Increased sulfate-reducing bacteria can drive microbial dysbiosis in bleached corals

AIMS

Coral bleaching occurs when coral colonies lose their Symbiodiniaceae partner and turn pale or white. Although this event is generally temperature-induced, there is also the possibility of holobiont microbial infection and dysbiosis. To address this issue, this study was conducted to investigate the diversity and composition of Symbiodiniaceae and bacteria in healthy and bleached colonies of Porites lutea collected from eastern Shenzhen.

METHODS AND RESULTS

Internal transcribed spacer 2 and 16S amplicon sequencing analysis were used to explore the diversity and composition of Symbiodiniaceae and bacteria in healthy and bleached colonies of P. lutea. Bacterial diversity and richness were significantly higher in bleached colonies than in healthy colonies (P < 0.05), whereas the diversity and richness of Symbiodiniaceae showed no significant changes. The bleaching event exerted a more significant impact on Symbiodiniaceae composition, which differed between healthy and bleached colonies (PERMANOVA, F = 8.246, P < 0.05). In terms of composition, Clade C (Cladocopium) was the predominant Symbiodiniaceae, whereas subclade C116 and C2r were significantly less abundant in bleached colonies than in healthy colonies (P < 0.05). The phyla Bacteroidetes, Acidobacteria, and Actinobacteria were significantly more abundant in bleached colonies than in healthy colonies (P < 0.05). The sulfate-reducing bacteria (SRB) Desulfobulbus and Desulfobacter at the genus level and Desulfobacterales and Desulfuromonadales at the order level were significantly more abundant in bleached colonies than in healthy colonies (P < 0.05). The co-occurrence patterns of Symbiodiniaceae and bacteria revealed a negative correlation of Desulfofaba, Desulfovibrio, Desulfarculus, and Desulfobulbus with Endozoicomonas, a very common symbiotic bacterial genus found in corals.

CONCLUSION

Coral bleaching may be associated with significant shifts in microbial communities, including increased SRB abundance, which may disrupt microbial balance and contribute to bleaching.

Photobacterium obscurum sp. nov., a marine bacterium isolated from the coast of Qingdao

A Gram-stain-negative, facultative anaerobic, rod-shaped strain, named SDRW27T, was isolated from offshore seawater collected near Qingdao. Strain SDRW27T was able to grow at 16-37 °C (optimum, 28 °C), pH 6.0-9.0 (optimum, pH 6.0) and in the presence of 1-7 % (w/v) NaCl (optimum, 3 %). Phylogenetic analysis using 16S rRNA gene sequences indicated that strain SDRW27T was most closely related to Photobacterium toruni H01100410BT (97.89 % sequence similarity), Photobacterium andalusiense H01100409BT (97.89 %) and Photobacterium leiognathi ATCC 25521T (97.82 %). The predominant fatty acids were summed feature 3 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH), summed feature 8 (C18 : 1  ω7c and/or C18 : 1  ω6c) and C16 : 0. The polar lipids of strain SDRW27T comprised phosphatidylglycerol, phosphatidylinositol dimannoside, phosphatidylcholine, phosphatidylethanolamine and three unidentified lipids. The major respiratory quinone was ubiquinone-8. The G+C content was 47.71 mol%. The genome size was 5.84 Mbp, including 85 contigs with an N50 value of 223 542. The average nucleotide identity (ANI) values of SDRW27T with its three most similar strains, P. toruni H01100410BT, P. andalusiense H01100409BT and P. leiognathi ATCC 25521T, were 71.36, 71.58 and 72.23 %, respectively (all lower than the 95-96 % ANI threshold), and the DNA-DNA hybridization (DDH) values were 20.4, 20.8 and 20.4 % (all lower than the 70 % DDH threshold). The obtained results of polyphasic analysis demonstrate that strain SDRW27T represents a novel species, for which the name Photobacterium obscurum sp. nov. is proposed. The type strain is SDRW27T (=MCCC 1K06286T=KCTC 82892T).

