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Rhizobium alvei sp. nov., isolated from a freshwater river.
Int. J. Syst. Evol. Microbiol.
PUBLISHED: 11-12-2014
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A bacterial strain designated TNR-22T was isolated from freshwater river in Taiwan and characterized using the polyphasic taxonomy approach. Cells of strain TNR-22T were faculative anaerobic, Gram-stain-negative, rod-shaped, motile by a single polar flagellum and forming cream colored colonies. Growth occurred at 4-45 °C (optimum, 25-30 °C), with 0-1.0 % NaCl (optimum, 0.5 %) and at pH 7.0-8.0 (optimum, pH 7.0). Strain TNR-22T did not form nodules on a legume plant, Macroptilium atropurpureum. The nifH gene encoding denitrogenase reductase was not detected by PCR. The major fatty acids (?10 %) of strain TNR-22T were C18:1 ?7c and C16:0. The DNA G+C content was 60.3 mol%. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, diphosphatidylglycerol, an uncharacterized aminoglycolipid and an uncharacterized phospholipid. Comparative analysis of the 16S rRNA gene sequences showed that strain TNR-22T constituted a distinct branch within the genus Rhizobium, showing the highest level of sequence similarity with respect to Rhizobium rosettiformans W3T (96.3 %). Phenotypic characteristics of the novel strain also differed from those of the closest related species of the genus Rhizobium. On the basis of the genotypic, chemotaxonomic and phenotypic data, strain TNR-22T represents a novel species in the genus Rhizobium, for which the name Rhizobium alvei sp. nov. is proposed. The type strain is TNR-22T (=BCRC 80408T =LMG 26895T =KCTC 23919T).
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Hanstruepera neustonica gen. nov., sp. nov., a zeaxanthin-producing member of the family Flavobacteriaceae isolated from estuarine water, and emendation of Sediminibacter furfurosus Khan et al. 2007 emend. Kwon et al. 2014, Mangrovimonas yunxiaonensis Li et al. 2013, An
Int. J. Syst. Evol. Microbiol.
PUBLISHED: 10-30-2014
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A Gram-staining-negative, strictly aerobic, yellowish-orange-pigmented, flexirubin-positive, rod-shaped, non-flagellated, non-spore-forming and non-gliding marine bacterium, designated strain CC-PY-50T, was isolated from estuarine water off Pingtung, Taiwan. Strain produced zeaxanthin as a major carotenoid pigment, and showed highest pairwise 16S rRNA gene sequence similarity to Bizionia hallyeonensis T-y7T (93.9 %) followed by Corallibacter vietnamensis KMM 6217T (93.8 %), Geojedonia litorea YCS-16T (93.7 %) and other Flavobacteriaceae members (<93.7 %). Strain CC-PY-50T established a distinct phyletic lineage associated with Mangrovimonas yunxiaonensis LYYY01T (93.1 % sequence similarity) with poor bootstrap support during neighbor-joining and maximum-likelihood phylogenetic analyses (37 % for each). The polar lipid profile of strain CC-PY-50T characterized to accommodate large number of unknown lipids including major amounts of three unidentified aminolipids and two unidentified lipids, and moderate amounts of an unidentified phospholipid, an unidentified glycolipid and an unidentified lipid. In addition, phosphatidylethanolamine was also detected in significant amounts. The major (>5 % of total) fatty acids were iso-C15:0, iso-C15:1 G, iso-C17:0 3-OH, C16:0 and C16:1 ?6c and/or C16:1 ?7c. The DNA G + C content was 37.1 mol% and menaquinone-6 (MK-6) was the sole respiratory quinone. Based on the phylogenetic evidence and several distinguishing phenotypic and chemotaxonomic features, strain CC-PY-50T is proposed to represent a novel genus and species of the family Flavobacteriaceae, for which the name Hanstruepera neustonica gen. nov., sp. nov. is proposed. The type strain of the type species Hanstruepera neustonica is CC-PY-50T (=JCM 19743T =BCRC 80747T). The emended descriptions of the species Sediminibacter furfurosus, Mangrovimonas yunxiaonensis, Antarcticimonas flava and Hoppeia youngheungensis are also proposed.
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Cribrihabitans neustonicus sp. nov., isolated from coastal surface seawater, and emended description of the genus Cribrihabitans Chen et al. 2014.
Int. J. Syst. Evol. Microbiol.
