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Reevaluation of the taxonomy of Vibrio, beneckea, and Photobacterium: Abolition of the genus Beneckea

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Abstract

As a result of studies on the evolution of glutamine synthetase and superoxide dismutase, the genusBeneckea has been abolished and its constituent species, along withPhotobacterium fischeri andP. logei, assigned to the genusVibrio. The definitions ofVibrio andPhotobacterium have been modified accordingly.
... Four novel PET hydrolase genes (PET2, PET5, PET6, and PET12) were functionally verified by cloning and expressing them heterologously in E. coli, with active clones producing halos on PET nanoparticles or PCL. Among these active enzymes, PET2 was derived from a marine metagenomics dataset [187], and PET6 was derived from Vibrio gazogenes strain DSM-21264 [188]. Both enzymes showed traits of thermostability, with optimal temperature at 70 • C for PET2 and 55 • C for PET6. ...
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... SWC is an artificial seawater medium containing sodium chloride (2.33%), magnesium sulfate (1.85%), calcium chloride (0.22%), and potassium chloride (0.11%), with peptone (0.50%), glycerol (0.30%), and yeast extract (0.05%) as carbon sources (25)(26)(27). V. harveyi strain SFP118, derived from B392 (MAV/Photobacterium fischeri/Beneckea harveyi) (28,29), and a spontaneous nalidixic acid-resistant mutant (SFP119) were utilized for this study. SFP119, the spontaneous nalidixic acid-resistant strain, was isolated from SFP118 using a previously published protocol (19,30,31). ...
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The bioluminescent marine bacterium Vibrio harveyi can exist within a host, acting as a mutualist or a parasitic microbe, and as planktonic cells in open seawater. This study demonstrates the ability of V. harveyi populations to survive and adapt under nutrient stress conditions in the laboratory, starting in an initially rich medium. V. harveyi populations remain viable into long-term stationary phase, for at least 1 month, without the addition of nutrients. To determine whether these communities are dynamic, populations were sampled after 10, 20, and 30 days of incubation and examined for their competitive ability when cocultured with an unaged, parental population. While populations incubated for 10 or 20 days showed some fitness advantage over parental populations, only after 30 days of incubation did all populations examined outcompete parental populations in coculture, fully expressing the growth advantage in stationary phase (GASP) phenotype. The ability to express GASP, in the absence of additional nutrients after inoculation, verifies the dynamism of long-term stationary-phase V. harveyi populations, implies the ability to generate genetic diversity, and demonstrates the plasticity of the V. harveyi genome, allowing for rapid adaptation for survival in changing culture environments. Despite the dynamism, the adaptation to the changing culture environment occurs less rapidly than in Escherichia coli, possibly due to Vibrio harveyi's lower mutation frequency. IMPORTANCE Vibrio harveyi populations exist in many different niches within the ocean environment, as free-living cells, symbionts with particular squid and fish species, and parasites to other marine organisms. It is important to understand V. harveyi's ability to survive and evolve within each of these niches. This study focuses on V. harveyi's lifestyle outside the host environment, demonstrating this microbe's ability to survive long-term culturing after inoculation in an initially rich medium and revealing increased competitive fitness correlated with incubation time when aged V. harveyi populations are cocultured with unaged, parental cultures. Thus, this study highlights the development of the growth advantage in stationary phase (GASP) phenotype in V. harveyi populations suggesting a dynamic population with fluctuating genotype frequencies throughout long-term, host-independent incubation.
... Интенсивность люминесценции зависит от большого количества внешних факторов, в частности, температуры, рН, степени аэрации, гидростатического давления, состава среды, воздействующих на метаболизм клеток и в целом на их структуру. Светящиеся бактерии -это самые маленькие источ ники биолюминесцен ции, способные излу чать 10 3 -10 4 квант/с · клетку [3][4][5]. Спектр эмиссии большинства люминесцентных бактерий характеризуется отдельной широкой полосой с пиком 490-495 нм. Благодаря таким особенностям биолюминесцентные бактерии являются перспективными тест-объектами в современных аналитических технологиях. ...
