Identification of a novel monocyclic carotenoid and prediction of its biosynthetic genes in Algoriphagus sp. oki45.

Bacteria belonging to the genus Algoriphagus have been isolated from various sources, such as Antarctic sea ice, seawater, and sediment, and some strains are known to produce orange to red pigments. However, the pigment composition and biosynthetic genes have not been fully elucidated. A new red-pigmented Algoriphagus sp. strain, oki45, was isolated from the surface of seaweed collected from Senaga-Jima Island, Okinawa, Japan. Genome comparison revealed oki45's average nucleotide identity of less than 95% to its closely related species, Algoriphagus confluentis NBRC 111222 T and Algoriphagus taiwanensis JCM 19755 T. Comprehensive chemical analyses of oki45's pigments, including 1H and 13C nuclear magnetic resonance and circular dichroism spectroscopy, revealed that the pigments were mixtures of monocyclic carotenoids, (3S)-flexixanthin ((3S)-3,1'-dihydroxy-3',4'-didehydro-1',2'-dihydro-ß,ψ-caroten-4-one) and (2R,3S)-2-hydroxyflexixanthin ((2R,3S)-2,3,1'-trihydroxy-3',4'-didehydro-1',2'-dihydro-ß,ψ-caroten-4-one); in particular, the latter compound was new and not previously reported. Both monocyclic carotenoids were also found in A. confluentis NBRC 111222 T and A. taiwanensis JCM 19755 T. Further genome comparisons of carotenoid biosynthetic genes revealed the presence of eight genes (crtE, crtB, crtI, cruF, crtD, crtYcd, crtW, and crtZ) for flexixanthin biosynthesis. In addition, a crtG homolog gene encoding 2,2'-ß-hydroxylase was found in the genome of the strains oki45, A. confluentis NBRC 111222 T, and A. taiwanensis JCM 19755 T, suggesting that the gene is involved in 2-hydroxyflexixanthin synthesis via 2-hydroxylation of flexixanthin. These findings expand our knowledge of monocyclic carotenoid biosynthesis in Algoriphagus bacteria. KEY POINTS: • Algoriphagus sp. strain oki45 was isolated from seaweed collected in Okinawa, Japan. • A novel monocyclic carotenoid 2-hydroxyflexixanthin was identified from strain oki45. • Nine genes for 2-hydroxyflexixanthin biosynthesis were found in strain oki45 genome.

Robiginitalea aurantiaca sp. nov. and Algoriphagus sediminis sp. nov., isolated from coastal sediment.

Two novel rod-shaped, Gram-stain-negative, aerobic and non-motile bacterial strains, designated M39T and C2-7T, were isolated from the coastal sediment of Xiaoshi Island, Weihai, PR China. Growth of strain M39T occurred at 15-37 °C, at pH 6.0-9.0 and in the presence of 1.0-9.0 % (w/v) NaCl. Strain C2-7T grew at 15-40 °C, at pH 6.0-8.0 and in the presence of 0.5-8.0 % (w/v) NaCl. Phylogenetic analysis based 16S rRNA gene sequences revealed that strains M39T and C2-7T belong to the phylum Bacteroidota. Based on the results of 16S rRNA gene sequence analysis, the closest relative of strain M39T was Robiginitalea marina KCTC 92035T (95.4 %), and the closest relative of strain C2-7T was Algoriphagus namhaensis DPG-3T (97.0 %). The percentage of conserved protein and average nucleotide identity values between strain M39T and some species of the genus Robiginitalea were 66.9-77.6% and 69.3-71.0 %, respectively, while those between strain C2-7T and some species of the genus Algoriphagus were 68.0-70.1% and 56.1-72.6 %, respectively. The major cellular fatty acids (>10 %) of strain M39T consisted of iso-C15 : 1 F, iso-C15 : 0 and iso-C17 : 0 3-OH, while those of strain C2-7T were iso-C15 : 0 and C16 : 1 ω7c/C16 : 1 ω6c. MK-6 was the only respiratory quinone that was compatible with the genus of strain M39T. The predominant menaquinone of strain C2-7T was MK-7. The major polar lipids of strain M39T were phosphatidylethanolamine and glycolipids, and those of strain C2-7T were phosphatidylethanolamine, one unidentified aminolipid and four unidentified lipids. The DNA G+C contents of strains M39T and C2-7T were 46.9 and 40.8 mol%, respectively. Based upon the results presented in this study, strains M39T and C2-7T represent novel species of the genera Robiginitalea and Algoriphagus, respectively, for which the names Robiginitalea aurantiaca sp. nov. and Algoriphagus sediminis sp. nov. are proposed with the type strains M39T (=MCCC 1H00498T=KCTC 92014T) and C2-7T (=MCCC 1H00414T=KCTC 92027T).