PUBLISHED: 09-01-2014
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A Gram-stain-negative, strictly aerobic, rod- or oval-shaped, motile, non-spore-forming bacterium, designated strain CC-AMHB-3(T), was isolated from coastal surface seawater off Hualien, Taiwan. The novel strain showed high pairwise 16S rRNA gene sequence similarities to Ruegeria mobilis NBRC 101030(T) (96.5?%), Ruegeria scottomollicae LMG 24367(T) (96.4?%), Phaeobacter aquaemixtae SSK6-1(T) (96.2?%), Phaeobacter daeponensis TF-218(T) (96.2?%), Cribrihabitans marinus CZ-AM5(T) (96.1?%) and other species of the family Rhodobacteraceae (?95.9?%). However, strain CC-AMHB-3(T) formed a distinct phyletic lineage associated with C. marinus CZ-AM5(T) during phylogenetic analyses. The polar lipid profile of strain CC-AMHB-3(T) included major amounts of diphosphatidylglycerol, phosphatidylglycerol and phosphatidylcholine; moderate amounts of phosphatidylethanolamine, an unidentified aminolipid, an unidentified phospholipid and an unidentified lipid; and trace amounts of an unidentified lipid and an unidentified phospholipid, which was qualitatively almost in line with that of C. marinus CZ-AM5(T) but remarkably distinct as compared with the type species of the genera Ruegeria (Ruegeria atlantica JCM 21234(T)) and Phaeobacter (Phaeobacter gallaeciensis JCM 21319(T)). In line with the fatty acid profile of C. marinus CZ-AM5(T), the major (>5?% of total) fatty acids of strain CC-AMHB-3(T) were C18?:?1?7c and/or C18?:?1?6c (summed feature 8), 11-methyl C18?:?1?7c and C16?:?0. The DNA G+C content was 66.7 mol%. Ubiquinone-10 (Q-10) was the sole respiratory quinone. Thus, based on the results of the polyphasic study presented here, strain CC-AMHB-3(T) is considered to represent a novel species of the genus Cribrihabitans, for which the name Cribrihabitans neustonicus sp. nov. is proposed; the type strain is CC-AMHB-3(T) (?=?JCM 19537(T)?=?BCRC 80695(T)). In addition, an emended description of the genus Cribrihabitans is also proposed.
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Description of Algoriphagus taiwanensis sp. nov., a xylanolytic bacterium isolated from surface seawater, and emended descriptions of Algoriphagus mannitolivorans, Algoriphagus olei, Algoriphagus aquatilis and Algoriphagus ratkowskyi.
Antonie Van Leeuwenhoek
PUBLISHED: 06-17-2014
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A novel, Gram-stain negative, strictly aerobic, oval or rod-shaped, red-pigmented, non-spore-forming xylanolytic bacterial strain, designated CC-PR-82(T), was isolated from surface seawater of Pingtung coast, Taiwan, and characterized by polyphasic taxonomy. Strain CC-PR-82(T) shared highest pairwise 16S rRNA gene sequence similarity to Algoriphagus mannitolivorans IMSNU 14012(T) (97.0 %) followed by 'A. boseongensis' BS-R1(T) (96.5 %) and A. olei CC-Hsuan-617(T) (95.6 %), whereas other (n = 26) Algoriphapus species shared 95.6-92.6 % sequence similarities. The novel strain further established a distinct phyletic lineage tightly associated with Algoriphagus species. The DNA-DNA hybridization value obtained between CC-PR-82(T) and A. mannitolivorans DSM 15301(T) was 29.0 % (33.4 % reciprocal using A. mannitolivorans DSM 15301(T) probe). The major (>5 % of total) fatty acids were identified as iso-C15:0, C16:1 ?6c and/or C16:1 ?7c, iso-C16:0, iso-C17:1 ?9c and/or C16:0 10-methyl, anteiso-C15:0 and C17:1 ?6c. Polar lipids included major amounts of an unidentified aminolipid and an unidentified lipid; moderate amounts of phosphatidylethanolamine, phosphatidylserine and an unidentified aminolipid; trace amounts of an unidentified phospholipid, an unidentified lipid and an unidentified glycolipid. The DNA G+C content was determined to be 42.3 mol%. Menaquinone-7 was the sole respiratory quinone. Based on the polyphasic characteristics, that are in line with those of Algoriphagus species, in addition to distinguishing phylogenetic and phenotypic features, strain CC-PR-82(T) appears to represent a novel species of the genus Algoriphagus, for which the name Algoriphagus taiwanensis sp. nov. (type strain CC-PR-82(T) = JCM 19755(T) = BCRC 80746(T)) is proposed. In addition, emended descriptions of the species A. mannitolivorans, A. aquatilis, A. olei and A. ratkowskyi are also proposed.
