrane lipids were similar for both clusters. All strains grew by fermentation (glucose, organic acids) and all but five by anaerobic respiration (nitrate, dimethyl sulfoxide, anthraquinone disulfonate, or humic acids). These results indicate that the genus Photobacterium forms subsurface populations well adapted to life in the deep biosphere.
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Affiliation(s)
- Jacqueline Süss
- Institut für Chemie und Biologie des Meeres, Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
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18
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Ast JC, Cleenwerck I, Engelbeen K, Urbanczyk H, Thompson FL, De Vos P, Dunlap PV. Photobacterium kishitanii sp. nov., a luminous marine bacterium symbiotic with deep-sea fishes. Int J Syst Evol Microbiol 2007; 57:2073-2078. [PMID: 17766874 DOI: 10.1099/ijs.0.65153-0] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Six representatives of a luminous bacterium commonly found in association with deep, cold-dwelling marine fishes were isolated from the light organs and skin of different fish species. These bacteria were Gram-negative, catalase-positive, and weakly oxidase-positive or oxidase-negative. Morphologically, cells of these strains were coccoid or coccoid-rods, occurring singly or in pairs, and motile by means of polar flagellation. After growth on seawater-based agar medium at 22 °C for 18 h, colonies were small, round and white, with an intense cerulean blue luminescence. Analysis of 16S rRNA gene sequence similarity placed these bacteria in the genus Photobacterium. Phylogenetic analysis based on seven housekeeping gene sequences (16S rRNA gene, gapA, gyrB, pyrH, recA, rpoA and rpoD), seven gene sequences of the lux operon (luxC, luxD, luxA, luxB, luxF, luxE and luxG) and four gene sequences of the rib operon (ribE, ribB, ribH and ribA), resolved the six strains as members of the genus Photobacterium and as a clade distinct from other species of Photobacterium. These strains were most closely related to Photobacterium phosphoreum and Photobacterium iliopiscarium. DNA–DNA hybridization values between the designated type strain, Photobacterium kishitanii
pjapo.1.1T, and P. phosphoreum LMG 4233T, P. iliopiscarium LMG 19543T and Photobacterium indicum LMG 22857T were 51, 43 and 19 %, respectively. In AFLP analysis, the six strains clustered together, forming a group distinct from other analysed species. The fatty acid C17 : 0 cyclo was present in these bacteria, but not in P. phosphoreum, P. iliopiscarium or P. indicum. A combination of biochemical tests (arginine dihydrolase and lysine decarboxylase) differentiates these strains from P. phosphoreum and P. indicum. The DNA G+C content of P. kishitanii pjapo.1.1T is 40.2 %, and the genome size is approximately 4.2 Mbp, in the form of two circular chromosomes. These strains represent a novel species, for which the name Photobacterium kishitanii sp. nov. is proposed. The type strain, pjapo.1.1T (=ATCC BAA-1194T=LMG 23890T), is a luminous symbiont isolated from the light organ of the deep-water fish Physiculus japonicus.
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MESH Headings
- Animal Structures/microbiology
- Animals
- Bacterial Proteins/genetics
- Bacterial Typing Techniques
- Base Composition
- Catalase/biosynthesis
- Chromosomes, Bacterial
- Cluster Analysis
- DNA Fingerprinting
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Circular
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Fatty Acids/analysis
- Fishes/microbiology
- Fishes/physiology
- Flagella
- Genes, rRNA
- Locomotion/physiology
- Luminescence
- Luminescent Proteins/biosynthesis
- Molecular Sequence Data
- Nucleic Acid Amplification Techniques
- Nucleic Acid Hybridization
- Oxidoreductases/biosynthesis
- Photobacterium/classification
- Photobacterium/genetics
- Photobacterium/isolation & purification
- Photobacterium/physiology
- Phylogeny
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Skin/microbiology
- Symbiosis
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Affiliation(s)
- Jennifer C Ast
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Ilse Cleenwerck
- Laboratory of Microbiology and BCCM/LMG Bacteria Collection, Ghent University, K. L. Ledeganckstraat 35, Ghent 9000, Belgium
| | - Katrien Engelbeen
- Laboratory of Microbiology and BCCM/LMG Bacteria Collection, Ghent University, K. L. Ledeganckstraat 35, Ghent 9000, Belgium
| | - Henryk Urbanczyk
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Fabiano L Thompson
- Department of Genetics, Federal University of Rio de Janeiro, Ilha do Fundão, CEP 21944-970, Rio de Janeiro, Brazil
| | - Paul De Vos
- Laboratory of Microbiology and BCCM/LMG Bacteria Collection, Ghent University, K. L. Ledeganckstraat 35, Ghent 9000, Belgium
| | - Paul V Dunlap
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
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García-Rosado E, Cano I, Martín-Antonio B, Labella A, Manchado M, Alonso MC, Castro D, Borrego JJ. Co-occurrence of viral and bacterial pathogens in disease outbreaks affecting newly cultured sparid fish. Int Microbiol 2007; 10:193-199. [PMID: 18076001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Several microbial disease outbreaks in farm stocks of newly cultured sparid fish species, such as common seabream, redbanded seabream, and white seabream, were recorded from 2004 to 2006. This study describes the isolation and characterization of the potential causative agents, either bacteria or viruses, of these outbreaks. The isolated bacterial strains were characterized according to traditional taxonomical analyses and sequencing of a 16S rDNA fragment. Most bacteria were identified as Vibrio spp. and Photobacterium damselae subsp. damselae. The development of cytopathic effects (CPE) on different fish cell lines, the application of specific nested-PCR tests for infectious pancreatic necrosis virus (IPNV), viral nervous necrosis virus (VNNV) and viral hemorrhagic septicemia virus (VHSV), and subsequent sequence analyses were used for virus detection and identification. VNNV, related to the striped jack neural necrosis virus (SJNNV) genotype, and VHSV, related to the genotype Ia, were the only viruses detected. VNNV was isolated from the three fish species under study in five different outbreaks, whereas VHSV was isolated from common seabream and white seabream during two of these outbreaks. IPNV was not detected in any case.
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Abstract
We describe a case of a urinary tract infection with an unusual pathogen,
Photobacterium damsela, in a pregnant female. This pathogen has been described as
having a virulent life threatening nature, so a detailed history and prompt treatment is
needed.
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Affiliation(s)
- Jesus R. Alvarez
- Obstetrics, Gynecology, and Women's Health Department, University of Medicine and Dentistry of New Jersey, Newark, NJ 07103, USA
- *Jesus R. Alvarez:
| | - Sangeeta Lamba
- Obstetrics, Gynecology, and Women's Health Department, University of Medicine and Dentistry of New Jersey, Newark, NJ 07103, USA
| | - Keisha Y. Dyer
- Obstetrics, Gynecology, and Women's Health Department, University of Medicine and Dentistry of New Jersey, Newark, NJ 07103, USA
| | - Joseph J. Apuzzio
- Obstetrics, Gynecology, and Women's Health Department, University of Medicine and Dentistry of New Jersey, Newark, NJ 07103, USA
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Abstract
We performed the first broad study aiming at the reconstruction of the evolutionary history of vibrios by means of multilocus sequence analysis of nine genes. Overall, 14 distinct clades were recognized using the SplitsTree decomposition method. Some of these clades may correspond to families, e.g., the clades Salinivibrio and Photobacteria, while other clades, e.g., Splendidus and Harveyi, correspond to genera. The common ancestor of all vibrios was estimated to have been present 600 million years ago. We can define species of vibrios as groups of strains that share >95% gene sequence similarity and >99.4% amino acid identity based on the eight protein-coding housekeeping genes. The gene sequence data were used to refine the standard online electronic taxonomic scheme for vibrios (http://www.taxvibrio.lncc.br).
