Major Hydroxy Fatty Acid Research Articles

Sphingomonas molluscorum sp. nov., a novel marine isolate with antimicrobial activity

An aerobic, Gram-negative, yellow-pigmented, non-motile bacterium, designated strain KMM 3882T, was isolated from a marine bivalve (Anadara broughtoni) collected from Peter the Great Bay, Sea of Japan, and was subjected to phenotypic and phylogenetic analyses. Strain KMM 3882T was found to exert a remarkable inhibitory activity against a number of Gram-positive micro-organisms. Phylogenetic analysis based on 16S rRNA gene sequences placed strain KMM 3882T within the genus Sphingomonas, as an independent lineage adjacent to Sphingomonas dokdonensis DS-4T and Sphingomonas panni DSM 15761T. Strain KMM 3882T showed the highest 16S rRNA gene sequence similarity to Sphingomonas dokdonensis DS-4T (97.3 %); similarities of 96.5-96.7 % were obtained with Sphingomonas pituitosa DSM 13101T, Sphingomonas azotifigens NBRC 15497T, Sphingomonas asaccharolytica NBRC 15499T, Sphingomonas trueperi DSM 7225T and Sphingomonas panni DSM 15761T. Chemotaxonomically, strain KMM 3882T contained sphingoglycolipid, C(16 : 0) and C(18 : 1) as predominant fatty acids and 2-OH C(14 : 0) as a major 2-hydroxy fatty acid, confirming the affiliation of strain KMM 3882T with the genus Sphingomonas. On the basis of phylogenetic analysis, DNA-DNA hybridization and physiological and biochemical characterization, strain KMM 3882T should be classified as representing a novel species of the genus Sphingomonas, for which the name Sphingomonas molluscorum sp. nov. is proposed. The type strain is KMM 3882T (=An 18T=NRIC 0685T=JCM 14122T=CIP 109223T).

Description of Sphingobium fuliginis sp. nov., a phenanthrene-degrading bacterium from a fly ash dumping site, and reclassification of Sphingomonas cloacae as Sphingobium cloacae comb. nov.

A phenanthrene-degrading bacterium, strain TKP(T), was isolated from a fly ash dumping site of the thermal power plant in Panki, Kanpur, India, by an enrichment culture method using phenanthrene as the sole source of carbon and energy. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain belonged to the genus Sphingobium, as it showed highest sequence similarity to Sphingobium herbicidovorans DSM 11019(T) (97.3 %) and Sphingomonas cloacae JCM 10874(T) (96.5 %), compared with only 91-93 % similarity to members of other genera such as Sphingomonas sensu stricto, Novosphingobium, Sphingopyxis and Sphingosinicella. In DNA-DNA hybridization experiments with strains that were closely related phylogenetically and in terms of 16S rRNA gene sequences, i.e. Sphingobium herbicidovorans DSM 11019(T) and Sphingomonas cloacae JCM 10874(T), strain TKP(T) showed less than 70 % relatedness. Strain TKP(T) contained sphingoglycolipids SGL-1 and SGL-2 and 18 : 1omega7c as the predominant fatty acid, with 16 : 0 as a minor component and 14 : 0 2-OH as the major 2-hydroxy fatty acid. Thus, phylogenetic analysis, DNA-DNA hybridization, fatty acid and polar lipid profiles and differences in physiological and morphological features from the most closely related members of the Sphingobium group showed that strain TKP(T) represents a distinct species of Sphingobium. The name Sphingobium fuliginis sp. nov. is proposed, with the type strain TKP(T) (=MTCC 7295(T)=CCM 7327(T)). Sphingomonas cloacae JCM 10874(T) formed a coherent cluster with members of Sphingobium, did not reduce nitrate to nitrite and had a fatty acid profile similar to those of Sphingobium species; hence Sphingomonas cloacae should be transferred to the genus Sphingobium as Sphingobium cloacae comb. nov., with the type strain JCM 10874(T) (=DSM 14926(T)).

