<Emphasis Type="Italic">Lysobacter daecheongensis</Emphasis> sp. nov., isolated from sediment of stream near the Daechung dam in South Korea

A Gram-negative, aerobic, rod shaped, non-spore-forming bacterial strain, designated Dae08^T, was isolated from sediment of the stream near Daechung dam in South Korea, and was characterized in order to determine its taxonomic position, using a polyphasic approach. Comparative 16S rRNA gene sequence analysis showed that strain Dae08^T belongs to the family Xanthomonadaceae of the Gammaproteobacteria, and is related to Lysobacter brunescens ATCC 29482^T (97.3%). The phylogenetic distances from any other species with validly published names within the genus Lysobacter were greater than 3.7%. The G+C contents of the genomic DNA of strain Dae08^T was 69.3 mol%. The detection of a quinone system with Q-8 as the predominant compound and a fatty acid profile with iso-C_15:0, iso-C_17:1, ω9c, iso-C_17:0, iso-C_16:0, and iso-C_11:0 3-OH as the major acids supported the affiliation of strain Dae08^T to the genus Lysobacter. DNA-DNA relatedness between strain Dae08^T and its phylogenetically closest neighbour was 28%. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain Dae08^T (= KCTC 12600^T) should be classified in the genus Lysobacter as the novel species, for which the name Lysobacter daecheongensis sp. nov. is proposed.     

<Emphasis Type="Italic">Streptomyces</Emphasis><Emphasis Type="Italic">mayteni</Emphasis> sp. nov., a novel actinomycete isolated from a Chinese medicinal plant

An actinomycete strain, designated YIM 60475^T, was isolated from the roots of Maytenus austroyunnanensis and was characterized by using a polyphasic approach. The strain was determined to belong to the genus Streptomyces, based on its phenotypic and phylogenetic characteristics. The strain produced spiral spore chains on aerial mycelium. The cell wall contained ll-diaminopimelic acid. Whole-cell hydrolysates contained galactose, glucose, and xylose. The phospholipid was type II. The DNA G+C content of the type strain was 73.3 mol%. DNA–DNA hybridization and comparison of physiological and chemical characteristics suggested that strain YIM 60475^T is a new Streptomyces species, for which the name Streptomyces mayteni sp. nov. is proposed. The type strain is YIM 60475^T (=CCTCC AA 207005^T = KCTC 19383^T). Hua-Hong Chen and Sheng Qin contributed equally to this work.     

Novel Production of Isochainin by a Strain of <Emphasis Type="Italic">Streptomyces </Emphasis>sp<Emphasis Type="Italic">.</Emphasis> Isolated from Rhizosphere Soil of the Indigenous Moroccan Plant <Emphasis Type="Italic">Argania Spinosa</Emphasis> L

Summary An actinomycete strain (designated Ap1) isolated from the rhizosphere soil of Argania spinosa L. strongly inhibited the growth of two plant pathogens: Fusarium oxysporum f.sp. albedinis and Verticillium dahliae. The spore morphology suggested that the Ap1 strain belonged to the genus Streptomyces. The antifungal compound produced by Ap1 was purified by HPLC and identified as the polyene macrolide, isochainin, by NMR and mass spectroscopy. Ap1 showed normal biosynthesis of isochainin in comparison with S. cellulosae ATTC 12625, in which precursor-directed biosynthesis by feeding ethyl (Z)-16-phenylhexadec-9-enoate to the culture medium is required. In addition, Streptomyces sp. strain Ap1 produces isochainin with a 6.5-fold higher concentration than Streptomyces cellulosae ATTC 12625.     

