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At least 19 recordsLinked to original sources
PubMed2004

Transfer of Hyphomicrobium indicum to the genus Photobacterium as Photobacterium indicum comb. nov.

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.

Bacterial Proteins↗
PubMed1991

Evaluation of the genus Listonella and reassignment of Listonella damsela (Love et al.) MacDonell and Colwell to the genus Photobacterium as Photobacterium damsela comb. nov. with an emended description.

The genus Listonella, which was recently described on the basis of 5S rRNA sequence data, was found to be of dubious value on the basis of the results of a comparison of a number of taxonomic studies involving members of the Vibrionaceae. The available data suggest that 5S rRNA sequences may be of limited taxonomic use at the intra- and intergeneric levels, at least for apparently recently evolved groups, such as the Vibrionaceae. In this light, we assessed the generic assignment of the species Listonella damsela. Phenotypic characterization of 12 strains of bacteria assigned to L. damsela, including type strain ATCC 33539, revealed a strong resemblance to members of the genus Photobacterium. All of the strains conformed to major characteristics common to all known Photobacterium species. The characteristics of these organisms included the absence of a flagellar sheath and accumulation of poly-beta-hydroxybutyrate during growth on glucose coupled with the inability to utilize DL-beta-hydroxybutyrate as a sole carbon source. On the basis of the phenotypic data, we propose that L. damsela should be reassigned to the genus Photobacterium as Photobacterium damsela comb. nov.

Animals↗
PubMed1980

Proteolytic inactivation of luciferases from three species of luminous marine bacteria, Beneckea harveyi, Photobacterium fischeri, and Photobacterium phosphoreum: evidence of a conserved structural feature.

Upon limited proteolysis of luciferases from the luminous marine bacteria Photobacterium fischeri, Photobacterium phosphoreum, and Beneckea harveyi, the rate of loss of luciferase activity is the same as the rate of loss of the heavier subunit of all three enzymes. It thus appears that the larger subunit of the luciferase from P. phosphoreum should be designated alpha based on its apparent homology with the alpha subunits of the luciferases from B. harveyi and P. fischeri. The luciferase from B. harveyi is more sensitive to chymotrypsin than to trypsin; the luciferases of the Photobacterium species are more sensitive to trypsin than to chymotrypsin. Proteolytic inactivation of all three luciferases results from hydrolysis of a few peptide bonds in the alpha subunit; the proteolytic fragments from the three luciferases in 0.50 M phosphate are approximately the same size, indicating that the three enzymes have a protease-labile region at about the same position in the primary structure of their alpha subunits. Phosphate stabilizes all three luciferases against inactivation by proteases. Formation and degradation of intermediate species derived from the alpha subunits are readily observable in all three luciferases. Phosphate alters both the rate of product formation and the sites of peptide bond scission. The beta subunits of the luciferases from the two Photobacterium species, unlike the enzyme of B. harveyi, appear to be degraded in buffers containing low concentrations of phosphate; in high-phosphate buffers, the beta subunits of all three luciferases appear to resist proteases. Analysis of native and chymotrypsin-inactivated P. fischeri and P. phosphoreum luciferases in the analytical ultracentrifuge indicates that, as with B. harveyi luciferase, the products of limited proteolysis do not dissociate under nondenaturing conditions. The fact that the luciferases from evolutionarily diverse species of luminous bacteria have protease-sensitive bonds in the same region of the alpha subunit that are stabilized by anions strongly suggests that the protease-labile region of the alpha subunit is either an integral component of or in close proximity to the active center.

Binding Sites↗
PubMed1985

Purification of lumazine proteins from Photobacterium leiognathi and Photobacterium phosphoreum: bioluminescence properties.