Algoriphagus algorifonticola sp. nov., a marine bacterium isolated from cold spring area of South China Sea.

A Gram-stain-negative, aerobic, non-motile, short-rod-shaped bacterium, designated strain hg1T, was isolated from marine sediment within the cold spring area of South China Sea and subjected to a polyphasic taxonomic investigation. Colonies were circular and 1.0-2.0 mm in diameter, coral in colour, convex and smooth after growth on marine agar at 28 °C for 3 days. Strain hg1T was found to grow at 4-40 °C (optimum, 35-37 °C), at pH 6.5-9.0 (optimum, pH 7.5) and with 0-8 % (w/v) NaCl (optimum, 1.5-2 %). Chemotaxonomic analysis showed the sole respiratory quinone was MK-7, and the principal fatty acids are iso-C15 : 0, summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), and iso-C16 : 0. The major polar lipids are phosphatidylethanolamine, an unidentified phospholipid and five unidentified glycolipids. The DNA G+C content of strain hg1T was 39.6 mol% based on the genome sequence. The comparison of 16S rRNA gene sequence similarities showed that hg1T was closely related to Algoriphagus ornithinivorans DSM 15282T (98.6 % sequence similarity), Algoriphagus zhangzhouensis MCCC 1F01099T (97.9 %) and Algoriphagus vanfongensis DSM 17529T (97.2 %); it exhibited 97.0 % or less sequence similarity to the type strains of other species of the genus Algoriphagus with validly published names. Phylogenetic trees reconstructed with the neighbour-joining, maximum-parsimony and maximum-likelihood methods based on 16S rRNA gene sequences showed that strain hg1T constituted a separate branch with A. ornithinivorans, A. zhangzhouensis, A. vanfongensis in a clade of the genus Algoriphagus. OrthoANI values between strain hg1T and A. ornithinivorans, A. zhangzhouensis and A. vanfongensis were 94.3, 74.1, 73.2 %, respectively, and in silico DNA-DNA hybridization values were 56.2, 18.5 and 18.3 %, respectively. Differential phenotypic properties, together with phylogenetic distinctiveness, demonstrated that strain hg1T is clearly distinct from recognized species of genus Algoriphagus. On the basis of these features, we propose that strain hg1T (=MCCC 1K03570T=KCTC 72111T) represents a novel species of the genus Algoriphagus with the name Algoriphagus algorifonticola sp. nov.

Algoriphagus pacificus sp. nov. and Algoriphagus oliviformis sp. nov., isolated from a mariculture fishpond.

Two Gram-stain-negative, catalase-positive, oxidase-negative, rod-shaped, non-flagellated, non-spore-forming and non-motile strains (YJ13CT and H41T) were isolated from a mariculture fishpond in PR China. Comparisons based on 16S rRNA gene sequences indicated that YJ13CT and H41T shared 16S rRNA gene sequences similarities between 92.6 and 99.2 % with species of the genus Algoriphagus. YJ13CT only shared 93.8 % 16S rRNA gene sequence similarity with H41T. The reconstructed phylogenetic and phylogenomic trees indicated that YJ13CT and H41T clustered closely with species of the genus Algoriphagus. The calculated pairwise orthologous average nucleotide identity with usearch (OrthoANIu) values between strains YJ13CT and H41T and other related strains were all less than 79.5 %. The OrthoANIu value between YJ13CT and H41T was only 69.9 %. MK-7 was the predominant respiratory quinone of YJ13CT and H41T and their major cellular fatty acids contained iso-C15 : 0, C16 : 1 ω7c and C17 : 1 ω9c. The polar lipids profiles of YJ13CT and H41T consisted of phosphatidylethanolamine and several kinds of unidentified lipids. Combining the above descriptions, strains YJ13CT and H41T represent two distinct novel species of the genus Algoriphagus, for which the names Algoriphagus pacificus sp. nov. (type strain YJ13CT=GDMCC 1.2178T=KCTC 82450T) and Algoriphagus oliviformis sp. nov. (type strain H41T=GDMCC 1.2179T=KCTC 82451T) are proposed.