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Affiliation(s)
- Tomoo Sawabe
- Laboratory of Microbiology, Faculty of Fisheries, Hokkaido University, 3-1-1 Minato-cho, Hakodate 041-8611, Japan.
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Mancuso M, Avendaño-Herrera R, Zaccone R, Toranzo AE, Magariños B. Evaluation of different DNA-based fingerprinting methods for typing Photobacterium damselae ssp. piscicida. Biol Res 2007; 40:85-92. [PMID: 17657358 DOI: 10.4067/s0716-97602007000100009] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
This study evaluates the effectiveness of three different molecular techniques, repetitive extragenic palindromic PCR (REP-PCR), enterobacterial repetitive intergenic consensus sequence PCR (ERIC-PCR) and the random amplified polymorphic DNA (RAPD-PCR) for rapid typing of Photobacterium damselae ssp. piscicida strains isolated from different species of marine fish and geographic areas. The results obtained by the three methods showed that RAPD and ERIC-PCR were more discriminative for suitable rapid typing of Ph. damselae ssp. piscicida than REP-PCR. The analysis of DNA banding patterns generated by both molecular methods (RAPD and ERIC-PCR) clearly separated the strains into two main groups that strongly correlated with their geographic origin. Moreover, the REP-PCR analysis was less reproducible than the RAPD and ERIC-PCR methods and does not allow the establishment of genetic groups. RAPD and ERIC-PCR constitute valuable tools for molecular typing of Ph. damselae ssp. piscicida strains, which can be used in epidemiological studies of photobacteriosis infections.
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Affiliation(s)
- Monique Mancuso
- Istituto per l'Ambiente Marino Costiero, CNR Sezione di Messina, Italy
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Vaseeharan B, Sundararaj S, Murugan T, Chen JC. Photobacterium damselae ssp. damselae associated with diseased black tiger shrimp Penaeus monodon Fabricius in India. Lett Appl Microbiol 2007; 45:82-6. [PMID: 17594465 DOI: 10.1111/j.1472-765x.2007.02139.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AIM To characterize and identify Photobacterium damselae ssp. damselae present in black gill diseased Penaeus monodon collected from east coast of India. METHODS AND RESULTS Photobacterium damselae ssp. damselae was isolated from hepatopancreas, muscles and gills by using the thiosulfate citrate bile salts sucrose agar supplemented with 1.5% NaCl (TCBS-1) medium. A total of 32 Ph. damselae ssp. damselae isolates were studied together with two reference strains. The biochemical tests and analysis of ureC and 16S rRNA genes confirmed the phenotypic characterization of the isolates as Ph damselae ssp. damselae. Experimental infection studies revealed that the LD50 values of P. monodon and P. indicus ranged from 2x10(3) to 5x10(5) CFU per shrimp and from 4x10(2) to 2x10(4) CFU per shrimp, respectively. CONCLUSIONS Photobacterium damselae ssp. damselae was found in the internal organs of P. monodon and it showed pathogenic to shrimp. SIGNIFICANCE AND IMPACT OF THE STUDY This is the first study on the Ph. damselae ssp. damselae present in the black gill diseased P. monodon in India and therefore might serve as a basis for future studies and diagnosis purpose to shrimp culturists.
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Affiliation(s)
- B Vaseeharan
- Department of Aquaculture, College of Life Sciences, National Taiwan Ocean University, Keelung, Taiwan, ROC.
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24
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Kaeding AJ, Ast JC, Pearce MM, Urbanczyk H, Kimura S, Endo H, Nakamura M, Dunlap PV. Phylogenetic diversity and cosymbiosis in the bioluminescent symbioses of "Photobacterium mandapamensis". Appl Environ Microbiol 2007; 73:3173-82. [PMID: 17369329 PMCID: PMC1907103 DOI: 10.1128/aem.02212-06] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2006] [Accepted: 03/12/2007] [Indexed: 11/20/2022] Open
Abstract
"Photobacterium mandapamensis" (proposed name) and Photobacterium leiognathi are closely related, phenotypically similar marine bacteria that form bioluminescent symbioses with marine animals. Despite their similarity, however, these bacteria can be distinguished phylogenetically by sequence divergence of their luminescence genes, luxCDAB(F)E, by the presence (P. mandapamensis) or the absence (P. leiognathi) of luxF and, as shown here, by the sequence divergence of genes involved in the synthesis of riboflavin, ribBHA. To gain insight into the possibility that P. mandapamensis and P. leiognathi are ecologically distinct, we used these phylogenetic criteria to determine the incidence of P. mandapamensis as a bioluminescent symbiont of marine animals. Five fish species, Acropoma japonicum (Perciformes, Acropomatidae), Photopectoralis panayensis and Photopectoralis bindus (Perciformes, Leiognathidae), Siphamia versicolor (Perciformes, Apogonidae), and Gadella jordani (Gadiformes, Moridae), were found to harbor P. mandapamensis in their light organs. Specimens of A. japonicus, P. panayensis, and P. bindus harbored P. mandapamensis and P. leiognathi together as cosymbionts of the same light organ. Regardless of cosymbiosis, P. mandapamensis was the predominant symbiont of A. japonicum, and it was the apparently exclusive symbiont of S. versicolor and G. jordani. In contrast, P. leiognathi was found to be the predominant symbiont of P. panayensis and P. bindus, and it appears to be the exclusive symbiont of other leiognathid fishes and a loliginid squid. A phylogenetic test for cospeciation revealed no evidence of codivergence between P. mandapamensis and its host fishes, indicating that coevolution apparently is not the basis for this bacterium's host preferences. These results, which are the first report of bacterial cosymbiosis in fish light organs and the first demonstration that P. leiognathi is not the exclusive light organ symbiont of leiognathid fishes, demonstrate that the host species ranges of P. mandapamensis and P. leiognathi are substantially distinct. The host range difference underscores possible differences in the environmental distributions and physiologies of these two bacterial species.
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Affiliation(s)
- Allison J Kaeding
- Department of Ecology and Evolutionary Biology, 830 North University Avenue, University of Michigan, Ann Arbor, MI 48109-1048, USA
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Abstract
A Gram-negative, motile, pale-yellow-pigmented, oval-shaped bacterial strain, DF-42T, was isolated from a tidal flat sediment in Korea. Strain DF-42T grew optimally at 25–30 °C and in the presence of 2–3 % (w/v) NaCl. It contained Q-8 as the predominant ubiquinone and C16 : 0, C18 : 1
ω7c and summed feature 3 (C16 : 1
ω7c and/or iso-C15 : 0 2-OH) as the major fatty acids. The DNA G+C content was 48.3 mol%. Phylogenetic trees based on 16S rRNA gene sequences showed that strain DF-42T falls within the evolutionary radiation enclosed by the genus Photobacterium. Strain DF-42T exhibited 16S rRNA gene sequence similarity values of 93.8–97.9 % to the type strains of Photobacterium species with validly published names. DNA–DNA relatedness data and differential phenotypic properties made it possible to categorize strain DF-42T as representing a species that is separate from previously described Photobacterium species. The name Photobacterium lutimaris sp. nov. is proposed, with strain DF-42T (=KCTC 12723T=JCM 13586T) as the type strain.
