<i>Vibrio communis</i> sp. nov., isolated from the marine animals <i>Mussismilia hispida, Phyllogorgia dilatata, Palythoa caribaeorum, Palythoa variabilis</i> and <i>Litopenaeus vannamei</i>

Eight Vibrio isolates originating from the marine corals Mussismilia hispida and Phyllogorgia dilatata and the zoanthids Palythoa caribaeorum and Palythoa variabilis in Brazil and the Pacific white shrimp (Litopenaeus vannamei) in Ecuador were studied by means of a polyphasic approach. The novel isolates formed a tight monophyletic group in the genus Vibrio and were closely related to species of the Vibrio harveyi group, to which they showed more than 99?% 16S rRNA gene sequence similarity. Analysis based on concatenated sequences of the following seven genes, 16S rRNA, gyrB, recA, rpoA, topA, pyrH and mreB (5633 bp in length), showed clear separation between the isolates and species of the V. harveyi group. Amplified fragment length polymorphism (AFLP) analysis, performed previously, revealed that a representative isolate of this group, LMG 20370, was clearly separate from known Vibrio species (it belonged to the so-called AFLP cluster A31). DNA–DNA hybridization (DDH) experiments with representative isolates and type strains of the V. harveyi species group revealed high DDH between the novel isolates (more than 74?%) and less than 70?% DDH towards type strains of related Vibrio species, proving the novel species status of the isolates. Phenotypically, the novel species belongs to the arginine dihydrolase (A)-negative, lysine decarboxylase (L)-positive and ornithine decarboxylase (O)-positive (A-/L+/O+) cluster reported previously. Most species of the V. harveyi group (i.e. Vibrio rotiferianus, V. harveyi, V. parahaemolyticus and V. alginolyticus) also belong to this A-/L+/O+ cluster. However, several phenotypic features can be used for the identification of the novel species. In contrast to its closest phylogenetic neighbours, the novel species exhibits esterase (C4) and N-acetyl-ß-glucosaminidase activities, but it does not produce acetoin, does not use citrate, a-ketoglutaric acid or propionic acid and does not ferment melibiose. The novel species can also be differentiated on the basis of the presence of the fatty acids C17?:?0, C17?:?1?8c, iso-C17?:?0 and iso-C13?:?0 and the absence of the fatty acid C18?:?0. The name Vibrio communis sp. nov. is proposed for this taxon. Strain R-40496T (=LMG 25430T =CAIM 1816T) is the type strain

Marinomonas Brasilensis Sp. Nov., Isolated From The Coral Mussismilia Hispida, And Reclassification Of Marinomonas Basaltis As A Later Heterotypic Synonym Of Marinomonas Communis

A Gram-negative, aerobic bacterium, designated strain R-40503 T, was isolated from mucus of̃oChannel,SãoPaulo, Brazil. Phylogenetic analyses revealed that strain R-40503 T belongs to the genus Marinomonas. The 16S rRNA gene sequence similarity of R-40503 T was above 97% with the type strains of Marinomonas vaga, M. basaltis, M. communis and M. pontica, and below 97% with type strains of the other Marinomonas species. Strain R-40503 T showed less than 35% DNA-DNA hybridization (DDH) with the type strains of the phylogenetically closest Marinomonas species, demonstrating that it should be classified into a novel species. Amplified fragment length polymorphism (AFLP), chemotaxonomic and phenotypic analyses provided further evidence for the proposal of a novel species. Concurrently, a close genomic relationship between M. basaltis and M. communis was observed. The type strains of these two species showed 78% DDH and 63% AFLP pattern similarity. Their phenotypic features were very similar, and their DNA G+C contents were identical (46.3 mol%). Collectively, these data demonstrate unambiguously that Marinomonas basaltis is a later heterotypic