Comparative Genomic Analyses of the Genus Photobacterium Illuminate Biosynthetic Gene Clusters Associated with Antagonism

The genus Photobacterium is known for its ecophysiological versatility encompassing free-living, symbiotic, and pathogenic lifestyles. Photobacterium sp. CCB-ST2H9 was isolated from estuarine sediment collected at Matang Mangrove, Malaysia. In this study, the genome of CCB-ST2H9 was sequenced, and the pan-genome of 37 Photobacterium strains was analysed. Phylogeny based on core genes showed that CCB-ST2H9 clustered with P. galatheae, forming a distinct clade with P. halotolerans, P. salinisoli, and P. arenosum. The core genome of Photobacterium was conserved in housekeeping functions, while the flexible genome was well represented by environmental genes related to energy production and carbohydrate metabolism. Genomic metrics including 16S rRNA sequence similarity, average nucleotide identity, and digital DNA–DNA hybridization values were below the cut-off for species delineation, implying that CCB-ST2H9 potentially represents a new species. Genome mining revealed that biosynthetic gene clusters (BGCs) involved in producing antimicrobial compounds such as holomycin in CCB-ST2H9 could contribute to the antagonistic potential. Furthermore, the EtOAc extract from the culture broth of CCB-ST2H9 exhibited antagonistic activity against Vibrio spp. Intriguingly, clustering based on BGCs profiles grouped P. galatheae, P. halotolerans, P. salinisoli, P. arenosum, and CCB-ST2H9 together in the heatmap by the presence of a large number of BGCs. These BGCs-rich Photobacterium strains represent great potential for bioactive secondary metabolites production and sources for novel compounds.

Exploring the Diversity and Biotechnological Potential of Cultured and Uncultured Coral-Associated Bacteria

Coral-associated microbes are crucial for the biology of their hosts, contributing to nutrient cycling, adaptation, mitigation of toxic compounds, and biological control of pathogens. Natural products from coral-associated micro-organisms (CAM) may possess unique traits. Despite this, the use of CAM for biotechnological purposes has not yet been adequately explored. Here, we investigated the production of commercially important enzymes by 37 strains of bacteria isolated from the coral species Mussismilia braziliensis, Millepora alcicornis, and Porites astreoides. In-vitro enzymatic assays showed that up to 56% of the isolates produced at least one of the seven enzymes screened (lipase, caseinase, keratinase, cellulase, chitinase, amylase, and gelatinase); one strain, identified as Bacillus amyloliquefaciens produced all these enzymes. Additionally, coral species-specific cultured and uncultured microbial communities were identified. The phylum Firmicutes predominated among the isolates, including the genera Exiguobacterium, Bacillus, and Halomonas, among others. Next-generation sequencing and bacteria culturing produced similar but also complementary data, with certain genera detected only by one or the other method. Our results demonstrate the importance of exploring different coral species as sources of specific micro-organisms of biotechnological and industrial interest, at the same time reinforcing the economic and ecological importance of coral reefs as reservoirs of such diversity.

Photobacterium arenosum sp. nov., isolated from marine sediment sand

A Gram-stain-negative, aerobic, motile, short rod-shaped, catalase-negative and oxidase-positive bacterium, strain CAU 1568^T, was isolated from marine sediment sand sampled at Sido Island in the Republic of Korea. The optimum conditions for growth were at 25-30 °C, at pH 6.5-8.5 and with 0-4.0 % (w/v) NaCl. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain CAU 1568^T was a member of the genus Photobacterium with high similarity to Photobacterium salinisoli JCM 30852^T (97.7 %), Photobacterium halotolerans KACC 17089^T (97.3 %) and Photobacterium galatheae LMG F28894^T (97.3 %). The predominant cellular fatty acids were C_16 : 0, summed feature 3 (C_16 : 1  ω6c and/or C_16 : 1  ω7c) and summed feature 8 (C_18 : 1  ω7c and/or C_18 : 1  ω6c), with Q-8 as the major of isoprenoid quinone. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerols, phosphatidylcholine, phosphatidylethanolamine, phospholipid, two aminophospholipids and three unidentified lipids. The whole genome size of strain CAU 1568^T was 4.8 Mb with 50.1 mol% G+C content; including 38 contigs and 4233 protein-coding genes. These taxonomic data support CAU 1568^T as representing a novel Photobacterium species, for which the name Photobacterium arenosum sp. nov. is proposed. The type strain of this novel species is CAU 1568^T (=KCTC 82404^T=MCCC 1K05668^T).