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Affiliation(s)
- Seo-Youn Jung
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, South Korea
| | - Yong-Taek Jung
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, South Korea
| | - Tae-Kwang Oh
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, South Korea
| | - Jung-Hoon Yoon
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, South Korea
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Chiu HH, Chou HH, Jean WD, Shieh WY. Isolation and characterization of marine luminous bacteria from shallow coastal waters of Taiwan. J Microbiol Immunol Infect 2007; 40:14-23. [PMID: 17332902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
BACKGROUND AND PURPOSE Marine luminous bacteria were isolated and identified from samples in shallow coastal waters of Taiwan during the relatively warm seasons. METHODS Identification of the luminous isolates was performed based on differences of phenotypic and genotypic characteristics together with data from phylogenetic analysis. RESULTS Twenty seven strains of marine luminous bacteria were isolated. They were divided into five types based on differences of phenotypic characteristics. However, they could be clustered into only two genotypes according to the analysis of restriction patterns of polymerase chain reaction-amplified 16S rRNA genes digested with various restriction enzymes. The characterization data together with the 16S rRNA gene-based phylogenetic analysis revealed that the isolates included in phenotype I (seven isolates) could be Photobacterium leiognathi, and those included in phenotypes II-V (twenty isolates) might be classified as Vibrio harveyi. However, phylogeny based on gyrB sequences indicated that phenotypes II-V could be classified into two species, V. harveyi and Vibrio campbellii. CONCLUSION Culturable luminous bacteria in the shallow coastal waters of Taiwan during the sampling period are dominated by V. harveyi/campbellii and P. leiognathi, and the former species appeared to be more prevalent and numerous than the latter species in general.
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Affiliation(s)
- Hsiu Hui Chiu
- Institute of Oceanography, National Taiwan University, Taipei, Taiwan
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Park YD, Baik KS, Seong CN, Bae KS, Kim S, Chun J. Photobacterium ganghwense sp. nov., a halophilic bacterium isolated from sea water. Int J Syst Evol Microbiol 2006; 56:745-749. [PMID: 16585687 DOI: 10.1099/ijs.0.63811-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A marine bacterial strain, designated FR1311T, was isolated from a sea-water sample from Ganghwa Island, South Korea. Cells were Gram-negative, facultatively anaerobic, catalase- and oxidase-positive, motile, oval or rod-shaped and halophilic (optimum sea-salt concentration for growth of 5-6 %). Phylogenetic analysis of its 16S rRNA gene sequence revealed that it represented a distinct line of descent within the genus Photobacterium. The major fatty acids were straight-chain saturated (C(16 : 0)) and monounsaturated fatty acids (C(16 : 1)omega7c and C(18 : 1)omega7c). The predominant respiratory lipoquinone was Q-8. The DNA G+C content was 44 mol%. The phenotypic features of strain FR1199T were similar to those of Photobacterium damselae subsp. damselae and Photobacterium damselae subsp. piscicida, but several physiological and chemotaxonomic properties readily distinguish the new isolate from them. On the basis of the polyphasic results revealed in this study, FR1311T is considered to be the type strain of a novel species, for which the name Photobacterium ganghwense sp. nov. is proposed. The type strain is FR1311T (=IMSNU 60287T = KCTC 12328T = JCM 12487T).
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Affiliation(s)
- Yoon-Dong Park
- School of Biological Sciences and Institute of Microbiology, Seoul National University, 56-1 Shillim-dong, Kwanak-gu, Seoul 151-742, Republic of Korea
| | - Keun Sik Baik
- Department of Biology, College of Natural Sciences, Sunchon National University, Sunchon 540-742, Republic of Korea
| | - Chi Nam Seong
- Department of Biology, College of Natural Sciences, Sunchon National University, Sunchon 540-742, Republic of Korea
| | - Kyung Sook Bae
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, Taejon 305-600, Republic of Korea
| | - Sanggoo Kim
- School of Biological Sciences and Institute of Microbiology, Seoul National University, 56-1 Shillim-dong, Kwanak-gu, Seoul 151-742, Republic of Korea
| | - Jongsik Chun
- School of Biological Sciences and Institute of Microbiology, Seoul National University, 56-1 Shillim-dong, Kwanak-gu, Seoul 151-742, Republic of Korea
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Kita-Tsukamoto K, Wada M, Yao K, Kamiya A, Yoshizawa S, Uchiyama N, Kogure K. Rapid identification of marine bioluminescent bacteria by amplified 16S ribosomal RNA gene restriction analysis. FEMS Microbiol Lett 2006; 256:298-303. [PMID: 16499620 DOI: 10.1111/j.1574-6968.2006.00129.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
To rapidly identify natural isolates of marine bioluminescent bacteria, we developed amplified ribosomal DNA restriction analysis (ARDRA) methods. ARDRA, which is based on the restriction patterns of 16S rRNA gene digested with five enzymes (EcoRI, DdeI, HhaI, HinfI, RsaI), clearly distinguished the 14 species of marine bioluminescent bacteria currently known, which belong to the genera Vibrio, Photobacterium, and Shewanella. When we applied ARDRA to 129 natural isolates from two cruises in Sagami Bay, Japan, 127 were grouped into six ARDRA types with distinctive restriction patterns; these isolates represented the bioluminescent species, P. angustum, P. leiognathi, P. phosphoreum, S. woodyi, V. fischeri, and V. harveyi. The other two isolates showing unexpected ARDRA patterns turned out to have 16S rRNA gene sequences similar to P. leiognathi and P. phosphoreum. Nevertheless, ARDRA provides a simple and fairly robust means for rapid identification of the natural isolates of marine bioluminescent bacteria, and is therefore useful in studying their diversity.
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Wada M, Kamiya A, Uchiyama N, Yoshizawa S, Kita-Tsukamoto K, Ikejima K, Yu R, Imada C, Karatani H, Mizuno N, Suzuki Y, Nishida M, Kogure K. LuxA gene of light organ symbionts of the bioluminescent fish Acropoma japonicum (Acropomatidae) and Siphamia versicolor (Apogonidae) forms a lineage closely related to that of Photobacterium leiognathi ssp. mandapamensis. FEMS Microbiol Lett 2006; 260:186-92. [PMID: 16842343 DOI: 10.1111/j.1574-6968.2006.00322.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
A molecular phylogenetic analysis of luxA gene sequences of light organ symbionts of the fish Acropoma japonicum (Acropomatidae) and Siphamia versicolor (Apogonidae) revealed that the sequences were related to those of Photobacterium leiognathi ssp. mandapamensis, which is not known to occur as a light organ symbiont among bioluminescent P. leiognathi clades. The presence of another lux gene element, luxF, coding for nonfluorescent protein, provided additional support for the identity of the light organ symbionts of the fish. Cladogenesis of the light organ symbiont P. leiognathi may be influenced by the radiation of host fishes.
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Affiliation(s)
- Minoru Wada
- Ocean Research Institute, The University of Tokyo, Tokyo, Japan.