Algoriphagus kandeliae sp. nov., isolated from mangrove rhizosphere soil.

Strain XY-J91T, a Gram-stain-negative, reddish orange, non-spore-forming and short-rod-shaped marine bacterium, was isolated from rhizosphere soil of the mangrove plant Kandelia candel (L.) Druce in Mai Po Nature Reserve, Hong Kong. The strain showed growth at 15-50 °C (optimum 40 °C), at pH 5.5-9.5 (optimum 7.0-8.0) and with 0-8 % (w/v) NaCl (optimum 1-2 %). The only respiratory quinone was MK-7 and the major fatty acids were iso-C15 : 0 and iso-C17 : 0 3-OH. The major polar lipids were phosphatidylethanolamine, an unidentified aminolipid and an unidentified phospholipid. The G+C content of strain XY-J91T was 40.4 mol%. Strain XY-J91T exhibited highest 16S rRNA gene sequence similarities to the type strains of Algoriphagus marincola SW-2T (96.66 %), Algoriphagus taiwanensis CC-PR-82T (96.21%), Algoriphagus ornithinivorans JC2052T (96.16%), Algoriphagus confluentis HJM-2T (95.73%) and Algoriphagus zhangzhouensis 12C11T (95.52 %). Based on the phylogenetic, phenotypic and chemotaxonomic evidence presented, strain XY-J91T represents a novel species of the genus Algoriphagus, for which the name Algoriphagus kandeliae sp. nov. is proposed. The type strain is XY-J91T (=MCCC 1K03612T=KCTC 72216T).

Algoriphagus lacus sp. nov., isolated from a freshwater lake.

A Gram-stain-negative, non-motile, rod-shaped, oxidase-positive, red-pigmented bacterium, strain N3T, was isolated from Fuxian lake, a freshwater lake in Yunnan Province, PR China. Strain N3T was facultatively anaerobic, heterotrophic and negative for catalase. Optimal growth occurred at 30 °C (range 4-45 °C), pH 7.0-8.0 (range 6.5-9.5) and in the presence of 0-3 % (w/v) NaCl (range 0-3 %). The results of phylogenetic analysis based on 16S rRNA gene sequencing revealed that strain N3T was close to the type strains of Algoriphagus aquaeductus, Algoriphagus shivajiensis and Algoriphagus alkaliphilus with sequence similarities of 97.4, 97.3 and 97.2 % respectively. The G+C content of the genomic DNA was 43.9 mol%. The quinone system contained menaquinone MK-7 as the sole component. The major fatty acids were iso-C15 : 0, summed feature 9 (10-methyl C16 : 0 and/or iso-C17 : 1 ω9c), summed feature 3 (C16 : 1 ω6c and/or C16 : 1 ω 7c) and iso-C16 : 0. Major polar lipids were phosphatidylcholine, phosphatidylethanolamine, an unidentified glycolipid, one unidentified phospholipid, two unidentified aminolipids and four unidentified lipids. On the basis of physiological, chemotaxonomic and molecular properties as well as phylogenetic distinctiveness, strain N3T should be placed into the genus Algoriphagus as a novel species, for which the name Algoriphagus lacus sp. nov. is proposed. The type strain is N3T (=KCTC 62622T=MCCC 1H00308T).

Algoriphagus aquimaris sp. nov., isolated from seashore sand.

