Genomic and phylogenetic characterization of luminous bacteria symbiotic with the deep-sea fish Chlorophthalmus albatrossis (Aulopiformes: Chlorophthalmidae)

Insight to the diversity of Photobacterium spp. isolated from European plaice (Pleuronectes platessa) based on phylogenetic analysis, phenotypic characterisation and spoilage potential

This study aimed to explore the diversity of fifty-four Photobacterium strains isolated from muscle tissue of European plaice (Pleuronectes platessa) caught at different fishing seasons and stored 14-days under various conditions. Single phylogenetic markers (16S rRNA, gapA, gyrB and recA) and multilocus sequence analysis (MLSA) were employed to classify isolates at species level. Furthermore, intra- and interspecies variability in the phenotypic traits, maximum specific growth rate (μmax) and spoilage potential of the Photobacterium isolates were investigated. The isolates were classified into the P. iliopiscarium (53.7 %), P. phosphoreum (40.7 %) and P. piscicola (5.6 %) clades using MLSA. Two housekeeping genes, gyrB and recA, exhibited a consistent phylogenetic relationship with MLSA, suggesting that they might be used as individual phylogenetic markers for the Photobacterium genus. Intra- and interspecies variability in the expression of phenotypic characteristics and the production of trimethylamine (TMA), inosine (HxR), and hypoxanthine (Hx) were observed. A growth optimum temperature for P. iliopiscarium was approximately 20 °C, while those for P. phosphoreum and P. piscicola were closer to 15 °C. All isolates exhibited the highest growth density at 1.5 % NaCl, followed by 0.5 %, 3 %, and 6 % NaCl. However, P. phosphoreum demonstrated a higher NaCl tolerance than the other two species. Although, the high CO2 atmosphere significantly inhibited the growth of all strains at 4 °C, P. phosphoreum and P. piscicola showed higher growth density at 15 °C than P. iliopiscarium. Notably, all strains demonstrated H2S production. The μmax varied considerably within each species, highlighting the significance of strain-level variability. This study demonstrates that P. iliopiscarium and P. piscicola, alongside P. phosphoreum, are efficient TMA-, HxR-, Hx-, and H2S-producers, suggesting their potential contribution to synergistic off-odour generation and spoilage. Moreover, the Photobacterium isolates seem to exhibit diverse adaptations to their environments, resulting in fluctuated growth and spoilage potential. Understanding intra- and interspecies variability will facilitate modelling seafood spoilage in microbial risk assessments and developing targeted hurdles to prolong products' shelf-life.

Comparative genomics of symbiotic Photobacterium using highly contiguous genome assemblies from long read sequences

This study presents the assembly and comparative genomic analysis of luminous Photobacterium strains isolated from the light organs of 12 fish species using Oxford Nanopore Technologies (ONT) sequencing. The majority of assemblies achieved chromosome-level continuity, consisting of one large (>3 Mbp) and one small (~1.5 Mbp) contig, with near complete BUSCO scores along with varying plasmid sequences. Leveraging this dataset, this study significantly expanded the available genomes for P. leiognathi and its subspecies P. 'mandapamensis', enabling a comparative genomic analysis between the two lineages. An analysis of the large and small chromosomes unveiled distinct patterns of core and accessory genes, with a larger fraction of the core genes residing on the large chromosome, supporting the hypothesis of secondary chromosome evolution from megaplasmids in Vibrionaceae. In addition, we discovered a proposed new species, Photobacterium acropomis sp. nov., isolated from an acropomatid host, with an average nucleotide identify (ANI) of 93 % compared to the P. leiognathi and P. 'mandapamensis' strains. A comparison of the P. leiognathi and P. 'mandapamensis' lineages revealed minimal differences in gene content, yet highlighted the former's larger genome size and potential for horizontal gene transfer. An investigation of the lux-rib operon, responsible for light production, indicated congruence between the presence of luxF and host family, challenging its role in differentiating P. 'mandapamensis' from P. leiognathi. Further insights were derived from the identification of metabolic differences, such as the presence of the NADH:quinone oxidoreductase respiratory complex I in P. leiognathi as well as variations in the type II secretion system (T2S) genes between the lineages, potentially impacting protein secretion and symbiosis. In summary, this study advances our understanding of Photobacterium genome evolution, highlighting subtle differences between closely related lineages, specifically P. leiognathi and P. 'mandapamensis'. These findings highlight the benefit of long read sequencing for bacterial genome assembly and pangenome analysis and provide a foundation for exploring early bacterial speciation processes of these facultative light organ symbionts.