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Rivas R, García-Fraile P, Mateos PF, Martínez-Molina E, Velázquez E. Photobacterium halotolerans sp. nov., isolated from Lake Martel in Spain. Int J Syst Evol Microbiol 2006; 56:1067-1071. [PMID: 16627656 DOI: 10.1099/ijs.0.64099-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A halotolerant bacterium was isolated from a saline lake located in Mallorca, Spain. Cells of the strain, designated MACL01T, were Gram-negative, rod-shaped and motile by means of polar flagella. Colonies of strain MACL01T were white to cream in TSA medium, turning brown after 7 days of incubation; they were blue in thiosulphate/citrate/bile salts/sucrose agar medium. A neighbour-joining phylogenetic analysis based on 16S rRNA gene sequences showed that strain MACL01T belongs to the genus Photobacterium, in which it forms a distinct lineage together with Photobacterium rosenbergii and Photobacterium ganghwense (showing 96.9 and 96.2 % similarity, respectively). The most closely related taxon according to phylogenetic analysis of the rpoA gene is also P. rosenbergii (90 % similarity). The recA gene also showed low similarity (83.7, 83.4 and 82.4 %, respectively) with respect to those of Vibrio proteolyticus LMG 3772T, Photobacterium leiognathii LMG 4228T and P. rosenbergii LMG 22223T. Neighbour-joining phylogenetic analysis of the rpoA and recA genes confirms that strain MACL01T belongs to the genus Photobacterium, forming a branch together with P. rosenbergii. Strain MACL01T was able to grow in 0–8 % NaCl. Growth occurred between 4 and 37 °C (optimum, 28 °C) and at pH 5–8.5. Luminescence was negative on marine agar. Strain MACL01T was found to be sensitive to the vibriostatic agent O/129. It reduced nitrate to nitrite, produced β-galactosidase and hydrolysed gelatin, but did not produce arginine dihydrolase, indole or acetoin. Strain MACL01T used several carbohydrates and fermented glucose, l-arabinose and sucrose. The most abundant fatty acids were summed feature 3 (32.6 %; comprising C16 : 1
ω7c and/or C15 : 0 iso 2-OH), C16 : 0 (21.2 %) and C18 : 1
ω7c (19.9 %). The G+C content of the genomic DNA was 49.8 mol%. On the basis of genotypic, phenotypic, chemotaxonomic and phylogenetic results, strain MACL01T (=LMG 22194T=CECT 5860T) should be classified as the type strain of a novel species of the genus Photobacterium, for which the name Photobacterium halotolerans sp. nov. is proposed.
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Affiliation(s)
- Raúl Rivas
- Departamento de Microbiología y Genética, Lab. 209, Edificio Departamental de Biología, Campus Miguel de Unamuno, Universidad de Salamanca, 37007 Salamanca, Spain
| | - Paula García-Fraile
- Departamento de Microbiología y Genética, Lab. 209, Edificio Departamental de Biología, Campus Miguel de Unamuno, Universidad de Salamanca, 37007 Salamanca, Spain
| | - Pedro F Mateos
- Departamento de Microbiología y Genética, Lab. 209, Edificio Departamental de Biología, Campus Miguel de Unamuno, Universidad de Salamanca, 37007 Salamanca, Spain
| | - Eustoquio Martínez-Molina
- Departamento de Microbiología y Genética, Lab. 209, Edificio Departamental de Biología, Campus Miguel de Unamuno, Universidad de Salamanca, 37007 Salamanca, Spain
| | - Encarna Velázquez
- Departamento de Microbiología y Genética, Lab. 209, Edificio Departamental de Biología, Campus Miguel de Unamuno, Universidad de Salamanca, 37007 Salamanca, Spain
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Labella A, Vida M, Alonso MC, Infante C, Cardenas S, Lopez-Romalde S, Manchado M, Borrego JJ. First isolation of Photobacterium damselae ssp. damselae from cultured redbanded seabream, Pagrus auriga Valenciennes, in Spain. J Fish Dis 2006; 29:175-9. [PMID: 16533303 DOI: 10.1111/j.1365-2761.2006.00697.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Affiliation(s)
- A Labella
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain
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Abstract
Substantial ambiguity exists regarding the phylogenetic status of facultatively psychrophilic luminous bacteria identified as Photobacterium phosphoreum, a species thought to be widely distributed in the world's oceans and believed to be the specific bioluminescent light-organ symbiont of several deep-sea fishes. Members of the P. phosphoreum species group include luminous and non-luminous strains identified phenotypically from a variety of different habitats as well as phylogenetically defined lineages that appear to be evolutionarily distinct. To resolve this ambiguity and to begin developing a meaningful knowledge of the geographic distributions, habitats and symbiotic relationships of bacteria in the P. phosphoreum species group, we carried out a multilocus, fine-scale phylogenetic analysis based on sequences of the 16S rRNA, gyrB and luxABFE genes of many newly isolated luminous strains from symbiotic and saprophytic habitats, together with previously isolated luminous and non-luminous strains identified as P. phosphoreum from these and other habitats. Parsimony analysis unambiguously resolved three evolutionarily distinct clades, phosphoreum, iliopiscarium and kishitanii. The tight phylogenetic clustering within these clades and the distinct separation between them indicates they are different species, P. phosphoreum, Photobacterium iliopiscarium and the newly recognized 'Photobacterium kishitanii'. Previously reported non-luminous strains, which had been identified phenotypically as P. phosphoreum, resolved unambiguously as P. iliopiscarium, and all examined deep-sea fishes (specimens of families Chlorophthalmidae, Macrouridae, Moridae, Trachichthyidae and Acropomatidae) were found to harbour 'P. kishitanii', not P. phosphoreum, in their light organs. This resolution revealed also that 'P. kishitanii' is cosmopolitan in its geographic distribution. Furthermore, the lack of phylogenetic variation within 'P. kishitanii' indicates that this facultatively symbiotic bacterium is not cospeciating with its phylogenetically divergent host fishes. The results of this fine-scale phylogenetic analysis support the emerging view that bacterial species names should designate singular historical entities, i.e. discrete lineages diagnosed by a significant divergence of shared derived nucleotide characters.
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Affiliation(s)
- Jennifer C Ast
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
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33
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Flodgaard LR, Dalgaard P, Andersen JB, Nielsen KF, Givskov M, Gram L. Nonbioluminescent strains of Photobacterium phosphoreum produce the cell-to-cell communication signal N-(3-Hydroxyoctanoyl)homoserine lactone. Appl Environ Microbiol 2005; 71:2113-20. [PMID: 15812045 PMCID: PMC1082519 DOI: 10.1128/aem.71.4.2113-2120.2005] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bioluminescence is a common phenotype in marine bacteria, such as Vibrio and Photobacterium species, and can be quorum regulated by N-acylated homoserine lactones (AHLs). We extracted a molecule that induced a bacterial AHL monitor (Agrobacterium tumefaciens NT1 [pZLR4]) from packed cod fillets, which spoil due to growth of Photobacterium phosphoreum. Interestingly, AHLs were produced by 13 nonbioluminescent strains of P. phosphoreum isolated from the product. Of 177 strains of P. phosphoreum (including 18 isolates from this study), none of 74 bioluminescent strains elicited a reaction in the AHL monitor, whereas 48 of 103 nonbioluminescent strains did produce AHLs. AHLs were also detected in Aeromonas spp., but not in Shewanella strains. Thin-layer chromatographic profiles of cod extracts and P. phosphoreum culture supernatants identified a molecule similar in relative mobility (Rf value) and shape to N-(3-hydroxyoctanoyl)homoserine lactone, and the presence of this molecule in culture supernatants from a nonbioluminescent strain of P. phosphoreum was confirmed by high-performance liquid chromatography-positive electrospray high-resolution mass spectrometry. Bioluminescence (in a non-AHL-producing strain of P. phosphoreum) was strongly up-regulated during growth, whereas AHL production in a nonbioluminescent strain of P. phosphoreum appeared constitutive. AHLs apparently did not influence bioluminescence, as the addition of neither synthetic AHLs nor supernatants delayed or reduced this phenotype in luminescent strains of P. phosphoreum. The phenotypes of nonbioluminescent P. phosphoreum strains regulated by AHLs remains to be elucidated.
