Vibrio chanodichtyis sp. nov., isolated from the intestine of swordfish Chanodichthys dabryi

A Gram-stain-negative, facultatively anaerobic, motile, curved-rod-shaped flagellated bacterium, designated DSL-7T, was isolated from the intestine of Chanodichthys dabryi in the Yangtze river, PR China. The strain grew optimally in tryptone soy broth medium at 37 °C, pH 7.0 and with 1 % (w/v) NaCl. Strain DSL-7T showed less than 96.2 % 16S rRNA gene sequence similarity to type strains of the genus Vibrio. Phylogenetic analysis based on genomes indicated that strain DSL-7T belonged to the genus Vibrio and formed a subclade with Vibrio mimicus NCTC 11435T, Vibrio metoecus OP3HT, Vibrio cholerae ATCC 14035T, Vibrio albensis ATCC14547T, Vibrio paracholerae OP3HEDC-792T and Vibrio tarriae 2521-89T. The average nucleotide identity (ANI) and in digital DNA-DNA hybridization (dDDH) values between DSL-7T and closely related type strains were below the accepted threshold to delineate a new species of 95 and 70 %, respectively. The major cellular fatty acids were summed feature 3 (C16 : 1  ω7c and/or C16 : 1  ω6c), C16 : 0, summed feature 8 (C18 : 1  ω7c and/or C18 : 1  ω6c) and C14 : 0. The genomic DNA G+C content was 47.6 mol%. Based on the phenotypic, chemotaxonomic, phylogenetic and genomic data, strain DSL-7T represents a novel species of the genus Vibrio, for which the name Vibrio chanodichtyis sp. nov. is proposed, with strain DSL-7T (=KCTC 92851T=CCTCC AB 2022396T) as the type strain.

Vibrio methylphosphonaticus sp. nov., a methylphosphonate-decomposing bacterium isolated from surface seawater in the Xisha Islands, PR China

A Gram-stain-negative, facultative anaerobic, methylphosphonate-decomposing, motile by a polar flagellum and rod-shaped marine bacterium, designated S4B1T, was isolated from the surface seawater collected from the Yongle Atoll (Xisha Islands, PR China). The pairwise alignment showed the highest sequence similarity of 97.5 and 96.6 % to Vibrio aestuarianus subsp. cardii 12_122_3T3T and Vibrio atypicus HHS02T, respectively. Phylogenetic analysis based on 16S rRNA gene and the phylogenomic analysis of single-copy genes showed that strain S4B1T belonged to the genus Vibrio and formed a close branch with Vibrio qingdaonensis ZSDZ65T. Growth of strain S4B1T occurred at 4-30 °C (optimum, 28 °C), at pH 6.0-8.0 (optimum, pH 7.0) and in the presence of 2-7 % (w/v) NaCl (optimum, 3 %). The predominant fatty acids (>10 %) were C16 : 0, iso-C16 : 0 and summed feature 3 (C16 : 1  ω7c or/and C16 : 1  ω6c). The DNA G+C content of the assembled genomic sequence was 44.3 mol%. Average nucleotide identity (ANI) values between S4B1T and its reference species were lower than the threshold for species delineation (95-96 %), in which its highest ANI value with V. qingdaonensis ZSDZ65T was 87.0 %. In silico DNA-DNA hybridization further showed that strain S4B1T had less than 70 % similarity to its relatives. On the basis of the polyphasic evidence, strain S4B1T is proposed to represent a novel species of the genus Vibrio, for which the name Vibrio methylphosphonaticus sp. nov. is proposed. The type strain is S4B1T (=KCTC 92311T=MCCC 1K06168T).

Vibrio intestinalis sp. nov., isolated from intestine of seahorse

A novel Gram-stain-negative, catalase- and oxidase-positive, facultatively anaerobic, and rod-shaped motile bacterial strain, designated as YLB-11^T, was isolated from seahorse intestine. The 16S rRNA gene sequencing analysis showed that YLB-11^T was most closely related Vibrio mytili LMG 19157^T (98.9 % nucleotide sequence identity). Phylogenetic analysis placed strain YLB-11^T within the genus Vibrio. The major cellular fatty acids were summed feature 3 (C_16: 1 ω6c/C_16 : 1 ω7c, 36.4 %), C_16 : 0 (19.1 %) and summed feature 8 (C_18:1 ω6c/C_18:1 ω7c, 12.3 %). The DNA G+C content of YLB-11^T was 44.7 mol %. The in silico DNA-DNA hybridization and average nucleotide identity values for whole-genome sequence comparisons between YLB-11^T and related species were clearly below the thresholds used for the delineation of a novel species. Therefore, YLB-11^T is considered to represent novel species of the genus Vibrio, for which the name Vibrio intestinalis sp. nov. is proposed. The type strain is YLB-11^T (=MCCC 1A17441^T=KCTC 72604^T).