<Emphasis Type="Italic">Streptomyces serianimatus</Emphasis> sp. nov., isolated from a rhizophere soil

A novel actinomycete strain, designated YIM 45720^T, was isolated from a Cephalotaxus fortunei rhizophere soil sample collected from Yunnan Province, southwest China. The strain formed well-differentiated aerial and substrate mycelia. Chemotaxonomically, it contained LL-diaminopimelic acid in the cell wall. The cell-wall sugars contained ribose, mannose, and galactose with traces of glucose and xylose. Phospholipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and phosphatidylinositol. MK-9 (H₈) was the predominant menaquinone. The major fatty acids (>10%) were iso-C_16:0, iso-C_15:1 and anteiso-C_15:0. The G + C content of the DNA was 70 mol%. Phylogenetic analysis data based on 16S rRNA gene sequence showed that strain YIM 45720^T formed a distinct branch with the type strain of Streptomyces scabrisporus JCM 11712^T within the genus Streptomyces. On the basis of the phenotypic and genotypic characteristics, strain YIM 45720^T (=DSM 41883^T = CCTCC AA 206006^T) is proposed as the type strain of a novel species, Streptomyces serianimatus sp. nov.     

Characterization of Desulfomicrobium escambium sp. nov. and proposal to assign Desulfovibrio desulfuricans strain Norway 4 to the genus Desulfomicrobium

A sulfate-reducing bacterium, designated strain ESC1, was isolated and found to be a new species. Strain ESC1 is a strictly anaerobic, gram-negative, non-sporeforming, motile, short, round-ended rod often occurring in pairs. Of 31 fermentative substrates tested, only pyruvate was utilized. Sulfate enhanced growth with pyruvate and allowed growth with ethanol, lactate, formate and hydrogen. Both sulfate and thiosulfate were reduced. Lactate was incompletely oxidized to acetate and CO₂. The strain was desulfoviridin negative. The G+C content is 59.9%. These data suggested placement of strain ESC1 in the genus Desulfomicrobium. Comparative 16S rRNA analysis showed that strain ESC1 shares 98% rRNA sequence similarity with Desulfomicrobium baculatum and Desulfovibrio desulfuricans strain Norway 4. The latter two strains shared greater than 99% 16S rRNA sequence similarity. Strain ESC1 has been designated as the new species Desulfomicrobium escambium. We also recommend that D. desulfuricans strain Norway 4 be considered for reclassification as a Desulfomicrobium species.     

<Emphasis Type="Italic">Rhodotorula oryzae</Emphasis> sp. nov., a novel basidiomycetous yeast species isolated from paddy rice

A basidiomyetous yeast strain RO-203, which formed orange-red colored colonies, was isolated from a sample of paddy rice crops at the ripe stage in Japan. Morphological, physiological and biochemical characterization indicated that this strain belonged to the genus Rhodotorula. Molecular taxonomic analysis based on the 26S rDNA D1/D2 domain and internal transcribed spacer (ITS) region sequences showed that RO-203 represents an undescribed yeast species, for which the name Rhodotorula oryzae sp. nov. is proposed (type strain: AS 2.2363^T = MAFF 516128^T). The new species clustered in a branch together with Sakaguchia dacryoidea in phylogenetic trees based on the D1/D2 and ITS sequences. These two species differed by 2.3% and 12% nucleotide divergences in the D1/D2 and ITS regions, respectively.     

拟孢囊菌属放线菌的研究进展

拟孢囊菌属(Kibdelosporangium)是一个经典的丝状放线菌类群。自Shearer等于1986年建立该属以来,不断有新的菌株从不同生境中被纯培养分离得到,目前已有效发表8个种、2个亚种。拟孢囊菌属作为稀有放线菌属,是获得新型抗生素类次生代谢产物的重要资源。本文结合我们分离到的一株该属菌株的功能研究、基因组分析和相关文献资料,系统综述了拟孢囊菌属放线菌的建立、分类学特征、属内种的分布、活性次级代谢产物的发现以及其他功能应用和开发前景,以期为该属其他新分离菌株的分类鉴定、新颖次级代谢产物的发现、功能基因资源的挖掘与开发提供借鉴。     

<Emphasis Type="Italic">Aliihoeflea aestuarii</Emphasis> gen. nov., sp. nov., a novel bacterium isolated from tidal flat sediment