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Affiliation(s)
- L R Flodgaard
- Department of Seafood Research, Danish Institute for Fisheries Research, Kongens Lyngby, Denmark
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Seo HJ, Bae SS, Lee JH, Kim SJ. Photobacterium frigidiphilum sp. nov., a psychrophilic, lipolytic bacterium isolated from deep-sea sediments of Edison Seamount. Int J Syst Evol Microbiol 2005; 55:1661-1666. [PMID: 16014498 DOI: 10.1099/ijs.0.63338-0] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-negative, motile, rod-shaped, psychrophilic and weakly halophilic bacterial strain, SL13T, was isolated from deep-sea sediments (1450 m depth) of Edison Seamount in the western Pacific Ocean. Optimal growth of SL13Trequires the presence of 1·5 % (w/v) NaCl, a pH of 6·0 and a temperature of 14 °C. The whole-cell fatty acid profile of the isolate includes C16 : 1 and C16 : 0 as major fatty acids and contains C20 : 5ω3. This is consistent with corresponding data forPhotobacterium profundum. The DNA G+C content of strain SL13Tis 43·8 mol%. Phylogenetic analyses of 16S rRNA gene sequences place this bacterium in the ‘Gammaproteobacteria’, within the genusPhotobacterium. Sequence similarity analysis indicates that the closest relatives of strain SL13TarePhotobacterium indicum(99·3 %),P. profundum(98·5 %) andPhotobacterium lipolyticum(98·2 %). The DNA–DNA hybridization levels between the isolate and its closest known phylogenetic relatives,P. indicum,P. profundumandP. lipolyticum, are 27·1, 52·4 and 20·2 %, respectively. Thus strain SL13Trepresents a novel species of the genusPhotobacterium, for which the namePhotobacterium frigidiphilumsp. nov. is proposed. The type strain is SL13T(=KCTC 12384T=JCM 12947T).
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Affiliation(s)
- Hae Jeom Seo
- Marine Biotechnology Research Centre, Korea Ocean Research and Development Institute, PO Box 29, Ansan 425-600, Republic of Korea
| | - Seung Seob Bae
- Marine Biotechnology Research Centre, Korea Ocean Research and Development Institute, PO Box 29, Ansan 425-600, Republic of Korea
| | - Jung-Hyun Lee
- Marine Biotechnology Research Centre, Korea Ocean Research and Development Institute, PO Box 29, Ansan 425-600, Republic of Korea
| | - Sang-Jin Kim
- Marine Biotechnology Research Centre, Korea Ocean Research and Development Institute, PO Box 29, Ansan 425-600, Republic of Korea
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Abstract
Photobacterium damsela was identified in a blood culture taken from a child with sickle-cell disease. This is the first report of this organism in humans in the Caribbean. The microbiology of this organism and its identification are discussed. The clinical presentation in humans and the role of the immune status of the patient are reviewed.
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Affiliation(s)
- Jennifer M Knight-Madden
- Sickle Cell Unit, Tropical Medicine Research Institute, University of the West Indies, Kingston, Jamaica, West Indies.
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36
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Thompson FL, Thompson CC, Naser S, Hoste B, Vandemeulebroecke K, Munn C, Bourne D, Swings J. Photobacterium rosenbergii sp. nov. and Enterovibrio coralii sp. nov., vibrios associated with coral bleaching. Int J Syst Evol Microbiol 2005; 55:913-917. [PMID: 15774685 DOI: 10.1099/ijs.0.63370-0] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Six new Vibrio-like isolates originating from different species of bleached and healthy corals around Magnetic Island (Australia) were investigated using a polyphasic approach. Phylogenetic analyses based on 16S rRNA, recA and rpoA gene sequences split the isolates in two new groups. Strains LMG 22223(T), LMG 22224, LMG 22225, LMG 22226 and LMG 22227 were phylogenetic neighbours of Photobacterium leiognathi LMG 4228(T) (95.6 % 16S rRNA gene sequence similarity), whereas strain LMG 22228(T) was related to Enterovibrio norvegicus LMG 19839(T) (95.5 % 16S rRNA gene sequence similarity). The two new groups can be distinguished from closely related species on the basis of several phenotypic features, including fermentation of d-mannitol, melibiose and sucrose, and utilization of different compounds as carbon sources, arginine dihydrolase activity, nitrate reduction, resistance to the vibriostatic agent O/129 and the presence of fatty acids 15 : 0 iso and 17 : 0 iso. The names Photobacterium rosenbergii sp. nov. (type strain LMG 22223(T)=CBMAI 622(T)=CC1(T)) and Enterovibrio coralii sp. nov. (type strain LMG 22228(T)=CBMAI 623(T)=CC17(T)) are proposed to accommodate these new isolates. The G+C contents of the DNA of the two type strains are respectively 47.6 and 48.2 mol%.
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Affiliation(s)
- F L Thompson
- Microbial Resources Division and Brazilian Collection of Environmental and Industrial Micro-organisms (CBMAI), CPQBA, CP 6171, UNICAMP, CEP 13081-970, São Paulo, Brazil
| | - C C Thompson
- Microbial Resources Division and Brazilian Collection of Environmental and Industrial Micro-organisms (CBMAI), CPQBA, CP 6171, UNICAMP, CEP 13081-970, São Paulo, Brazil
| | - S Naser
- BCCM™/LMG Bacteria Collection, Laboratory for Microbiology, Ghent University, K. L. Ledeganckstraat 35, Ghent 9000, Belgium
- Laboratory for Microbiology, Ghent University, K. L. Ledeganckstraat 35, Ghent 9000, Belgium
| | - B Hoste
- BCCM™/LMG Bacteria Collection, Laboratory for Microbiology, Ghent University, K. L. Ledeganckstraat 35, Ghent 9000, Belgium
| | - K Vandemeulebroecke
- BCCM™/LMG Bacteria Collection, Laboratory for Microbiology, Ghent University, K. L. Ledeganckstraat 35, Ghent 9000, Belgium
| | - C Munn
- University of Plymouth, School of Biological Sciences, Drake Circus, Plymouth PL4 8AA, UK
| | - D Bourne
- Australian Institute of Marine Science, PMB 3, Townsville MC, Queensland 4810, Australia
| | - J Swings
- BCCM™/LMG Bacteria Collection, Laboratory for Microbiology, Ghent University, K. L. Ledeganckstraat 35, Ghent 9000, Belgium
- Laboratory for Microbiology, Ghent University, K. L. Ledeganckstraat 35, Ghent 9000, Belgium
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Osorio CR, Collins MD, Romalde JL, Toranzo AE. Variation in 16S-23S rRNA intergenic spacer regions in Photobacterium damselae: a mosaic-like structure. Appl Environ Microbiol 2005; 71:636-45. [PMID: 15691912 PMCID: PMC546723 DOI: 10.1128/aem.71.2.636-645.2005] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Phenotypically, Photobacterium damselae subsp. piscicida and P. damselae subsp. damselae are easily distinguished. However, their 16S rRNA gene sequences are identical, and attempts to discriminate these two subspecies by molecular tools are hampered by their high level of DNA-DNA similarity. The 16S-23S rRNA internal transcribed spacers (ITS) were sequenced in two strains of Photobacterium damselae subsp. piscicida and two strains of P. damselae subsp. damselae to determine the level of molecular diversity in this DNA region. A total of 17 different ITS variants, ranging from 803 to 296 bp were found, some of which were subspecies or strain specific. The largest ITS contained four tRNA genes (tDNAs) coding for tRNA(Glu(UUC)), tRNA(Lys(UUU)), tRNA(Val(UAC)), and tRNA(Ala(GGC)). Five amplicons contained tRNA(Glu(UUC)) combined with two additional tRNA genes, including tRNA(Lys(UUU)), tRNA(Val(UAC)), or tRNA(Ala(UGC)). Five amplicons contained tRNA(Ile(GAU)) and tRNA(Ala(UGC)). Two amplicons contained tRNA(Glu(UUC)) and tRNA(Ala(UGC)). Two different isoacceptor tRNA(Ala) genes (GGC and UGC anticodons) were found. The five smallest amplicons contained no tRNA genes. The tRNA-gene combinations tRNA(Glu(UUC))-tRNA(Val(UAC))-tRNA(Ala(UGC)) and tRNA(Glu(UUC))-tRNA(Ala(UGC)) have not been previously reported in bacterial ITS regions. The number of copies of the ribosomal operon (rrn) in the P. damselae chromosome ranged from at least 9 to 12. For ITS variants coexisting in two strains of different subspecies or in strains of the same subspecies, nucleotide substitution percentages ranged from 0 to 2%. The main source of variation between ITS variants was due to different combinations of DNA sequence blocks, constituting a mosaic-like structure.