Vibrio sinus sp. nov., a marine bacterium isolated from coastal seawater

A Gram-straining-negative, facultatively anaerobic, motile by means of a polar flagellum and rod-shaped marine bacterium, designated S4M6^T, was isolated from surface seawater collected in Dongshan Bay (Fujian, PR China). Phylogenetic analysis based on 16S rRNA genes, phylogenomic analysis of single-copy gene families and whole genome data indicated that S4M6^T represented a member of the genus Vibrio. The closest phylogenetic relatives of S4M6^T were Vibrio marisflavi CGMCC 1.8994^T (97.8 % 16S rRNA gene sequence pairwise similarity), Vibrio variabilis LMG 25438^T (96.9 %), Vibrio gangliei SZDIS-1^T (96.2 %) and Vibrio aestivus M22^T (96.1 %). The growth of S4M6^T occurred at 15-35 °C (optimum 28 °C), pH 4.0-9.0 (optimum 5.0-7.0) and in the presence of 2-5 % (w/v) NaCl (optimum 3 %). The predominant fatty acids (>10 %) are C_16 : 0, summed feature 3 (C_16 : 1ω7c and/or C_{16 :  1}ω6c) and summed feature 8 (C_18 : 1ω7c and/or C_{18 :  1}ω6c). The DNA G+C content of the assembled genomic sequences was 43.4 % for S4M6^T. Average nucleotide identity (ANI) values between S4M6^T and the reference species were lower than the threshold for species delineation (95-96 %); in silico DNA-DNA hybridization further indicated that S4M6^T had less than 70 % similarity to its relatives. On the basis of the polyphasic evidence, strain S4M6^T is proposed to represent a novel species of the genus Vibrio, for which the name Vibrio sinus sp. nov. is proposed. The type strain is S4M6^T (= KCTC 92312^T= MCCC 1K06167^T).

Vibrio amylolyticus sp. nov. and Vibrio gelatinilyticus sp. nov., two marine bacteria isolated from surface seawater of Qingdao

Two Gram-stain-negative, oxidase-positive, facultative anaerobic and rod-shaped motile bacteria, designated strains ZSDZ34 and ZSDE26, were isolated from offshore surface seawater collected near Qingdao. Phylogenetic analysis based on 16S rRNA gene sequences placed ZSDE26^T and ZSDZ34^T within the genus Vibrio, family Vibrionaceae, class Gammaproteobacteria. Strain ZSDE26^T was most closely related to Vibrio gallaecicus VB 8.9^T with 97.3 % sequence similarity, whereas ZSDZ34^T was most closely related to Vibrio aestuarianus subsp. cardii DSM 109723^T with 97.8 % sequence similarity. Strain ZSDE26^T grew with 1-5 % (w/v) NaCl (optimum, 4 %), at 16-28 °C (optimum, 28 °C) and at pH 6.0-9.0 (optimum, pH 7.0). Growth of strain ZSDZ34^T occurred with 1-6 % (w/v) NaCl (optimum, 3 %), at 16-37 °C (optimum, 28 °C) and at pH 6.0-9.0 (optimum, pH 7.0). Both strains shared the same major fatty acid components (more than 10 % of total fatty acids) of summed feature 3 (C_16 : 1 ω7c and/or C_16 : 1 ω6c), summed feature 8 (C_18 : 1 ω7c and/or C_18 : 1 ω6c) and C_16 : 0. Additionally, strain ZSDZ34^T contained a higher proportion of iso-C_16 : 0. The DNA G+C contents of strains ZSDE26^T and ZSDZ34^T were 42.8 and 44.5 mol%, respectively. On the basis of the results of polyphasic analysis, ZSDE26^T and ZSDZ34^T are considered to represent novel species within the genus Vibrio, for which the names Vibrio amylolyticus sp. nov. (type strain, ZSDE26^T=KCTC 82890^T=MCCC 1K06290^T) and Vibrio gelatinilyticus sp. nov. (type strain, ZSDZ34^T=KCTC 82888^T=MCCC 1K06292^T) are proposed, respectively.