A novel Gram-negative and rod-shaped bacterium, designated N8^T, was isolated from tidal flat sediment. Phylogenetic analysis based on 16S rRNA gene sequences showed that N8^T strain is associated with the family Phyllobacteriaceae: two uncultured clones (98.4 and 99.8% 16S rRNA gene sequence similarity) and the genus Mesorhizobium (≤97.0%). The novel strain formed a separate clade with uncultured clones in the phylogenetic tree based on 16S rRNA gene sequences. Cellular fatty acid profiles predominately comprised C_18:1 ω7c and C_19:0 cyclo ω8c. The major isoprenoid quinone is ubiquinone-10 and genomic DNA G+C content is 53.4 mol%. The polyphasic taxonomic study indicates that the novel strain N8^T represents a novel species of the new genus in the family Phyllobacteriaceae, named Aliihoeflea aestuarii. The type strain is N8^T (= KCTC 22052^T= JCM 15118^T= DSM 19536^T).     

<Emphasis Type="Italic">Virgibacillus litoralis</Emphasis> sp. nov., a moderately halophilic bacterium isolated from saline soil

A Gram-positive, moderately halophilic, endospore-forming, catalase- and oxidase-positive, motile, rod-shaped, aerobic bacterium, designated strain JSM 089168^T, was isolated from saline soil collected from Naozhou Island, Leizhou Bay, South China Sea. The organism was able to grow with 2–25% (w/v) total salts (optimum, 5–10%), at pH 6.0–10.0 (optimum, pH 8.0) and 10–45°C (optimum, 30°C). meso-Diaminopimelic acid was present in the cell-wall peptidoglycan. The strain contained MK-7 as the predominant menaquinone, and diphosphatidylglycerol and phosphatidylglycerol as the major polar lipids. The major cellular fatty acids were anteiso-C_15:0, iso-C_15:0 and anteiso-C_17:0, and the DNA G + C content was 40.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain JSM 089168^T should be assigned to the genus Virgibacillus, being related most closely to the type strains of Virgibacillus carmonensis (sequence similarity 97.6%), Virgibacillus necropolis (97.3%) and Virgibacillus halodenitrificans (97.1%). Levels of DNA–DNA relatedness between strain JSM 089168^T and the type strains of V. carmonensis, V. necropolis and V. halodenitrificans were 20.4, 14.3 and 12.0%, respectively. The combination of phylogenetic analysis, DNA–DNA relatedness, phenotypic characteristics and chemotaxonomic data supported the view that strain JSM 089168^T represents a novel species of the genus Virgibacillus, for which the name Virgibacillus litoralis sp. nov. is proposed. The type strain is JSM 089168^T (=DSM 21085^T =KCTC 13228^T). The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of strain JSM 089168^T is FJ425909.     

Isolation of the <Emphasis Type="Italic">opdE</Emphasis> gene that encodes for a new hydrolase of <Emphasis Type="Italic">Enterobacter</Emphasis> sp. capable of degrading organophosphorus pesticides

Microbial enzymes that can hydrolyze organophosphorus compounds have been isolated, identified and characterized from different microbial species in order to use them in biodegradation of organophosphorus compounds. We isolated a bacterial strain Cons002 from an agricultural soil bacterial consortium, which can hydrolyze methyl-parathion (MP) and other organophosphate pesticides. HPLC analysis showed that strain Cons002 is capable of degrading pesticides MP, parathion and phorate. Pulsed-field gel electrophoresis and 16S rRNA amplification were performed for strain characterization and identification, respectively, showing that the strain Cons002 is related to the genus Enterobacter sp. which has a single chromosome of 4.6 Mb and has no plasmids. Genomic library was constructed from DNA of Enterobacter sp. Cons002. A gene called opdE (Organophosphate Degradation from E nterobacter) consists of 753 bp and encodes a protein of 25 kDa, which was isolated using activity methods. This gene opdE had no similarity to any genes reported to degrade organophosphates. When kanamycin-resistance cassette was placed in the gene opdE, hydrolase activity was suppressed and Enterobacter sp. Cons002 had no growth with MP as a nutrients source.     

