Flavobacterium foetidum sp. nov., isolated from ginseng soil.

A Gram-staining-negative bacterial strain, designated CJ42T, was isolated from ginseng soil in Anseong, Republic of Korea. Cells were rod-shaped, yellow-pigmented, aerobic and devoid of flagella but showed gliding motility. Strain CJ42T grew optimally at 30 °C and pH 7.0 in the absence of NaCl on tryptic soy agar. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain CJ42T belonged to the genus Flavobacterium within the family Flavobacteriaceae and was most closely related to Flavobacterium tistrianum KCTC 42679T (97.3 % similarity). Flexirubin-type pigments were produced. The only respiratory quinone was menaquinone 6. The predominant polar lipids were phosphatidylethanolamine, an unknown aminolipid and two unknown lipids. The major fatty acids of strain CJ42T were iso-C15 : 0 and summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c). The G+C content of the genomic DNA was 30.7 mol%. Based on the polyphasic analyses, strain CJ42T represents a novel species in the genus Flavobacterium, for which the name Flavobacteriumfoetidum sp. nov. is proposed. The type strain is CJ42T (=KACC 19302=JCM 32085).

Flavobacterium panacis sp. nov., isolated from rhizosphere of Panax ginseng.

A novel bacterial strain, designated DCY106(T), was isolated from soil collected from the rhizosphere of ginseng (Panax ginseng), in Gochang, Republic of Korea. Strain DCY106(T) is Gram-negative, yellow-pigmented, non-flagellate, motile, non-spore-forming, rod-shaped, and strictly aerobic. The strain grows optimally at 25-30 °C and pH 6.5-7.5. Phylogenetically, strain DCY106(T) is closely related to Flavobacterium arsenitoxidans KCTC 22507(T) (98.41 %), followed by Flavobacterium cutihirudini LMG 26922(T) (97.67 %), Flavobacterium nitrogenifigens LMG 28694(T) (97.59 %), Flexibacter auranticus LMG 3987(T) (97.38 %), Flavobacterium defluvi KCTC 12612(T) (97.21 %) and Flavobacterium chilense LMG 26360(T) (97.05 %). The 16S rRNA gene sequence similarities to all other Flavobacterium species were below 97 %. The DNA G+C content of strain DCY106(T) is 34.2 mol% and the DNA-DNA relatedness between strain DCY106(T) and F. cutihirudini LMG 26922(T), F. auranticus LMG 3987(T), F. defluvi KCTC 12612(T) and F. chilense LMG 26360(T) were below 40.0 %. The menaquinone of the type MK-6 was found to be the predominant respiratory quinone. The major polar lipids were identified as phosphatidylethanolamine, phosphatidylserine, two unidentified aminolipids (APL1, APL6) and one unidentified lipid L2. C15:0, iso-C15:0 and summed feature 3 (iso-C15:0 2OH/C16:1 ω7c) were identified as the major fatty acids present in DCY106(T). The results of physiological and biochemical tests allowed strain DCY106(T) to be differentiated phenotypically from other recognized species belonging to the genus Flavobacterium. Therefore, it is suggested that the newly isolated organism represents a novel species, for which the name Flavobacterium panacis sp. nov. is proposed with the type strain designated as DCY106(T) (= JCM 31468(T)= KCTC 42747(T)).

Flavobacterium panacisoli sp. nov., isolated from soil of a ginseng field.