Zoantharia (Cnidaria: Hexacorallia) of the Dutch Caribbean and One New Species of Parazoanthus

Species of the anthozoan order Zoantharia (=Zoanthidea) are common components of subtropical and tropical shallow water coral reefs. Despite a long history of research on their species diversity in the Caribbean, many regions within this sea remain underexamined. One such region is the Dutch Caribbean, including the islands of St. Eustatius, St. Maarten, Saba, Aruba, Bonaire, and Curaçao, as well as the Saba Bank, for which no definitive species list exists. Here, combining examinations of specimens housed in the Naturalis Biodiversity Center collection with new specimens and records from field expeditions, we provide a list of zoantharian species found within the Dutch Caribbean. Our results demonstrate the presence at least 16 described species, including the newly described Parazoanthus atlanticus, and the additional potential presence of up to four undescribed species. These records of new and undescribed species demonstrate that although the zoantharian research history of the Caribbean is long, further discoveries remain to be found. In light of biodiversity loss and increasing anthropogenic pressure on declining coral reefs, documenting the diversity of zoantharians and other coral reef species to provide baseline data takes on a new urgency.

Photobacterium salinisoli sp. nov., isolated from a sulfonylurea herbicide-degrading consortium enriched with saline soil

A Gram-stain-negative, aerobic, motile, rod-shaped bacterium, designated strain LAM9072^T, was isolated from a sample of a sulfonylurea herbicide-degrading consortium enriched with saline soil. The optimal temperature and pH for the growth of strain LAM9072^T were 35 °C and 7.0, respectively. Strain LAM9072^T could grow in the presence of NaCl up to 9 % (w/v). Comparative analysis of the 16S rRNA gene sequences revealed that strain LAM9072^T was closely related to members of the family Vibrionaceae, with the highest similarities to Photobacterium halotolerans MACL01^T (97.7 %) and Photobacterium galatheae S2753^T (97.7 %). Strain LAM9072^T formed a distinct phylogenetic subclade within the genus Photobacterium in the 16S rRNA gene phylogenetic trees. The results of multi-locus sequence analysis revealed a distinct lineage with P. halotolerans MACL01^T as its closest relative. The genomic G+C content was 50.2 mol%. The DNA-DNA hybridization values between strain LAM9072^T and P. halotolerans LMG 22194^T and P. galatheae LMG 28894^T were 41.6 and 22.2 %, respectively. The average nucleotide identity values were 90.9 and 78.8 %, respectively, by comparing the draft genome sequences of strain LAM9072^T and P. halotolerans LMG 22194^T and P. galatheae LMG 28894^T. The major fatty acids were summed feature 3 (C_16 : 1ω6c and/or C_16 : 1ω7c), C_16 : 0 and summed feature 8 (C_18 : 1ω7c and/or C_18 : 1ω6c). Ubiquinone 8 was detected as the predominant respiratory quinone. The main polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, aminophospholipid and four unidentified lipids. Based on its phenotypic characteristics and the results of genotypic analyses, we propose that strain LAM9072^T represents a novel species, for which the name Photobacteriumsalinisoli sp. nov. is proposed. The type strain is LAM9072^T (=ACCC 19961^T=JCM 30852^T).

Virulence properties of three new Photobacterium species affecting cultured fish

AIMS

Several virulence factors of three new Photobacterium species: Photobacterium toruni, Photobacterium malacitanum and Photobacterium andalusiense associated with diseases of cultured redbanded seabream (Pagrus auriga) were studied. The exoenzymatic activities, adherence and cytotoxic capabilities, and iron-uptake mechanisms were determined both in bacterial extracellular products (ECP) and whole bacterial cells. The histopathology damages provoked on redbanded seabream by the ECP was also studied.

METHODS AND RESULTS

The highest exoenzymatic activities of the ECP were alkaline- and acid-phosphatase, phosphohydrolase and lipase. The ECP were strongly lethal for fish at 4-96 h post-inoculation (p.i). Histological changes were evident at 96 hpi of ECP, affecting head kidney, splenic parenchyma and heart. Cytotoxicity assays, on three fish lines and one human cell line, were conducted using whole bacterial cells and their ECP. The new species tested were cytotoxic only for fish cell lines using whole bacterial cells. Bacterial adherence showed an adherence index moderate on CHSE-214 cell line. All strains showed variable haemolytic activity, and were able to grow under iron-limiting conditions, although the CAS reactivitiy was very low. However, all strains produced high amounts of extracelullar citrate that could be used as iron carrier, and use haem as iron source, except the P. toruni strains because a deletion in the genomic region encoding this ability in all Vibrionaceae members.