<Emphasis Type="Italic">Dwiroopa</Emphasis>, a coelomycetous genus with two species

The coelomycete Dwiroopa was determined to be the correct genus for Harknessia lythri, and a new combination is made for this species. The type species of Dwiroopa, D. ramya, is redescribed and illustrated based on the type specimen for which a lectotype is designated. A key to the two species of Dwiroopa is presented along with a discussion of their similarities and differences. The genus Dwiroopa is distinguished from Harknessia by conidial characteristics. In Dwiroopa the macroconidia have widely spaced, longitudinal slits around the conidia and lack a basal appendage, whereas in Harknessia the macroconidia are smooth or have closely spaced, longitudinal slits on only one side of the conidia and often have a true basal appendage. Both Dwiroopa and Harknessia are included in the Diaporthales.     

<Emphasis Type="Italic">Halobacillus naozhouensis</Emphasis> sp. nov., a moderately halophilic bacterium isolated from a sea anemone

A moderately halophilic, Gram-positive, catalase- and oxidase-positive, rod-shaped, aerobic bacterium, designated strain JSM 071068^T, was isolated from a sea anemone (Anthopleura xanthogrammica) collected from the Naozhou Island on the Leizhou Bay in the South China Sea. Cells were motile by means of peritrichous flagella and formed ellipsoidal endospores lying in subterminal swollen sporangia. Strain JSM 071068^T was able to grow with 1–20% (w/v) total salts (optimum, 6–9%), at pH values of 6.0–10.0 (optimum, pH 7.5) and a temperature range of 10–35°C (optimum, 25°C). meso-Diaminopimelic acid was present in the cell-wall peptidoglycan. The predominant menaquinone was MK-7 and the major cellular fatty acids were anteiso-C_15:0, anteiso-C_17:0 and iso-C_15:0. The genomic DNA G + C content was 42.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain JSM 071068^T belonged to the genus Halobacillus. The 16S rRNA gene sequence similarities between strain JSM 071068^T and the type strains of the recognized Halobacillus species ranged from 97.9% (with Halobacillus alkaliphilus) to 95.3% (with Halobacillus kuroshimensis). The levels of DNA–DNA relatedness between the new isolate and the type strains of H. alkaliphilus, Halobacillus campisalis, Halobacillus halophilus and Halobacillus seohaensis were 25.6, 22.1, 10.8 and 13.2%, respectively. The combination of phylogenetic analysis, DNA–DNA relatedness, phenotypic characteristics and chemotaxonomic data supported the view that strain JSM 071068^T represents a new species of the genus Halobacillus, for which the name Halobacillus naozhouensis sp. nov. is proposed, with JSM 071068^T (=DSM 21183^T =KCTC 13234^T) as the type strain. The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of strain JSM 071068^T is EU925615.     

<Emphasis Type="Italic">Candida patagonica</Emphasis> sp. nov., a new species of yeast from cellar surfaces

A novel anamorphic yeast species belonging to the genus Candida has been isolated from cellar surfaces in North Patagonia. Morphological and physiological observation and phylogenetic analysis were performed. Pseudomycelium was plentifully produced. No sexual reproduction was observed. From sequence analysis of the 26S rDNA D1/D2 region, Candida bituminiphila and Zygoascus hellenicus were the closest species with 40 and 79 bp substitutions, respectively. C. bituminiphila differed physiologically from the novel species in its ability to assimilate sucrose and erythritol, in not fermenting any sugars, in growing without some vitamin compounds, and in growing at 40°C. All these data support the hypothesis that the new yeast, named Candida patagonica, is a novel species related to C. bituminiphila. The type strain is UNCOMA 159.5 (= CECT 12029 = CBS 10443).     