First record of isolation and characterization of Vibrio sinaloensis from diseased orange-spotted grouper Epinephelus coioides

A dominant bacterium, ZYL-12, isolated from the liver of a diseased orange-spotted grouper Epinephelus coioides, was identified as Vibrio sinaloensis, based on phenotypic and molecular analysis. The median lethal dosage of ZYL-12 was calculated as 1.6 × 105 CFU g-1 fish weight. The infection experiment indicated that ZYL-12 caused noticeable histological lesions to the liver, kidney and spleen of the fish. Growth characteristics showed that ZYL-12 possessed strong environmental adaptability. This note is the first report about the pathogenicity of V. sinaloensis isolated from diseased fish.

Vibrio agarilyticus sp. nov., an agar-digesting marine bacterium isolated from coastal seawater in Daya Bay (Guangdong, China)

A Gram-strain-negative, facultatively anaerobic, motile, rod-shaped and flagellated marine bacterium, designated SM6^T, was isolated from surface seawater collected in Daya Bay (Guangdong, China). Phylogenetic analysis based on 16S rRNA gene sequences, multilocus sequence analysis, phylogenomic analysis of single-copy gene families and whole genome data showed that strain SM6^T belonged to the genus Vibrio. The closest phylogenetic relatives of SM6^T were Vibrio plantisponsor MSSRF60^T (97.38 % 16S rRNA gene sequence pairwise similarity), Vibrio variabilis R-40492^T (97.27 %), Vibrio aestuarianus ATCC 35048^T (97.21 %) and Vibrio sagamiensis LC2-047^T (97.3 %). Growth of strain SM6^T occurred at 10-45 °C (optimum 30 °C), at pH 6.0-9.0 (optimum 6.0) and in the presence of 0-10 % (w/v) NaCl (optimum 3-8 %). The predominant fatty acids (>10 %) were summed feature 3 (C_{16 : 1} ω7c or/and C_{16 : 1} ω6c), C_{16 : 0} and summed feature 8 (C_{18 : 1} ω7c or/and C_{18 : 1} ω6c). The DNA G+C content of the assembled genomic sequences was 47.37 % for strain SM6^T. Average nucleotide identity values between SM6^T and its reference species were lower than the threshold for species delineation (95-96 %); in silico DNA-DNA hybridization further showed that the strains shared less than 70 % similarity. On the basis of evidence from the present polyphasic study, strain SM6^T is considered to represent a novel species of the genus Vibrio, for which the name Vibrio agarilyticus sp. nov. is proposed. The type strain is SM6^T (=KCTC 82076^T=MCCC 1K04327 ^T).

Epidemiology of a SKin Ulceration Disease (SKUD) in the sea cucumber Holothuria scabra with a review on the SKUDs in Holothuroidea (Echinodermata)

Aquacultivated sea cucumbers often suffer from SKin Ulceration Diseases (SKUDs). SKUDs have been observed in six holothuroid species from nine countries. All SKUDs present a similar symptom-the skin ulceration-and can be induced by bacteria, viruses, or abiotic factors. We here provide an update on SKUDs in holothuroids and analyse the case of the SKUD observed in Holothuria scabra in Madagascar. Field observations revealed a seasonality of the disease (i.e. wintertime maximum peak). Morphological analyses of integument ulcers showed that sea cucumbers react by forming a collagen fibre plug. Metagenomic analyses revealed a higher proportion of Vibrionaceae (Gammaproteobacteria) in ulcers in comparison to the healthy integument of the same individuals. Experimental infection assays were performed with ulcer crude extracts and bacteria isolated from these extracts (e.g. Vibrio parahaemolyticus) but did not significantly induce skin ulceration. Our results suggest that the disease is not induced by a pathogen or, at the very least, that the pathogen is not found within the ulcers as the disease is not transmissible by contact. An initial cause of the SKUD in Madagascar might be the repeated and prolonged exposures to cold temperatures. Opportunistic bacteria could settle in the dermis of ulcerated individuals and promote the ulcer extension. We propose a general nomenclature for SKUDs based on the acronym of the disease, the affected sea cucumber species (e.g. Hs for Holothuria scabra), the concerned region using an ISO code 3166-2 (e.g. MG for Madagascar), the description date (e.g. 20 for the year 2020), and, when known, the inducing agent (first letter of the general taxon, b for bacteria, v for virus in currently known cases; a a if it is an abiotic inducing parameter; nothing if the inducing cause has not been precisely identified). The disease described in this work will be designated under the name SKUD Hs-MG-20.