Deciphering the growth responses and genotypic diversity of bioluminescent Photobacterium phosphoreum on chicken meat during aerobic refrigerated storage

The advent of high-throughput sequencing technologies in recent years has revealed the unexpected presence of genus Photobacterium within the chicken meat spoilage ecosystem. This study was undertaken to decipher the occurrence, the growth patterns and the genotypic biodiversity of Photobacterium phosphoreum on chicken breast fillets stored aerobically at 4 °C through conventional microbiological methods and molecular techniques. Samples were periodically cultured on marine broth agar (MA; supplemented with meat extract and vancomycin) for the enumeration of presumptive bioluminescent Photobacterium spp. In total, 90 bioluminescent bacteria were recovered from the initial (time of first appearance), middle and end stages of storage. Concomitantly, 95 total psychrotrophic/psychrophilic bacteria were isolated from the same medium to assess the presence and diversity of non-luminous photobacteria. Genetic diversity between bioluminescent isolates was assessed with two PCR-based DNA fingerprinting methods, i.e. RAPD and rep-PCR. Moreover, the characterization of selected bacterial isolates at the genus and/or species level was performed by sequencing of the 16S rRNA and/or gyrB gene. Bioluminescent bacteria were scarcely encountered in fresh samples at population levels of ca. 2.0 log CFU/g, whilst total psychrotrophic/psychrophilic bacteria were found at levels of ca. 4.4 log CFU/g. As time proceeded and close to shelf-life end, bioluminescent bacteria were encountered at higher populations, and were found at levels of 5.3 and 7.0 log CFU/g in samples from the second and third batch, respectively. In the first batch their presence was occasional and at levels up to 3.9 log CFU/g. Accordingly, total psychrotrophic/psychrophilic bacteria exceeded 8.4 log CFU/g at the end of storage, suggesting the possible underestimation of bioluminescent populations following the specific cultivation conditions. Sequence analysis assigned bioluminescent isolates to Photobacterium phosphoreum, while genetic fingerprinting revealed high intra-species variability. Respectively, total psychrotrophs/psychrophiles were assigned to genera Pseudomonas, Shewanella, Psychrobacter, Acinetobacter, Vibrio and Photobacterium. Non-luminous photobacteria were not identified within the psychrotrophs/psychrophiles. Results of the present study reveal the intra- and inter-batch variability on the occurrence and growth responses of P. phosphoreum and highlight its potential role in the chicken meat spoilage consortium.

16S rRNA Gene Amplicon Sequencing of Gut Microbiota in Three Species of Deep-Sea Fish in Suruga Bay, Japan

We report here 16S rRNA gene amplicon sequence analysis of the gut microbiota in three species of deep-sea fish collected from Suruga Bay, Japan. Of the three species, two were dominated by the phylum Proteobacteria (genus Photobacterium), while one was dominated by the phyla Spirochaetes (genus Brevinema) and Tenericutes (unclassified Mycoplasmataceae).

We report here 16S rRNA gene amplicon sequence analysis of the gut microbiota in three species of deep-sea fish collected from Suruga Bay, Japan. Of the three species, two were dominated by the phylum Proteobacteria (genus Photobacterium), while one was dominated by the phyla Spirochaetes (genus Brevinema) and Tenericutes (unclassified Mycoplasmataceae).