A novel bacterial strain, designated DCY70(T), was isolated from soil of a ginseng field in Republic of Korea and was characterized in order to determine its taxonomic position. The strain was Gram-reaction negative, yellow-pigmented, rod-shaped and catalase- and oxidase-positive. Based on the 16S rRNA gene sequence similarity, strain DCY70(T) was shown to belong to the genus Flavobacterium, most closely related to Flavobacterium oncorhynchi 631-08(T) (98.4 %), Flavobacterium plurextorum 1126-1H-08(T) (97.9 %), Flavobacterium chilense LM-09-Fp(T) (97.9 %) and Flavobacterium chungangense CJ(T) (97.7 %). The chemotaxonomic characteristics showed only menaquinone-6 (MK-6), iso-C15:0, iso-C15:0 3OH, iso-C17:0 3OH and summed feature 3 as major cellular fatty acids. Polar lipids were phosphatidylethanolamine (PE), two unidentified aminolipids, four unidentified polar lipids and one unidentified phospholipid. The DNA G+C content was 34.9 mol%. Based on the phylogenetic, phenotypic and genotypic data, a novel species, Flavobacterium panacisoli sp. nov., is proposed (=KCTC 32393(T) = JCM 19162(T)).

Enrichment and isolation of Flavobacterium strains with tolerance to high concentrations of cesium ion.

Interest in the interaction of microorganisms with cesium ions (Cs(+)) has arisen, especially in terms of their potent ability for radiocesium bioaccumulation and their important roles in biogeochemical cycling. Although high concentrations of Cs(+) display toxic effects on microorganisms, there have been only limited reports for Cs(+)-tolerant microorganisms. Here we report enrichment and isolation of Cs(+)-tolerant microorganisms from soil microbiota. Microbial community analysis revealed that bacteria within the phylum Bacteroidetes, especially Flavobacterium spp., dominated in enrichment cultures in the medium supplemented with 50 or 200 mM Cs(+), while Gammaproteobacteria was dominant in the control enrichment cultures (in the presence of 50 and 200 mM K(+) instead of Cs(+)). The dominant Flavobacterium sp. was successfully isolated from the enrichment culture and was closely related to Flavobacterium chungbukense with 99.5% identity. Growth experiments clearly demonstrated that the isolate has significantly higher tolerance to Cs(+) compared to its close relatives, suggesting the Cs(+)-tolerance is a specific trait of this strain, but not a universal trait in the genus Flavobacterium. Measurement of intracellular K(+) and Cs(+) concentrations of the Cs(+)-tolerant isolate and its close relatives suggested that the ability to maintain low intracellular Cs(+) concentration confers the tolerance against high concentrations of external Cs(+).

Flavobacterium panaciterrae sp. nov., a ß-glucosidase producing bacterium with ginsenoside-converting activity isolated from the soil of a ginseng field.

The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of strain DCY69(T) is JX233806. A Gram-reaction-negative, oxidase- and catalase-positive, non-gliding motile strain, designated strain DCY69(T), was isolated from the soil of a ginseng field in the Republic of Korea. Colonies of strain DCY69(T) were circular, 0.5-1.5 mm diameter, yellow, and convex on an R2A agar plate after 2 days. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain DCY69(T) belonged to the genus Flavobacterium with 90.5-98.3% gene sequence similarity. The major predominant quinone was MK-6. The major cellular fatty acids were iso-C15:0, iso-C17:0 3-OH, iso-C15:0 3-OH and summed feature 3 (containing C16:1ω7c and/or C16:1ω6c). The major polar lipids were phosphatidylethanolamine, one unidentified aminolipid and unidentified polar lipids (L1, L2). The genomic DNA G+C content of strain DCY69(T) was 35.0mol%. The strain DCY69(T) transformed ginsenoside Rb1 into Rd and F2. Based on the polyphasic taxonomic data, strain DCY69(T) is considered to represent a novel species of the genus Flavobacterium, for which the name Flavobacterium panaciterrae sp. nov. is proposed. The type strain is DCY69(T)(= KCTC 32392(T) = JCM 19161(T)), isolated from the soil of a ginseng field in the Republic of Korea.

Isolation and identification of phytate-degrading bacteria and their contribution to phytate mineralization in soil.