CONCLUSIONS

The toxic activity of the bacterial ECPs was thermolabile, and not associated with their thermoresistant lipopolysaccharide content. The virulence of the strains tested could not be related to the haemolytic activity. Iron uptake could be based on the use of endogenous citrate as iron carrier and P. toruni lacks the ability to use haem as iron source.

SIGNIFICANCE AND IMPACT OF THE STUDY

The study analyses for the first time the virulence properties of three new species of Photobacterium pathogenic for fish.

Photobacterium chitinilyticum sp. nov., a marine bacterium isolated from seawater at the bottom of the East China Sea

A Gram-stain-negative, facultative aerobic, motile by a polar flagellum, rod-shaped strain, designated BEI247^T, was isolated from seawater at the bottom of the East China Sea. Phylogenetic analysis of the 16S rRNA gene and whole genome data affiliated it with the genus Photobacterium. It was most closely related to Photobacterium alginatilyticum P03D4^T (97.36 % 16S rRNA gene similarity). Multi-locus sequence analysis (MLSA) revealed a distinct lineage with P. alginatilyticum P03D4^T as its closest relative. Strain BEI247^T was found to have lower than 86.0 % similarities to the type strains of its most closely related species in MLSA, less than 82.3 % using genome average nucleotide identities, and less than 25.3 % in DNA-DNA relatedness studies. Growth occurred at 10-37 °C (optimum, 24 °C), pH 5.0-8.0 (pH 7.0) and in the presence of 1-5 % (w/v) NaCl (3 %). The dominant fatty acids were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0. The polar lipids of strain BEI247^T comprised phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, two phospholipids and one unknown lipid. The major respiratory quinone was ubiquinone-8 (Q-8). The DNA G+C content of strain BEI247^T was 46.45 mol%. On the basis of the polyphasic evidence, strain BEI247^T is proposed as representing a novel species of the genus Photobacterium, for which the name Photobacterium chitinilyticum sp. nov. is proposed. The type strain is BEI247^T (=JCM 32689^T=MCCC 1K03517^T=KCTC 62619^T).

Description of New and Amended Clades of the Genus Photobacterium

Phylogenetic relationships between species in the genus Photobacterium have been poorly studied despite pathogenic and ecological relevance of some of its members. This is the first phylogenetic study that includes new species of Photobacterium (validated or not) that have not been included in any of the previously described clades, using 16S rRNA sequences and multilocus sequence analysis (MLSA) in concatenated sequences of gyrB, gapA, topA, ftsZ and mreB housekeeping genes. Sequence analysis has been implemented using Maximum-parsimony (MP), Neighbour-joining (NJ) and Maximum likelihood (ML) treeing methods and the predicted evolutionary relationship between the Photobacterium clades was established on the basis of bootstrap values of >75% for 16S rRNA sequences and MLSA. We have grouped 22 species of the genus Photobacterium into the following 5 clades: Phosphoreum (comprises P. aquimaris, “P. carnosum,” P. iliopiscarium, P. kishitanii, P. phosphoreum, “P. piscicola” and “P. toruni”); clade Profundum (composed of P. aestuarii, P. alginatilyticum, P. frigidiphilum, P. indicum, P. jeanii, P. lipolyticum, “P. marinum,” and P. profundum); clade Damselae (two subspecies of P. damselae, damselae and piscicida); and two new clades: clade Ganghwense (includes P. aphoticum, P. aquae, P. galatheae, P. ganghwense, P. halotolerans, P. panuliri and P. proteolyticum); and clade Leiognathi (composed by P. angustum, P. leiognathi subsp. leiognathi and “P. leiognathi subsp. mandapamensis”). Two additional clades, Rosenbergii and Swingsii, were formed using a phylogenetic method based on 16S rRNA gene, although they are not confirmed by any MLSA methods. Only P. aplysiae could not be included in none of the established clade, constituting an orphan clade.

The biology and the importance of Photobacterium species

Photobacterium species are Gram-negative coccobacilli which are distributed in marine habitats worldwide. Some species are unique because of their capability to produce luminescence. Taxonomically, about 23 species and 2 subspecies are validated to date. Genomes from a few Photobacterium spp. have been sequenced and studied. They are considered a special group of bacteria because some species are capable of producing essential polyunsaturated fatty acids, antibacterial compounds, lipases, esterases and asparaginases. They are also used as biosensors in food and environmental monitoring and detectors of drown victim, as well as an important symbiont.