Strain F21T, a marine, aerobic, Gram-negative, rod-shaped bacterium, was isolated from seashore sand sampled in Pohang, Republic of Korea. Cells of strain F21T were non-motile, catalase-positive, oxidase-positive, non-spore-forming and formed pinkish-red colonies on marine agar. The strain grew optimally at 37°C, pH 7 and in the presence of 2-3 % NaCl (w/v). Analysis of the 16S rRNA gene sequence of strain F21T revealed that it belonged to the genus Algoriphagus, family Cyclobacteriaceae, with similarity values of 98.1 and 96.8 % to Algoriphagus marincola DSM 16067T and Algoriphagus ornithinivorans IMSNU 14014T, respectively. When comparing the genome sequence of F21 T with those of the type strains of six species of the genus Algoriphagus, the values obtained were below the thresholds for analyses of average nucleotide identity (71.8-92.7 %) and in silico DNA-DNA hybridization using the Genome-to-Genome Distance Calculator (14.7-75.2 %). The DNA G+C content of strain F21T was 42.0 mol%. The chemotaxonomic characteristics of F21T included MK-7 as the predominant isoprenoid quinone, iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c) as major cellular fatty acids, and phosphatidylcholine and phosphatidylethanolamine as major polar lipids. On the basis of phenotypic and chemotaxonomic properties, phylogenetic distinctiveness, and genomic data, we named strain F21T as Algoriphagus aquimaris sp. nov. and proposed that strain F21T (=KEMB 2250-007T= KCTC 72106T=JCM 33187T) in the genus Algoriphagus represents a novel species.

Algoriphagus litoralis sp. nov., isolated from the junction between the ocean and a freshwater lake.

A Gram-stain negative, non-motile and short rod shaped bacterium, designated strain DSL-12T, was isolated from seawater of the East China Sea and characterised phylogenetically and phenotypically. Optimal growth was found to occur at 28 °C (range 4-40 °C), pH 7 (range 6-12) and with 3% (w/v) NaCl (range 0-8%). Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain DSL-12T is related to members of the genus Algoriphagus and shares high sequence similarities with Algoriphagus boritolerans DSM 17298T (97.6%) and Algoriphagus alkaliphilus DSM 22703T (97.6%). The 16S rRNA gene sequence identities between strain DSL-12T and other current members of the genus Algoriphagus were below 96.4%. The digital DNA-DNA hybridization values between strain DSL-12T and the type strains A. boritolerans DSM 17298T and A. alkaliphilus DSM 22703T were found to be 21.2 ± 2.4% and 20.2 ± 2.4%, respectively. The average nucleotide identity (ANI) values between strain DSL-12T and A. boritolerans DSM 17298T and A. alkaliphilus DSM 22703T were found to be 83.2% and 82.8%, respectively. The sole respiratory quinone was identified as MK-7. The major polar lipids were identified as phosphatidylethanolamine, diphosphatidylglycerol, one unidentified phospholipid and two unidentified lipids. The major fatty acids identified as were iso-C15:0, summed feature 8 (C18:1ω7c and/or C18:1ω6c), C16:0, summed feature 3 (C16:1ω7c and/or C16:1ω6c) and iso-C17:0. The G+C content of the genomic DNA was determined to be 43.3 mol%. The combined genotypic and phenotypic data indicate that strain DSL-12T represents a novel species of the genus Algoriphagus, for which the name Algoriphagus litoralis sp. nov. is proposed, with the type strain DSL-12T (= KCTC 62647T = MCCC 1K03536T).

Algoriphagus formosus sp. nov., isolated from coastal sediment.

