Endozoicomonas numazuensis sp. nov., a gammaproteobacterium isolated from marine sponges, and emended description of the genus Endozoicomonas Kurahashi and Yokota 2007.

Two non-motile, rod-shaped gammaproteobacteria were isolated from marine sponges collected from the coast of Japan at Numazu. The isolates were oxidase- and catalase-positive facultative anaerobes that fermented carbohydrates. They required sodium ions for growth and were slightly halophilic, growing in the presence of 1.0-5.0 % (w/v) NaCl (optimum of 2.0 % NaCl). Under aerobic conditions, the major isoprenoid quinones were ubiquinone-9 and menaquinone-9 and the minor quinones were ubiquinone-8 and menaquinone-8. The major cellular fatty acids were C(18 : 1)ω7c, C(16 : 1)ω7c and C(16 : 0) and the hydroxy acids were C(10 : 0) 3-OH and C(12 : 0) 3-OH. The DNA G+C content was 48.3-48.7 mol%. Phylogenetic analysis of 16S rRNA gene sequences placed the isolates within the radiation of the genus Endozoicomonas in a broad clade of uncultured clones recovered from various marine invertebrates. The isolates exhibited 96.5-96.9 % 16S rRNA gene sequence similarity with Endozoicomonas elysicola MKT110(T) and Endozoicomonas montiporae CL-33(T), with which the isolates formed a monophyletic cluster with 100 % bootstrap support. The phenotypic features (carbohydrate fermentation, quinone system and some major cellular fatty acids) differed from those of members of the genus Endozoicomonas, which are aerobic, produce little or no menaquinone under aerobic conditions and possess different amounts of C(14 : 0) and C(18 : 1)ω7c. Although some phenotypic differences were identified, the isolates should be assigned to the genus Endozoicomonas on the basis of congruity of phylogeny and should be classified as representatives of a novel species, for which the name Endozoicomonas numazuensis sp. nov. is proposed. The type strain is HC50(T) ( = NBRC 108893(T)  = DSM 25634(T)). An emended description of the genus Endozoicomonas is presented.

Tunicatimonas pelagia gen. nov., sp. nov., a novel representative of the family Flammeovirgaceae isolated from a sea anemone by the differential growth screening method.

A Gram-negative, strictly aerobic, reddish-pink pigmented, non-motile, rod-shaped strain designated N5DB8-4(T), was isolated from an orange-striped sea anemone Diadumene lineata by a differential growth screening method. Phylogenetic analyses based on the 16S rRNA gene sequence revealed that the novel isolate was affiliated with the family Flammeovirgaceae of the phylum Bacteroidetes and that it showed highest sequence similarity (89.1%) to Porifericola rhodea N5EA6-3A2B(T). The strain could be differentiated phenotypically from recognized members of the family Flammeovirgaceae. The G+C content of the DNA is 52.6 mol%, the major respiratory quinone is menaquinone 7 (MK-7) and iso-C15:0, C16:1ω5c and iso-C15:1 G (the double-bond position indicated by capital letter is unknown) were the major fatty acids. From the distinct phylogenetic position and combination of genotypic and phenotypic characteristics, the strain represents a novel taxon for which the name Tunicatimonas pelagia gen. nov., sp. nov. is proposed. The type strain of Tunicatimonas pelagia is N5DB8-4(T) (=KCTC 23473(T )= NBRC 107804(T)).

Rubidimonas crustatorum gen. nov., sp. nov., a novel member of the family Saprospiraceae isolated from a marine crustacean.

A strictly aerobic, Gram-negative, reddish-orange pigmented, non-motile and rod-shaped bacterium, designated AK17-053(T) was isolated from a marine crustacean (Squillidae) living on tidal flats on the coast of the Ariake Sea, Nagasaki, Japan. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that the novel isolate could be affiliated with the family Saprospiraceae of the phylum Bacteroidetes and that it showed highest sequence similarity (84%) with Lewinella marina MKG-38(T). The strain could be differentiated phenotypically from recognized members of the family Saprospiraceae. The G+C content of DNA was 55.3 mol%, MK-7 was the major menaquinone and iso-C(15:0) and C(16:1)ω7c were the major fatty acids. On the basis of polyphasic taxonomic studies, it was concluded that strain AK17-053(T) represents a new genus of the family Saprospiraceae. We propose the name Rubidimonas crustatorum gen. nov., sp. nov. for this strain; its type strain is AK17-053(T) (= MBIC08356(T) = NBRC 107717(T)).