synonym of Marinomonas communis. Several phenotypic features can be used to discriminate between Marinomonas species. The novel strain R-40503 T is clearly distinguishable from its neighbours. For instance, it shows oxidase and urease activity, utilizes L-asparagine and has the fatty acid C 12: 1 3-OH but lacks C 10: 0 and C 12: 0. The name Marinomonas brasilensis sp. nov. is proposed, with the type strain R-40503 T (5R-278 T 5LMG 25434 T 5CAIM 1459 T). The DNA G+C content of strain R-40503 T is 46.5 mol%. © 2011 IUMS Printed in Great Britain.61511701175Alves Jr., N., Neto, O.S.M., Silva, B.S.O., de Moura, R.L., Francini-Filho, R.B., Castro, C.B.E., Paranhos, R., Kruger, R.H., Diversity and pathogenic potential of vibrios isolated from Abrolhos Bank corals (2010) Environ Microbiol Rep, 2, pp. 90-95. , Other authorsBaumann, L., Baumann, P., Mandel, M., Allen, R.D., Taxonomy of aerobic marine eubacteria (1972) J Bacteriol, 110, pp. 402-429Hidalgo, R.B., Cleenwerck, I., Balboa, S., Wachter, M.D., Thompson, F.L., Swings, J., Vos, P.D., Romalde, J.L., Diversity of vibrios associated with reared clams in Galicia (NW Spain) (2008) Syst Appl Microbiol, 31, pp. 215-222Brady, C., Venter, S., Cleenwerck, I., Vancanneyt, M., Swings, J., Coutinho, T., A FAFLP system for the improved identification of plant-pathogenic and plant-associated species of the genus Pantoea (2007) Syst Appl Microbiol, 30, pp. 413-417Chang, H.-W., Roh, S.W., Kim, K.-H., Nam, Y.-D., Yoon, J.-H., Oh, H.-M., Bae, J.-W., Marinomonas basaltis sp. nov., a marine bacterium isolated from black sand (2008) Int J Syst Evol Microbiol, 58, pp. 2743-2747Chenna, R., Sugawara, H., Koike, T., Lopez, R., Gibson, T.J., Higgins, D.G., Thompson, J.D., Multiple sequence alignment with the CLUSTAL series of programs (2003) Nucleic Acids Res, 31, pp. 3497-3500Chimetto, L.A., Brocchi, M., Thompson, C.C., Martins, R.C.R., Ramos, H.R., Thompson, F.L., Vibrios dominate as culturable nitrogen-fixing bacteria of the Brazilian coral Mussismilia hispida (2008) Syst Appl Microbiol, 31, pp. 312-319Chimetto, L.A., Brocchi, M., Gondo, M., Thompson, C.C., Gomez-Gil, B., Thompson, F.L., Genomic diversity of vibrios associated with the Brazilian coral Mussismilia hispida and its sympatric zoanthids (Palythoa caribaeorum, Palythoa variabilis and Zoanthus solanderi) (2009) J Appl Microbiol, 106, pp. 1818-1826de Castro, A.P., Araújo Jr, S.D., Reis, A.M., Moura, R.L., Francini-filho, R.B., Pappas Jr., G., Rodrigues, T.B., KrüGer R., H., Bacterial community associated with healthy and diseased reef coral Mussismilia hispida from eastern Brazil (2010) Microb Ecol, 59, pp. 658-667Dinsdale, E.A., Pantos, O., Smriga, S., Edwards, R.A., Angly, F., Wegley, L., Hatay, M., Brown, E., Microbial ecology of four coral atolls in the Northern Line Islands (2008) PLoS ONE, p. 3. , Other authorsEck, R.V., Dayhoff, M.O., Atlas of Protein Sequence and Structure (1966) Silver Springs, , MD: National Biomedical Research FoundationEspinosa, E., Marco-Noales, E., Gómez, D., Lucas-Elío, P., Ordax, M., Garcías-Bonet, N., Duarte, C.M., Sanchez-Amat, A., Taxonomic study of Marinomonas strains isolated from the seagrass Posidonia oceanica, with descriptions of Marinomonas balearica sp. nov. and Marinomonas pollencensis sp. nov (2010) Int J Syst Evol Microbiol, 60, pp. 93-98Ezaki, T., Hashimoto, Y., Yabuuchi, E., Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains (1989) Int J Syst Bacteriol, 39, pp. 224-229Felsenstein, J., Confidence limits on phylogenies: An approach using the bootstrap (1985) Evolution, 39, pp. 783-791Francini-Filho, R.B., Moura, R.L., Thompson, F.L., Reis, R.M., Kaufman, L., Kikuchi, R.K.P., Diseases leading to accelerated decline of reef corals in the largest South Atlantic reef complex (Abrolhos Bank, eastern