A Gram-stain negative, facultative anaerobic, non-motile, strongly orange-pigmented and rod-shaped bacterium, designated XAY3209T, was isolated from a marine sediment sample collected from the coast of Weihai, China. Strain XAY3209T was found to grow optimally at 30 °C, at pH 7.0 and in the presence of 2.0% (w/v) NaCl. Its genomic DNA G+C content was 41.9 mol%. On the basis of 16S rRNA gene sequence similarity, the novel isolate belongs to the family Cyclobacteriaceae and is related to the genus Algoriphagus. It shares 98.1% 16S rRNA sequence identity with Algoriphagus marincola, its close phylogenetic relative, but did not show similarities more than 97% with other members of the genus Algoriphagus with validly published names. It contained menaquinone-7 (MK-7) as the sole respiratory quinone, iso-C15:0, iso-C17:1 ω9c and Summed feature 3 (C16:1 ω7c and/or iso-C15:0 2-OH) as the major fatty acids. The major polar lipids were phosphatidylethanolamine, one unidentified aminolipid, one unidentified phospholipid and five unidentified lipids. Results of physiological experiments, biochemical tests and genome average nucleotide identity value (with A. marincola MCCC 1F01203T) indicate that strain XAY3209T is genetically and phenotypically distinct from the species of the genus Algoriphagus with validly published names. Strain XAY3209T therefore represents a novel species, for which the name Algoriphagus formosus sp. nov. is proposed. The type strain is XAY3209T (= KCTC 52842T = MCCC 1H00189T).

Algoriphagus marisflavi sp. nov., isolated from water of an estuary environment.

A Gram-stain-negative, non-motile, aerobic and rod-shaped or ovoid bacterial strain, designated KEM-106T, was isolated from water of an estuary environment on the Yellow Sea, South Korea, and subjected to a polyphasic taxonomic study. Strain KEM-106T grew optimally at 30 °C and pH 7.0-8.0 and in the presence of 1.0-2.0 % (w/v) NaCl. Phylogenetic trees based on 16S rRNA gene sequences revealed that strain KEM-106T belonged to the genus Algoriphagus, clustering with the type strains of Algoriphagus litorisediminis and Algoriphagus aquaemixtae. Strain KEM-106T exhibited 16S rRNA gene sequence similarities of 96.5, 96.2 and 96.0 % to the type strains of Algoriphagus boritolerans, A. litorisediminis and A. aquaemixtae, respectively, and of 92.5-95.8 % to the type strains of the other Algoriphagus species. Strain KEM-106T contained MK-7 as the predominant menaquinone and iso-C15 : 0 and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) as the major fatty acids. The major polar lipids were phosphatidylethanolamine and phosphatidylcholine. The DNA G+C content of strain KEM-106T was 42.7 mol%. Differential phenotypic properties, together with its phylogenetic distinctiveness, revealed that strain KEM-106T is separated from recognized species of the genus Algoriphagus. On the basis of the data presented, strain KEM-106T is considered to represent a novel species of the genus Algoriphagus, for which the name Algoriphagus marisflavi sp. nov. is proposed. The type strain is KEM-106T (=KCTC 52979T=NBRC 112904T).

Genome sequences of Vibrio diabolicus and Algoriphagus sp. isolated from the San Elijo coastal lagoons in San Diego.

We report two draft genome sequences related to the genera Vibrio and Algoriphagus, isolated from water samples at the San Elijo Lagoon Ecological Reserve, which is one of the largest remaining coastal wetlands in San Diego, California. The initial whole genome-based comparison illustrates the uniqueness of these species.

Enhancing the Thermotolerance of Isochrysis zhangjiangensis Through Co-culturing With Algoriphagus marincola.

Isochrysis zhangjiangensis is an important microalgal species used as bait in aquaculture. However, its optimal cultivation temperature is around 25 °C, limiting its use in summer when temperature is higher. To overcome this limitation, we aimed to develop a consortia of I. zhangjiangensis and bacteria that are more resistant to heat stress. Here, six thermotolerance-promoting bacterial strains were isolated from the culture of a heat-tolerant mutant strain of I. zhangjiangensis (IM), and identified as Algoriphagus marincola, Nocardioides sp., Pseudidiomarina sp., Labrenzia alba, Nitratireductor sp., and Staphylococcus haemolyticus. Further, co-culturing I. zhangjiangensis with A. marincola under high temperature conditions increased cell density, chlorophyll a, PSII maximum photochemical efficiency (Fv/Fm), and soluble protein content of microalgae. The presence of A. marincola positively influenced the activities of superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), and total antioxidant capacity (T-AOC) in I. zhangjiangensis cells, while concurrently reducing the levels of reactive oxygen species (ROS). Additionally, gene expression studies confirmed that co-culturing with A. marincola upregulated the expression of antioxidant-related genes (sod and pod) and stress tolerance genes (heat shock protein genes). Our findings indicate that A. marincola effectively helps I. zhangjiangensis withstand high temperature stress, leading to improved yield of microalgae during high temperature conditions. The thermotolerance-promoting bacteria can be exploited as potential inoculants for enhancing the productivity and sustainability of bait microalgae in aquaculture.