To better understand the phosphorus (P) cycling in an agricultural soil environment, amounts of total, organic and inorganic P in 10 agricultural soil samples were analyzed. Since a large proportion (57.8%) of the total P in the soils was in organic form, a method was developed to evaluate the mineralization rate of organic P in the soil by adding phytate to the soil and analyzing the change in water-soluble P (WSP) content after incubating it for 3 days. Moreover, the relationship between the phytate mineralization activity and bacterial biomass in 60 agricultural soils was also investigated, where the phytate mineralization activity ranged from 0 to 61.7% (average: 18.8%), and the R² value between phytate mineralization activity and indigenous bacterial biomass was 0.11 only. Phytate-degrading bacteria were isolated from the soil environment, and identified as Pseudomonas rhodesiae JT29, JT32, JT33, JT34, JT35, Pseudomonas sp. JT30, and Flavobacterium johnsoniae JT31. When P. rhodesiae JT29 and F. johnsoniae JT31 were inoculated into the agricultural soils, the phytate mineralization activities were increased up to 16 and 27 times, respectively. It was concluded that promotion of effective phytate-degrading bacterial strains could improve the sustainable P management in the agricultural soils.

Flavobacterium kyungheensis sp. nov., isolated from soil of a ginseng field.

A Gram-staining negative, strictly aerobic, motile by gliding, non-spore-forming, pale yellow pigmented and rod-shaped bacterium designated strain THG-107(T) was isolated from soil of a ginseng field on Ganghwa Island in the Republic of Korea and its taxonomic position was investigated by using a polyphasic study. Growth of strain THG-107(T) was found to occur at 4-37 °C (optimum, 20-30 °C), at pH 5.5-10 (optimum, pH 7.0) and in the presence of 0-1 % (w/v) NaCl (optimum, absence) on R2A agar. On the basis of 16S rRNA gene sequence similarity, strain THG-107(T) was shown to belong to the family Flavobacteriaceae and was related to Flavobacterium denitrificans ED5(T) (99.1 % similarity). The G+C content of the genomic DNA was determined to be 34.2 mol%. These results are consistent with characteristics of members of the genus Flavobacterium. The only isoprenoid quinone detected in strain THG-107(T) was menaquinone-6 (MK-6) and the major polyamine was identified as homospermidine (82.9 %). The major polar lipid detected was phosphatidylethanolamine and the major cellular fatty acids were identified as iso-C15:0 (26.3 %), iso-C17:0 3OH (12.6 %) and summed feature 3 (comprising C16:1 ω7c and/or C16:1 ω6c; 11.6 %). Flexirubin-type pigments were found to be present. Strain THG-107(T) has ß-glucosidase activity to convert ginsenosides Rb1 and Rd into Gyp17 and F2. DNA-DNA hybridization with F. denitrificans ED5(T) was 52 %. Strain THG-107(T) could be distinguished from F. denitrificans ED5(T) and the other species of the genus Flavobacterium by its phylogenetic and genetic distinctiveness and by several phenotypic properties. Therefore, strain THG-107(T) is considered to represent a novel species in the genus Flavobacterium, for which the name Flavobacterium kyungheensis sp. nov. is proposed (type strain THG-107(T) = KACC 16219(T) = LMG 26575(T)).

Flavobacterium ginsengisoli sp. nov., isolated from soil of a ginseng field.

A novel bacterial strain, designated DCY54(T), was isolated from a field cultivated with ginseng in Yongin, Republic of Korea. Cells were Gram-reaction-negative, yellow-pigmented, rod-shaped, non-spore-forming, and strictly aerobic. They were motile by gliding and produced flexirubin-type pigments. Growth occurred optimally at 25-30 °C, at pH 5.0-7.0 and in the presence of 0-1 % NaCl. The 16S rRNA sequence analysis demonstrated that strain DCY54(T) was most closely related to Flavobacterium defluvii EMB117(T) (96.9 %). The only isoprenoid quinone of strain DCY 54(T) was menaquinone-6 (MK-6) and the major polar lipids were phosphatidylethanolamine, one unidentified aminolipid and one unidentified lipid. The major cellular fatty acids (>15 %) were iso-C15 : 0, summed feature 3 (comprising C16 : 1ω7c and/or iso-C15 : 0 2-OH) and C16 : 0. The DNA G+C content was 33.3 mol%. Phylogenetic inference and phenotypic data supported affiliation of strain DCY54(T) to the genus Flavobacterium. Several physiological and biochemical tests differentiated strain DCY54(T) from the species of the genus Flavobacterium with validly published names. On the basis of data from a polyphasic study, strain DCY54(T) represents a novel species of the genus Flavobacterium for which the name Flavobacterium ginsengisoli sp. nov. is proposed. The type strain is DCY54(T) ( = KCTC 23318(T) = JCM 17336(T)).