Zoantharia (Cnidaria: Hexacorallia) of the Dutch Caribbean and One New Species of Parazoanthus

Species of the anthozoan order Zoantharia (=Zoanthidea) are common components of subtropical and tropical shallow water coral reefs. Despite a long history of research on their species diversity in the Caribbean, many regions within this sea remain underexamined. One such region is the Dutch Caribbean, including the islands of St. Eustatius, St. Maarten, Saba, Aruba, Bonaire, and Curaçao, as well as the Saba Bank, for which no definitive species list exists. Here, combining examinations of specimens housed in the Naturalis Biodiversity Center collection with new specimens and records from field expeditions, we provide a list of zoantharian species found within the Dutch Caribbean. Our results demonstrate the presence at least 16 described species, including the newly described Parazoanthus atlanticus, and the additional potential presence of up to four undescribed species. These records of new and undescribed species demonstrate that although the zoantharian research history of the Caribbean is long, further discoveries remain to be found. In light of biodiversity loss and increasing anthropogenic pressure on declining coral reefs, documenting the diversity of zoantharians and other coral reef species to provide baseline data takes on a new urgency.

Classification and structural insight into vibriolysin-like proteases of Vibrio pathogenicity

Vibriolysin-like proteases (VLPs) are important virulence agents in the arsenal of Vibrio causing instant cytotoxic effects during infection. Most of Vibrio secreted VLPs show serious pathogenicity, while some species of Vibrio with VLPs are non-pathogenic, like Vibrio tasmaniensis and Vibrio pacinii. To investigate the relation between VLPs and Vibrio pathogenicity, one phylogenetic tree of VLPs was constructed and compared consensus sequences at the N-terminus of VLPs. Based on these results, VLPs were defined into nine phylogenetic clades. Pathogenicity analysis of Vibrio showed that Vibrio species with VLPs III, VI, VII or VIII are serious pathogenic bacteria, while species with VLPs I, II, IV or IX are opportunistic pathogens. Multiple sequence alignment showed that the N-terminal 5-16 nucleotides of each clade are highly conservative. Topological analysis of VLPs exhibited the structural differences in N-terminal regions of each VLP clade. These results suggest that structure of N-terminus might play a key role in the pathogenicity of VLPs. Our findings give new insights into the classification of VLPs and the relationship between VLPs and Vibrio pathogenicity.

Distribution of siderophore gene systems on a Vibrionaceae phylogeny: Database searches, phylogenetic analyses and evolutionary perspectives

Siderophores are small molecules synthesized and secreted by bacteria and fungi to scavenge iron. Extracellular ferri-siderohores are recognized by cognate receptors on the cell surface for transport over membranes. Several siderophore systems from Vibrionaceae representatives are known and well understood, e.g., the molecular structure of the siderophore, the biosynthesis gene cluster and pathway, and the gene expression pattern. Less is known about how these systems are distributed among the ~140 Vibrionaceae species, and which evolutionary processes contributed to the present-day distribution. In this work, we compiled existing knowledge on siderophore biosynthesis systems and siderophore receptors from Vibrionaceae and used phylogenetic analyses to investigate their organization, distribution, origin and evolution. Through literature searches, we identified nine different siderophore biosynthesis systems and thirteen siderophore receptors in Vibrionaceae. Homologs were identified by BLAST searches, and the results were mapped onto a Vibrionaceae phylogeny. We identified 81 biosynthetic systems distributed in 45 Vibrionaceae species and 16 unclassified Vibrionaceae strains, and 409 receptors in 89 Vibrionaceae species and 49 unclassified Vibrionaceae strains. The majority of taxa are associated with at least one type of siderophore biosynthesis system, some (e.g., aerobactin and vibrioferrin) of which are widely distributed in the family, whereas others (i.e., bisucaberin and vibriobactin) are found in one lineage. Cognate receptors are found more widespread. Phylogenetic analysis of three siderophore systems (piscibactin, vibrioferrin and aerobactin) show that their present-day distribution can be explained by an old insertion into Vibrionaceae, followed mainly by stable vertical evolution and extensive loss, and some cases of horizontal gene transfers. The present work provides an up to date overview of the distribution of siderophore-based iron acquisition systems in Vibrionaceae, and presents phylogenetic analysis of these systems. Our results suggest that the present-day distribution is a result of several evolutionary processes, such as old and new gene acquisitions, gene loss, and both vertical and horizontal gene transfers.