Biodiversity of Photobacterium spp. Isolated From Meats

Photobacteria are common psychrophilic bacteria found in marine environments. Recently, several studies revealed high numbers of Photobacterium (P.) spp. on packaged fresh meat. Their occurrence appears relevant for the spoilage of meat, since species of the genus are already known as potent fish spoilage organisms. Here we report on distribution, biodiversity, and specific traits of P. carnosum (n = 31), P. phosphoreum (n = 24), and P. iliopiscarium (n = 3) strains from different foods. Biodiversity was assessed by genomic fingerprinting, diversity index analysis, growth dynamics, comparison of metabolic activities, and antibiotic resistance. We observed a ubiquitous occurrence of the species on all common meats independent of packaging conditions and producer, suggesting contamination during an established processing or packaging step. Regarding biodiversity, the three species differed clearly in their growth properties and metabolic characteristics, with P. phosphoreum growing the fastest and showing the strongest alkalization of the media. On strain level we also recorded variations in enzymatic reactions, acid production, and antibiotic resistances not restricted to specific meat types. This depicts high biodiversity on species and strain level on each contaminated meat sample. Our analysis showed that meat-borne strains of P. phosphoreum and P. iliopiscarium clearly differ from their type strains from a marine habitat. Additionally, we report for the first time isolation of P. carnosum strains from packaged fish, which in contrast showed comparable phenotypic properties to meat-borne strains. This hints at different initial origins of P. phosphoreum/P. iliopiscarium (marine background) and P. carnosum (no demonstrated marine background) contaminations on fish and meat, respectively.

Expression of genes encoding the luciferase from Photobacterium leiognathi in Escherichia coli Rosetta (DE3) and its application in NADH detection

Cloning of genes encoding the luciferase from Photobacterium leiognathi YL in Escherichia coli Rosetta (DE3) was performed successfully and the expressed forms of lux AB were purified to homogeneity. Experimental measurements revealed that luciferase from Photobacterium leiognathi YL has good thermal stability and a high residual activity at extreme pH values, which are extremely important for its various ecological, industrial and medical applications. Furthermore, we made a first attempt for quantitative detection of NADH by recombinant E. coli Rosetta (DE3) coupled enzyme system. A good linear relationship between luminescence intensity and NADH with low (1-12 nmol/L) and high (10-500 nmol/L) concentration was observed, whose standard curve was y = 772.97× + 4041.1, R²  = 0.9884 and y = 1710× + 4.99 × 10⁵ , R²  = 0.9727, respectively. Our results demonstrate a high sensitivity of recombinant E. coli coupled enzyme system to NADH on the basis of high soluble expression of recombinant luciferase and continuous and stable expression of some NAD(P)H-dependent flavin mononucleotide (FMN) reductases.

Genetic diversity analysis of isolates belonging to the Photobacterium phosphoreum species group collected from salmon products using AFLP fingerprinting

An accurate amplified fragment length polymorphism (AFLP) method, including three primer sets for the selective amplification step, was developed to display the phylogenetic position of Photobacterium isolates collected from salmon products. This method was efficient for discriminating the three species Photobacterium phosphoreum, Photobacterium iliopiscarium and Photobacterium kishitanii, until now indistinctly gathered in the P. phosphoreum species group known to be strongly responsible for seafood spoilage. The AFLP fingerprints enabled the isolates to be separated into two main clusters that, according to the type strains, were assigned to the two species P. phosphoreum and P. iliopiscarium. P. kishitanii was not found in the collection. The accuracy of the method was validated by using gyrB-gene sequencing and luxA-gene PCR amplification, which confirmed the species delineation. Most of the isolates of each species were clonally distinct and even those that were isolated from the same source showed some diversity. Moreover, this AFLP method may be an excellent tool for genotyping isolates in bacterial communities and for clarifying our knowledge of the role of the different members of the Photobacterium species group in seafood spoilage.

