title: Photobacterium kishitanii sp. nov., a luminous marine bacterium symbiotic with deep-sea fishes.
abstract: Six representatives of a luminous bacterium commonly found in association with deep, cold-dwelling marine fishes were isolated from the light organs and skin of different fish species. These bacteria were Gram-negative, catalase-positive, and weakly oxidase-positive or oxidase-negative. Morphologically, cells of these strains were coccoid or coccoid-rods, occurring singly or in pairs, and motile by means of polar flagellation. After growth on seawater-based agar medium at 22 degrees C for 18 h, colonies were small, round and white, with an intense cerulean blue luminescence. Analysis of 16S rRNA gene sequence similarity placed these bacteria in the genus Photobacterium. Phylogenetic analysis based on seven housekeeping gene sequences (16S rRNA gene, gapA, gyrB, pyrH, recA, rpoA and rpoD), seven gene sequences of the lux operon (luxC, luxD, luxA, luxB, luxF, luxE and luxG) and four gene sequences of the rib operon (ribE, ribB, ribH and ribA), resolved the six strains as members of the genus Photobacterium and as a clade distinct from other species of Photobacterium. These strains were most closely related to Photobacterium phosphoreum and Photobacterium iliopiscarium. DNA-DNA hybridization values between the designated type strain, Photobacterium kishitanii pjapo.1.1(T), and P. phosphoreum LMG 4233(T), P. iliopiscarium LMG 19543(T) and Photobacterium indicum LMG 22857(T) were 51, 43 and 19 %, respectively. In AFLP analysis, the six strains clustered together, forming a group distinct from other analysed species. The fatty acid C(17 : 0) cyclo was present in these bacteria, but not in P. phosphoreum, P. iliopiscarium or P. indicum. A combination of biochemical tests (arginine dihydrolase and lysine decarboxylase) differentiates these strains from P. phosphoreum and P. indicum. The DNA G+C content of P. kishitanii pjapo.1.1(T) is 40.2 %, and the genome size is approximately 4.2 Mbp, in the form of two circular chromosomes. These strains represent a novel species, for which the name Photobacterium kishitanii sp. nov. is proposed. The type strain, pjapo.1.1(T) (=ATCC BAA-1194(T)=LMG 23890(T)), is a luminous symbiont isolated from the light organ of the deep-water fish Physiculus japonicus.
authors.affiliation: Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA.
authors.forename: Jennifer C
authors.initials: JC
authors.lastname: Ast
authors.affiliation: Laboratory of Microbiology and BCCM/LMG Bacteria Collection, Ghent University, K. L. Ledeganckstraat 35, Ghent 9000, Belgium.
authors.forename: Ilse
authors.initials: I
authors.lastname: Cleenwerck
authors.affiliation: Laboratory of Microbiology and BCCM/LMG Bacteria Collection, Ghent University, K. L. Ledeganckstraat 35, Ghent 9000, Belgium.
authors.forename: Katrien
authors.initials: K
authors.lastname: Engelbeen
authors.affiliation: Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA.
authors.forename: Henryk
authors.initials: H
authors.lastname: Urbanczyk
authors.affiliation: Department of Genetics, Federal University of Rio de Janeiro, Ilha do Fundão, CEP 21944-970, Rio de Janeiro, Brazil.
authors.forename: Fabiano L
authors.initials: FL
authors.lastname: Thompson
authors.affiliation: Laboratory of Microbiology and BCCM/LMG Bacteria Collection, Ghent University, K. L. Ledeganckstraat 35, Ghent 9000, Belgium.
authors.forename: Paul
authors.initials: P
authors.lastname: De Vos
authors.affiliation: Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA.
authors.forename: Paul V
authors.initials: PV
authors.lastname: Dunlap
mesh_terms: D000825:Animal Structures / Q000382:microbiology; D000818:Animals; D001426:Bacterial Proteins / Q000235:genetics; D015373:Bacterial Typing Techniques; D001482:Base Composition; D002374:Catalase / Q000096:biosynthesis; D002876:Chromosomes, Bacterial; D016000:Cluster Analysis; D016172:DNA Fingerprinting; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D004270:DNA, Circular; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D005227:Fatty Acids / Q000032:analysis; D005399:Fishes / Q000382:microbiology* / Q000502:physiology; D005407:Flagella; D020459:Genes, rRNA; D008124:Locomotion / Q000502:physiology; D049449:Luminescence; D008164:Luminescent Proteins / Q000096:biosynthesis*; D008969:Molecular Sequence Data; D021141:Nucleic Acid Amplification Techniques; D009693:Nucleic Acid Hybridization; D010088:Oxidoreductases / Q000096:biosynthesis; D010776:Photobacterium / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification* / Q000502:physiology; D010802:Phylogeny; D012329:RNA, Bacterial / Q000235:genetics; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA; D012689:Sequence Homology, Nucleic Acid; D012867:Skin / Q000382:microbiology; D013559:Symbiosis
chemical_list: D001426:Bacterial Proteins; D004269:DNA, Bacterial; D004270:DNA, Circular; D004275:DNA, Ribosomal; D005227:Fatty Acids; D008164:Luminescent Proteins; D012329:RNA, Bacterial; D012336:RNA, Ribosomal, 16S; D010088:Oxidoreductases; D002374:Catalase