Terpenoids produced by actinomycetes: isolation, structural elucidation and biosynthesis of new diterpenes, gifhornenolones A and B from Verrucosispora gifhornensis YM28-088.

New terpenoids named gifhornenolones A (1) and B (2) were isolated from the culture broth of Verrucosispora gifhornensis YM28-088, and their structures were established as hydroxylated isopimaradiene derivatives on the basis of extensive NMR and MS spectral analyses. In addition, a known sesquiterpene compound cyperusol C (3) was isolated. The absolute configuration of 1 was determined by nuclear Overhauser effect spectroscopy (NOESY) and CD spectra as 4R, 5S, 9R, 10S, 13R, and that of 2 was determined by NOESY experiments as 3R, 4R, 5R, 9R, 10S, 13R. Labeling experiments with [1-(13)C]glucose and [U-(13)C(6)]glucose confirmed that the MEP (2-C-methyl-D-erythritol-4-phosphate) pathway was used for the biosynthesis of terpenoids in this organism. 1 showed potent inhibitory activity to the androgen receptor with an IC(50) of 2.8 microg ml(-1).

Haloferula rosea gen. nov., sp. nov., Haloferula harenae sp. nov., Haloferula phyci sp. nov., Haloferula helveola sp. nov. and Haloferula sargassicola sp. nov., five marine representatives of the family Verrucomicrobiaceae within the phylum 'Verrucomicrobia'.

Six Gram-negative, non-motile, rod-shaped, chemoheterotrophic bacteria designated strains YM23-227(T), 06SJR1-1(T), AK18-024(T), 05IJR53-1(T), MN1-1037(T) and MN1-1047 were isolated from various marine environments and subjected to a polyphasic taxonomic study. Preliminary analysis based on 16S rRNA gene sequences revealed that the novel isolates could be affiliated with the family Verrucomicrobiaceae of the phylum 'Verrucomicrobia'. The strains shared approximately 94-100 % sequence similarity with each other and showed less than 94 % similarity with members of the family Verrucomicrobiaceae with validly published names. The DNA-DNA relatedness between strains YM23-227(T) and 06SJR1-1(T) was less than 70 %, a value that is accepted as a phylogenetic definition of a species. The cell wall peptidoglycan of the strains contained muramic acid and meso-diaminopimelic acid. The novel isolates produced carotenoid pigments and squalene. The DNA G+C contents of the six strains were 63-65 mol%. The major menaquinone was MK-9 and iso-C(14 : 0) was the major fatty acid. Based on the evidence from the polyphasic taxonomic study, it was concluded that the six strains should be classified as representing a new genus and five novel species of the family Verrucomicrobiaceae within the phylum 'Verrucomicrobia', for which the names Haloferula rosea gen. nov., sp. nov. (type strain 06SJR1-1(T)=MBIC08340(T)=KCTC 22201(T)), Haloferula harenae sp. nov. (type strain YM23-227(T)=MBIC08299(T)=KCTC 22198(T)), Haloferula phyci sp. nov. (type strain AK18-024(T)=MBIC08341(T)=KCTC 22200(T)), Haloferula helveola sp. nov. (type strain 05IJR53-1(T)=MBIC08342(T)=KCTC 22199(T)) and Haloferula sargassicola sp. nov. (type strain MN1-1037(T)=MBIC08343(T)=KCTC 22202(T)) are proposed.

Psychromonas heitensis sp. nov., a psychrotolerant bacterium isolated from seawater in Japan.