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Five isolates of luminous bacteria from aquatic organisms of the Azov and the Black Seas were isolated. The study of morphological, cultural, physiological and biochemical properties showed that isolates M1 and M4 were the representatives of the species harveyi, and isolates Fb, Sh1, and B were the representatives of the species P. leiognathi. It was found that the strain P. leiognathi Sh1 was the most sensitive to zinc sulfate when studying its effect on allocated luminescent bacteria. The effective concentration that reduced the bioluminescent index (BLI) by 50% (EC50) for zinc sulfate, when exposed to the test strain, was 4,0 0,1 g/ml. Experimental data allowed to consider the strain P. leiognathi Sh1 to be the test-object for determining the antimicrobial activity of benzylpenicillin, gentamicin, streptomycin, tetracycline and ceftriaxone. The results of evaluating the effect of antibiotics on the test object, revealed that after 15 minutes of incubation, the BLI values decreased by 50% only in samples containing benzylpenicillin, gentamicin, and tetracycline. Their EC50 were 500.0, 283.0 and 28.5 g/ml respectively. It was found that the exposure of test-strain to all antibacterial agents demonstrated resulted in decrease in BLI by 100% as compared to the control values. Strain P. leiognathi Sh1 can be used as a test-object for determining the antimicrobial activity of antibiotics.
... Figure 12: Photographies indiquant la morphologie des souches de Vibrio harveyi. A. Croissance de la souche VIB 391 sur marine agar 2216E ; B. Luminescence de la souche VIB 391 ; C. Croissance de la souche VIB 645 sur TCBS ; D. Microscopie électronique en transmission de la souche VIB 645 cultivée en marine broth, échelle = 1 µm(Zhang et al., 2020).Par la suite, elle a été identifiée en tant que Lucibacterium harveyi puis Beneckea harveyi pour finalement être assignée au genre Vibrio et nommée Vibrio harveyi(Baumann et al., 1980). Plus tard, grâce au développement des méthodes d'identification, en particulier AFLP, ribotypage et hybridation ADN-ADN, Vibrio carchariae et Vibrio trachuri ont été reconnues comme synonymesde V. harveyi ...
Thesis
Les bactéries du genre Vibrio et plus particulièrement celles du clade Harveyi, sont responsables de la vibriose, entraînant des mortalités de masse associées à des pertes économiques considérables pour le secteur aquacole. Vibrio Harveyi est un agent pathogène émergent pour le bar commun d'élevage (Dicentrarchus labrax), capable de former des biofilms. Etant donné qu'aucune méthode prophylactique n'est aujourd'hui commercialisée, la lutte contre la vibriose réside dans la prévention et le développement de méthodes de surveillance et de diagnostic. L'objectif de cette thèse consiste à apporter des éléments de compréhension, via la combinaison d'approches microbiologiques et moléculaires, visant à optimiser la gestion du risque Vibrio pour le bar commun d'élevage. Dans un premier temps, des méthodes de quantification et d'identification ont été mises au point. Une méthode de PCR en temps réel, ciblant le gène mreB, a été développée et optimisée pour quantifier V. harveyi à la fois dans l'eau et les biofilms. La "Luvibase", une base de données composée de 23 profils de spectres de masse de souches de Vibrio de collection a ensuite été élaborée, permettant d'identifier les espèces du clade Harveyi par MALDI-TOF MS. Dans un second temps, ces méthodes ont été appliquées lors d'une campagne hebdomadaire d'échantillonnage d'avril à octobre 2018 dans une ferme d'élevage de bars communs. Des échantillons d'eau et de biofilms ont été collectés à partir des bassins d'élevage et des arrivées d'eau chaude et froide, alimentant la ferme. L'abondance de V.harveyi et des Vibrionaceae cultivables à 37°C, mais aussi leur diversité relative ont ensuite été déterminées. Plusieurs espèces potentiellement pathogènes ont régulièrement été identifiées, dont V.harveyi, tout au long de la campagne. L'étude de l'influence des paramètres environnementaux a mis en évidence une corrélation positive entre la température de l'eau et l'abondance de ces bactéries à la fois dans l'eau et les biofilms. Sachant que ces biofilms peuvent induire une persistance de V.harveyi au sein de la ferme, et que leur abondance pourrait prochainement augmenter du fait du réchauffement climatique, il est urgent de développer des solutions anti-biofilms, afin de limiter le risque Vibrio.
... Forty-two bacteria species, including marine and non-marine bacteria, were tested on a minimal and an enriched medium for their susceptibility to 13 Halobacteriovorax isolates from coastal waters around Oahu, HI (United States) (Supplementary Table 2). The marine bacteria, primarily Beneckea, now classified as Vibrio species (Baumann et al., 1980), were most susceptible (95.7% exclusive of one outlier, B. nigrapulchrituda, which was not susceptible to any Halobacteriovorax isolates). The Photobacteria and related bacteria were also highly susceptible (80%). ...