Residence of habitat-specific anammox bacteria in the deep-sea subsurface sediments of the South China Sea: analyses of marker gene abundance with physical chemical parameters

Anaerobic ammonium oxidation (anammox) has been recognized as an important process for the global nitrogen cycle. In this study, the occurrence and diversity of anammox bacteria in the deep-sea subsurface sediments of the South China Sea (SCS) were investigated. Results indicated that the anammox bacterial sequences recovered from this habitat by amplifying both 16S rRNA gene and hydrazine oxidoreductase encoding hzo gene were all closely related to the Candidatus Scalindua genus. A total of 96 16S rRNA gene sequences from 346 clones were grouped into five subclusters: two subclusters affiliated with the brodae and arabica species, while three new subclusters named zhenghei-I, -II, and -III showed ≤ 97.4% nucleic acid sequence identity with other known Candidatus Scalindua species. Meanwhile, 88 hzo gene sequences from the sediments also formed five distant subclusters within hzo cluster 1c. Through fluorescent real-time PCR analysis, the abundance of anammox bacteria in deep-sea subsurface sediment was quantified by hzo genes, which ranged from 1.19 × 10(4) to 7.17 × 10(4) copies per gram of dry sediments. Combining all the information from this study, diverse Candidatus Scalindua anammox bacteria were found in the deep-sea subsurface sediments of the SCS, and they could be involved in the nitrogen loss from the fixed inventory in the habitat.

Photobacterium aphoticum sp. nov., isolated from coastal water

A facultatively anaerobic marine gammaproteobacterium, designated strain M46T, 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 M46T was closely related to P. rosenbergii CECT 7644T, P. halotolerans CECT 5860T and P. ganghwense CECT 7641T, 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 7641T with 87.4 and 85.0 % sequence similarity, respectively. Regardless of the gene used in phylogenetic analysis, strain M46T always formed a separate and stable clade containing these three species of the genus Photobacterium. Strain M46T 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 M46T was positive for arginine dihydrolase (ADH), β-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 C18 and C16, as in other members of the genus Photobacterium, but their relative amounts and the presence or absence of other fatty acids differentiated strain M46T from its closest relatives. Based on the results of this polyphasic taxonomic study, strain M46T represents a novel species of the genus Photobacterium, for which the name Photobacterium aphoticum is proposed. The type strain is M46T ( = CECT 7614T  = KCTC 23057T).

Phylogeny, genomics, and symbiosis of Photobacterium

Photobacterium comprises several species in Vibrionaceae, a large family of Gram-negative, facultatively aerobic, bacteria that commonly associate with marine animals. Members of the genus are widely distributed in the marine environment and occur in seawater, surfaces, and intestines of marine animals, marine sediments and saline lake water, and light organs of fish. Seven Photobacterium species are luminous via the activity of the lux genes, luxCDABEG. Much recent progress has been made on the phylogeny, genomics, and symbiosis of Photobacterium. Phylogenetic analysis demonstrates a robust separation between Photobacterium and its close relatives, Aliivibrio and Vibrio, and reveals the presence of two well-supported clades. Clade 1 contains luminous and symbiotic species and one species with no luminous members, and Clade 2 contains mostly nonluminous species. The genomes of Photobacterium are similar in size, structure, and organization to other members of Vibrionaceae, with two chromosomes of unequal size and multiple rrn operons. Many species of marine fish form bioluminescent symbioses with three Photobacterium species: Photobacterium kishitanii, Photobacterium leiognathi, and Photobacterium mandapamensis. These associations are highly, but not strictly species specific, and they do not exhibit symbiont-host codivergence. Environmental congruence instead of host selection might explain the patterns of symbiont-host affiliation observed from nature.

Bioluminescence in the sea

Bioluminescence spans all oceanic dimensions and has evolved many times--from bacteria to fish--to powerfully influence behavioral and ecosystem dynamics. New methods and technology have brought great advances in understanding of the molecular basis of bioluminescence, its physiological control, and its significance in marine communities. Novel tools derived from understanding the chemistry of natural light-producing molecules have led to countless valuable applications, culminating recently in a related Nobel Prize. Marine organisms utilize bioluminescence for vital functions ranging from defense to reproduction. To understand these interactions and the distributions of luminous organisms, new instruments and platforms allow observations on individual to oceanographic scales. This review explores recent advances, including the chemical and molecular, phylogenetic and functional, community and oceanographic aspects of bioluminescence.