Four bacterial strains, 04HE-4-40, A4I-9, A4I-21 and AK15-027(T), were isolated from Heita Bay off Kamaishi in Japan. Based on 16S rRNA gene sequence analysis, the isolates were placed as a new lineage within the genus Psychromonas. The 16S rRNA gene sequence similarity values between the isolates and type strains of recognized Psychromonas species were less than 97 %. The DNA G+C contents of the isolates were about 38 mol%. The major respiratory quinone was Q-8, and the predominant cellular fatty acids were 16 : 1omega7c and 16 : 0. The isolates were able to grow at 30 degrees C, unlike other Psychromonas species. Based on the results of the phylogenetic analysis and phenotypic characteristics and DNA-DNA hybridization data, the isolates represent a novel species, for which the name Psychromonas heitensis sp. nov. is proposed. The type strain is AK15-027(T) (=MBIC 06898(T)=NCIMB 14416(T)).

Robiginitalea myxolifaciens sp. nov., a novel myxol-producing bacterium isolated from marine sediment, and emended description of the genus Robiginitalea.

A marine, Gram-negative, deep-orange-coloured, rod/coccoid-shaped, strictly aerobic, non-motile, oxidase- and catalase-positive bacterial strain, designated YM6-073(T), was isolated from sediment collected in Okinawa, Japan. Strain YM6-073(T) produced the carotenoid (3R,2'S)-myxol. A phylogenetic analysis based on 16S rRNA gene sequences revealed that strain YM6-073(T) belonged to a distinct lineage in the family Flavobacteriaceae, the closest relative being Robiginitalea biformata HTCC2501(T) (93.7 % sequence similarity). Strain YM6-073(T) could be distinguished from other members of the family Flavobacteriaceae by means of a number of phenotypic characteristics. The DNA G+C content was 50.1 mol%. The predominant cellular fatty acids were iso-C(15 : 0), iso-C(15 : 1)omega10c, iso-C(17 : 0) 3-OH and C(15 : 0,) and menaquinone-6 was the only respiratory quinone. DNA-DNA hybridization between strain YM6-073(T) and R. biformata DSM 15991(T) showed less than 10 % DNA-DNA relatedness. On the basis of phenotypic, genotypic and phylogenetic features, strain YM6-073(T) represents a novel species of the genus Robiginitalea, for which the name Robiginitalea myxolifaciens sp. nov. is proposed. The type strain is YM6-073(T) (=MBIC 06409(T)=KCTC 22216(T)=DSM 21019(T)).

Structural determination and proposed biosynthesis of alcanivorone, a novel alpha-pyrone produced by Alcanivorax jadensis.

A novel alpha-pyrone designated as alcanivorone was found in a culture broth of the marine bacterium, Alcanivorax jadensis, and its structure was determined by an analysis of 1D NMR, 2D NMR and MS data. Alcanivorone was produced by A. jadensis only when sodium pyruvate was added to the culture medium as a carbon source. Incorporation experiments using stable isotope-labeled pyruvate indicated that alcanivorone was biosynthesized from four molecules of pyruvate.

Unnarmicins A and C, new antibacterial depsipeptides produced by marine bacterium Photobacterium sp. MBIC06485.

Two new antibiotic depsipeptides, unnarmicins C (1) and A (2), were isolated from the fermentation broth of a marine bacterium, Photobacterium sp. strain MBIC06485. The structure of 1 was established by spectroscopic studies and chiral analyses of its chemical degradation/conversion products, and that of 2 by comparing its NMR, MS, and CD data with those of 1. Both compounds selectively inhibited the growth of two strains belonging to the genus Pseudovibrio, one of the most prevalent genera in the marine environments within the class Alphaproteobacteria.

Rubritalea squalenifaciens sp. nov., a squalene-producing marine bacterium belonging to subdivision 1 of the phylum 'Verrucomicrobia'.