Photobacterium sanguinicancri sp. nov. isolated from marine animals

Six strains were isolated from the hemolymph of the spider crab Maja brachydactyla, captured in Spain, and one from a diseased blue mussel, Mytilus edulis. The 16S rRNA gene sequences showed close similarity to the recently described Photobacterium swingsii (98.1 %) and to a lesser degree to Photobacterium aquimaris (97.8 %). MLSA analyses showed a monophyletic group including P. swingsii that form a new subclade. All genomic analyses (Average Nucleotide Identity, Average Amino Acid Identity, and in silico DNA-DNA) clearly separate the strains analysed from P. swingsii with values below the thresholds to delimit a new species. The phenotypic, genotypic and genomic data presented here clearly place these strains as a coherent group within the genus Photobacterium, for which we propose the name Photobacterium sanguinicancri sp. nov. Strain CAIM 1827(T) (=CECT 7579(T), =DSM 24670(T)) is proposed as the type strain of the species.

Finding diagnostic phenotypic features of Photobacterium in the genome sequences

Photobacterium species are ubiquitous in the aquatic environment and can be found in association with animal hosts including pathogenic and mutualistic associations. The traditional phenotypic characterization of Photobacterium is expensive, time-consuming and restricted to a limited number of features. An alternative is to infer phenotypic information directly from whole genome sequences. The present study evaluates the usefulness of whole genome sequences as a source of phenotypic information and compares diagnostic phenotypes of the Photobacterium species from the literature with the predicted phenotypes obtained from whole genome sequences. All genes coding for the specific proteins involved in metabolic pathways responsible for positive phenotypes of the seventeen diagnostic features were found in the majority of the Photobacterium genomes. In the Photobacterium species that were negative for a given phenotype, at least one or several genes involved in the respective biochemical pathways were absent.

Vibrio crosai sp. nov., isolated from a cultured oyster Crassostrea gigas

A motile, facultative anaerobic, marine bacterial isolate (CAIM 1437(T)) was obtained from a cultured oyster (Crassostrea gigas) in Sonora, México. The strain was studied by a phylogenetic analysis based on sequences of the 16S rRNA and five housekeeping genes, i.e. ftsZ, gapA, pyrH, recA, and topA. Comparison of the almost-complete 16S rRNA gene sequence with those of other type strains of the genus Vibrio showed a close relationship with the type strains of Vibrio orientalis and Vibrio rotiferianus, with similarity values ranging from 98.4 to 98.3 %, respectively. MLSA placed this strain within the Orientalis clade. The DNA-DNA hybridization value of strain CAIM 1437(T) with V. orientalis was 59 % and with V. rotiferianus 55 %. The DNA G+C content was determined to be 45.6 mol %. Phenotypic characteristics also showed differences with the species analysed. The results presented here support the description of a novel species, for which the name Vibrio crosai sp. nov. is proposed, with CAIM 1437(T) (= DSM 27145(T)) as the type strain.

Photobacterium panuliri sp. nov., an alkalitolerant marine bacterium isolated from eggs of spiny lobster, Panulirus penicillatus from Andaman Sea

A facultative anaerobe, alkalitolerant, gram-negative marine bacterium strain LBS5(T), was isolated from eggs carried on the pleopods of female spiny lobster (Panulirus penicillatus) in Andaman Sea from a depth of 3.5 m. Heterotrophic growth was observed at 15-38 °C and pH 5.5-11. Optimum growth occurred at 28 °C and pH 7.5. It can grow in the presence of 0.5-7 % NaCl (w/v), and the optimal NaCl required for growth was 2-4 %. 16S rRNA gene sequence analysis revealed the strain LBS5(T) belongs to the genus Photobacterium and showed 99.6 % similarity with P. aquae AE6(T), 98.2 % with P. aphoticum M46(T), 97 % with P. rosenbergii CC1(T), 96.9 % with P. lutimaris DF-42(T), and 96.6 % with P. halotolerans MACL01(T). The DNA-DNA similarities between strains LBS5(T) with other closely related strains were well below 70 %. The DNA G + C content was 50.52 (±0.9) mol%. The major fatty acids were C16:1w7c/w6c, C18:1w6c/w7c, C16:0, C15:0 iso, C16:0 10-methyl/17:1 iso w9c, C17:0 iso. Polar lipids included a phosphatidylglycerol, a diphosphatidylglycerol, a phosphatidylethanolamine, and one unidentified lipid. Based on the polyphasic evidences, strain LBS5(T) represents a novel species of the genus Photobacterium for which Photobacterium panuliri sp. nov. is proposed. The type strain is LBS5(T) (=DSM 27646(T) = LMG 27617(T) = JCM 19199(T)).