Developmental and microbiological analysis of the inception of bioluminescent symbiosis in the marine fish Nuchequula nuchalis (Perciformes: Leiognathidae)

Many marine fish harbor luminous bacteria as bioluminescent symbionts. Despite the diversity, abundance, and ecological importance of these fish and their apparent dependence on luminous bacteria for survival and reproduction, little is known about developmental and microbiological events surrounding the inception of their symbioses. To gain insight on these issues, we examined wild-caught larvae of the leiognathid fish Nuchequula nuchalis, a species that harbors Photobacterium leiognathi as its symbiont, for the presence, developmental state, and microbiological status of the fish's internal, supraesophageal light organ. Nascent light organs were evident in the smallest specimens obtained, flexion larvae of 6.0 to 6.5 mm in notochord length (NL), a developmental stage at which the stomach had not yet differentiated and the nascent gasbladder had not established an interface with the light organ. Light organs of certain of the specimens in this size range apparently lacked bacteria, whereas light organs of other specimens of 6.5 mm in NL and of all larger specimens harbored large populations of bacteria, representatives of which were identified as P. leiognathi. Bacteria identified as Vibrio harveyi were also present in the light organ of one larval specimen. Light organ populations were composed typically of two or three genetically distinct strain types of P. leiognathi, similar to the situation in adult fish, and the same strain type was only rarely found in light organs of different larval, juvenile, or adult specimens. Light organs of larvae carried a smaller proportion of strains merodiploid for the lux-rib operon, 79 of 249 strains, than those of adults (75 of 91 strains). These results indicate that light organs of N. nuchalis flexion and postflexion larvae of 6.0 to 6.7 mm in NL are at an early stage of development and that inception of the symbiosis apparently occurs in flexion larvae of 6.0 to 6.5 mm in NL. Ontogeny of the light organ therefore apparently precedes acquisition of the symbiotic bacteria. Furthermore, bacterial populations in larval light organs near inception of the symbiosis are genetically diverse, like those of adult fish.

Mutations in the lux operon of natural dark mutants in the genus Vibrio

Bacterial bioluminescence can display a wide range of intensities among strains, from very bright to undetectable, and it has been shown previously that there are nonluminous vibrios that possess lux genes. In this paper, we report the isolation and characterization of completely dark natural mutants in the genus Vibrio. Screening of over 600 Vibrio isolates with a luxA gene probe revealed that approximately 5% carried the luxA gene. Bioluminescence assays of the luxA-positive isolates, followed by repetitive extragenic palindromic-PCR fingerprinting, showed three unique genotypes that are completely dark. The dark mutants show a variety of lesions, including an insertion sequence, point mutations, and deletions. Strain BCB451 has an IS10 insertion sequence in luxA, a mutated luxE stop codon, and a truncated luxH. Strain BCB494 has a 396-bp deletion in luxC, and strain BCB440 has a frameshift in luxC. This paper represents the first molecular characterization of natural dark mutants and the first demonstration of incomplete lux operons in natural isolates.

Photobacterium kishitanii sp. nov., a luminous marine bacterium symbiotic with deep-sea fishes

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 °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.1.1T, and P. phosphoreum LMG 4233T, P. iliopiscarium LMG 19543T and Photobacterium indicum LMG 22857T 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 C17 : 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.1.1T 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.1.1T (=ATCC BAA-1194T=LMG 23890T), is a luminous symbiont isolated from the light organ of the deep-water fish Physiculus japonicus.

Natural merodiploidy of the lux-rib operon of Photobacterium leiognathi from coastal waters of Honshu, Japan