Bright strains of the marine bioluminescent bacterium Photobacterium leiognathi produce a "lumazine protein" in amounts comparable to that previously found in Photobacterium phosphoreum. New protocols are developed for the purification to homogeneity of the proteins from both species in yields up to 60%. In dimmer strains the amounts of lumazine protein in extracts are less, and also there is an accompanying shift of the bioluminescence spectral maximum to longer wavelength, 492 nm. Both types of lumazine proteins have identical fluorescence spectra, with maxima at 475 nm, so it is suggested that, whereas lumazine protein is the major emitter in bright strains, there is a second emitter also present with a fluorescence maximum at longer wavelength. The two species of lumazine protein have the same 276 nm/visible absorbance ratio, 2.2, but differ in visible maxima: P. phosphoreum, 417 nm; P. leiognathi, 420 nm. For the latter the bound lumazine has epsilon 420 = 10 100 M-1 cm-1, practically the same as in free solution. The two lumazine proteins also differ quantitatively in their effect on the in vitro bioluminescence reaction, i.e., at blue shifting the bioluminescence spectrum or altering the kinetics. The P. phosphoreum lumazine protein is more effective with its homologous luciferase or with P. leiognathi luciferase than is the lumazine protein from P. leiognathi. These differences may have an electrostatic origin.

Bacterial Proteins↗
PubMed1985

Chemical characterization of lumazine protein from Photobacterium leiognathi: comparison with lumazine protein from Photobacterium phosphoreum.

The properties of lumazine proteins purified from the marine bioluminescent bacteria Photobacterium phosphoreum, a psychrophile, and Photobacterium leiognathi, a relatively thermophilic species, are compared. An accurate 1:1 stoichiometry of binding of the ligand 6,7-dimethyl-8-ribityllumazine to each lumazine protein is established by back-titration of the apoprotein with the authentic ligand, using both fluorescence and absorption measurements. Neither protein contains metal cofactors, organic phosphorus, or carbohydrate. Both proteins are anionic and hydrophilic. They each contain a single Trp residue and have blocked amino terminals but otherwise differ in amino acid composition and other properties (P. phosphoreum and P. leiognathi, respectively): Met (internal), 1, 2; Cys, 2, 1; Arg, 4, 7; pI, 4.78 and 4.83, 4.38 and 4.45; Mr, 19 750, 21 300. In the P. phosphoreum protein both Cys residues are accessible, but in the P. leiognathi protein the single Cys is "buried". Modification of this buried Cys and at least one Cys in the P. phosphoreum protein prevents binding of the ligand. The UV and visible absorption spectra of both lumazine proteins denatured in 6 M guanidine hydrochloride can be accurately modeled by using the number of equivalents of the lumazine derivative and blocked aromatic amino acid model compounds determined by chemical and spectrophotometric analyses for Trp, Tyr, and Phe.

Amino Acids↗
PubMed1995

Small-subunit rRNA sequences and whole DNA relatedness concur for the reassignment of Pasteurella piscicida (Snieszko et al.) Janssen and Surgalla to the genus Photobacterium as Photobacterium damsela subsp. piscicida comb. nov.

The taxonomic status of Pasteurella piscicida (strain NCIMB 2058T [T = type strain] and a strain isolated from the environment) was investigated by performing phylogenetic analyses of small-subunit rRNA sequences, DNA-DNA hybridization analyses, and biochemical characterization analyses. The results of the phylogenetic analyses and the levels of DNA-DNA complementarity demonstrated conclusively that Pasteurella piscicida is extremely closely related to Photobacterium damsela ATCC 33539T. Since the two taxa exhibited a level of DNA-DNA relatedness of 80%, they are members of the same species. The high level of DNA relatedness and the presence of specific morphological and biochemical characteristics support the hypothesis that two subspecies should be recognized. On the basis of its phylogenetic position, we concluded that Pasteurella piscicida should be renamed Photobacterium damsela subsp. piscicida comb. nov.

Base Sequence↗
PubMed2000

Photobacterium histaminum Okuzumi et al. 1994 is a later subjective synonym of Photobacterium damselae subsp. damselae (Love et al. 1981) Smith et al. 1991.

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.