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Rhizobium straminoryzae sp. nov., isolated from the surface of rice straw.
Int. J. Syst. Evol. Microbiol.
PUBLISHED: 06-04-2014
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An aerobic, Gram-stain-negative, rod-shaped bacterium, designated strain CC-LY845(T), was isolated from the surface of rice straw in Taiwan. Cells were non-motile, and no flagellum was detected. Comparison of 16S rRNA gene sequences indicated that the strain was phylogenetically related to species of the genus Rhizobium, with closest similarity to Rhizobium pseudoryzae KCTC 23294(T) (97.6?%), R. rhizoryzae KCTC 23652(T) (97.0?%) and R. oryzae LMG 24253(T) (96.7?%); other species showed lower levels of similarity (<96.6?%). The DNA-DNA relatedness of strain CC-LY845(T) and R. pseudoryzae KCTC 23294(T) was 34.8±3.1?% (reciprocal value 39.2±2.2?%). Phylogenetic analysis based on the housekeeping atpD and recA genes showed that the novel strain could be distinguished from R. pseudoryzae KCTC 23294(T) (92.7 and 91.5?%, respectively) and other species of the genus Rhizobium. The temperature range for growth was 25-42 °C, the pH range was 5.0-9.0 and NaCl concentrations up to 4.0?% (w/v) were tolerated. Strain CC-LY845(T) did not form nodules on four different legumes, and the nodD and nifH genes were not detected by PCR. The major fatty acids were C16?:?0 and summed feature 8 (C18?:?1?7c/C18?:?1?6c). The polyamine pattern of strain CC-LY845(T) showed spermidine and putrescine as major polyamines. The predominant quinone system was ubiquinone 10 (Q-10). The DNA G+C content was 68.3±2.4 mol%. Base on its phylogenetic, phenotypic and chemotaxonomic features, strain CC-LY845(T) is proposed to represent a novel species within the genus Rhizobium, for which the name Rhizobium straminoryzae sp. nov. is proposed. The type strain is strain CC-LY845(T) (?=?BCRC 80698(T)?=?JCM 19536(T)).
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Gramella oceani sp. nov., a zeaxanthin-producing bacterium of the family Flavobacteriaceae isolated from marine sediment.
Int. J. Syst. Evol. Microbiol.
PUBLISHED: 05-16-2014
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A Gram-staining-negative, yellow-pigmented, strictly aerobic, zeaxanthin-producing, rod-shaped, non-endospore-forming, appendaged bacterial strain that exhibits gliding motility, designated CC-AMSZ-T(T), was isolated from marine sediment off coastal Kending, Taiwan. Strain CC-AMSZ-T(T) shared 94.9% and 96.7-94.1% 16S rRNA gene sequence similarities with Gramella echinicola KMM 6050(T) and other species of the genus Gramella, respectively, and formed a distinct phyletic lineage in phylogenetic trees. The major (?5% of the total) fatty acids were C(16?:?0), iso-C(15?:?0), anteiso-C(15?:?0), C(16?:?1)?6c and/or C(16?:?1)?7c and iso-C(17?:?1)?9c and/or C(16?:?0) 10-methyl. Phosphatidylethanolamine, six unidentified lipids and three unidentified aminolipids were the polar lipid components. The DNA G+C content was 38.6 mol%. The predominant respiratory quinone was menaquinone-6 (MK-6). Based on the phylogenetic distinctiveness and distinguishing phenotypic characteristics, strain CC-AMSZ-T(T) represents a novel species of the genus Gramella, for which the name Gramella oceani sp. nov. is proposed. The type strain is CC-AMSZ-T(T) (?=?JCM 18809(T)?=?BCRC 80547(T)).
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Paludibacterium paludis sp. nov., isolated from a marsh.
Int. J. Syst. Evol. Microbiol.