Dyella yeojuensis sp. nov., isolated from greenhouse soil in Korea

A novel strain, R2A16-10(T), was isolated from greenhouse soil in Yeoju, Korea. The taxonomy of strain R2A16-10(T) was studied by using polyphasic methods. On the basis of 16S rRNA gene sequence analyses, strain R2A16-10(T) was found to be phylogenetically related to type strains of Dyella species (96.7-96.9 %), Frateuria aurantia DSM 6220(T) (96.5 %), Fulvimonas soli LMG 19981(T) (96.3 %) and Rhodanobacter species (94.9-95.7 %). Strain R2A16-10(T), which produced yellow-coloured colonies, was Gram-negative, rod-shaped (0.3-0.4x1.5-3.5 mum) and motile. The predominant fatty acids were 17 : 1 iso omega9c (25.5 %), 15 : 0 iso (18.7 %) and 17 : 0 iso (14.6 %), and the major hydroxy fatty acids were 11 : 0 iso 3-OH (5.0 %), 13 : 0 iso 3-OH (3.4 %) and 17 : 0 iso 3-OH (1.0 %). The major isoprenoid quinone was Q-8. The G+C content of the DNA of the type strain was 63.0 mol%. On the basis of the data from this study, strain R2A16-10(T) represents a novel species of the genus Dyella, for which the name Dyella yeojuensis sp. nov. is proposed. The type strain is R2A16-10(T) (=KACC 11405(T)=DSM 17673(T)).

Endozoicomonas elysicola gen. nov., sp. nov., a γ-proteobacterium isolated from the sea slug Elysia ornata

A Gram-negative, strictly aerobic, rod-formed bacterium, strain MKT110 T, was isolated from a mollusk, the sea slug Elysia ornata collected in seawater off the coast of Izu-Miyake Island, Japan at a depth of 15 m. Comparative 16S rRNA gene sequences analysis indicated that the isolate MKT110 T constituted a novel lineage in γ-proteobacteria related to the genera Zooshikella, Oceanospirillum, Microbulbifer, Marinobacter, Saccharospirillum and Pseudomonas. The strain MKT110 T was closely related to the clones from marine sponge Halichondria okadai (AB054136, AB054161) and the coral Pocillopora damicornis (AY700600, AY700601). The phylogenetic tree based on the 16S rRNA gene sequences showed that MKT110 T and four clones formed a sub-lineage related to the genus Zooshikella, with a bootstrap value of 100%. MKT110 T required salt for its growth and was mesophilic. The bacterium contained 16:1 ω7c, 16:0 and 14:0 as major cellular fatty acids, and 3-OH 14:0, 3-OH 10:0 and 3-OH 12:0 as major hydroxy fatty acids. The DNA base composition of the isolate was 50.4 mol% G+C. The major quinone was Q-9. The bacterium is distinguished from currently recognized bacterial genera based on phylogenetic and phenotypic features and should be classified in a novel genus for which the name Endozoicomonas elysicola gen. nov., sp. nov. is proposed. (type strain MKT110 T=IAM 15107 T=KCTC 12372 T; GenBank accession no. AB196667).

Zoogloea oryzae sp. nov., a nitrogen-fixing bacterium isolated from rice paddy soil, and reclassification of the strain ATCC 19623 as Crabtreella saccharophila gen. nov., sp. nov.

Two strains of free-living diazotrophs isolated from soil from a rice paddy field were characterized by using a polyphasic approach. The novel strains, A-7T and A-4, were found to be very closely related, with 99.9% 16S rRNA gene sequence similarity and a DNA-DNA hybridization value of 89.5%, suggesting that they represent a single species. 16S rRNA gene sequence analyses indicated that the two strains fell within the Zoogloea lineage, with less than 96.7 % sequence similarity to other Zoogloea species. Chemotaxonomic characteristics of the novel strains, including DNA G + C content (65.1 mol%), the major quinone system (Q-8), predominant fatty acids (16:1omega7c and 16:0) and major hydroxy fatty acids (3-OH 10:0 and 3-OH 12:0), are similar to those of the genus Zoogloea. The novel strains showed positive results for floc formation which is accepted as confirmatory for species of the genus Zoogloea. However, the novel strains can be distinguished from the other species of Zoogloea by physiological characteristics. The name Zoogloea oryzae sp. nov. is therefore proposed for the novel strains with strain A-7T (= IAM 15218T = CCTCC AB 2052005T) as the type strain. Phylogenetic and chemotaxonomic analyses indicate that strain ATCC 19623, designated as a reference strain of Zoogloea ramigera, does not belong to the genus Zoogloea but to a new genus of Alphaproteobacteria. The name Crabtreella saccharophila gen. nov., sp. nov. is proposed for strain ATCC 19623T (= IAM 12669T).