DNA, Bacterial↗
PubMed2005

Photobacterium lipolyticum sp. nov., a bacterium with lipolytic activity isolated from the Yellow Sea in Korea.

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 degrees 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 C(16 : 1)omega7c and/or iso-C(15 : 0) 2-OH and C(16 : 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.

Bacterial Typing Techniques↗
PubMed2006

Photobacterium halotolerans sp. nov., isolated from Lake Martel in Spain.

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 degrees C (optimum, 28 degrees 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 beta-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 : 1omega7c and/or C15 : 0 iso 2-OH), C16 : 0 (21.2 %) and C18 : 1omega7c (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.

Base Composition↗
PubMed2000

Application of AFLP for taxonomic and epidemiological studies of Photobacterium damselae subsp. piscicida.

A collection of 106 Photobacterium damselae subsp. piscicida strains and 19 Photobacterium damselae subsp. damselae strains, including reference and type strains, were genetically characterized using AFLP. The total genomic DNA of each bacterial strain was digested using restriction endonucleases HindIII and TaqI. Using numerical analysis, six clusters were recognized. The largest cluster (n = 106) contained the majority of the strains tested and consisted exclusively of Photobacterium damselae subsp. piscicida. The Photobacterium damselae subsp. damselae strains fell outside this cluster. DNA-DNA hybridization experiments showed 77% DNA binding between the two subspecies, indicating a close genetic relationship. This clearly demonstrates the applicability of AFLP in studying the taxonomic position of Photobacterium damselae subsp. piscicida. In addition, AFLP proved to be a useful genotypic technique for epidemiological surveys of the pathogen, since it was able to discriminate between Mediterranean and Japanese Photobacterium damselae subsp. piscicida isolates.

Animals↗
PubMed2005

Photobacterium frigidiphilum sp. nov., a psychrophilic, lipolytic bacterium isolated from deep-sea sediments of Edison Seamount.

A Gram-negative, motile, rod-shaped, psychrophilic and weakly halophilic bacterial strain, SL13(T), was isolated from deep-sea sediments (1450 m depth) of Edison Seamount in the western Pacific Ocean. Optimal growth of SL13(T) requires the presence of 1.5% (w/v) NaCl, a pH of 6.0 and a temperature of 14 degrees C. The whole-cell fatty acid profile of the isolate includes C16:1 and C16:0 as major fatty acids and contains C20:5omega3. This is consistent with corresponding data for Photobacterium profundum. The DNA G+C content of strain SL13(T) is 43.8 mol%. Phylogenetic analyses of 16S rRNA gene sequences place this bacterium in the 'Gammaproteobacteria', within the genus Photobacterium. Sequence similarity analysis indicates that the closest relatives of strain SL13(T) are Photobacterium indicum (99.3%), P. profundum (98.5%) and Photobacterium lipolyticum (98.2%). The DNA-DNA hybridization levels between the isolate and its closest known phylogenetic relatives, P. indicum, P. profundum and P. lipolyticum, are 27.1, 52.4 and 20.2%, respectively. Thus strain SL13(T) represents a novel species of the genus Photobacterium, for which the name Photobacterium frigidiphilum sp. nov. is proposed. The type strain is SL13(T) (=KCTC 12384(T)=JCM 12947(T)).

Bacterial Typing Techniques↗
PubMed1998

Phenotypic characterization of the marine pathogen Photobacterium damselae subsp. piscicida.

The taxonomic position of Photobacterium damselae subsp. piscicida, the causative agent of fish pasteurellosis, is controversial as this organism has also been described as 'Pasteurella piscicida'. To clarify the taxonomic position of the pathogen, a total of 113 P. damselae subsp. piscicida strains and 20 P. damselae subsp. damselae strains, isolated from different geographical areas and from the main affected fish species, were analysed using 129 morphological and biochemical tests, including the commercial API 20E and API CH50 test systems. For comparison, the type strains of other Photobacterium species (i.e. Photobacterium leiognathi and Photobacterium angustum) were included in the analyses. The results were statistically analysed by unweighted pair group average clustering and the distance between the different clusters was expressed as the percentage disagreement. The analyses showed that, based on morphological and biochemical identification tests, P. damselae subsp. piscicida is related to other Photobacterium species. However, it is clearly distinguishable from P. damselae subsp. damselae and no phenotypic evidence was found to include P. damselae subsp. piscicida as a subspecies in the species P. damselae.

