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Applied Microbiology and Biotechnology Jun 2017Photobacterium species are Gram-negative coccobacilli which are distributed in marine habitats worldwide. Some species are unique because of their capability to produce... (Review)
Review
Photobacterium species are Gram-negative coccobacilli which are distributed in marine habitats worldwide. Some species are unique because of their capability to produce luminescence. Taxonomically, about 23 species and 2 subspecies are validated to date. Genomes from a few Photobacterium spp. have been sequenced and studied. They are considered a special group of bacteria because some species are capable of producing essential polyunsaturated fatty acids, antibacterial compounds, lipases, esterases and asparaginases. They are also used as biosensors in food and environmental monitoring and detectors of drown victim, as well as an important symbiont.
Topics: Bacterial Proteins; Biosensing Techniques; DNA, Bacterial; Ecosystem; Genome, Bacterial; Luminescence; Photobacterium; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Symbiosis
PubMed: 28497204
DOI: 10.1007/s00253-017-8300-y -
International Microbiology : the... Mar 2017The genus Photobacterium, one of the eight genera included in the family Vibrionaceae, contains 27 species with valid names and it has received attention because of the... (Review)
Review
The genus Photobacterium, one of the eight genera included in the family Vibrionaceae, contains 27 species with valid names and it has received attention because of the bioluminescence and pathogenesis mechanisms that some of its species exhibit. However, the taxonomy and phylogeny of this genus are not completely elucidated; for example, P. logei and P. fischeri are now considered members of the genus Aliivibrio, and previously were included in the genus Vibrio. In addition, P. damselae subsp. piscicida was formed as a new combination for former Vibrio damsela and Pasteurella piscicida. Moreover, P. damselae subsp. damselae is an earlier heterotypic synonym of P. histaminum. To avoid these incovenences draft and complete genomic sequences of members of Photobacterium are increasingly becoming available and their use is now routine for many research laboratories to address diverse goals: species delineation with overall genomic indexes, phylogenetic analyses, comparative genomics, and phenotypic inference. The habitats and isolation source of the Photobacterium species include seawater, sea sediments, saline lake waters, and a variety of marine organisms with which the photobacteria establish different relationships, from symbiosis to pathogenic interactions. Several species of this genus contain bioluminescent strains in symbiosis with marine fish and cephalopods; in addition, other species enhance its growth at pressures above 1 atmosphere, by means of several high-pressure adaptation mechanisms and for this, they may be considered as piezophilic (former barophilic) bacteria. Until now, only P. jeanii, P. rosenbergii, P. sanctipauli, and the two subspecies of P. damselae have been reported as responsible agents of several pathologies on animal hosts, such as corals, sponges, fish and homeothermic animals. In this review we have revised and updated the taxonomy, ecology and pathogenicity of several members of this genus. [Int Microbiol 20(1): 1-10 (2017)].
Topics: Animals; Fish Diseases; Fishes; Photobacterium; Phylogeny; Symbiosis
PubMed: 28581017
DOI: 10.2436/20.1501.01.280 -
International Journal of Systematic and... Oct 2021A Gram-stain-negative, aerobic, motile, short rod-shaped, catalase-negative and oxidase-positive bacterium, strain CAU 1568, was isolated from marine sediment sand...
A Gram-stain-negative, aerobic, motile, short rod-shaped, catalase-negative and oxidase-positive bacterium, strain CAU 1568, was isolated from marine sediment sand sampled at Sido Island in the Republic of Korea. The optimum conditions for growth were at 25-30 °C, at pH 6.5-8.5 and with 0-4.0 % (w/v) NaCl. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain CAU 1568 was a member of the genus with high similarity to JCM 30852 (97.7 %), KACC 17089 (97.3 %) and LMG F28894 (97.3 %). The predominant cellular fatty acids were C, summed feature 3 (C 6 and/or C 7) and summed feature 8 (C 7 and/or C 6), with Q-8 as the major of isoprenoid quinone. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerols, phosphatidylcholine, phosphatidylethanolamine, phospholipid, two aminophospholipids and three unidentified lipids. The whole genome size of strain CAU 1568 was 4.8 Mb with 50.1 mol% G+C content; including 38 contigs and 4233 protein-coding genes. These taxonomic data support CAU 1568 as representing a novel species, for which the name sp. nov. is proposed. The type strain of this novel species is CAU 1568 (=KCTC 82404=MCCC 1K05668).
Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Geologic Sediments; Islands; Phospholipids; Photobacterium; Phylogeny; RNA, Ribosomal, 16S; Republic of Korea; Sand; Seawater; Sequence Analysis, DNA; Ubiquinone
PubMed: 34605765
DOI: 10.1099/ijsem.0.005034 -
FEMS Microbiology Reviews Mar 2011Photobacterium comprises several species in Vibrionaceae, a large family of Gram-negative, facultatively aerobic, bacteria that commonly associate with marine animals.... (Review)
Review
Photobacterium comprises several species in Vibrionaceae, a large family of Gram-negative, facultatively aerobic, bacteria that commonly associate with marine animals. Members of the genus are widely distributed in the marine environment and occur in seawater, surfaces, and intestines of marine animals, marine sediments and saline lake water, and light organs of fish. Seven Photobacterium species are luminous via the activity of the lux genes, luxCDABEG. Much recent progress has been made on the phylogeny, genomics, and symbiosis of Photobacterium. Phylogenetic analysis demonstrates a robust separation between Photobacterium and its close relatives, Aliivibrio and Vibrio, and reveals the presence of two well-supported clades. Clade 1 contains luminous and symbiotic species and one species with no luminous members, and Clade 2 contains mostly nonluminous species. The genomes of Photobacterium are similar in size, structure, and organization to other members of Vibrionaceae, with two chromosomes of unequal size and multiple rrn operons. Many species of marine fish form bioluminescent symbioses with three Photobacterium species: Photobacterium kishitanii, Photobacterium leiognathi, and Photobacterium mandapamensis. These associations are highly, but not strictly species specific, and they do not exhibit symbiont-host codivergence. Environmental congruence instead of host selection might explain the patterns of symbiont-host affiliation observed from nature.
Topics: Animals; Fishes; Genomics; Molecular Sequence Data; Photobacterium; Phylogeny; Symbiosis; Water Microbiology
PubMed: 20883503
DOI: 10.1111/j.1574-6976.2010.00250.x -
International Microbiology : the... Mar 2002Pasteurellosis, or pseudotuberculosis, is a bacterial septicaemia caused by the halophilic bacterium Photobacterium damselae subsp. piscicida (formerly Pasteurella... (Review)
Review
Pasteurellosis, or pseudotuberculosis, is a bacterial septicaemia caused by the halophilic bacterium Photobacterium damselae subsp. piscicida (formerly Pasteurella piscicida). Although this disease was first described in wild populations of white perch and striped bass, currently the natural hosts of the pathogen are a wide variety of marine fish. The disease has great economic impact both in Japan, where it affects mainly yellowtail cultures, and in the Mediterranean area, due to the losses it causes in seabream and seabass farms. This microorganism serves as a perfect model to study a bacterial fish pathogen, either at an applied level, to resolve or to mitigate the high economic losses of fish farmers, or at a basic level, for a better understanding of P. damselae subsp. piscicida biology. This article discusses the methods employed in our laboratory to study the causative agent of pasteurellosis. It reviews important aspects, from the diverse procedures for the detection and isolation of the pathogen to the latest molecular studies that have allowed its correct taxonomic allocation. Characterization of some virulence mechanisms and the available methods to prevent the disease are also presented.
Topics: Animals; Bacteremia; Fish Diseases; Gram-Negative Bacterial Infections; Molecular Diagnostic Techniques; Pasteurella Infections; Phenotype; Photobacterium; Virulence
PubMed: 12102234
DOI: 10.1007/s10123-002-0051-6 -
Journal of Bioscience and Bioengineering Jul 2019An efficient heterotrophic nitrifying/aerobic denitrifying strain, Photobacterium sp. NNA4 was isolated from a recirculating aquaculture system (RAS). NNA4 was capable...
An efficient heterotrophic nitrifying/aerobic denitrifying strain, Photobacterium sp. NNA4 was isolated from a recirculating aquaculture system (RAS). NNA4 was capable of utilizing ammonia, nitrate or nitrite as sole N-source with maximal removal rates of 12.5 mg/L/h for NHN, 16.4 mg/L/h for NO-N, and 4.5 mg/L/h for NO-N, respectively. Optimal nitrification conditions were: sodium succinate as C-source, 30-37°C, NaCl 1-4%, pH 7.0-8.0, dissolved oxygen 5.89 mg/L, C/N > 10. Gas chromatography/mass spectrometry and gas chromatography/isotope ratio mass spectrometry analyses showed that N and NO were aerobic denitrification products of nitrite and nitrate. NNA4 could tolerate high concentration of hydroxylamine and displayed efficient hydroxylamine-transforming capability. Hydroxylamine oxidoreductase activity using potassium ferricyanide as electron acceptor was 0.042 U. Results revealed that strain NNA4 could oxidize NHOH directly to NO at aerobic conditions. In view of its high removal ability of inorganic nitrogen pollutants and broad salinity tolerance range, NNA4 has great potential in denitrification treatment of types of wastewater with either low salinity (e.g., municipal facilities) or high salinity (e.g., aquaculture, seafood processing).
Topics: Aerobiosis; Ammonia; Animals; Aquaculture; Denitrification; Equipment Reuse; Heterotrophic Processes; Humans; Hydroxylamine; Nitrates; Nitrification; Nitrogen; Oxidoreductases; Photobacterium; Wastewater; Water Pollutants, Chemical; Water Purification
PubMed: 30709706
DOI: 10.1016/j.jbiosc.2018.12.014 -
Current Microbiology Jun 2020Two bacterial strains were isolated from the hepatopancreas of a cultured shrimp (Penaeus vannamei) in Sinaloa, México. Their partial 16S rRNA gene sequences clustered...