Photobacterium sanctipauli sp. nov. isolated from bleached Madracis decactis (Scleractinia) in the St Peter & St Paul Archipelago, Mid-Atlantic Ridge, Brazil

Five novel strains of Photobacterium (A-394T, A-373, A-379, A-397 and A-398) were isolated from bleached coral Madracis decactis (scleractinian) in the remote St Peter & St Archipelago (SPSPA), Mid-Atlantic Ridge, Brazil. Healthy M. decactis specimens were also surveyed, but no strains were related to them. The novel isolates formed a distinct lineage based on the 16S rRNA, recA, and rpoA gene sequences analysis. Their closest phylogenetic neighbours were Photobacterium rosenbergii, P. gaetbulicola, and P. lutimaris, sharing 96.6 to 95.8% 16S rRNA gene sequence similarity. The novel species can be differentiated from the closest neighbours by several phenotypic and chemotaxonomic markers. It grows at pH 11, produces tryptophane deaminase, presents the fatty acid C18:0, but lacks C16:0 iso. The whole cell protein profile, based in MALDI-TOF MS, distinguished the strains of the novel species among each other and from the closest neighbors. In addition, we are releasing the whole genome sequence of the type strain. The name Photobacterium sanctipauli sp. nov. is proposed for this taxon. The G + C content of the type strain A-394(T) (= LMG27910(T) = CAIM1892(T)) is 48.2 mol%.

Photobacterium aquae sp. nov., isolated from a recirculating mariculture system

A Gram-staining-negative, heterotrophic, facultatively anaerobic bacterium, designated AE6T, was isolated from a grouper (Epinephelus malabaricas) culture tank in a recirculating mariculture system located in Tianjin, China. Strain AE6T was able to grow at 15–40 °C (optimum, 30–35 °C), at pH 5.5–10.0 (optimum, pH 7.0–7.5) and in the presence of 0.5–7 % (w/v) NaCl (optimum, 2–3 %). It contained Q-8 as the predominant respiratory quinone, phosphatidylethanolamine (PE) and phosphatidylglycerol (PG) as the major polar lipids and C16 : 1ω7c/C16 : 1ω6c (40.4 %), C18 : 1ω7c (15.5 %) and C16 : 0 (13.5 %) as the predominant cellular fatty acids. The genomic DNA G+C content was 47.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain AE6T belonged to the genus Photobacterium (94.2–96.8 % of 16S rRNA gene sequence similarity) and formed a distinct phylogenetic lineage within the genus and exhibited the highest sequence similarity to Photobacterium aphoticum CECT 7614T (96.8 %). Multilocus sequence analysis (MLSA) using four loci (gyrB, rpoA, pyrH and recA) also revealed that strain AE6T was phylogenetically related to the genus Photobacterium . Based on the phylogenetic, chemotaxonomic and phenotypic evidence, strain AE6T is considered to represent a novel species of the genus Photobacterium , for which the name Photobacterium aquae sp. nov. is proposed. The type strain is AE6T ( = CGMCC 1.12159T = JCM 18480T).

Photobacterium aestuarii sp. nov., a marine bacterium isolated from a tidal flat

A Gram-staining-negative, motile, weakly halophilic and facultatively aerobic bacterium, designated strain YA11T, was isolated from tidal flat sediment at Yeongam Bay, South Korea. Strain YA11T grew at 10–30 °C (optimum, 20 °C), at pH 6.0–10.0 (optimum, pH 6.5–7.5) and in the presence of 1–6 % (w/v) NaCl (optimum, 2–3 %). The major cellular fatty acids of the strain were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C16 : 0. The DNA G+C content of the genomic DNA was 44.2 mol%. Strain YA11T contained Q-8 as the sole respiratory quinone. A phylogenetic tree based on 16S rRNA gene sequences showed that strain YA11T formed a distinct phyletic lineage within the genus Photobacterium and the 16S rRNA gene sequence similarities between strain YA11T and the type strains of species of the genus Photobacterium ranged between 94.0 and 96.4 %. Based on the phenotypic, chemotaxonomic and molecular properties, strain YA11T represents a novel species of the genus Photobacterium , for which the name Photobacterium aestuarii sp. nov. is proposed, with strain YA11T( = KACC 16912T = JCM 18592T) as the type strain.