Azospirillum oryzae sp. nov., a nitrogen-fixing bacterium isolated from the roots of the rice plant Oryza sativa

The taxonomic position of the free-living diazotrophic strain COC8(T) isolated from rice was investigated based on phylogenetic analyses. 16S rRNA gene sequence analyses indicated that strain COC8(T) was closely related to the genus Azospirillum (96% similarity). Chemotaxonomic characteristics (G+C content of the DNA 66.8 mol%, Q-10 quinone system, 18:1omega7c as the major fatty acid and 14:0 3-OH and 16:0 3-OH as the major hydroxy fatty acids) were also similar to those of the genus Azospirillum. Based on its physiological characteristics, strain COC8(T) can clearly be differentiated from recognized species of Azospirillum. The name Azospirillum oryzae sp. nov. is proposed to accommodate this bacterial strain; the type strain is COC8(T) (=IAM 15130(T)=CCTCC AB204051(T)).

Pleomorphomonas oryzae gen. nov., sp. nov., a nitrogen-fixing bacterium isolated from paddy soil of Oryza sativa

Five strains of free-living diazotrophs isolated from rice were characterized by using a polyphasic approach. The strains were found to be very closely related, with 99-100 % 16S rRNA gene sequence similarity and DNA-DNA hybridization values greater than 70 %, suggesting that they represent a single species. When compared with other recognized species, they showed not more than 93 and 89 % similarity for the 16S rRNA and nifH gene sequences, respectively. Phylogenetic distances showed that these isolates were distinct from other taxa within the alpha-Proteobacteria. Chemotaxonomic characteristics of these isolates included the DNA G + C content (62.1-63.1 mol%), the major quinone system (Q-10), predominant fatty acids (18 : 1omega7c, cyclo 19 : 0omega8c and 16 : 0) and major hydroxy fatty acids (14 : 0 3-OH, 18 : 0 3-OH and 16 : 0 3-OH). Based on phylogenetic and phenotypic analyses, these isolates are considered to represent a novel genus and species, for which the name Pleomorphomonas oryzae gen. nov., sp. nov. is proposed. The type strain is F-7(T) (=IAM 15079(T) = ATCC BAA-940(T) = DSM 16300(T)).

Sphingomonas oligophenolica sp. nov., a halo- and organo-sensitive oligotrophic bacterium from paddy soil that degrades phenolic acids at low concentrations

The taxonomic position of a halo- and organo-sensitive, oligotrophic soil bacterium, strain S213(T), was investigated. Cells were Gram-negative, non-motile, strictly aerobic, yellow-pigmented rods of short to medium length on diluted nutrient broth. When 0.1-0.4 % (w/v) NaCl was added to diluted media composed of peptone and meat extract, growth was inhibited with increasing NaCl concentration and the cells became long aberrant forms. When 6 mM CaCl(2) was added, the cells grew quite normally and aberrant cells were no longer found at 0.1-0.5 % (w/v) NaCl. Chemotaxonomically, strain S213(T) contains chemical markers that indicate its assignment to the Sphingomonadaceae: the presence of ubiquinone Q-10 as the predominant respiratory quinone, C(18 : 1) and C(16 : 0) as major fatty acids, C(14 : 0) 2-OH as the major 2-hydroxy fatty acid and sphingoglycolipids. 16S rRNA gene sequence analysis indicated that strain S213(T) belongs to the genus Sphingomonas, exhibiting high sequence similarity to the 16S rRNA gene sequences of Sphingomonas mali IFO 15500(T) (98.3 %), Sphingomonas pruni IFO 15498(T) (98.0 %), Sphingomonas asaccharolytica IFO 15499(T) (97.9 %) and Sphingomonas echinoides DSM 1805(T) (97.8 %). The results of DNA-DNA hybridization experiments and its phenotypic characteristics clearly distinguished the strain from its nearest neighbours and demonstrate that strain S213(T) represents a novel Sphingomonas species, for which the name Sphingomonas oligophenolica sp. nov. is proposed. The type strain is S213(T) (=JCM 12082(T)=CIP 107926(T)).