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Affiliation(s)
- Carlos R Osorio
- Departamento de Microbioloxía e Parasitoloxía e Instituto de Acuicultura, Universidade de Santiago de Compostela, Campus Sur, 15782 Santiago de Compostela, Galicia, Spain.
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Dunlap PV, Ast JC. Genomic and phylogenetic characterization of luminous bacteria symbiotic with the deep-sea fish Chlorophthalmus albatrossis (Aulopiformes: Chlorophthalmidae). Appl Environ Microbiol 2005; 71:930-9. [PMID: 15691950 PMCID: PMC546735 DOI: 10.1128/aem.71.2.930-939.2005] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2004] [Accepted: 09/25/2004] [Indexed: 11/20/2022] Open
Abstract
Bacteria forming light-organ symbiosis with deep-sea chlorophthalmid fishes (Aulopiformes: Chlorophthalmidae) are considered to belong to the species Photobacterium phosphoreum. The identification of these bacteria as P. phosphoreum, however, was based exclusively on phenotypic traits, which may not discriminate between phenetically similar but evolutionarily distinct luminous bacteria. Therefore, to test the species identification of chlorophthalmid symbionts, we carried out a genomotypic (repetitive element palindromic PCR genomic profiling) and phylogenetic analysis on strains isolated from the perirectal light organ of Chlorophthalmus albatrossis. Sequence analysis of the 16S rRNA gene of 10 strains from 5 fish specimens placed these bacteria in a cluster related to but phylogenetically distinct from the type strain of P. phosphoreum, ATCC 11040(T), and the type strain of Photobacterium iliopiscarium, ATCC 51760(T). Analysis of gyrB resolved the C. albatrossis strains as a strongly supported clade distinct from P. phosphoreum and P. iliopiscarium. Genomic profiling of 109 strains from the 5 C. albatrossis specimens revealed a high level of similarity among strains but allowed identification of genomotypically different types from each fish. Representatives of each type were then analyzed phylogenetically, using sequence of the luxABFE genes. As with gyrB, analysis of luxABFE resolved the C. albatrossis strains as a robustly supported clade distinct from P. phosphoreum. Furthermore, other strains of luminous bacteria reported as P. phosphoreum, i.e., NCIMB 844, from the skin of Merluccius capensis (Merlucciidae), NZ-11D, from the light organ of Nezumia aequalis (Macrouridae), and pjapo.1.1, from the light organ of Physiculus japonicus (Moridae), grouped phylogenetically by gyrB and luxABFE with the C. albatrossis strains, not with ATCC 11040(T). These results demonstrate that luminous bacteria symbiotic with C. albatrossis, together with certain other strains of luminous bacteria, form a clade, designated the kishitanii clade, that is related to but evolutionarily distinct from P. phosphoreum. Members of the kishitanii clade may constitute the major or sole bioluminescent symbiont of several families of deep-sea luminous fishes.
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Affiliation(s)
- Paul V Dunlap
- Department of Ecology and Evolutionary Biology, University of Michigan, 830 North University Ave., Ann Arbor, MI 48109-1048, USA.
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Yoon JH, Lee JK, Kim YO, Oh TK. Photobacterium lipolyticum sp. nov., a bacterium with lipolytic activity isolated from the Yellow Sea in Korea. Int J Syst Evol Microbiol 2005; 55:335-339. [PMID: 15653897 DOI: 10.1099/ijs.0.63215-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-negative, motile, non-spore-forming, pleomorphic and lipolytic bacterial strain, M37T, was isolated from an intertidal sediment of the Yellow Sea in Korea. This organism grew optimally at 25–28 °C and in the presence of 1–2 % NaCl. It did not grow without NaCl or in the presence of more than 6 % NaCl. Strain M37T was characterized chemotaxonomically by having Q-8 as the predominant respiratory lipoquinone and C16 : 1
ω7c and/or iso-C15 : 0 2-OH and C16 : 0 as the major fatty acids. The DNA G+C content was 47 mol%. Phylogenetic analyses based on 16S rRNA gene sequences placed strain M37T within the clade comprising Photobacterium species, forming a coherent cluster with the type strains of Photobacterium profundum and Photobacterium indicum (16S rRNA gene similarity levels of 97·5–98·0 %). The mean DNA–DNA relatedness levels between strain M37T and P. profundum JCM 10084T and P. indicum DSM 5151T were in the range 12–15 %. Similarities between 16S rRNA gene sequences of strain M37T and those of the type strains of the other Photobacterium species ranged from 93·9 % (with Photobacterium fischeri) to 96·2 % (with Photobacterium phosphoreum). On the basis of phenotypic properties and phylogenetic and genomic distinctiveness, strain M37T (=KCTC 10562BPT=DSM 16190T) should be placed in the genus Photobacterium as a novel species, for which the name Photobacterium lipolyticum sp. nov. is proposed.
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Affiliation(s)
- Jung-Hoon Yoon
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, Korea
| | - Jung-Kee Lee
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, Korea
| | - Young-Ok Kim
- Biotechnology Research Centre, National Fisheries Research and Development Institute, Gijang-gun, Busan, Korea
| | - Tae-Kwang Oh
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, Korea
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Abstract
Hyphomicrobium indicum Johnson and Weisrock 1969 lacks true budding and hyphal branching, and some phenotypic characteristics are in contrast to other true hyphomicrobia. The major quinone system (ubiquinone Q-8), the G+C content of the DNA (40 mol%) and the cellular fatty acid composition (16 : 0, 16 : 1 and 18 : 1 as the major components, and 12 : 0 3-OH and 14 : 0 3-OH as the hydroxy fatty acids) of H. indicum are different from the genus Hyphomicrobium, but similar to the genus Photobacterium. Like the marine bacteria Photobacterium, H. indicum can be tolerant of sea water, while Hyphomicrobium cannot. Phylogenetic analyses of 16S rRNA and gyrB gene sequences revealed that H. indicum is most closely related to the genus Photobacterium of the gamma-Proteobacteria. Based on the phylogenetic, phenotypic and chemotaxonomic evidence, the results indicate that H. indicum should be transferred to the genus Photobacterium, and the name Photobacterium indicum comb. nov. (type strain, NBRC 14233(T)=ATCC 19614(T)) is proposed.