Genomic insight into Algoriphagus limi sp. nov. isolated from a mudflat on the Yellow Sea coast.

A Gram-negative, non-motile, and reddish-orange colored bacterium, designated CAU 1643T, was isolated from a mudflat collected in Ganghwa Island, Republic of Korea. The bacterium was found to grow optimally at 30°C, pH 9.0-9.5, and with 0%-1% (w/v) NaCl. The highest 16S rRNA gene sequence similarities to the bacterium were Algoriphagus kandeliae XY-J91T (97.9%), A. aquimaris F21T (97.1%), A. formosus XAY3209T (97.0%), and A. marincola DSM 16067T (96.2%). The DNA G + C content of the type strain was 40.35 mol%. The average nucleotide identity and digital DNA-DNA hybridization values between strain CAU 1643T and the reference strains were below the threshold value for species demarcation. The predominant cellular fatty acids were iso-C15:0, iso-C17:0 3-OH, and Summed Feature 9. The major respiratory quinone was menaquinone-7. The genome showed three putative biosynthetic gene clusters that are responsible for different secondary metabolites. Moreover, CAU 1643T contains 72 genes that encode carbohydrate-active enzymes. Based on phenotypic, phylogenetic, and chemotaxonomic evidence, strain CAU 1643T represents novel species in the genus Algoriphagus, for which the name A. limi sp. nov. is proposed. The type strain is CAU 1643T ( = KCTC 92080T, = MCCC 1K07150T).

Complete genome sequence of a nitrate reducing bacteria, Algoriphagus sp. Y33 isolated from the water of the Indian Ocean.

Algoriphagus sp. Y33, is a nitrate-reducing bacterium isolated from the water of Indian Ocean. Here, we present the complete genome sequence of strain Y33. The genome has one circular chromosome of 6,378,979 bp, with an average GC content of 41.86%, and 5757 coding sequences. According to the annotation analysis, strain Y33 encodes 32 proteins related to nitrogen metabolism. To our knowledge, this is the first report of Algoriphagus sp. isolated from the Indian Ocean with the capacity of nitrate reduction, which will provide insights into regulatory mechanisms of nitrate uptake by heterotrophic bacteria and the global nitrogen cycling.

Molecular clue links bacteria to the origin of animals.

Bacteria have a role in the formation of colonies by a species of single-celled organisms whose ancestors gave rise to the animals, which suggests that bacteria might also have influenced the origin of multicellularity in animals.

A bacterial sulfonolipid triggers multicellular development in the closest living relatives of animals.

Bacterially-produced small molecules exert profound influences on animal health, morphogenesis, and evolution through poorly understood mechanisms. In one of the closest living relatives of animals, the choanoflagellate Salpingoeca rosetta, we find that rosette colony development is induced by the prey bacterium Algoriphagus machipongonensis and its close relatives in the Bacteroidetes phylum. Here we show that a rosette inducing factor (RIF-1) produced by A. machipongonensis belongs to the small class of sulfonolipids, obscure relatives of the better known sphingolipids that play important roles in signal transmission in plants, animals, and fungi. RIF-1 has extraordinary potency (femtomolar, or 10(-15) M) and S. rosetta can respond to it over a broad dynamic range-nine orders of magnitude. This study provides a prototypical example of bacterial sulfonolipids triggering eukaryotic morphogenesis and suggests molecular mechanisms through which bacteria may have contributed to the evolution of animals.DOI:http://dx.doi.org/10.7554/eLife.00013.001.