Sequence analysis of the bacterial luminescence (lux) genes has proven effective in helping resolve evolutionary relationships among luminous bacteria. Phylogenetic analysis using lux genes, however, is based on the assumptions that the lux genes are present as single copies on the bacterial chromosome and are vertically inherited. We report here that certain strains of Photobacterium leiognathi carry multiple phylogenetically distinct copies of the entire operon that codes for luminescence and riboflavin synthesis genes, luxCDABEG-ribEBHA. Merodiploid lux-rib strains of P. leiognathi were detected during sequence analysis of luxA. To define the gene content, organization, and sequence of each lux-rib operon, we constructed a fosmid library of genomic DNA from a representative merodiploid strain, lnuch.13.1. Sequence analysis of fosmid clones and genomic analysis of lnuch.13.1 defined two complete, physically separate, and apparently functional operons, designated lux-rib1 and lux-rib2. P. leiognathi strains lelon.2.1 and lnuch.21.1 were also found to carry lux-rib1 and lux-rib2, whereas ATCC 25521T apparently carries only lux-rib1. In lnuch.13.1, lelon.2.1, lnuch.21.1, and ATCC 25521T, lux-rib1 is flanked upstream by lumQ and putA and downstream by a gene for a hypothetical multidrug efflux pump. In contrast, transposase genes flank lux-rib2 of lnuch.13.1, and the chromosomal location of lux-rib2 apparently differs in lnuch.13.1, lelon.2.1, and lnuch.21.1. Phylogenetic analysis demonstrated that lux-rib1 and lux-rib2 are more closely related to each other than either one is to the lux and rib genes of other bacterial species, which rules out interspecies lateral gene transfer as the origin of lux-rib2 in P. leiognathi; lux-rib2 apparently arose within a previously unsampled or extinct P. leiognathi lineage. Analysis of 170 additional strains of P. leiognathi, for a total of 174 strains examined from coastal waters of Japan, Taiwan, the Philippine Islands, and Thailand, identified 106 strains that carry only a single lux-rib operon and 68 that carry multiple lux-rib operons. Strains bearing a single lux-rib operon were obtained throughout the geographic sampling range, whereas lux-rib merodiploid strains were found only in coastal waters of central Honshu. This is the first report of merodiploidy of lux or rib genes in a luminous bacterium and the first indication that a natural merodiploid state in bacteria can correlate with geography.

Phylogenetic diversity and cosymbiosis in the bioluminescent symbioses of "Photobacterium mandapamensis"

"Photobacterium mandapamensis" (proposed name) and Photobacterium leiognathi are closely related, phenotypically similar marine bacteria that form bioluminescent symbioses with marine animals. Despite their similarity, however, these bacteria can be distinguished phylogenetically by sequence divergence of their luminescence genes, luxCDAB(F)E, by the presence (P. mandapamensis) or the absence (P. leiognathi) of luxF and, as shown here, by the sequence divergence of genes involved in the synthesis of riboflavin, ribBHA. To gain insight into the possibility that P. mandapamensis and P. leiognathi are ecologically distinct, we used these phylogenetic criteria to determine the incidence of P. mandapamensis as a bioluminescent symbiont of marine animals. Five fish species, Acropoma japonicum (Perciformes, Acropomatidae), Photopectoralis panayensis and Photopectoralis bindus (Perciformes, Leiognathidae), Siphamia versicolor (Perciformes, Apogonidae), and Gadella jordani (Gadiformes, Moridae), were found to harbor P. mandapamensis in their light organs. Specimens of A. japonicus, P. panayensis, and P. bindus harbored P. mandapamensis and P. leiognathi together as cosymbionts of the same light organ. Regardless of cosymbiosis, P. mandapamensis was the predominant symbiont of A. japonicum, and it was the apparently exclusive symbiont of S. versicolor and G. jordani. In contrast, P. leiognathi was found to be the predominant symbiont of P. panayensis and P. bindus, and it appears to be the exclusive symbiont of other leiognathid fishes and a loliginid squid. A phylogenetic test for cospeciation revealed no evidence of codivergence between P. mandapamensis and its host fishes, indicating that coevolution apparently is not the basis for this bacterium's host preferences. These results, which are the first report of bacterial cosymbiosis in fish light organs and the first demonstration that P. leiognathi is not the exclusive light organ symbiont of leiognathid fishes, demonstrate that the host species ranges of P. mandapamensis and P. leiognathi are substantially distinct. The host range difference underscores possible differences in the environmental distributions and physiologies of these two bacterial species.

The bacterial flora of vacuum-packed cold-smoked salmon stored at 7°C, identified by direct 16S rRNA gene analysis and pure culture technique

AIMS

The indigenous flora of freshly chilled cold-smoked salmon just after the vacuum packaging, and the spoilage flora after storage, in vacuum package at 7 degrees C for 19 days, were to be investigated with two different sampling strategies.