Photobacterium marinum sp. nov., a marine bacterium isolated from a sediment sample from Palk Bay, India

The novel, cream colored, Gram-staining-negative, rod-shaped, motile bacteria, designated strains AK15(T) and AK18, were isolated from sediment samples collected from Palk Bay, India. Both strains were positive for arginine dihydrolase, lysine decarboxylase, oxidase, nitrate reduction and methyl red test. The major fatty acids were C16:0, C18:1 ω7c, C16:1 ω7c and/or C16:1 ω6c and/or iso-C15:0 2-OH (summed feature 3). Polar lipids content of strains AK15(T) and AK18 were found to bephosphatidylethanolamine (PE), two unidentified phospholipids (PL1 and PL2) and three unidentified lipids (L1-L3). The 16S rRNA gene sequence analysis indicated strains AK15(T) and AK18 as the members of the genus Photobacterium and closely related to the type strain Photobacterium jeanii with pair-wise sequence similarity of 96.7%. DNA-DNA hybridization between strain AK15(T) and AK18 showed a relatedness of 87%. Based on data from the current polyphasic study, strains AK15(T) and AK18 are proposed as novel species of the genus Photobacterium, for which the name Photobacterium marinum sp. nov. is proposed. The type strain of Photobacterium marinum is AK15(T) (=MTCC 11066(T)=DSM 25368(T)).

Usefulness of a real-time PCR platform for G+C content and DNA–DNA hybridization estimations in vibrios

The aim of this study was to evaluate the utility of a real-time PCR platform to estimate the DNA G+C content (mol%) and DNA–DNA hybridization (DDH) values in the genus Vibrio. In total, nine vibrio strains were used to determine the relationship between genomic DNA G+C content and T m (°C). The T m and HPLC datasets fit a linear regression curve with a significant correlation coefficient, corroborating that this methodology has a high correlation with the standard methodology based on HPLC (R2 = 0.94). Analysis of 31 pairs of vibrios provided a wide range of ΔT m values, varying between 0.72 and 12.5 °C. Pairs corresponding to strains of the same species or strains from sister species showed the lowest ΔT m values. For instance, the ΔT m of the sister species Vibrio harveyi LMG 4044T and Vibrio campbellii LMG 11216T was 5.2 °C, whereas the ΔT m of Vibrio coralliilyticus LMG 20984T and Vibrio neptunius LMG 20536T was 8.75 °C. The mean ΔT m values corresponding to pairs of strains with DDH values lower than 60 % or higher than 80 % were, respectively, 8.29 and 2.21 °C (significant difference, P<0.01). The high correlation between DDH values obtained in previous studies and the ΔT m values (R2 = 0.7344) indicates that the fluorimetric methodology is a reliable alternative for the estimation of both DNA G+C content and ΔT m in vibrios. We suggest that strains of the same Vibrio species will have less than 4 °C ΔT m. The use of a real-time PCR platform represents a valuable alternative for the development of the taxonomy of vibrios.

Photobacterium atrarenae sp. nov. a novel bacterium isolated from sea sand

The gram-reaction-negative, motile, facultatively anaerobic, catalase-positive, oxidase-positive bacterial strain M3-4(T) was isolated from black sea sand and subjected to a taxonomic study. Cells of strain M3-4(T) have monotrichous flagella, grow optimally at 37°C and at pH 7-8 in the presence of 1-4% (w/v) NaCl and hydrolyze casein, starch and L: -tyrosine. According to phylogenetic analyses using 16S rRNA gene sequences, strain M3-4(T) belongs to the genus Photobacterium and is most closely related to Photobacterium rosenbergii LMG 22223(T) (97.4%) and P. gaetbulicola KCTC 22804(T) (96.6%). The DNA-DNA relatedness value between M3-4(T) and P. rosenbergii LMG 22223(T) was 21.5%. The DNA G+C mol% of strain M3-4(T) was 53.6. The major cellular fatty acid of strain M3-4(T) was a summed feature 3 consisting of C(16:1) ω7c and/or iso-C(15:0) 2-OH (35.0%), followed by C(16:0) (25.4%) and C(18:1)ω7c (16.8%). These data suggest that strain M3-4(T) represents a novel species in genus Photobacterium, for which the name P. atrarenae sp. nov. is proposed. The type strain is M3-4(T) (= KCTC 23265(T) = NCAIM B 02414(T)).

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.