Degradation of <Emphasis Type="Italic">o</Emphasis>-xylene and <Emphasis Type="Italic">m</Emphasis>-xylene by a novel sulfate-reducer belonging to the genus <Emphasis Type="Italic">Desulfotomaculum</Emphasis>

A strictly anaerobic bacterium, strain OX39, was isolated with o-xylene as organic substrate and sulfate as electron acceptor from an aquifer at a former gasworks plant contaminated with aromatic hydrocarbons. Apart from o-xylene, strain OX39 grew on m-xylene and toluene and all three substrates were oxidized completely to CO₂. Induction experiments indicated that o-xylene, m-xylene, and toluene degradation were initiated by different specific enzymes. Methylbenzylsuccinate was identified in supernatants of cultures grown on o-xylene and m-xylene, and benzylsuccinate was detected in supernatants of toluene-grown cells, thus indicating that degradation was initiated in all three cases by fumarate addition to the methyl group. Strain OX39 was sensitive towards sulfide and depended on Fe(II) in the medium as a scavenger of the produced sulfide. Analysis of the PCR-amplified 16S rRNA gene revealed that strain OX39 affiliates with the gram-positive endospore-forming sulfate reducers of the genus Desulfotomaculum and is the first hydrocarbon-oxidizing bacterium in this genus.     

<Emphasis Type="Italic">Nocardioides islandiensis</Emphasis> sp. nov., isolated from soil in Bigeum Island Korea

A novel actinobacterium designated as MSL-26^T was isolated from soil in Bigeum Island Korea. A polyphasic study was undertaken to establish the taxonomic position of isolate MSL-26^T. Strain MSL-26^T was found to have chemical and morphological characteristics similar to Nocardioides. The strain grew optimally at pH 7·5 and 28°C. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain MSL-26^T forms a distinct line of descent within the radiation enclosed by the genus Nocardioides. The cell wall of strain MSL-26^T contained LL-2, 6-diaminopimelic acid. The principal menaquinone was MK-8 (H₄). The phospholipids detected were diphosphatidylglycerol, phosphatidylglycerol and some unidentified lipids. C_18:1 w7c (50.38%) was the major fatty acid. The DNA G + C content of strain MSL-26^T was 71.4 mol%. The 16S rRNA gene sequence of strain MSL-26^T shares the highest sequence similarity with Nocardioides kribbensis KCTC 19038^T (95.78%) and Nocardioides aquaticus DSM 11439^T (95.52%). Based on the morphological, physiological, biochemical and chemotaxonomical data presented in this study, strain MSL-26^T should be classified as a novel species, for which the name Nocardioides islandiensis sp. nov. is proposed. The type strain is MSL-26^T (=KCTC 19275^T =DSM 19321^T)     

Trichosporon insectorum sp. nov., a new anamorphic basidiomycetous killer yeast

Three killer yeasts, isolated from the gut of insects in Panama and artisanal cheese in Brazil, were shown to be related to the Ovoides clade of the genus Trichosporon. Sequencing of the D1/D2 region of the LSU rDNA and physiological characterization revealed a distinct taxonomic position in relation to known species of the genus. Conspecificity of the three killer isolates was reinforced by similar M13 fingerprinting and killer profiles. We propose a new species in this genus: Trichosporon insectorum. The type strain is CBS 10422^T (syn. NRRL Y-48120). This anamorphic species produces arthroconidia but not appressoria, and its killer character seems to be associated with dsRNA.     

Isolation and characterization of a novel bacterium, <Emphasis Type="Italic">Sphingomonas bisphenolicum</Emphasis> strain AO1, that degrades bisphenol A