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The impact of key environmental factors, salinity, prey, and temperature, on the survival and ecology of Bdellovibrio and like bacteria (BALOs), including the freshwater/terrestrial, non-halotolerant group and the halophilic Halobacteriovorax strains, has been assessed based on a review of data in the literature. These topics have been studied by numerous investigators for nearly six decades now, and much valuable information has been amassed and reported. The collective data shows that salinity, prey, and temperature play a major role in, not only the growth and survival of BALOs, but also the structure and composition of BALO communities and the distribution of the predators. Salinity is a major determinant in the selection of BALO habitats, distribution, prey bacteria, and systematics. Halophilic BALOs require salt for cellular functions and are found only in saltwater habitats, and prey primarily on saltwater bacteria. To the contrary, freshwater/terrestrial BALOs are non-halotolerant and inhibited by salt concentrations greater than 0.5%, and are restricted to freshwater, soils, and other low salt environments. They prey preferentially on bacteria in the same habitats. The halophilic BALOs are further separated on the basis of their tolerance to various salt concentrations. Some strains are found in low salt environments and others in high salt regions. In situ studies have demonstrated that salinity gradients in estuarine systems govern the type of BALO communities that will persist within a specific gradient. Bacterial prey for BALOs functions more than just being a substrate for the predators and include the potential for different prey species to structure the BALO community at the phylotype level. The pattern of susceptibility or resistance of various bacteria species has been used almost universally to differentiate strains of new BALO isolates. However, the method suffers from a lack of uniformity among different laboratories. The use of molecular methods such as comparative analysis of the 16S rDNA gene and metagenomics have provided more specific approaches to distinguished between isolates. Differences in temperature growth range among different BALO groups and strains have been demonstrated in many laboratory experiments. The temperature optima and growth range for the saltwater BALOs is typically lower than that of the freshwater/terrestrial BALOs. The collective data shows not only that environmental factors have a great impact on BALO ecology, but also how the various factors affect BALO populations in nature.
... Besides the potential for association of bacteria from sewage with crabs, the possible accumulation of indigenous marine bacteria that may be human pathogens has been investigated. Detailed taxonomic studies of Vibrio species from marine ecosystems have led to a reevaluation of the taxonomy of this group and the definition of several new species that are potential human pathogens (4,39,41). Several investigators have found Vibrio species associated with tissues of blue crabs collected in temperate waters (10,12,37,42). Recent studies have shown that V. cholerae naturally occurs in temperate estuaries and that cases of cholera in the Gulf Coast region of the United States have resulted from the ingestion of contaminated shellfish, including inadequately cooked crab meat (5,26,44). ...
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Vibrio harveyi is recognized as one of the major causes of vibriosis, a disease that threatens the long-term sustainability of aquaculture. Current research shows that the Mediterranean strains of V . harveyi are serologically heterogeneous, though research comparing the traits of different strains is scarce. This study aims to describe the biochemical, physiological and genetic characteristics of three serologically different strains of V . harveyi isolated from farmed European Sea bass ( Dicentrarchus labrax ) from the Adriatic Sea. A total of 32 morphological and biochemical markers were examined and, the susceptibility to 13 antimicrobials tested, and then compared the results of high-throughput sequencing and in silico analyses. This study also presents the first whole genome sequences of V . harveyi isolated from European sea bass. A large number of nonsynonymous variations were detected among sequences of the three strains. The prediction analysis of resistance genes did not correspond with the in vitro antimicrobial susceptibility tests. Six virulence genes previously unrelated to virulence of vibrios were detected in all three studied strains. The results show that differences were detected at every level of comparison among the three studied strains isolated from the same fish species originating from a small geographic area.
Chapter
A.li.li.vi'bri.o. L. masc. adj. alius other, another; N.L. masc. n. Vibrio a bacterial genus name; N.L. masc. n. Aliivibrio the other Vibrio. Proteobacteria / Gammaproteobacteria / Vibrionales / Vibrionaceae / Aliivibrio The genus Aliivibrio accommodates six species. Cells are Gram‐negative, facultatively anaerobic, motile by means of polar flagella, and rod shaped. Strains are oxidase‐positive, fermentative, and able to grow on glucose as the sole carbon source. Require NaCl for growth, with optimal concentration 1–3% (w/v). Some strains are luminous. The major fatty acids are C15:0 iso 2‐OH and C16:1 ω8c. Found in marine environment, some strains form mutualistic symbioses with marine fish and squids, and some are pathogens of fish. DNA G + C content (mol%): 38–42 (Tm). Type species: Aliivibrio fischeri Urbanczyk et al. 2007VP (Photobacterium fischeri Beijerinck 1889, Vibrio fischeri Lehmann and Neumann 1896).
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Relationships among species of Beneckea and Photobacterium, as well as Vibrio cholerae, Escherichia coli, Enterobacter aerogenes, Serratia marcescens, Proteus vulgaris, and Aeromonas hydrophila were determined using a method involving in vitro, DNA/ribosomal RNA competition experiments. The results indicated an evolutionary divergence between the marine and terrestrial enterobacteria and were consistent with the generic separation of Beneckea, Photobacterium, and Vibrio cholerae. The latter organism was found to be more closely related to the marine than to the terrestrial enterobacteria, suggesting that this pathogen may have evolved from a marine ancestor.