Two bacterial strains were isolated from the hepatopancreas of a cultured shrimp (Penaeus vannamei) in Sinaloa, México. Their partial 16S rRNA gene sequences clustered within those of the genus Photobacterium, showing high similarity to the type strains of Photobacterium angustum and Photobacterium leiognathi, were 87.1% and 97.5%, respectively. Multilocus sequence analysis using eight housekeeping genes (ftsZ, gapA, gyrB, mreB, pyrH, recA, rpoA, topA and 16S rRNA) and phylogenetic analysis with 139 single-copy genes showed that the new strains form an independent branch whole genome sequencing and genomic analyses (average nucleotide identity, average amino acid identity, and in silico DNA-DNA hybridization) produced values well below the thresholds for species delineation with all methods tested. In addition, a phenotypic characterization was performed to support the description and differentiation of the novel strains from related taxa. The results obtained demonstrate that the two strains represent a novel species for which the name Photobacterium lucens sp. nov. is proposed.
Topics: Animals; DNA, Bacterial; Genes, Essential; Genome, Bacterial; Mexico; Nucleic Acid Hybridization; Penaeidae; Phenotype; Photobacterium; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA
PubMed: 31982966
DOI: 10.1007/s00284-020-01893-9 -
Systematic and Applied Microbiology Jul 2014Five isolates from marine fish (W3(T), WM, W1S, S2 and S3) and three isolates misclassified as Photobacterium phosphoreum, originating from spoiled modified atmosphere...
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.
Topics: Amplified Fragment Length Polymorphism Analysis; Animals; Aquatic Organisms; Bacterial Proteins; Bacterial Typing Techniques; Cluster Analysis; DNA, Bacterial; DNA, Ribosomal; Food Microbiology; Gadiformes; Molecular Sequence Data; Nucleic Acid Hybridization; Photobacterium; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA
PubMed: 24951451
DOI: 10.1016/j.syapm.2014.05.003 -
International Journal of Systematic and... Dec 2019A Gram-stain-negative, aerobic, motile, rod-shaped bacterium, designated strain LAM9072, was isolated from a sample of a sulfonylurea herbicide-degrading consortium...
A Gram-stain-negative, aerobic, motile, rod-shaped bacterium, designated strain LAM9072, 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 LAM9072 were 35 °C and 7.0, respectively. Strain LAM9072 could grow in the presence of NaCl up to 9 % (w/v). Comparative analysis of the 16S rRNA gene sequences revealed that strain LAM9072 was closely related to members of the family , with the highest similarities to MACL01 (97.7 %) and S2753 (97.7 %). Strain LAM9072 formed a distinct phylogenetic subclade within the genus in the 16S rRNA gene phylogenetic trees. The results of multi-locus sequence analysis revealed a distinct lineage with MACL01 as its closest relative. The genomic G+C content was 50.2 mol%. The DNA-DNA hybridization values between strain LAM9072 and LMG 22194 and LMG 28894 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 LAM9072 and LMG 22194 and LMG 28894. The major fatty acids were summed feature 3 (Cω6 and/or Cω7), C and summed feature 8 (Cω7 and/or Cω6). 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 LAM9072 represents a novel species, for which the name sp. nov. is proposed. The type strain is LAM9072 (=ACCC 19961=JCM 30852).
Topics: Bacterial Typing Techniques; Base Composition; Biodegradation, Environmental; China; DNA, Bacterial; Fatty Acids; Herbicides; Nucleic Acid Hybridization; Phospholipids; Photobacterium; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Sulfonylurea Compounds; Ubiquinone
PubMed: 31693472
DOI: 10.1099/ijsem.0.003705 -
Annals of the New York Academy of... Feb 2010The deep-sea bacterium, Photobacterium profundum SS9, has been adopted as a model organism to understand the molecular basis of cold-adapted high-pressure-loving... (Review)
Review
The deep-sea bacterium, Photobacterium profundum SS9, has been adopted as a model organism to understand the molecular basis of cold-adapted high-pressure-loving (piezophilic) growth. Despite growing optimally at 28 MPa (15 degrees C), P. profundum SS9 can grow over a wide range of pressures and temperatures. The ability to grow at atmospheric pressure has enabled a limited set of genetic tools to be developed, which has provided genetic insights into the mechanism of piezophilic growth in P. profundum SS9. This review focuses on how genetic studies have uncovered the importance of processes affecting the DNA and the bacterial cell envelope in the piezophilic growth of P. profundum SS9. In addition, a method was developed to assess quantitative piezophilic colony growth of P. profundum SS9 on solid agar. Future studies, using this methodology, could provide novel insights into the molecular basis of piezophilic, surface-attached growth.
Topics: Adaptation, Physiological; Bacterial Proteins; Cell Membrane; Cold Temperature; DNA, Bacterial; Genes, Bacterial; Hydrostatic Pressure; Models, Biological; Photobacterium; Seawater
PubMed: 20233381
DOI: 10.1111/j.1749-6632.2009.05178.x