Proposal of Pseudorhodobacter ferrugineus gen nov, comb nov, for a non-photosynthetic marine bacterium, Agrobacterium ferrugineum, related to the genus Rhodobacter.

The marine gram-negative non-photosynthetic bacterium, Agrobacterium ferrugineum IAM 12616(T) forms one cluster with the species of the photosynthetic genus Rhodobacter in phylogenetic trees based on molecules of 16S rRNA, 23S rRNA and DNA gyrases. Agrobacterium ferrugineum and Rhodobacter species are similar in that growth occurs without NaCl in the culture medium (optimal NaCl concentration for growth of P. ferrugineus is 1%) and their major hydroxy fatty acid compositions are 3-hydroxy decanoic acids (3-OH 10:0) and 3-hydroxy tetradecanoic acids (3-OH 14:1). However, A. ferrugineum differs from Rhodobacter species in G+C content (58 mol% in A. ferrugineum versus 64-73 mol% in Rhodobacter species), in having an insertion in its 16S rRNA gene sequence, and in lacking photosynthetic abilities, bacteriochlorophyll a and intracytoplasmic membrane systems. Furthermore, experiments using PCR and Southern hybridization show that A. ferrugineum does not have puhA gene and puf genes localized near the opposite ends of the photosynthesis gene cluster of Rhodobacter capsulatus. It suggests that A. ferrugineum may not have any genes for photosynthesis. We propose the transfer of A. ferrugineum IAM 12616(T) to the genus Pseudorhodobacter gen. nov. as Pseudorhodobacter ferrugineus comb. nov. Although Pseudorhodobacter ferrugineus disturbs the phylogenetic monophyly of the genus Rhodobacter, this taxonomic proposal seems adequate until it has been clarified whether P. ferrugineus possesses an incomplete photosynthetic apparatus.

Importance of Xanthobacter autotrophicus in Toluene Biodegradation within a Contaminated Stream

Toluene-degrading strains T101 and T102 were isolated from rock surface biomass in a toluene-contaminated freshwater stream. These organisms were present at a density of 5.5 x 10(6) cells/g of rock surface biomass. Both are aerobic, rod-shaped, Gram-negative, non-motile, catalase-positive, oxidase-positive, with yellow pigments, and can grow on benzene. Phylogenetic analyses show that strains T101 and T102 have 16S rDNA sequences identical to Xanthobacter autotrophicus. Fatty acid analyses indicate that they are different strains of the same species Xanthobacter autotrophicus, and that they have high levels of cis-11-octadecenoic acid and cis-9-hexadecenoic acid; 3-hydroxyhexadecanoic acid is the major hydroxy fatty acid present. Strains T101 and T102 had maximal velocities (Vmax) for toluene biodegradation of 3.8 +/- 0.5 and 28.3 +/- 2.2 mumoles toluene/mgprotein-hr, and half-saturation constants (Ks) of 0.8 +/- 0.5 and 11.5 +/- 2.4 microM, respectively. Strain T102 has a higher capacity than strain T101 to degrade toluene, and kinetic calculations suggest that strain T102 may be a major contributor to toluene biodegradation in the stream.

Taxonomic study of aromatic-degrading bacteria from deep-terrestrial-subsurface sediments and description of Sphingomonas aromaticivorans sp. nov., Sphingomonas subterranea sp. nov., and Sphingomonas stygia sp. nov.

Phylogenetic analyses of 16S rRNA gene sequences by distance matrix and parsimony methods indicated that six strains of bacteria isolated from deep saturated Atlantic coastal plain sediments were closely related to the genus Sphingomonas. Five of the strains clustered with, but were distinct from, Sphingomonas capsulata, whereas the sixth strain was most closely related to Blastobacter natatorius. The five strains that clustered with S. capsulata, all of which could degrade aromatic compounds, were gram-negative, non-spore-forming, non-motile, rod-shaped organisms that produced small, yellow colonies on complex media. Their G + C contents ranged from 60.0 to 65.4 mol%, and the predominant isoprenoid quinone was ubiquinone Q-10. All of the strains were aerobic and catalase positive. Indole, urease, and arginine dihydrolase were not produced. Gelatin was not liquified, and glucose was not fermented. Sphingolipids were present in all strains; 2OH14:0 was the major hydroxy fatty acid, and 18:1 was a major constituent of cellular lipids. Acid was produced oxidatively from pentoses, hexoses, and disaccharides, but not from polyalcohols and indole. All of these characteristics indicate that the five aromatic-degrading strains should be placed in the genus Sphingomonas as currently defined. Phylogenetic analysis of 16S rRNA gene sequences, DNA-DNA reassociation values, BOX-PCR genomic fingerprinting, differences in cellular lipid composition, and differences in physiological traits all indicated that the five strains represent three previously undescribed Sphingomonas species. Therefore, we propose the following new species: Sphingomonas aromaticivorans (type strain, SMCC F199), Sphingomonas subterranea (type strain, SMCC B0478), and Sphingomonas stygia (type strain, SMCC B0712).