PUBLISHED: 05-06-2014
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A bacterial strain, designated KBP-21(T), was isolated from a water sample taken from the Banping Lake Wetland Park in Taiwan and characterized in a taxonomic study using a polyphasic approach. Cells of strain KBP-21(T) were Gram-stain-negative, facultatively anaerobic, poly-?-hydroxybutyrate-accumulating, motile rods that formed yellow colonies. Growth occurred at 15-40 °C (optimum, 30 °C), at pH 5.0-8.0 (optimum, pH 8.0) and with 0-2% NaCl (optimum, 0%). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain KBP-21(T) belonged to the genus Paludibacterium within the family Neisseriaceae of the class Betaproteobacteria and the closest related neighbour was Paludibacterium yongneupense 5YN8-15(T) with a 16S rRNA gene sequence similarity value of 96.4%. Strain KBP-21(T) contained summed feature 3 (comprising C16 : 1?7c and/or C16 : 1?6c), C16 : 0 and C18 : 1?7c as the predominant fatty acids. The major respiratory quinone was Q-8. The DNA G+C content of the genomic DNA was 62.1 mol%. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, one uncharacterized aminophospholipid and several uncharacterized phospholipids. On the basis of the genotypic, chemotaxonomic and phenotypic data, strain KBP-21(T) represents a novel species in the genus Paludibacterium, for which the name Paludibacterium paludis sp. nov. is proposed. The type strain is KBP-21(T) (?= BCRC 80514(T)? = LMG 27230(T) ?= KCTC 32182(T)).
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Pseudomonas hussainii sp. nov., isolated from droppings of a seashore bird, and emended descriptions of Pseudomonas pohangensis, Pseudomonas benzenivorans and Pseudomonas segetis.
Int. J. Syst. Evol. Microbiol.
PUBLISHED: 04-17-2014
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Two Gram-staining-negative, aerobic, rod-shaped, non-spore-forming bacterial strains that are motile by a monopolar flagellum, designated CC-AMH-11(T) and CC-AMHZ-5, were isolated from droppings of a seashore bird off the coast of Hualien, Taiwan. The strains showed 99.7% mutual pairwise 16S rRNA gene sequence similarity, while exhibiting <96.2% sequence similarity to strains of other species of the genus Pseudomonas (95.7-95.9% similarity with type species, Pseudomonas aeruginosa LMG 1242T), and formed a distinct co-phyletic lineage in the phylogenetic trees. The common major fatty acids (>5% of the total) were C18 : 1?7c and/or C18 : 1?6c (summed feature 8), C16 : 1?6c and/or C16 : 1?7c (summed feature 3), C16 : 0 and C12 : 0. Phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylserine, an unidentified lipid and an unidentified phospholipid were detected as common polar lipids. The DNA G+C contents of strains CC-AMH-11(T) and CC-AMHZ-5 were 61.1 and 61.6 mol%, respectively. The common major respiratory quinone was ubiquinone 9 (Q-9), and the predominant polyamine was putrescine. The DNA-DNA hybridization obtained between the two strains was 79.0% (reciprocal value 89.4% using CC-AMHZ-5 DNA as the probe). The very high 16S rRNA gene sequence similarity and DNA-DNA relatedness and the poorly distinguishable phenotypic features witnessed between CC-AMH-11(T) and CC-AMHZ-5 suggested unambiguously that they are two distinct strains of a single genomic species. However, the strains also showed several genotypic and phenotypic characteristics that distinguished them from other closely related species of Pseudomonas. Thus, the strains are proposed to represent a novel species of Pseudomonas, for which the name Pseudomonas hussainii sp. nov. is proposed. The type strain is CC-AMH-11(T) (?= JCM 19513(T)?= BCRC 80696(T)); a second strain of the same species is CC-AMHZ-5 (?= JCM 19512 = BCRC 80697). In addition, emended descriptions of the species Pseudomonas pohangensis, Pseudomonas benzenivorans and Pseudomonas segetis are also proposed.
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Description of Niveispirillum fermenti gen. nov., sp. nov., isolated from a fermentor in Taiwan, transfer of Azospirillum irakense (1989) as Niveispirillum irakense comb. nov., and reclassification of Azospirillum amazonense (1983) as Nitrospirillum amazonense gen. nov.