Brazil) (2008) Mar Pollut Bull, 56, pp. 1008-1014Goris, J., Suzuki, K., de Vos, P., Nakase, T., Kersters, K., Evaluation of a microplate DNA-DNA hybridization method compared with the initial renaturation method (1998) Can J Microbiol, 44, pp. 1148-1153Gupta, P., Chaturvedi, P., Pradhan, S., Delille, D., Shivaji, S., Marinomonas polaris sp. nov., a psychrohalotolerant strain isolated from coastal sea water off the subantarctic Kerguelen islands (2006) Int J Syst Evol Microbiol, 56, pp. 361-364Huys, G., Vancanneyt, M., Coopman, R., Janssen, P., Falsen, E., Altwegg, M., Kersters, K., Cellular fatty-acid composition as a chemotaxonomic marker for the differentiation of phenospecies and hybridization groups in the genus Aeromonas (1994) Int J Syst Bacteriol, 44, pp. 651-658Ivanova, E.P., Onyshchenko, O.M., Christen, R., Lysenko, A.M., Zhukova, N.V., Shevchenko, L.S., Kiprianova, E.A., Marinomonas pontica sp. nov., isolated from the Black Sea (2005) Int J Syst Evol Microbiol, 55, pp. 275-279Janssen, P., Coopman, R., Huys, G., Swings, J., Bleeker, M., Vos, P., Zabeau, M., Kersters, K., Evaluation of the DNA fingerprinting method AFLP as an new tool in bacterial taxonomy (1996) Microbiology, 142, pp. 1881-1893KováCs, N., Identification of Pseudomonas pyocyanea by the oxidase reaction (1956) Nature, 178, p. 703Lau, K.W.K., Ren, J., Wai, N.L.M., Lau, S.C.L., Qian, P.-Y., Wong, P.-K., Wu, M., Marinomonas ostreistagni sp. nov., isolated from a pearl-oyster culture pond in Sanya, Hainan Province, China (2006) Int J Syst Evol Microbiol, 56, pp. 2271-2275Leão, Z.M.A.N., Kikuchi, R.K.P., A relic coral fauna threatened by global changes and human activities, Eastern Brazil (2005) Mar Pollut Bull, pp. 599-611Macián, M.C., Arahal, D.R., Garay, E., Pujalte, M.J., Marinomonas aquamarina sp. nov., isolated from oysters and seawater (2005) Syst Appl Microbio, 28, pp. 145-150Mesbah, M., Premachandran, U., Whitman, W.B., Precise measurement of the G+C content of deoxyribonucleic acid by highperformance liquid chromatography (1989) Int J Syst Bacteriol, 39, pp. 159-167On, S.L.W., Harrington, C.S., Atabay, H.I., Differentiation of Arcobacter species by numerical analysis of AFLP profiles and description of a novel Arcobacter from pig abortions and turkey faeces (2003) J Appl Microbiol, 95, pp. 1096-1105Prabagaran, S.R., Suresh, K., Manorama, R., Delille, D., Shivaji, S., Marinomonas ushuaiensis sp. nov., isolated from coastal sea water in Ushuaia, Argentina, sub-Antarctica (2005) Int J Syst Evol Microbiol, 55, pp. 309-313Raina, J.-B., Tapiolas, D., Willis, B.L., Bourne, D.G., Coralassociated bacteria and their role in the biogeochemical cycling of sulfur (2009) Appl Environ Microbiol, 75, pp. 3492-3501Rohwer, F., Breitbart, M., Jara, J., Azam, F., Knowlton, N., Diversity of bacteria associated with the Caribbean coral Montastraea franski (2001) Coral Reefs, 20, pp. 85-91Romanenko, L.A., Uchino, M., Mikhailov, V.V., Zhukova, N.V., Uchimura, T., Marinomonas primoryensis sp. nov., a novel psychrophile isolated from coastal sea-ice in the Sea of Japan (2003) Int J Syst Evol Microbiol, 53, pp. 829-832Romanenko, L.A., Tanaka, N., Frolova, G.M., Marinomonas arenicola sp. nov., isolated from marine sediment (2009) Int J Syst Evol Microbiol, 59, pp. 2834-2838Rosenberg, E., Koren, O., Reshef, L., Efrony, R., Zilber-Rosenberg, I., The role of microorganisms in coral health, disease and evolution (2007) Nat Rev Microbiol, 5, pp. 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Vibrio Variabilis Sp. Nov. And Vibrio Maritimus Sp. Nov., Isolated From Palythoa Caribaeorum