Vibrio barjaei sp. nov., a new species of the Mediterranei clade isolated in a shellfish hatchery

Seven isolates were obtained from different culture stages of carpet shell clam (Ruditapes decussatus) reared in a bivalve hatchery (Galicia, NW Spain). Three groups were differentiated by genotyping techniques and phenotypic profiles and representative trains were selected to further taxonomic studies. These strains were studied by a polyphasic approach and in basis of the phylogenetic analysis based on concatenated sequences of the five housekeeping genes ftsZ, gyrB, pyrH, recA and rpoA formed a tight group into the Mediterranei clade of the genus Vibrio. Percentages of genomic resemblance, including average nucleotide identity, in silico genome-to-genome comparison and wet DNA-DNA hybridization between the type strain and the closest relatives Vibrio mediterranei and Vibrio thalassae were below of the proposed boundaries for the definition of species. The novel isolates could be also differentiated from the related taxa on the basis of several phenotypic traits and fatty acid profiles. Results obtained support the description of a novel species into the Mediterranei clade, for which the name Vibrio barjaei sp. nov. is proposed, with strain 3062^T (=CECT 9090^T=CAIM 1921T^T=LMG 29358^T) as the type strain.

Rohul A, Sato K, Sato K, Mino S, Suda W, Oshima K, Hattori M, Ohkuma M, Meirelles PM, Thompson FL, Thompson C, A. Filho GM, Gomez-Gil B, Sawabe T, Sawabe T. Advanced Microbial Taxonomy Combined with Genome-Based-Approaches Reveals that Vibrio astriarenae sp. nov., an Agarolytic Marine Bacterium, Forms a New Clade in Vibrionaceae

Advances in genomic microbial taxonomy have opened the way to create a more universal and transparent concept of species but is still in a transitional stage towards becoming a defining robust criteria for describing new microbial species with minimum features obtained using both genome and classical polyphasic taxonomies. Here we performed advanced microbial taxonomies combined with both genome-based and classical approaches for new agarolytic vibrio isolates to describe not only a novel Vibrio species but also a member of a new Vibrio clade. Two novel vibrio strains (Vibrio astriarenae sp. nov. C7T and C20) showing agarolytic, halophilic and fermentative metabolic activity were isolated from a seawater sample collected in a coral reef in Okinawa. Intraspecific similarities of the isolates were identical in both sequences on the 16S rRNA and pyrH genes, but the closest relatives on the molecular phylogenetic trees on the basis of 16S rRNA and pyrH gene sequences were V. hangzhouensis JCM 15146T (97.8% similarity) and V. agarivorans CECT 5085T (97.3% similarity), respectively. Further multilocus sequence analysis (MLSA) on the basis of 8 protein coding genes (ftsZ, gapA, gyrB, mreB, pyrH, recA, rpoA, and topA) obtained by the genome sequences clearly showed the V. astriarenae strain C7T and C20 formed a distinct new clade protruded next to V. agarivorans CECT 5085T. The singleton V. agarivorans has never been included in previous MLSA of Vibrionaceae due to the lack of some gene sequences. Now the gene sequences are completed and analysis of 100 taxa in total provided a clear picture describing the association of V. agarivorans into pre-existing concatenated network tree and concluded its relationship to our vibrio strains. Experimental DNA-DNA hybridization (DDH) data showed that the strains C7T and C20 were conspecific but were separated from all of the other Vibrio species related on the basis of both 16S rRNA and pyrH gene phylogenies (e.g., V. agarivorans CECT 5085T, V. hangzhouensis JCM 15146T V. maritimus LMG 25439T, and V. variabilis LMG 25438T). In silico DDH data also supported the genomic relationship. The strains C7T also had less than 95% average amino acid identity (AAI) and average nucleotide identity (ANI) towards V. maritimus C210, V. variabilis C206, and V. mediterranei AK1T, V. brasiliensis LMG 20546T, V. orientalis ATCC 33934T, and V. sinaloensis DSM 21326. The name Vibrio astriarenae sp. nov. is proposed with C7 as the type strains. Both V. agarivorans CECT 5058T and V. astriarenae C7T are members of the newest clade of Vibrionaceae named Agarivorans.