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Affiliation(s)
- Cheng-Hui Xie
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-Ku, Tokyo 113-0032, Japan
| | - Akira Yokota
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-Ku, Tokyo 113-0032, Japan
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Ast JC, Dunlap PV. Phylogenetic analysis of the lux operon distinguishes two evolutionarily distinct clades of Photobacterium leiognathi. Arch Microbiol 2004; 181:352-61. [PMID: 15034641 DOI: 10.1007/s00203-004-0663-7] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2003] [Revised: 02/18/2004] [Accepted: 02/26/2004] [Indexed: 10/26/2022]
Abstract
The luminous marine bacterium Photobacterium mandapamensis was synonymized several years ago with Photobacterium leiognathi based on a high degree of phenotypic and genetic similarity. To test the possibility that P. leiognathi as now formulated, however, actually contains two distinct bacterial groups reflecting the earlier identification of P. mandapamensis and P. leiognathi as separate species, we compared P. leiognathi strains isolated from light-organ symbiosis with leiognathid fishes (i.e., ATCC 25521(T), ATCC 25587, lequu.1.1 and lleuc.1.1) with strains from seawater originally described as P. mandapamensis and later synonymized as P. leiognathi (i.e., ATCC 27561(T) and ATCC 33981) and certain strains initially identified as P. leiognathi (i.e., PL-721, PL-741, 554). Analysis of the 16S rRNA and gyrB genes did not resolve distinct clades, affirming a close relationship among these strains. However, strains ATCC 27561(T), ATCC 33981, PL-721, PL-741 and 554 were found to bear a luxF gene in the lux operon ( luxABFE), whereas ATCC 25521(T), ATCC 25587, lequu.1.1 and lleuc.1.1 lack this gene ( luxABE). Phylogenetic analysis of the luxAB(F)E region confirmed this distinction. Furthermore, ATCC 27561(T), ATCC 33981, PL-721, PL-741 and 554 all produced a higher level of luminescence on high-salt medium, as previously described for PL-721, whereas ATCC 25521(T), ATCC 25587, lequu.1.1 and lleuc.1.1 all produced a higher level of luminescence on low-salt medium, a characteristic of P. leiognathi from leiognathid fish light organs. These results demonstrate that P. leiognathi contains two evolutionarily and phenotypically distinct clades, P. leiognathi subsp. leiognathi (strains ATCC 25521(T), ATCC 25587, lequu.1.1 and lleuc.1.1), and P. leiognathi subsp. mandapamensis (strains ATCC 27561(T), ATCC 33981, PL-721, PL-741 and 554).
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Affiliation(s)
- Jennifer C Ast
- Department of Ecology and Evolutionary Biology, Kraus Natural Science Building, 830 North University Avenue, University of Michigan, Ann Arbor, MI 48109-1048, USA
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Abstract
An outbreak of serious mortality among the cultured cobia Rachycentron canadum (weighing 3 kg) characterized by the presence of whitish granulomatous deposits on the kidney, liver and spleen occurred in July of 2000 in Taiwan. A non-motile strain CP1 was isolated from kidney and/or liver on tryptic soy agar and/or brain heart infusion agar plates (both supplemented with 1% NaCl, w/v). This strain was characterized and identified as Photobacterium damselae subsp. piscicida using biochemical characteristics and Bionor mono-Pp tests. The bacterium and its extracellular products (ECP) were lethal to the cobia (weighing 10 g) with LD50 values of 1.03 x 10(4) colony forming units and 1.26 microg protein/g fish body weight, respectively. All the moribund/dead fish exhibited darkness in color with no gross or internal leasions. However, the bacteria could be reisolated from kidney and liver after bacterial challenge. The present results reveal that Ph. damselae subsp. piscicida is the causative agent of fish photobacteriosis in the cobia and the bacterium isolated from sub-adult cobia (chronic form) is virulent to young cobia causing acute form of the disease.
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Affiliation(s)
- Ping-Chung Liu
- Department of Aquaculture, National Taiwan Ocean University, Keelung, Taiwan
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Abstract
Six luminous bacteria were isolated from migrating salmon in the Yukon River, Alaska. All isolates were identified as Photobacterium phosphoreum. Previous studies suggest that P. phosphoreum is an exclusively marine bacterium, while our Alaskan isolates are from salmon which migrated up to 1,228 km from the marine environment.
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Affiliation(s)
- K J Budsberg
- Institute of Arctic Biology and Department of Biology and Wildlife, University of Alaska Fairbanks, Fairbanks, Alaska 99775, USA
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Abstract
Photobacterium leiognathi forms a bioluminescent symbiosis with leiognathid fishes, colonizing the internal light organ of the fish and providing its host with light used in bioluminescence displays. Strains symbiotic with different species of the fish exhibit substantial phenotypic differences in symbiosis and in culture, including differences in 2-D PAGE protein patterns and profiles of indigenous plasmids. To determine if such differences might reflect a genetically based symbiont-strain/host-species specificity, we profiled the genomes of P. leiognathi strains from leiognathid fishes using PFGE. Individual strains from 10 species of leiognathid fishes exhibited substantial genomic polymorphism, with no obvious similarity among strains; these strains were nonetheless identified as P. leiognathi by 16S rDNA sequence analysis. Profiling of multiple strains from individual host specimens revealed an oligoclonal structure to the symbiont populations; typically one or two genomotypes dominated each population. However, analysis of multiple strains from multiple specimens of the same host species, to determine if the same strain types consistently colonize a host species, demonstrated substantial heterogeneity, with the same genomotype only rarely observed among the symbiont populations of different specimens of the same host species. Colonization of the leiognathid light organ to initiate the symbiosis therefore is likely to be oliogoclonal, and specificity of the P. leiognathi/leiognathid fish symbiosis apparently is maintained at the bacterial species level rather than at the level of individual, genomotypically defined strain types.
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Affiliation(s)
- Paul V Dunlap
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA.
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Abstract
AIMS To detect Photobacterium damselae ssp. piscicida using the PCR technique and plating method. METHODS AND RESULTS Two strains of P. damselae ssp. piscicida were isolated from cultured cobia (Rachycentron canadum) at two different fish farms in Taiwan. A pair of primers was designed to detect the capsular polysaccharide gene of P. damselae ssp. piscicida by PCR. Reference strains of different genus and different clinical strains were used for this study. The expected product (410 bp) was obtained from both P. damselae ssp. piscicida and P. damselae ssp. damselae, and they were differentiated by culturing on thiosulphate citrate bile salts-sucrose agar (TCBS-1). Photobacterium damselae ssp. damselae grew on TCBS-1 producing green colonies whereas P. damselae ssp. piscicida did not grow. CONCLUSIONS The methods used are cost and labour effective when compared with the other methods and commercially available kits. SIGNIFICANCE AND IMPACT OF THE STUDY This work provides an integrated set of methods to identify the species P. damselae and to differentiate P. damselae ssp. piscicida from P. damselae ssp. damselae.