Two novel vibrio isolates (R-40492 T and R-40493 T) originating from the zoanthid Palythoa caribaeorum in Brazil in 2005 were taxonomically characterized by means of a polyphasic approach comprising multilocus sequence analysis (MLSA), DNA-DNA hybridization (DDH), ΔTm analysis and phenotypic characterization. Phylogenetic analysis based on 16S rRNA gene sequences showed that R-40492 T and R-40493 T fell within the genus Vibrio and were most closely related to each other with 99% similarity; similarities of these two novel isolates towards Vibrio neptunius LMG 20536 T, Vibrio coralliilyticus LMG 20984 T, Vibrio nigripulchritudo LMG 3896 T, Vibrio sinaloensis LMG 25238 T and Vibrio brasiliensis LMG 20546 T varied between 97.1 and 98.5%. DDH experiments showed that the two isolates had less than 15% relatedness to the phylogenetically most closely related Vibrio species. R-40492 T and R-40493 T had 55-57% relatedness to each other. The ΔTm between R-40492 T and R-40493 T was 6.12 °6C. In addition, MLSA of concatenated sequences (16S rRNA, ftsZ, gyrB, recA, rpoA, topA, pyrH and mreB; 6035 bp in length) showed that the two novel isolates formed a separate branch with less than 92% concatenated gene sequence similarity towards known species of vibrios. Two novel species are proposed to accommodate these novel isolates, namely Vibrio variabilis sp. nov. (type strain, R-40492 T=LMG 25438 T=CAIM 1454 T) and Vibrio maritimus sp. nov. (type strain, R-40493 T=LMG 25439 T=CAIM 1455 T)., © 2011 IUMS.611230093015Baumann, P., Schubert, R.H.W., Genus I.Vibrio.In Bergey's Manual of Systematic Bacteriology (1984), 1, pp. 518-538. , Edited by N. R. Krieg J. G. Holt. Baltimore: Williams WilkinsBen-Haim, Y., Thompson, F.L., Thompson, C.C., Cnockaert, M.C., Hoste, B., Swings, J., Rosenberg, E., Vibrio coralliilyticus sp.nov.,a temperature-dependent pathogen of the coral Pocillopora damicornis (2003) Int J Syst Evol Microbiol, 53, pp. 309-315Bourne, D.G., Garren, M., Work, T.M., Rosenberg, E., Smith, G.W., Harvell, C.D., Microbial disease and the coral holobiont (2009) Trends Microbiol, 17, pp. 554-562Chimetto, L.A., Brocchi, M., Thompson, C.C., Martins, R.C.R., Ramos, H.R., Thompson, F.L., Vibrios dominate as culturable nitrogen-fixing bacteria of the Brazilian coral Mussismilia hispida (2008) Syst Appl Microbiol, 31, pp. 312-319Chimetto, L.A., Brocchi, M., Gondo, M., Thompson, C.C., Gomez-Gil, B., Thompson, F.L., Genomic diversity of vibrios associated with the Brazilian coral Mussismilia hispida and its sympatric zoanthids (Palythoa caribaeorum, Palythoa variabilis and Zoanthus solanderi) (2009) J Appl Microbiol, 106, pp. 1818-1826Chimetto, L.A., Cleenwerck, I., Alves Jr., N., Silva, B.S., Brocchi, M., Willems, A., de Vos, P., Thompson, F.L., Vibrio communis sp.nov.,isolated from the marine animals Mussismilia hispida, Phyllogorgia dilatata, Palythoa caribaeorum, Palythoa variabilis and Litopenaeus vannamei (2011) Int J Syst Evol Microbiol, 61, pp. 362-368Eck, R.V., Dayhoff, M.O., (1966) Atlas of Protein Sequence and Structure, , Silver Springs, MD: National Biomedical Research FoundationEzaki, T., Hashimoto, Y., Yabuuchi, E., Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains (1989) Int J Syst Bacteriol, 39, pp. 224-229Felsenstein, J., Confidence limits on phylogenies: An approach using the bootstrap (1985) Evolution, 39, pp. 783-791Gomez-Gil, B., Fajer-Avila, E., Garcia-Vargas, F., Vibrios of the spotted rose snapper Lutjanus guttatus Steindachner, 1869 from northwestern Mexico (2007) J Appl Microbiol, 102, pp. 1518-1526Gomez-Gil, B., Fajer-Avila, E., Pascual, J., Macian, M.C., Pujalte, M.J., Garay, E., Roque, A., Vibrio sinaloensis sp.nov.,isolated from the spotted rose snapper,Lutjanus guttatus Steindachner, 1869 (2008) Int J Syst Evol Microbiol, 58, pp. 1621-1624Goris, J., Suzuki, K., de Vos, P., Nakase, T., Kersters, K., Evaluation of a microplate DNA-DNA hybridization method compared with the initial renaturation method (1998) Can J Microbiol, 