Vibrio panuliri sp. nov., a marine bacterium isolated from spiny lobster, Panulirus penicillatus and transfer of Vibrio ponticus from Scophthalmi clade to the newly proposed Ponticus clade

A novel marine bacterium, strain LBS2(T) was isolated from eggs carried on pleopods of the spiny lobster collected from Andaman Sea. Heterotrophic growth occurred at 1-7% NaCl. 16S rRNA gene sequence similarity revealed the strain LBS2(T) belonged to the genus Vibrio and showed above 97% similarity with eight type strains of the genus Vibrio. Multilocus analysis based on ftsZ, gapA, gyrB, mreB, pyrH recA, rpoA, and topA revealed LBS2(T) formed a separate cluster with Vibrio ponticus DSM 16217(T) with 89.8% multilocus gene sequence similarity. However, strain LBS2(T) is distantly related with other members of the Scophthalmi clade in terms of 16S rRNA signatures, phenotypic variations and multilocus gene sequence similarity, for which we propose LBS2(T) belongs to a new clade i.e. Ponticus clade with V. ponticus DSM 16217(T) as the representative type strain of the clade. DNA-DNA homologies between strain LBS2(T) and closely related strains were well below 70%. DNA G + C content was 45.3 mol%. On the basis of our polyphasic study, strain LBS2(T) represents a novel species of the genus Vibrio, for which the name Vibrio panuliri sp. nov. is proposed. The type strain is LBS2(T) (= JCM 19500(T) = DSM 27724(T) = LMG 27902(T)).

Vibrio madracius sp. nov. isolated from Madracis decactis (Scleractinia) in St Peter & St Paul Archipelago, Mid-Atlantic Ridge, Brazil

Three novel isolates (A-354(T), A-328, and A-384) were retrieved from apparently healthy scleractinian Madracis decactis in the remote St Peter & St Paul Archipelago, Mid-Atlantic Ridge, Brazil. The novel isolates formed a distinct lineage based on the phylogenetic reconstruction using the 16S rRNA and pyrH gene sequences. They fell into the Mediterranei clade and their closest phylogenetic neighbour was V. mediterranei species, sharing upto 98.1 % 16S rRNA gene sequence similarity. Genomic analysis including in silico DDH, MLSA, AAI and genomic signature distinguished A-354(T) from V. mediterranei LMG 19703 (=AK1) with values of 33.3, 94.2, 92 %, and 11.3, respectively. Phenotypically, the novel isolates can be differentiated from V. mediterranei based on the four following features. They do not grow at 8 % NaCl; use D-gluconic acid but not L-galactonic acid lactone as carbon source; and do not have the fatty acid C18:0. Differentiation from both the other Mediterranei clade species (V. maritimus and V. variabilis) is supported by fifteen features. The novel species show lysine decarboxylase and tryptophan deaminase, but not gelatinase and arginine dihydrolase activity; produce acetoin; use α-D-lactose, N-acetyl-D-galactosamine, myo-Inositol, D-gluconic acid, and β-hydroxy-D,L-butyric acid; and present the fatty acids C14:0 iso, C15:0 anteiso, C16:0 iso, C17:0 anteiso, and C17:1x8c . Whole-cell protein profiles, based on MALDI-TOF, showed that the isolates are not clonal and also distinguished them from the closes phylogenetic neighbors. The name Vibrio madracius sp. nov. is proposed to encompass these novel isolates. The G+C content of the type strain A-354(T) (=LMG 28124(T)=CBAS 482(T)) is 44.5 mol%.