Animals↗
PubMed2005

Photobacterium aplysiae sp. nov., a lipolytic marine bacterium isolated from eggs of the sea hare Aplysia kurodai.

A bacterium, named GMD509T, showing lipolytic activity was isolated from the eggs of the sea hare Aplysia kurodai collected at Mogiyeo (depth, 12 m), an uninhabited small island in the South Sea of Korea. The strain is Gram-negative, motile, facultatively anaerobic, mesophilic and weakly halophilic. Optimal growth of strain GMD509T occurs in the presence of 3.0 % (w/v) NaCl and at pH 8 and 25 degrees C. The whole-cell fatty acid profile of the isolate includes C16 : 1, C16 : 0 and C18 : 1 as major fatty acids and its DNA G+C content is 45 mol%. Phylogenetic analyses of 16S rRNA gene sequences place this bacterium in the gamma-Proteobacteria, within the genus Photobacterium. The 16S rRNA gene sequence of strain GMD509T is most similar to those of Photobacterium frigidiphilum (97.8 %), Photobacterium profundum (97.5 %) and Photobacterium indicum (97.4 %). DNA-DNA relatedness levels between the isolate and its closest known phylogenetic relatives, P. frigidiphilum and P. indicum, are 25.3 and 13.7 %, respectively. Strain GMD509T therefore represents a novel species, for which the name Photobacterium aplysiae sp. nov. is proposed, with the type strain GMD509T (=KCTC 12383T=JCM 12948T).

Animals↗
PubMed1998

A new approach to separate the genus Photobacterium from Vibrio with RFLP patterns by HhaI digestion of PCR-amplified 16S rDNA.

A new approach to separate members of the genus Photobacterium from the genus Vibrio with RFLP (Restriction Fragment Length Polymorphism) patterns by HhaI digestion of PCR-amplified 16S rDNA was developed in the present study. It was clearly shown that these patterns of the genus Photobacterium were unique and distinguishable from Vibrio species. This method is very simple and does not need other supporting procedures, such as Southern transfer and probe hybridization. It can be applied not only to luminous species, but also to non-luminous Photobacterium spp. This result promises a rapid tool to distinguish the genus Photobacterium from Vibrio and should be useful in routine identification system.

DNA, Ribosomal↗
PubMed1998

Photobacterium profundum sp. nov., a new, moderately barophilic bacterial species isolated from a deep-sea sediment.

A novel, moderately barophilic bacterium was isolated from a sediment sample obtained from the Ryukyu Trench, at a depth of 5110 m. The isolate, designated strain DSJ4, is a Gram-negative rod capable of growth between 4 degrees C and 18 degrees C under atmospheric pressure, with optimum growth displayed at 10 degrees C, and capable of growth at pressures between 0.1 MPa and 70 MPa at 10 degrees C, with optimum growth displayed at 10 MPa. Strain DSJ4 is a moderately barophilic bacterium, and shows no significant change in growth at pressures up to 50 MPa. Phylogenetic analysis of the 16S rRNA sequence of strain DSJ4 places this strain within the Photobacterium subgroup of the family Vibrionaceae, closely related to the strain SS9 that was independently isolated from the Sulu Trough. The temperature and pressure ranges for growth, cellular fatty acid composition, and assorted physiological and biochemical characteristics indicate that these strains differ from other Photobacterium species. Furthermore, both SS9 and DSJ4 displayed a low level of DNA similarity to other Photobacterium type strains. Based on these differences, these strains are proposed to represent a new deep-sea-type species. The name Photobacterium profundum (JCM10084) is proposed.

Base Composition↗