METHODS AND RESULTS

Identification was performed using 16S rRNA sequencing of both isolated bacteria and bacterial DNA from tissue extract. The indigenous flora of fresh cold-smoked vacuum-packed salmon was dominated by, in order, Brochothrix thermosphacta, Yersinia ruckeri, Photobacterium and Carnobacterium, whereas the spoilage flora of the same product stored at 7 degrees C for 19 days was dominated by Lactobacillus and Photobacterium. The two sampling strategies showed similar results on the fish flora. Several new types of Photobacterium sequences, closely related to Photobacterium iliopiscarium and Photobacterium phosphoreum, were found from both the freshly processed and the stored salmon, indicating that smoked salmon harbours at least three different, as yet unknown, Photobacterium species.

CONCLUSIONS

Ten per cent of the bacterial flora multiplying on chilled, vacuum-packed, cold-smoked salmon comprised unknown species. The two sampling strategies complement each other.

SIGNIFICANCE AND IMPACT OF THE STUDY

As cold-smoked salmon is consumed without heat-treatment, the presence of undefined bacteria in high numbers should be considered in public health assessments.

Phylogenetic resolution and habitat specificity of members of the Photobacterium phosphoreum species group

Substantial ambiguity exists regarding the phylogenetic status of facultatively psychrophilic luminous bacteria identified as Photobacterium phosphoreum, a species thought to be widely distributed in the world's oceans and believed to be the specific bioluminescent light-organ symbiont of several deep-sea fishes. Members of the P. phosphoreum species group include luminous and non-luminous strains identified phenotypically from a variety of different habitats as well as phylogenetically defined lineages that appear to be evolutionarily distinct. To resolve this ambiguity and to begin developing a meaningful knowledge of the geographic distributions, habitats and symbiotic relationships of bacteria in the P. phosphoreum species group, we carried out a multilocus, fine-scale phylogenetic analysis based on sequences of the 16S rRNA, gyrB and luxABFE genes of many newly isolated luminous strains from symbiotic and saprophytic habitats, together with previously isolated luminous and non-luminous strains identified as P. phosphoreum from these and other habitats. Parsimony analysis unambiguously resolved three evolutionarily distinct clades, phosphoreum, iliopiscarium and kishitanii. The tight phylogenetic clustering within these clades and the distinct separation between them indicates they are different species, P. phosphoreum, Photobacterium iliopiscarium and the newly recognized 'Photobacterium kishitanii'. Previously reported non-luminous strains, which had been identified phenotypically as P. phosphoreum, resolved unambiguously as P. iliopiscarium, and all examined deep-sea fishes (specimens of families Chlorophthalmidae, Macrouridae, Moridae, Trachichthyidae and Acropomatidae) were found to harbour 'P. kishitanii', not P. phosphoreum, in their light organs. This resolution revealed also that 'P. kishitanii' is cosmopolitan in its geographic distribution. Furthermore, the lack of phylogenetic variation within 'P. kishitanii' indicates that this facultatively symbiotic bacterium is not cospeciating with its phylogenetically divergent host fishes. The results of this fine-scale phylogenetic analysis support the emerging view that bacterial species names should designate singular historical entities, i.e. discrete lineages diagnosed by a significant divergence of shared derived nucleotide characters.

Opinion: Re-evaluating prokaryotic species

There is no widely accepted concept of species for prokaryotes, and assignment of isolates to species is based on measures of phenotypic or genome similarity. The current methods for defining prokaryotic species are inadequate and incapable of keeping pace with the levels of diversity that are being uncovered in nature. Prokaryotic taxonomy is being influenced by advances in microbial population genetics, ecology and genomics, and by the ease with which sequence data can be obtained. Here, we review the classical approaches to prokaryotic species definition and discuss the current and future impact of multilocus nucleotide-sequence-based approaches to prokaryotic systematics. We also consider the potential, and difficulties, of assigning species status to biologically or ecologically meaningful sequence clusters.