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A numerical taxonomic study was carried out to establish: the relationship of freshly isolated, oxidase-negative, vibrio-like organisms to strains listed in certain culture collections as Vibrio metschnikovii and V. proteus; the relationship of all these oxidase-negative organisms to the genus Vibrio and related organisms. Eighty-three strains were tested for their abilities to grow on 49 compounds as the sole organic source of carbon, their fermentation of carbohydrates, and their production of extracellular enzymes; various physiological tests were also carried out. In all, 130 characters were determined for each strain. The collection of strains were of Vibrio and Aeromonas species, certain other possibly related organisms, and 40 oxidase-negative organisms from a wide range of habitats. It was concluded that all of the oxidase-negative, vibrio-like strains except one belong to the species Vibrio metschnikovii Gamaleia 1888 (synonyms V. proteus Buchner 1885; V. cholerae biotype proteus Shewan and Veron 1974). The lectotype is NCTC 8443.
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Twenty-five strains of marine bacteria pathogenic for fish, which had been shown by means of in vitro DNA/DNA hybridization to comprise two biotypes of the speciesBeneckea anguillara, were subjected to a phenotypic characterization. A numerical analysis of the data segregated the strains into two phenotypically distinct clusters coincident with the biotypes established by DNA homology studies. The two biotypes were distinguishable fromPhotobacterium and other species ofBeneckea by a number of unrelated phenotypic properties.
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Eleven marine luminous isolates, which could not be identified with previously studied species of luminous marine bacteria, were subjected to an extensive characterization. The results indicated that these strains were phenotypically similar, had a G+C content in their DNA of 45 mol%, and differed from all previously characterized luminous species by their inability to ferment sugars. On the basis of these and other properties, the 11 luminous strains were assigned to the genusAlteromonas and given the species designationA hanedai. Strain 281 (ATCC 33224) has been designated as the type strain of this new species.
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Glutamine synthetase (GS) fromBeneckea alginolytica strain 90 was purified to homogeneity as indicated by sodium dodecyl sulface polyacrylamide gel electrophoresis. The purified enzyme was injected into rabbits, and the antiserum, as well as previously prepared antiserum against the GS fromEscherichia coli, was used in Ouchterlony double diffusion experiments. From the results of these studies, the marine and terrestrial enterobacteria could be separated into five major groups consisting of (i)Beneckea and related organisms, (ii)Photobacterium phosphoreum, P. leiognathi, andP. angustum, (iii) species ofAeromonas, (iv)Xenorhabdus luminescens, and (v) species of terrestrial enterobacteria. Evidence is presented that inB. alginolytica, as in other Gramnegative eubacteria, GS activity is regulated by adenylylation and deadenylylation.
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One hundred and seventy-three strains of marine, luminous bacteria isolated from sea water, surfaces and intestines of fish, as well as from the luminous organs of fish and squid were submitted to an extensive phenotypic characterization. A numerical analysis of the results grouped these strains into four clusters which were formed on the basis of overall phenotypic similarity. One cluster, which was given the designationBeneckea harveyi, consisted of strains which had a moles% GC content in their DNAs of 46.51.3 and a single, sheathed, polar flagellum when grown in liquid medium. Most of these strains had unsheathed, peritrichous flagella in addition to the sheathed, polar flagellum when grown on solid medium. The two phenotypically similar clusters which were assigned the species designationsPhotobacterium phosphoreum andP. mandapamensis consisted of strains which had 1–3 unsheathed, polar flagella and moles % GC contents in their DNAs of 41.50.7 and 42.90.5, respectively. The cluster designatedP. fischeri contained strains having 2–8 sheathed, polar flagella and a moles % GC content of 39.81.1. These four species could be further distinguished on the basis of a number of nutritional properties as well as other phenotypic traits. The assignment of the luminous, marine bacteria to four species was supported by differences in the properties of the luminous system as well as differences in the pattern of regulation of spartokinase activity which are discussed. The speciesB. harveyi was found to be phenotypically similar to a number of previously characterized, non-luminous strains ofBeneckea which should probably be assigned to this species.
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It is proposed that the species Vibrio fischeri (Beijerinck 1889) Lehmann and Neumann 1896 and Vibrio marinus (Russell 1891) Ford 1927 be combined as a single species on the basis of their overall similarity. The correct name of this species is V. fischeri, of which V. marinus is a later, subjective synonym. NCMB 1281 (= ATCC 7744) is designated as the neotype strain of V. fischeri.