Recharacterization and Emended Description of the Genus Mycoplana and Description of Two New Species, Mycoplana ramosa and Mycoplana segnis

The phenotypic and chemotaxonomic characteristics of Mycoplana strains were examined. These strains were gram-negative, peritrichously flagellated, branching, filament-forming bacteria. The cellular fatty acids consisted of large amounts of straight-chain unsaturated C18:1 acid, as well as straight-chain saturated C16:0 acid and unsaturated C16:1 acid. The major ubiquinone was ubiquinone Q-10. The Mycoplana strains were divided into four groups, including one group containing Mycoplana dimorpha ATCC 4279T (= IFO 13291T = NCIB 9439T) (T = type strain) and another group containing Mycoplana bullata ATCC 4278T (= IFO 13290T = NCIB 9440T), on the basis of DNA base composition, major hydroxy fatty acid composition, mucosity of colonies, acid production from sugars, and utilization of carbon compounds. This division into groups was supported by the results of DNA-DNA homology experiments. Two new species, Mycoplana ramosa and Mycoplana segnis, are proposed. The type strain of M. ramosa is strain TK0053 (= NCIB 9440), and the type strain of M. segnis is strain TK0059 (= IFO 13240 = ATCC 21756).

Chemical composition of a lipopolysaccharide from Legionella pneumophila.

Lipopolysaccharide isolated from Legionella pneumophila (Phil. 1) was examined for chemical composition. The polysaccharide split off by mild acid hydrolysis contained rhamnose, mannose, glucose, quinovosamine, glucosamine and 2-keto-3-deoxyoctonate, in molar proportions 1.6:1.8:1.0:1.5:4.1:2.7. Heptoses were absent and glucose was probably mainly phosphorylated. The carbohydrate backbone of the lipid A part consisted of glucosamine, quinovosamine and glycerol, in the molar ratios 3.9:1.0:3.4, with glycerol as a phosphorylated moiety. A complex fatty acid substitution pattern comprising eight O-ester-linked, exclusively nonhydroxylated acids, and nineteen amide-linked, exclusively 3-hydroxylated acids was revealed. Both straight- and branched (iso and anteiso) carbon chains occurred. The major hydroxy fatty acid was 3-hydroxy-12-methyltridecanoic acid and six others were of a chain-length above 20 carbon atoms, with 3-hydroxy-20-methyldocosanoic acid as the longest. Two dihydroxy fatty acids, 2,3-dihydroxy-12-methyltridecanoic and 2,3-dihydroxytetradecanoic acids, were also detected. These results suggest that L. pneumophila contains a rather complex and unusual lipopolysaccharide structure of considerable biological and chemotaxonomic interest.

Occurrence of 2‐ and 3‐hydroxy fatty acids in high concentrations in the extractable and bound lipids ofFlavobacterium meningosepticum andFlavobacterium IIb

The major hydroxy fatty acids of cellular lipids in Flavobacterium meningosepticum and Flavobacterium sp. King's group UUb were identified as 2-hydroxy 13-methyltetradecanoic, 3-hydroxy 13-methyltetradecanoic, 3-hydroxy palmitic, and 3-hydroxy 15-methylhexadecanoic acids using gas chromatography-mass spectrometry and GC-mass fragmentography. The concentration of these hydroxy fatty acids comprised up to 30-40% of the total extractable and 20-30% of the bound lipid fatty acids, respectively. From the stability for mild alkaline hydrolysis, 2-hydroxy fatty acids seemed to be attached with ester linkage, and 3-hydroxy fatty acids with amide linkage.