Bisphenol A (2,2-bis(4-hydroxyphenyl) propane, BPA), which is used as a synthetic resin material or a plasticizer, is a pollutant that␣possesses endocrine-disrupting activity. Bioremediation of BPA is used to decrease its polluting effects, and here we report a novel bacterial strain AO1, which is able to degrade BPA. This strain was isolated using enrichment cultivation from a soil sample from a vegetable-growing field; the sample was one of 500 soil samples collected across Japan. Strain AO1 degraded 100 mg/l BPA to an undetectable level within 6 h in MYPG medium (containing malt extract, yeast extract, peptone, and glucose) and within 48 h in minimum medium containing 1% glucose at 30°C. Strain AO1 can utilize BPA as a sole source of carbon and as an energy source under aerobic conditions. The estrogenic activity of BPA in MYPG medium was ultimately reduced by strain AO1, although the activity initially increased. Taxonomical analysis showed that strain␣AO1 is closely related to Sphingomonas chlorophenolicum and S. herbicidovorans, neither of which have a capacity for BPA degradation. DNA–DNA hybridization showed that strain AO1 is a novel species of the Sphingomonas genus, and we designated AO1 as S. bisphenolicum.     

<Emphasis Type="Italic">Arthrobacter halodurans</Emphasis> sp. nov., a new halotolerant bacterium isolated from sea water

A novel Gram-positive, halotolerant, non-sporulating, non-motile, catalase-positive, oxidase-negative and aerobic bacterium, designated strain JSM 078085^T, was isolated from sea water collected from the South China Sea. Strain JSM 078085^T exhibited a rod-coccus growth cycle and produced a yellow pigment. The strain was able to grow in the presence of 0–12% (w/v) NaCl and at pH 6.0–9.5 and 4–35°C; optimum growth was observed at pH 7.0 and 25–30°C in the absence of NaCl. The peptidoglycan type was A4α (l-Lys–l-Ala–l-Glu). Cell-wall sugars contained galactose and glucose. Strain JSM 078085^T contained menaquinone MK-9(H₂) as the major respiratory quinone and diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol as the major polar lipids. The major cellular fatty acids were anteiso-C_15:0, iso-C_15:0 and anteiso-C_17:0 and the DNA G + C content was 63.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain JSM 078085^T should be assigned to the genus Arthrobacter, being most closely related to the type strain of Arthrobacter rhombi (sequence similarity 97.1%), and the two strains formed a distinct lineage in the phylogenetic tree. The level of DNA–DNA relatedness between strain JSM 078085^T and the type strain of Arthrobacter rhombi was 10.6%. The combination of phylogenetic analysis, DNA–DNA relatedness, phenotypic characteristics and chemotaxonomic data supported the view that strain JSM 078085^T represents a novel species of the genus Arthrobacter, for which the name Arthrobacter halodurans sp. nov. is proposed. The type strain is JSM 078085^T (=DSM 21081^T=KCTC 19430^T). The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of strain JSM 078085^T is EU583729.     

<Emphasis Type="Italic">Henriciella marina</Emphasis> gen. nov., sp. nov., a novel member of the family <Emphasis Type="Italic">Hyphomonadaceae</Emphasis> isolated from the East Sea

A bacterial strain, designated Iso4^T, was isolated from the East Sea of Korea and was subjected to a poly-phasic taxonomy study including phenotypic and chemotaxonomic characteristics as well as 16S rRNA gene sequence analysis. Cells of the strain were Gram-negative, motile, non-budding, non-stalked, and strictly aerobic. Strain Iso4^T grew optimally at 20°C in the presence of 1∼2% (w/v) NaCl and at pH 6.9∼7.6. The major respiratory quinone was Q-10 and the major cellular fatty acids were C_18:1 ω7c (53.5%), C_17:1 ω5c (11.7%), C_17:1 ω6c (8.1%), C_16:0 (7.8%), C_17:0 (4.8%), C_15:0 (2.9%), and C_16:1 ω5c (2.2%). The DNA G+C content of strain Iso4^T was 56.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain Iso4^T formed a monophyletic clade in the family Hyphomonadaceae, supported by high bootstrap value and was most closely related to the genus Hyphomonas (92∼94%), a member of marine bacteria in the family. The phenotypic, genotypic, and chemotaxonomic evidences also suggest strain Iso4^T represents a novel genus and species in the family Hyphomonadaceae, for which the name Henriciella gen. nov., sp. nov. is proposed. The type strain is Iso4^T (=KCTC 12513^T =DSM 19595^T =JCM 15116^T).