Jellyfish modulate bacterial dynamic and community structure.

Jellyfish blooms have increased in coastal areas around the world and the outbreaks have become longer and more frequent over the past few decades. The Mediterranean Sea is among the heavily affected regions and the common bloom-forming taxa are scyphozoans Aurelia aurita s.l., Pelagia noctiluca, and Rhizostoma pulmo. Jellyfish have few natural predators, therefore their carcasses at the termination of a bloom represent an organic-rich substrate that supports rapid bacterial growth, and may have a large impact on the surrounding environment. The focus of this study was to explore whether jellyfish substrate have an impact on bacterial community phylotype selection. We conducted in situ jellyfish-enrichment experiment with three different jellyfish species. Bacterial dynamic together with nutrients were monitored to assess decaying jellyfish-bacteria dynamics. Our results show that jellyfish biomass is characterized by protein rich organic matter, which is highly bioavailable to 'jellyfish-associated' and 'free-living' bacteria, and triggers rapid shifts in bacterial population dynamics and composition. Based on 16S rRNA clone libraries and denaturing gradient gel electrophoresis (DGGE) analysis, we observed a rapid shift in community composition from unculturable Alphaproteobacteria to culturable species of Gammaproteobacteria and Flavobacteria. The results of sequence analyses of bacterial isolates and of total bacterial community determined by culture independent genetic analysis showed the dominance of the Pseudoalteromonadaceae and the Vibrionaceae families. Elevated levels of dissolved proteins, dissolved organic and inorganic nutrient release, bacterial abundance and carbon production as well as ammonium concentrations characterized the degradation process. The biochemical composition of jellyfish species may influence changes in the amount of accumulated dissolved organic and inorganic nutrients. Our results can contribute insights into possible changes in bacterial population dynamics and nutrient pathways following jellyfish blooms which have important implications for ecology of coastal waters.

Flavobacterium ginsenosidimutans sp. nov., a bacterium with ginsenoside converting activity isolated from soil of a ginseng field.

A Gram-negative, aerobic, non-motile, non-spore-forming, yellow-pigmented, rod-shaped bacterium, designated strain THG 01(T), was isolated from the soil of a ginseng field in Pocheon province, South Korea, and its taxonomic position was investigated by using a polyphasic approach. Strain THG 01(T) grew well at 25-37 °C and pH 6.0-7.5 in the absence of NaCl on nutrient agar. On the basis of 16S rRNA gene sequence similarity data, strain THG 01(T) was shown to belong to the family Flavobacteriaceae and was related to Flavobacterium anhuiense D3(T) (97.5 % similarity), Flavobacterium johnsoniae UW101(T) (96.8 %) and Flavobacterium denitrificans ED5(T) (96.7 %). 16S rRNA gene sequence similarities between the novel strain and members of other recognized species within the family Flavobacteriaceae were less than 96.7 %. The G+C content of the genomic DNA of strain THG 01(T) was 32.1 mol%. Phenotypic and chemotaxonomic data (major menaquinone was MK-6 and major fatty acids were iso-C(15 : 0), iso-C(15 : 0) 3-OH and C(16 : 1)ω7c and/or C(16 : 1)ω6c ) supported the affiliation of strain THG 01(T) to the genus Flavobacterium. DNA-DNA hybridization experiments showed that DNA-DNA relatedness values between strain THG 01(T) and its closest phylogenetic neighbours were below 11 %. The results of physiological and biochemical tests enabled strain THG 01(T) to be differentiated genotypically and phenotypically from recognized species of the genus Flavobacterium. The isolate therefore represents a novel species, for which the name Flavobacterium ginsenosidimutans sp. nov. is proposed, with THG 01(T) ( = KACC 14525(T) = JCM 16720(T)) as the type strain.