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Affiliation(s)
- P R Rajan
- Institute of BioAgricultural Sciences, Academia Sinica, Nankang, Taipei, Taiwan
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Botella S, Pujalte MJ, Macián MC, Ferrús MA, Hernández J, Garay E. Amplified fragment length polymorphism (AFLP) and biochemical typing of Photobacterium damselae subsp. damselae. J Appl Microbiol 2002; 93:681-8. [PMID: 12234352 DOI: 10.1046/j.1365-2672.2002.01748.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
AIMS The aim of the present study was to characterize subspecifically Photobacterium damselae subsp. damselae strains isolated from cultured Sparus aurata and Dicentrarchus labrax by means of phenotypic and molecular typing techniques (amplified fragment length polymorphism, AFLP). METHODS AND RESULTS Seventy-one strains of P. damselae subsp. damselae were isolated from 38 cultured fishes at different fish farms located on the Mediterranean coast near Valencia, Spain. Most fish studied were asymptomatic and some were recovered during infectious outbreaks. Phenotypic characterization revealed a considerable degree of variability within the subspecies, including some characters, such as production of urease, which are used to differentiate P. damselae subsp. damselae from P. damselae subsp. piscicida. Genetic characterization was conducted on a selection of 33 strains, including two reference strains. Dice coefficient (Sd) and the unweighted pair group method with average linkage (UPGMA) were used for numerical analysis of banding patterns. AFLP type was defined on the basis of 100% similarity in the dendrogram obtained, yielding 24 distinct AFLP profiles. At 70% similarity, 13 clusters were defined, thus confirming the great variability observed for the phenotypic traits. CONCLUSIONS The AFLP variability shown by the isolates was high enough to discriminate between different strains which colonize the same fish. However, closely related AFLP types were usually derived from strains isolated at the same fish farm, indicating an epidemiological relationship. SIGNIFICANCE AND IMPACT OF THE STUDY This study has confirmed that the AFLP technique allows discrimination of individual strains within P. damselae subsp. damselae for epidemiological studies, and that this subspecies exhibits greater variability than that described for subspecies piscicida.
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Affiliation(s)
- S Botella
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva and Departamento de Microbiología y Ecología, Universitat de València, Spain
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Kvitt H, Ucko M, Colorni A, Batargias C, Zlotkin A, Knibb W. Photobacterium damselae ssp. piscicida: detection by direct amplification of 16S rRNA gene sequences and genotypic variation as determined by amplified fragment length polymorphism (AFLP). Dis Aquat Organ 2002; 48:187-195. [PMID: 12033705 DOI: 10.3354/dao048187] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
A PCR protocol for the rapid diagnosis of fish 'pasteurellosis' based on 16S rRNA gene sequences was developed. The procedure combines low annealing temperature that detects low titers of Photobacterium damselae but also related species, and high annealing temperature for the specific identification of P. damselae directly from infected fish. The PCR protocol was validated on 19 piscine isolates of P. damselae ssp. piscicida from different geographic regions (Japan, Italy, Spain, Greece and Israel), on spontaneously infected sea bream Sparus aurata and sea bass Dicentrarchus labrax, and on closely related American Type Culture Collection (ATCC) reference strains. PCR using high annealing temperature (64 degrees C) discriminated between P. damselae and closely related reference strains, including P. histaminum. Sixteen isolates of P. damselae ssp. piscicida, 2 P. damselae ssp. piscicida reference strains and 1 P. damselae ssp. damselae reference strain were subjected to Amplified Fragment Length Polymorphism (AFLP) analysis, and a similarity matrix was produced. Accordingly, the Japanese isolates of P. damselae ssp. piscicida were distinguished from the Mediterranean/European isolates at a cut-off value of 83% similarity. A further subclustering at a cut-off value of 97% allowed discrimination between the Israeli P. damselae ssp. piscicida isolates and the other Mediterranean/European isolates. The combination of PCR direct amplification and AFLP provides a 2-step procedure, where P. damselae is rapidly identified at genus level on the basis of its 16S rRNA gene sequence and then grouped into distinct clusters on the basis of AFLP polymorphisms. The first step of direct amplification is highly sensitive and has immediate practical consequences, offering fish farmers a rapid diagnosis, while the AFLP is more specific and detects intraspecific variation which, in our study, also reflected geographic correspondence. Because of its superior discriminative properties, AFLP can be an important tool for epidemiological and taxonomic studies of this highly homogeneous genus.
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Affiliation(s)
- H Kvitt
- Israel Oceanographic & Limnological Research Ltd., National Center for Mariculture, Eilat.
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Lucangeli C, Morabito S, Caprioli A, Achene L, Busani L, Mazzolini E, Fabris A, Macrì A. Molecular fingerprinting of strains of Yersinia ruckeri serovar O1 and Photobacterium damsela subsp. piscicida isolated in Italy. Vet Microbiol 2000; 76:273-81. [PMID: 10973701 DOI: 10.1016/s0378-1135(00)00241-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We studied the ribotypes, patterns of pulsed-field gel electrophoresis (PFGE) and interspersed repeated sequences (IRS)-PCR of 30 strains of Yersinia ruckeri O1 and 20 strains of Photobacterium damsela subsp. piscicida isolated from apparently unrelated epizootic outbreaks occurring on Italian fish farms between 1993 and 1999. All of the Y. ruckeri O1 strains had similar profiles, as demonstrated by all three typing methods, thus confirming the clonal structure of this species. The strains of P. damsela subsp. piscicida showed similar profiles when tested with ribotyping and PFGE; however, two slightly different profiles were distinguished by IRS-PCR using the primer ERIC2. The two profiles appeared to be related to the geographic origin of the strains, since each of them was specific to isolates from a certain area (i.e. northern or southern Italy). This result suggests that PCR fingerprinting may be a valuable tool in typing fish bacterial pathogens, which often present a great degree of genetic homogeneity.
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Affiliation(s)
- C Lucangeli
- Laboratorio di Medicina Veterinaria, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
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Magariños B, Toranzo AE, Barja JL, Romalde JL. Existence of two geographically-linked clonal lineages in the bacterial fish pathogen Photobacterium damselae subsp. piscicida evidenced by random amplified polymorphic DNA analysis. Epidemiol Infect 2000; 125:213-9. [PMID: 11057980 PMCID: PMC2869590 DOI: 10.1017/s0950268899004252] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In this work, we applied the random amplified polymorphic DNA (RAPD) technique to evaluate the genetic diversity in Photobacterium damselae subsp. piscicida (formerly Pasteurella piscicida), an important pathogen for different marine fish. Regardless of the oligonucleotide primer employed, the 29 isolates of Ph. damselae subsp. piscicida tested were separated into two groups, the RAPD-PCR analysis differentiated the European strains from the Japanese strains. The similarity between both groups estimated on the basis of the Dice coefficient was 75-80%. These results show that European and Japanese isolates of Ph. damselae subsp. piscicida, regardless of their host fish species, belong to two different clonal lineages. Our findings also indicate that RAPD profiling constitutes a useful tool for epidemiological studies of this fish pathogen.
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Affiliation(s)
- B Magariños
- Departamento de Microbiología y Parasitología, Facultad de Biología, Universidad de Santiago, Santiago de Compostela, Spain
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Kimura B, Hokimoto S, Takahashi H, Fujii T. Photobacterium histaminum Okuzumi et al. 1994 is a later subjective synonym of Photobacterium damselae subsp. damselae (Love et al. 1981) Smith et al. 1991. Int J Syst Evol Microbiol 2000; 50 Pt 3:1339-1342. [PMID: 10843080 DOI: 10.1099/00207713-50-3-1339] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The type strain of Photobacterium histaminum, JCM 8968T (= ATCC 51805T), and that of Photobacterium damselae subsp. damselae, ATCC 33539T, exhibit 100% identity in their 16S rRNA sequence, more than 80% DNA-DNA homology and only one phenotypic difference. Also, like P. histaminum, P. damselae subsp. damselae was shown to excrete a large amount of histamine when cells were grown on medium containing excessive histidine under acidic conditions. Therefore, the name P. histaminum should be considered to be a later subjective synonym of P. damselae subsp. damselae.
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