Vibrio trends in the ecology of the Venice lagoon

Vibrio is a very diverse genus that is responsible for different human and animal diseases. The accurate identification of Vibrio at the species level is important to assess the risks related to public health and diseases caused by aquatic organisms. The ecology of Vibrio spp., together with their genetic background, represents an important key for species discrimination and evolution. Thus, analyses of population structure and ecology association are necessary for reliable characterization of bacteria and to investigate whether bacterial species are going through adaptation processes. In this study, a population of Vibrionaceae was isolated from shellfish of the Venice lagoon and analyzed in depth to study its structure and distribution in the environment. A multilocus sequence analysis (MLSA) was developed on the basis of four housekeeping genes. Both molecular and biochemical approaches were used for species characterization, and the results were compared to assess the consistency of the two methods. In addition, strain ecology and the association between genetic information and environment were investigated through statistical models. The phylogenetic and population analyses achieved good species clustering, while biochemical identification was demonstrated to be imprecise. In addition, this study provided a fine-scale overview of the distribution of Vibrio spp. in the Venice lagoon, and the results highlighted a preferential association of the species toward specific ecological variables. These findings support the use of MLSA for taxonomic studies and demonstrate the need to consider environmental information to obtain broader and more accurate bacterial characterization.

New Vibrio species associated to molluscan microbiota: a review

The genus Vibrio consists of more than 100 species grouped in 14 clades that are widely distributed in aquatic environments such as estuarine, coastal waters, and sediments. A large number of species of this genus are associated with marine organisms like fish, molluscs and crustaceans, in commensal or pathogenic relations. In the last decade, more than 50 new species have been described in the genus Vibrio, due to the introduction of new molecular techniques in bacterial taxonomy, such as multilocus sequence analysis or fluorescent amplified fragment length polymorphism. On the other hand, the increasing number of environmental studies has contributed to improve the knowledge about the family Vibrionaceae and its phylogeny. Vibrio crassostreae, V. breoganii, V. celticus are some of the new Vibrio species described as forming part of the molluscan microbiota. Some of them have been associated with mortalities of different molluscan species, seriously affecting their culture and causing high losses in hatcheries as well as in natural beds. For other species, ecological importance has been demonstrated being highly abundant in different marine habitats and geographical regions. The present work provides an updated overview of the recently characterized Vibrio species isolated from molluscs. In addition, their pathogenic potential and/or environmental importance is discussed.

Updating the Vibrio clades defined by multilocus sequence phylogeny: proposal of eight new clades, and the description of Vibrio tritonius sp. nov

To date 142 species have been described in the Vibrionaceae family of bacteria, classified into seven genera; Aliivibrio, Echinimonas, Enterovibrio, Grimontia, Photobacterium, Salinivibrio and Vibrio. As vibrios are widespread in marine environments and show versatile metabolisms and ecologies, these bacteria are recognized as one of the most diverse and important marine heterotrophic bacterial groups for elucidating the correlation between genome evolution and ecological adaptation. However, on the basis of 16S rRNA gene phylogeny, we could not find any robust monophyletic lineages in any of the known genera. We needed further attempts to reconstruct their evolutionary history based on multilocus sequence analysis (MLSA) and/or genome wide taxonomy of all the recognized species groups. In our previous report in 2007, we conducted the first broad multilocus sequence analysis (MLSA) to infer the evolutionary history of vibrios using nine housekeeping genes (the 16S rRNA gene, gapA, gyrB, ftsZ, mreB, pyrH, recA, rpoA, and topA), and we proposed 14 distinct clades in 58 species of Vibrionaceae. Due to the difficulty of designing universal primers that can amplify the genes for MLSA in every Vibrionaceae species, some clades had yet to be defined. In this study, we present a better picture of an updated molecular phylogeny for 86 described vibrio species and 10 genome sequenced Vibrionaceae strains, using 8 housekeeping gene sequences. This new study places special emphasis on (1) eight newly identified clades (Damselae, Mediterranei, Pectenicida, Phosphoreum, Profundum, Porteresiae, Rosenbergii, and Rumoiensis); (2) clades amended since the 2007 proposal with recently described new species; (3) orphan clades of genomospecies F6 and F10; (4) phylogenetic positions defined in 3 genome-sequenced strains (N418, EX25, and EJY3); and (5) description of V. tritonius sp. nov., which is a member of the “Porteresiae” clade.

Partial characterization of an exopolysaccharide secreted by a marine bacterium, Vibrio neocaledonicus sp. nov., from New Caledonia

AIMS

Exopolysaccharides (EPS) are industrially valuable molecules with numerous useful properties. This study describes the techniques used for the identification of a novel Vibrio bacterium and preliminary characterization of its EPS.