Flavobacterium ginsengiterrae sp. nov., isolated from a ginseng field.

A novel strain of Flavobacterium, DCY55(T), a Gram-negative, yellow-pigmented, rod-shaped, non-spore-forming and gliding-motile bacterium, was isolated from the soil of a ginseng field in South Korea. Phylogenetic analysis, based on the 16S rRNA sequence, demonstrated that strain DCY55(T) belongs to the genus Flavobacterium within the family Flavobacteriaceae. Strain DCY55(T) showed the highest similarity with F. johnsoniae UW101(T) (97.1%), F. ginsenosidimutans THG 01(T) (96.8%), F. defluvii EMB 117(T) (96.6%), F. banpakuense 15F3(T) (96.3%) and F. anhuiense D3(T) (95.8%). Chemotaxonomic results showed that strain DCY55(T) predominantly contains menaquinone MK-6, that its DNA G+C content is 36.1mol%, and that its major cellular fatty acids are iso-C(15:0), summed feature 3 (comprising iso-C(15:0) 2-OH and/or C(16:1) ω 7c) and C(16:0). The chemotaxonomic and genotypic characteristics support the taxonomic classification of strain DCY55(T) to the genus Flavobacterium. The results of physiological and biochemical tests confirmed that strain DCY55(T) is distinct from previously validated species. We conclude that strain DCY55(T) should be classified as a novel species of the genus Flavobacterium, for which the name Flavobacterium ginsengiterrae sp. nov. is proposed, with the type strain DCY55(T) (=KCTC 23319(T) = JCM 17337(T)).

Flavobacterium croceum sp. nov., isolated from activated sludge.

A Gram-negative, non-motile, rod-shaped bacterium, designated strain EMB47(T), was isolated from activated sludge performing enhanced biological phosphorus removal in a sequencing batch reactor. Growth was observed between 10 and 40 degrees C (optimum, 25-35 degrees C) and between pH 5.0 and 8.5 (optimum, pH 7.5-8.0). The predominant fatty acids of strain EMB47(T) were iso-C(16 : 0) 3-OH, iso-C(15 : 1) G, C(15 : 0), iso-C(15 : 0), iso-C(14 : 0) and iso-C(16 : 0) and it contained phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylcholine as polar lipids. The G+C content of the genomic DNA was 40.8 mol% and the major quinone was MK-6. Comparative 16S rRNA gene sequence analyses showed that strain EMB47(T) formed a distinct phyletic line within the genus Flavobacterium. The levels of 16S rRNA gene sequence similarity with respect to Flavobacterium species were below 94.7 %. On the basis of the phenotypic, chemotaxonomic and molecular data, strain EMB47(T) represents a novel species within the genus Flavobacterium, for which the name Flavobacterium croceum sp. nov. is proposed. The type strain is EMB47(T) (=KCTC 12611(T)=DSM 17960(T)).

Bacterial diversity in water samples from uranium wastes as demonstrated by 16S rDNA and ribosomal intergenic spacer amplification retrievals.

