Vibrio caribbeanicus sp. nov., isolated from the marine sponge Scleritoderma cyanea

Abstract

A Gram-negative, oxidase-positive, catalase-negative, facultatively anaerobic, motile, curved rodshaped bacterium, strain N384 T , was isolated from a marine sponge (Scleritoderma cyanea; phylum Porifera) collected from a depth of 795 feet (242 m) off the west coast of Curaç ao. On the basis of 16S rRNA gene sequencing, strain N384 T was shown to belong to the genus Vibrio, most closely related to Vibrio brasiliensis LMG 20546 T (98.8 % similarity), Vibrio nigripulchritudo ATCC 27043 T (98.5 %), Vibrio tubiashii ATCC 19109 T (98.6 %) and V. sinaloensis DSM 21326 T (98.2 %). The DNA G+C content of strain N384 T was 41.6 mol%. An analysis of concatenated sequences of five genes (gyrB, rpoA, pyrH, mreB and ftsZ; 4068 bp) demonstrated a clear separation between strain N384 T and its closest neighbours and clustered strain N384 T into the 'Orientalis' clade of vibrios. Phenotypically, the novel species belonged to the arginine dihydrolase-positive, lysine decarboxylase-and ornithine decarboxylase-negative (A+/L"/O") cluster. The novel species was also differentiated on the basis of fatty acid composition, specifically that the proportions of iso-C 13 : 0 , iso-C 15 : 0 , C 15 : 0 , iso-C 16 : 0 , C 16 : 0 , iso-C 17 : 0 , C 17 : 1 v8c and C 17 : 0 were significantly different from those found in V. brasiliensis and V. sinaloensis. The results of DNA-DNA hybridization, average nucleotide identity and physiological and biochemical tests further allowed differentiation of this strain from other described species of the genus Vibrio. Collectively, these findings confirm that strain N384 T represents a novel Vibrio species, for which the name Vibrio caribbeanicus sp. nov. is proposed, with the type strain N384 T (5ATCC BAA-2122 T 5DSM 23640 T ).The family Vibrionaceae is a member of the class Gammaproteobacteria and consists of the genera Vibrio, Photobacterium, Salinivibrio, Grimontia, Enterovibrio and Aliivibrio (Chimetto et al., 2011). At the time of writing, the genus Vibrio consisted of 89 species (http://www.vibriobiology.net). Some vibrios, such as Vibrio cholerae, V. parahaemolyticus and V. vulnificus, are well-known human pathogens (FDA, 2004). Generally, Vibrio species are halophilic, mesophilic and chemo-organotrophic in nature and have a facultatively fermentative metabolism (Thompson et al., 2004). Typically, vibrios are inhabitants of aquatic environments that show a remarkable degree of biodiversity, persisting in a variety of geographical locales and eukaryotic hosts, including corals, molluscs, sponges and zooplankton (Thompson et al., 2004).Sponges can maintain diverse symbiotic microbe populations that differ in composition from the microbial communities Abbreviations: ANI, average nucleotide identity; HGT, horizontal gene transfer; ILD, incongruence length difference; ML, maximum-likelihood; MLSA, multilocus sequence analysis; MP, maximum parsimony. The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA gene, topA, ftsZ, gapA, gyrB, mreB, pyrH, recA and rpoA gene sequences derived in this study are H...

Characterization of the Biosynthetic Operon for the Antibacterial Peptide Herbicolin in Pantoea vagans Biocontrol Strain C9-1 and Incidence in Pantoea Species

“…BLAST search (NCBI) revealed the presence of highly similar gene clusters in the genomes of P. agglomerans CU0119 (7) and Serratia proteamaculans 568 (43) and a distantly related gene cluster in Vibrio caribbeanicus ATCC BAA-2122 (14). The sequence of the gene cluster of P. agglomerans 48b/90 is not available, but the operon structure of P. agglomerans CU0119 (7) is very similar to that for P. vagans C9-1 (Fig.…”

The Rebirth of Culture in Microbiology through the Example of Culturomics To Study Human Gut Microbiota

“…An ANI value of Ն95% between genomes was proposed by those authors of to be equivalent to a DNA-DNA hybridization value of Ն70% (269). In 2009, Richter and Rossello-Mora (270) and, in 2010, Tindall et al (252) proposed that ANI could be used to replace DNA-DNA hybridization in characterizing prokaryotic species, and thus far, this method has been used to describe several new taxa (271)(272)(273). However, several drawbacks of using genomic sequences for taxonomic purposes have been highlighted.…”

New Vibrio species associated to molluscan microbiota: a review

“…To mention some examples, among the new species described as free-living seawater bacteria are V. agarivorans (Macián et al, 2001b), V. ruber (Shieh et al, 2003), V. aestivus and V. quintilis (Lucena et al, 2012), V. azureus (Yoshizawa et al, 2009), or V. sagamiensis (Yoshizawa et al, 2010). Associated to different marine organisms have been described, among others, V. caribbeanicus from sponges (Hoffmann et al, 2012), V. hemicentroti from sea urchin (Kim et al, 2013), V. corallilyticus, V. maritimus, V. shiloi, V. stylophorae , and V. variabilis from corals (Kushmaro et al, 2001; Ben-Haim et al, 2003; Chimetto et al, 2011; Sheu et al, 2011), V. rotiferianus from rotifers (Gomez-Gil et al, 2003a), V. comitans, V. gallicus, V. inusitatus, V. neonates, V. rarus , and V. superstes from abalones (Hayashi et al, 2003; Sawabe et al, 2004a, b, 2007a), V. atypicus, V. hispanicus, V. jasicida, V. owensii, V. pacinii, V. zhanjiangensis , and V. zhuhaiensis from crustaceans (Gomez-Gil et al, 2003b, 2004b; Cano-Gómez et al, 2010; Wang et al, 2010; Jin et al, 2012, 2013; Yoshizawa et al, 2012), V. hippocampi from sea horses (Bálcazar et al, 2010), and V. alfacsensis, V. sinaloensis , and V. tasmaniensis from fish (Thompson et al, 2003d; Gomez-Gil et al, 2008, 2012). …”