44, pp. 1148-1153Huys, G., Vancanneyt, M., Coopman, R., Janssen, P., Falsen, E., Altwegg, M., Kersters, K., Cellular fatty-acid composition as a chemotaxonomic marker for the differentiation of phenospecies and hybridization groups in the genus Aeromonas (1994) Int J Syst Bacteriol, 44, pp. 651-658Kovacs, N., Identification of Pseudomonas pyocyanea by the oxidase reaction (1956) Nature, 178, p. 703Macian, M.C., Ludwig, W., Aznar, R., Grimont, P.A.D., Schleifer, K.H., 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Kita-Tsukamoto, K., Thompson, F.L., Inferring the evolutionary history of vibrios by means of multilocus sequence analysis (2007) J Bacteriol, 189, pp. 7932-7936Sheu, S.Y., Jiang, S.R., Chen, C.A., Wang, J.T., Chen, W.M., Vibrio stylophorae sp.nov.,isolated from the reef-building coral Stylophora pistillata (2011) Int J Syst Evol Microbiol, 61, pp. 2180-2185Sussman, M., Willis, B.L., Victor, S., Bourne, D.G., Coral pathogens identified for White Syndrome (WS) epizootics in the Indo-Pacific (2008) PLoS ONE, 2393, p. 3Tamura, K., Dudley, J., Nei, M., Kumar, S., MEGA4:Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0 (2007) Mol Biol Evol, 24, pp. 1596-1599Thompson, F.L., Hoste, B., Vandemeulebroecke, K., Swings, J., Genomic diversity amongst Vibrio isolates from different sources determined by fluorescent amplified fragment length polymorphism (2001) Syst Appl Microbiol, 24, pp. 520-538Thompson, F.L., Hoste, B., Thompson, C.C., Huys, G., Swings, J., The coral bleaching Vibrio shiloi Kushmaro 2001 is a later synonym of Vibrio mediterranei Pujalte and Garay 1986 (2001) Syst Appl Microbiol, 24, pp. 516-519Thompson, F.L., Hoste, B., Vandemeulebroecke, K., Engelbeen, K., Denys, R., Swings, J., Vibrio trachuri Iwamoto 1995 is a junior synonym of Vibrio harveyi (Johnson and Shunk 1936) Baumann 1981 (2002) Int J Syst Evol Microbiol, 52, pp. 973-976Thompson, F.L., Li, Y., Gomez-Gil, B., Thompson, C.C., Hoste, B., Vandemeulebroecke, K., Rupp, G.S., de Bem, M.M., Vibrio neptunius sp.nov.,Vibrio brasiliensis sp.nov.and Vibrio xuii sp.nov.,isolated from the marine aquaculture environment (bivalves, fish, rotifers and shrimps) (2003) Int J Syst Evol Microbiol, 53, pp. 245-252Thompson, F.L., Iida, T., Swings, J., Biodiversity of vibrios (2004) Microbiol Mol Biol Rev, 68, pp. 403-431Thompson, F.L., Gevers, D., Thompson, C.C., Dawyndt, P., Naser, S., Hoste, B., Munn, C.B., Swings, J., Phylogeny and molecular identification of vibrios on the basis of multilocus sequence analysis (2005) Appl Environ Microbiol, 71, pp. 5107-5115Thompson, F.L., Gomez-Gil, B., Vasconcelos, A.T.R., Sawabe, T., Multilocus sequence analysis reveals that Vibrio harveyi and V.campbellii are distinct species (2007) Appl Environ Microbiol, 73, pp. 4279-4285Thompson, C.C., Vicente, A.C.P., Souza, R.C., Vasconcelos, A.T.R., Vesth, T., Alves Jr., N., Ussery, D.W., Thompson, F.L., Genomic taxonomy of vibrios (2009) BMC Evol Biol, 9, pp. 1-16Wang, H., Liu, J., Wang, Y., Zhang, X.H., Vibrio marisflavi sp.nov.,isolated from seawater (2011) Int J Syst Evol Microbiol, 61, pp. 568-573Waterhouse, A.M., Procter, J.B., Martin, D.M.A., Clamp, M., Barton, G.J., Jalview Version 2-a multiple sequence alignment editor and analysis workbench (2009) Bioinformatics, 25, pp. 1189-1191Wayne, L.G., Brenner, D.J., Colwell, R.R., Grimont, P.A.D., Kandler, O., Krichevsky, M.I., Moore, L.H., Murray, R.G.E., International Committee on Systematic Bacteriology.Report of the ad hoc committee on reconciliation of approaches to bacterial systematics (1987) Int J Syst Bacteriol, 37, pp. 463-464Willems, A., Doignon-Bourcier, F., Goris, J., Coopman, R., de Lajudie, P., de Vos, P., Gillis, M., DNA-DNA hybridization study of Bradyrhizobium strains (2001) Int J Syst Evol Microbiol, 51, pp. 1315-132