METHODS AND RESULTS

Bioprospection in marine intertidal areas of New Caledonia followed by screening for EPS producing brought to selection of the isolate NC470. Phylogenetic analysis (biochemical tests, gene sequencing and DNA-DNA relatedness) permitted to identify NC470 as a new member of the Vibrio genus. The EPS was produced in batch fermentation, purified using the ultrafiltration process and analysed by colorimetry, Fourier Transform Infrared spectroscopy, gas chromatography, Nuclear Magnetic Resonance and HPLC-size exclusion chromatography. This EPS exhibits a high N-acetyl-hexosamines and uronic acid content with a low amount of neutral sugar. The molecular mass was 672 × 10(3)  Da. These data are relevant for possible technological exploitation.

CONCLUSIONS

We propose the name Vibrio neocaledonicus sp. nov for this isolate NC470, producing an EPS with an unusual sugar composition. Comparison with other known polymers permitted to select applications for this polymer.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study contributes to evaluate the marine biodiversity of New Caledonia. It also highlights the biotechnological potential of New Caledonia marine bacteria.

Vibrio alfacsensis sp. nov., isolated from marine organisms

Five strains (CAIM 1831(T), CAIM 1832, CAIM 1833, CAIM 1834 and CAIM 1836) were isolated from cultured sole (Solea senegalensis) in two regions of Spain, two strains (CAIM 404 and CAIM 1294) from wild-caught spotted rose snapper (Lutjanus guttatus) in Mexico, and one strain (CAIM 1835) from corals in Brazil. The 16S rRNA gene sequences of the novel isolates showed similarity to Vibrio ponticus (98.2-98.3%, GenBank accession no. AJ630103) and to a lesser degree to Vibrio furnissii (97.2-97.3%, X76336) and to Vibrio fluvialis (96.9-97.1%, X74703). Multilocus sequence analysis clustered these strains closely together and clearly separated them from phylogenetically related species of the genus Vibrio. Genomic fingerprinting by rep-PCR clustered the novel strains according to their geographical origin. Phenotypic analyses showed a large variation among the new strains, but many tests enabled them to be differentiated from other species of the genus Vibrio. The mean ΔT(m) values between the strains analysed here and closely related type strains were above 6.79 °C. The values between the novel isolates were below 2.35 °C, well outside the limit suggested for the delineation of a bacterial species. The phenotypic and genotypic data presented here clearly place these new strains as a coherent group within the genus Vibrio, for which we propose the name Vibrio alfacsensis sp. nov. with CAIM 1831(T) ( = DSM 24595(T) = S277(T)) as the type strain.

Vibrio xiamenensis sp. nov., a cellulase-producing bacterium isolated from mangrove soil

A taxonomic study was carried out on a cellulase-producing bacterium, strain G21(T), isolated from mangrove soil in Xiamen, Fujian province, China. Cells were Gram-negative, slightly curved rods, motile with a single polar flagellum. The strain grew at 15-40 °C and in 0.5-10% (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain G21(T) belonged to the genus Vibrio and formed a clade with Vibrio furnissii ATCC 350116(T) (97.4% sequence similarity), V. fluvialis LMG 7894(T) (97.1%) and V. ponticus CECT 5869(T) (96.1%). However, multilocus sequence analysis (using rpoA, recA, mreB, gapA, gyrB and pyrH sequences) and DNA-DNA hybridization experiments indicated that the strain was distinct from the closest related Vibrio species. Additionally, strain G21(T) could be differentiated from them phenotypically by the ability to grow in 10% NaCl but not on TCBS plates, its enzyme activity spectrum, citrate utilization, oxidization of various carbon sources, hydrolysis of several substrates and its cellular fatty acid profile. The G+C content of the genomic DNA was 46.0 mol%. The major cellular fatty acids were summed feature 3 (C(16:1)ω7c and/or iso-C(15:0) 2-OH), C(16:0) and C(18:1)ω7c. The major polar lipids were phosphatidylethanolamine and phosphatidylglycerol, with trace amounts of diphosphatidylglycerol. The predominant quinones were Q-8 and Q-7. Based on phylogenetic, phenotypic and chemotaxonomic characteristics and DNA-DNA hybridization analysis, it is concluded that strain G21(T) represents a novel species of the genus Vibrio, for which the name Vibrio xiamenensis sp. nov. is proposed. The type strain is G21(T) ( = DSM 22851(T)  = CGMCC 1.10228(T)).