Photobacterium aphoticum sp. nov., isolated from coastal water

Abstract

A facultatively anaerobic marine gammaproteobacterium, designated strain M46 T , was isolated from Mediterranean seawater at Malvarrosa beach, Valencia, Spain. The strain was characterized by using a polyphasic approach and was found to be situated within the genus Photobacterium in the family Vibrionaceae. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain M46 T was closely related to P. rosenbergii CECT 7644 T , P. halotolerans CECT 5860 T and P. ganghwense CECT 7641 T , showing sequence similarities of 96.8, 96.4 and 96.2 %, respectively. According to the results of phylogenetic analyses based on recA and gyrB gene sequences, the most closely related taxon was P. ganghwense CECT 7641 T with 87.4 and 85.0 % sequence similarity, respectively. Regardless of the gene used in phylogenetic analysis, strain M46 T always formed a separate and stable clade containing these three species of the genus Photobacterium. Strain M46 T was not luminescent and produced a diffusible brown pigment. It required NaCl to grow, reduced nitrate to nitrite and oxidized a small number of substrates in Biolog GN plates. Strain M46 T was positive for arginine dihydrolase (ADH), b-galactosidase, aesculin hydrolysis and DNase activity. In API ZYM tests, the novel strain was positive for alkaline phosphatase, leucine arylamidase and acidic phosphatase activities. The major cellular fatty acids were unsaturated C 18 and C 16 , as in other members of the genus Photobacterium, but their relative amounts and the presence or absence of other fatty acids differentiated strain M46 T from its closest relatives. Based on the results of this polyphasic taxonomic study, strain M46 T represents a novel species of the genus Photobacterium, for which the name Photobacterium aphoticum is proposed. The type strain is M46 T (5CECT 7614 T 5KCTC 23057 T ).At the time of writing, the genus Photobacterium, of the family Vibrionaceae, contained sixteen species, most of which were isolated from seawater sampled at different depths, others having been isolated from marine animals. Defined as being facultatively anaerobic and weakly halophilic, species of the genus Photobacterium were originally thought to be mostly luminescent but more than half of the recognized species in the genus do not display this ecologically important character. Only P. phosphoreum, the type species of the genus, P. leiognathi, P. aquimaris, P. kishitanii and P. ganghwense have been described as being luminescent. Some of the luminescent species are symbionts of deep-sea fishes that hold them in specialized luminous organs , while other species, such as P. damselae, are pathogenic for marine animals. Phylogenetic positions of other members of the family Vibrionaceae showed members of the genus Photobacterium grouping with members of the genus Aliivibrio, whose earliest named species, A. fischerii and A. logei were once classified as species of the genus Photobacterium. Members of the recently described genera Grimontia and Enterovibrio also group with P. damselae in ...

Comparative Genomics Reveals High Genomic Diversity in the Genus Photobacterium

“…This study did not clarify the phylogenetic association of P. damselae as MLSA, fur , ANI, amino-acid usage analyses placed it in different branches, confirming its unstable association (Lucena et al, 2011). In contrast, although the species “P.…”

“…atrarenae” and “P. marinum” are not yet validly published names) (Gomez-Gil et al, 2011; Kim et al, 2011; Lucena et al, 2011; Urbanczyk et al, 2011; Srinivas et al, 2013; Figge et al, 2014; Liu et al, 2014; Lo et al, 2014; Moreira et al, 2014; Machado et al, 2015a). Of these 28, only 27 are available since no type strain was deposited for P. aplysiae , (Seo et al, 2005; Holmes and Farmer, 2008).…”

“…All species of this genus were originally thought to be luminescent, but it has become clear that a large number of species are not luminescent (Lucena et al, 2011; Urbanczyk et al, 2011). This ecological important characteristic is part of the symbiotic life style of some Photobacterium species and is attributed to the expression of the lux-rib operon (Dunlap, 2009).…”

Draft Genome Sequences of Two Vibrionaceae Species, Vibrio ponticus C121 and Photobacterium aphoticum C119, Isolated as Coral Reef Microbiota

“…However, the rapid expansion of the family has also demanded more reliable, reproducible, and informative schemes to define a new species that can be attained using microbial genomic taxonomy. While the type strains of V. ponticus (8) and P. aphoticum (9) were described in 2004 and 2011, respectively, no genome sequence has been reported since then. Our study reports the first draft genome sequences of V. ponticus C121 and P. aphoticum C119, which were isolated from water samples taken near the coral reef vicinity of Iriomote-Ishigaki National Park, Okinawa, Japan.…”

“…V. ponticus strain was isolated not only from seawater and mussels but also diseased sea bream (8) and Japanese sea bass (10). P. aphoticum was isolated from seawater (9). The species might be found closed as a clade of P. rosenbergii on the basis of multilocus sequence analysis (11).…”