A taxonomic study was carried out to clarify the status of a Gram-negative, heterotrophic mesophile that was isolated from the marine sponge Halichondria okadai. The strain, designated HOact23(T), was a non-motile, rod-shaped (0.44-0.53x0.65-0.79 microm) bacterium. The strain produced squalene and a red-pink carotenoid pigment. The cell-wall peptidoglycan contained meso-diaminopimelic acid, glutamic acid and alanine. The G+C content of the genomic DNA was 52.4 mol%. The major fatty acids were iso-C(14 : 0) (43.1 %), iso-C(16 : 0) (20.6 %) and anteiso-C(15 : 0) (18.1 %), and the major isoprenoid quinone was MK-9 (90.8 %). Based on 16S rRNA gene sequence data, the strain formed a distinct group within subdivision 1 in the phylum 'Verrucomicrobia'. It showed a range of phenotypic properties that distinguished it from its closest relative, Rubritalea marina Pol012(T) (94.3 % 16S rRNA gene sequence similarity). On the basis of polyphasic taxonomic evidence, it was concluded that strain HOact23(T) should be classified within a novel species in the genus Rubritalea. The name proposed for the taxon is Rubritalea squalenifaciens sp. nov., with the type strain HOact23(T) (=MBIC08254(T)=DSM 18772(T)).

Coraliomargarita akajimensis gen. nov., sp. nov., a novel member of the phylum 'Verrucomicrobia' isolated from seawater in Japan.

An obligately aerobic, Gram-negative, non-spore-forming, non-motile, spherical bacterium, designated strain 04OKA010-24(T), was isolated from seawater surrounding the hard coral Galaxea fascicularis L., collected at Majanohama, Akajima, Japan, and was subjected to a polyphasic taxonomic study. Phylogenetic analyses based on the 16S rRNA gene sequence indicated that the new strain represented a member of the phylum 'Verrucomicrobia' and shared 84-95 % sequence similarity with cultivated strains of 'Verrucomicrobia' subdivision 4. Amino acid analysis of the cell-wall hydrolysate indicated the absence of muramic acid and diaminopimelic acid, which suggested that the strain did not contain peptidoglycan in the cell wall. The G+C content of the DNA was 53.9 mol%. MK-7 was the major menaquinone and C(14 : 0), C(18 : 1)omega9c and C(18 : 0) were the major fatty acids. On the basis of these data, it was concluded that strain 04OKA010-24(T) represents a novel species in a new genus in subdivision 4 of the phylum 'Verrucomicrobia', for which the name Coraliomargarita akajimensis gen. nov., sp. nov. is proposed. The type strain of Coraliomargarita akajimensis is 04OKA010-24(T) (=MBIC06463(T)=IAM 15411(T)=KCTC 12865(T)).

Urukthapelstatin A, a novel cytotoxic substance from marine-derived Mechercharimyces asporophorigenens YM11-542. I. Fermentation, isolation and biological activities.

Urukthapelstatin A, a novel cyclic peptide, was isolated from the cultured mycelia of marine-derived Thermoactinomycetaceae bacterium Mechercharimyces asporophorigenens YM11-542. The peptide was purified by solvent extraction, silica gel chromatography, ODS flash chromatography, and finally by preparative HPLC. Urukthapelstatin A dose-dependently inhibited the growth of human lung cancer A549 cells with an IC(50) value of 12 nM. Urukthapelstatin A also showed potent cytotoxic activity against a human cancer cell line panel.

Smaragdicoccus niigatensis gen. nov., sp. nov., a novel member of the suborder Corynebacterineae.

A polyphasic taxonomic approach was applied to determine the taxonomic position of a hydrocarbon-degrading actinomycete, strain Hou_blueT, which was isolated from soil samples collected from an oil spring in Niigata, Japan. The results of 16S rRNA and gyrB gene sequence comparisons indicated that strain Hou_blueT represented a novel lineage in the suborder Corynebacterineae. Colonies were malachite green-like in colour on 1/10 trypticase soy agar and the cell morphology was coccoid in all growth phases. The cell-wall diamino acid and sugar indicated chemotype IV and variation A1gamma. The sugars of the peptidoglycan were glycolated. The polar lipids were composed of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside and some unspecified glycolipids. The organism contained two novel cyclic forms of menaquinone, smaragdiquinone A-8(H4, omega-cycl) and smaragdiquinone B-8(H4, dicycl). The major fatty acids were cis-9-18 : 1 (34.46 %) and 16 : 0 (25.1 %). Small amounts of 10-methyl-branched fatty acids were also present (10-methyl-17 : 0, 0.17 %), but not tuberculostearic acid (10-methyl-18 : 0), which has been shown to be present in all nocardiae. Gas-chromatographic analysis of the mycolic acid revealed a carbon-chain length of C43-C49. The DNA G+C content was 63.7 mol%. On the basis of phenotypic and phylogenetic distinctness, the organism is proposed to represent a novel genus and species, Smaragdicoccus niigatensis gen. nov., sp. nov., with the type strain Hou_blueT (=MBIC 06267T=DSM 44881T).