Bacterial diversity was assessed in water samples collected from several uranium mining wastes in Ger many and in the United States by using 16S rDNA and ribosomal intergenic spacer amplification retrievals. The results obtained using the 16S rDNA retrieval showed that the samples collected from the uranium mill tailings of Schlema/Alberoda, Germany, were predominated by Nitrospina-like bacteria, whereas those from the mill tailings of Shiprock, New Mexico, USA, were predominated by gamma-Pseudomonas and Frauteria spp. Additional smaller populations of the Cytophaga-Flavobacterium-Bacteroides group and alpha- and delta-Proteobacteria were identified in the Shiprock samples as well. Proteobacteria and Cytophaga-Flavobacterium-Bacteroides were also found in the third uranium mill tailings studied, Gittersee/Coschütz, Germany, but the groups of the predominant clones were rather small. Most of the clones of the Gittersee/Coschütz samples represented individual sequences, which indicates a high level of bacterial diversity. The samples from the fourth uranium waste studied, Steinsee Deponie B1, Germany, were predominantly occupied by Acinetobacter spp. The ribosomal intergenic spacer amplification retrieval provided results complementary to those obtained by the 16S rDNA analyses. For instance, in the Shiprock samples, an additional predominant bacterial group was identified and affiliated with Nitrosomonas sp., whereas in the Gittersee/Coschütz samples, anammox populations were identified that were not retrieved by the applied 16S rDNA approach.

Rapid mineralization of benzo[a]pyrene by a microbial consortium growing on diesel fuel.

A microbial consortium which rapidly mineralized the environmentally persistent pollutant benzo[a]pyrene was recovered from soil. The consortium cometabolically converted [7-(14)C]benzo[a]pyrene to (14)CO(2) when it was grown on diesel fuel, and the extent of benzo[a]pyrene mineralization was dependent on both diesel fuel and benzo[a]pyrene concentrations. Addition of diesel fuel at concentrations ranging from 0.007 to 0.2% (wt/vol) stimulated the mineralization of 10 mg of benzo[a]pyrene per liter 33 to 65% during a 2-week incubation period. When the benzo[a]pyrene concentration was 10 to 100 mg liter(-1) and the diesel fuel concentration was 0.1% (wt/vol), an inoculum containing 1 mg of cell protein per liter (small inoculum) resulted in mineralization of up to 17.2 mg of benzo[a]pyrene per liter in 16 days. This corresponded to 35% of the added radiolabel when the concentration of benzo[a]pyrene was 50 mg liter(-1). A radiocarbon mass balance analysis recovered 25% of the added benzo[a]pyrene solubilized in the culture suspension prior to mineralization. Populations growing on diesel fuel most likely promoted emulsification of benzo[a]pyrene through the production of surface-active compounds. The consortium was also analyzed by PCR-denaturing gradient gel electrophoresis of 16S rRNA gene fragments, and 12 dominant bands, representing different sequence types, were detected during a 19-day incubation period. The onset of benzo[a]pyrene mineralization was compared to changes in the consortium community structure and was found to correlate with the emergence of at least four sequence types. DNA from 10 sequence types were successfully purified and sequenced, and that data revealed that eight of the consortium members were related to the class Proteobacteria but that the consortium also included members which were related to the genera Mycobacterium and Sphingobacterium.

Application of gas-liquid chromatography to the routine identification of nonfermenting gram-negative bacteria in clinical specimens.

A total of 430 strains of glucose-nonfermenting gram-negative bacteria representing 35 species were analyzed for their cellular fatty acid composition by gas-liquid chromatography (GLC). On the basis of qualitative differences in their cellular fatty acid composition, these bacteria could be divided into 19 distinct chromatographic groups. Eight Pseudomonas species, Achromobacter xylosoxidans, group Vd, and Agrobacterium radiobacter were identified from their fatty acid compositions alone. The other glucose-nonfermenting gram-negative bacterial species studied here, classified within nine distinct GLC groups, were easily recognized by using the GLC fatty acid analysis supplemented with a limited number of conventional biochemical tests. The results support the hypothesis that bacterial fatty acid composition is rather specific and that qualitative GLC fatty acid analysis can be adapted in the clinical laboratory either to provide additional criteria for differentiation of closely related groups or to serve as a rapid and highly reproducible method for their routine identification.