Rare carotenoids, (3R)-saproxanthin and (3R,2'S)-myxol, isolated from novel marine bacteria (Flavobacteriaceae) and their antioxidative activities.

We isolated three orange or yellow pigment-producing marine bacteria, strains 04OKA-13-27 (MBIC08261), 04OKA-17-12 (MBIC08260), and YM6-073 (MBIC06409), off the coast of Okinawa Prefecture in Japan. These strains were classified as novel species of the family Flavobacteriaceae based on their 16S rRNA gene sequence. They were cultured, and the major carotenoids produced were purified by chromatographic methods. Their structures were determined by spectral data to be (3R)-saproxanthin (strain 04OKA-13-27), (3R,2'S)-myxol (strain YM6-073), and (3R,3'R)-zeaxanthin (strains YM6-073 and 04OKA-17-12). Saproxanthin and myxol, which are monocyclic carotenoids rarely found in nature, demonstrated significant antioxidative activities against lipid peroxidation in the rat brain homogenate model and a neuro-protective effect from L-glutamate toxicity.

Mechercharimyces mesophilus gen. nov., sp. nov. and Mechercharimyces asporophorigenens sp. nov., antitumour substance-producing marine bacteria, and description of Thermoactinomycetaceae fam. nov.

A study was carried out to clarify the taxonomy of four Gram-positive, heterotrophic mesophiles isolated from marine lakes in the Republic of Palau. The strains, designated YM3-251(T), YM3-653, YM3-671 and YM11-542(T), formed aerial and substrate mycelia. The cell-wall peptidoglycan contained meso-diaminopimelic acid, glutamic acid and alanine. The G+C content of their genomic DNA was approximately 45 mol%. The major fatty acid was iso-C(15 : 0) and the major isoprenoid quinone was MK-9. The strains formed a distinct group in the 16S rRNA gene tree and shared a range of phenotypic properties that distinguished them from members of related genera in Thermoactinomycetaceae fam. nov. The name proposed to accommodate the new isolates is Mechercharimyces gen. nov., comprising two species based on genotypic and phenotypic criteria, including comparative gyrB and DNA-DNA relatedness data. The names proposed for these taxa are Mechercharimyces mesophilus sp. nov., the type species, and Mechercharimyces asporophorigenens sp. nov., with the type strains YM3-251(T) (=MBIC06230(T)=DSM 44894(T)) and YM11-542(T) (=MBIC06487(T)=DSM 44955(T)), respectively.

Ferrimonas marina sp. nov.

A novel Ferrimonas species is described on the basis of phenotypic, chemotaxonomic and phylogenetic studies. Four halophilic organisms were isolated from marine sand and marine macroalgae samples by using high-pH marine agar 2216. An analysis of the nearly complete 16S rRNA gene sequences of these new isolates indicated that they were phylogenetically close (16S rRNA gene sequence similarity >99.5%, gyrB gene sequence similarity >97.8%), and were most closely related to Ferrimonas balearica (16S rRNA gene sequence similarity 97.1-97.3%, gyrB gene sequence similarity 84.4-85.0%). Chemotaxonomic data (major menaquinone MK7; major fatty acids C(16:0) and C(18:1)omega9c) supported the affiliation of the new isolates to the genus Ferrimonas. The results of physiological and biochemical tests allowed phenotypic differentiation of the isolates from F. balearica. It is therefore proposed that the new isolates represent a novel species with the name Ferrimonas marina sp. nov. and type strain A4D-4(T) (=MBIC06480(T)=DSM 16917(T)).