Antonie Van Leeuwenhoek
PUBLISHED: 04-15-2014
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A taxonomic study was carried out on a novel aerobic bacterial strain (designated CC-LY736(T)) isolated from a fermentor in Taiwan. Cells of strain CC-LY736(T) were Gram-stain negative, spiral-shaped and motile by means of a monopolar flagellum. Strain CC-LY736(T) shared the greatest degree of 16S rRNA gene sequence similarity to Azospirillum irakense DSM 11586(T) (97.2 %), Rhodocista centenaria JCM 21060(T) (96.3 %) and Rhodocista pekingensis JCM 11669(T) (96.1 %). The major fatty acids were C16:0, C16:1 ?5c, C19:0 cyclo ?8c, C18:1 ?7c/C18:1 ?6c, C16:0 3-OH and C18:1 2-OH. The predominant polar lipids included phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine, phosphatidyldimethylethanolamine and two unidentified glycolipids. The common major respiratory quinone was ubiquinone Q-10 and predominant polyamines were sym-homospermidine and putrescine. The DNA G+C content of strain CC-LY736(T) was 67.6 ± 0.1 mol %. During phylogenetic analysis, strain CC-LY736(T) formed a unique phyletic lineage associated with Rhodocista species. However, the combination of genetic, chemotaxonomic and physiological data clearly indicated that strain CC-LY736(T) was a novel representative of the family Rhodospirillaceae. Based on the polyphasic comparison, the name Niveispirillum fermenti gen. nov., sp. nov. is proposed; the type strain of the type species is CC-LY736(T) (= BCRC 80504(T) = LMG 27263(T)). In addition, the reclassifications of Azospirillum irakense as Niveispirillum irakense comb. nov. (type strain KBC1(T) = ATCC 51182(T) = BCRC 15764(T) = CIP 103311(T)), and Azospirillum amazonense as Nitrospirillum amazonense gen. nov., sp. nov. (type strain Am14(T) = ATCC 35119(T) = BCRC 14279(T) = DSM 3787(T)) are proposed based on the polyphasic taxonomic data obtained in this study.
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Rivicola pingtungensis gen. nov., sp. nov., a new member of the family Neisseriaceae isolated from a freshwater river.
Int. J. Syst. Evol. Microbiol.
PUBLISHED: 03-17-2014
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A bacterial strain, designated Npb-03(T), was isolated from a freshwater river in Taiwan and was characterized using a polyphasic taxonomic approach. The cells were Gram-reaction-negative, straight rod-shaped, non-motile, non-spore-forming and facultatively anaerobic. Growth occurred at 10-37 °C (optimum, 30-35 °C), at pH 6.0-8.0 (optimum, pH 6.0-7.0) and with 0-1.0% NaCl (optimum, 0%). The predominant fatty acids were summed feature 3 (comprising C(16?:?1)?7c and/or C(16?:?1)?6c) and C(16?:?0). The major isoprenoid quinone was Q-8 and the DNA G+C content was 64.1 mol%. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, an uncharacterized aminolipid and three uncharacterized phospholipids. The major polyamines were putrescine, 2-hydroxyputrescine, cadaverine and spermidine. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain Npb-03(T) forms a distinct lineage with respect to closely related genera within the family Neisseriaceae of the class Betaproteobacteria, most closely related to the genera Aquaspirillum, Laribacter, Leeia and Microvirgula, and the levels of 16S rRNA gene sequence similarity with respect to the type species of related genera are less than 93%. On the basis of the genotypic and phenotypic data, strain Npb-03(T) represents a novel genus and species of the family Neisseriaceae, for which the name Rivicola pingtungensis gen. nov., sp. nov. is proposed. The type strain is Npb-03(T) (?=?BCRC 80376(T)?=?LMG 26668(T)?=?KCTC 23712(T)).
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Gramella planctonica sp. nov., a zeaxanthin-producing bacterium isolated from surface seawater, and emended descriptions of Gramella aestuarii and Gramella echinicola.
Antonie Van Leeuwenhoek
PUBLISHED: 01-30-2014
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A Gram-stain negative, strictly aerobic, zeaxanthin-producing, rod-shaped, non-spore-forming bacterial strain which is motile by gliding, designated CC-AMWZ-3(T), was isolated from surface seawater off coastal Kending, Taiwan. Strain CC-AMWZ-3(T) was found to share 93.3 % and 96.0-92.4 % pairwise 16S rRNA gene sequence similarity to Gramella echinicola KMM 6050(T) and other Gramella species, respectively, and formed distinct phyletic lineage during phylogenetic analysis. The major fatty acids were identified as C16:0, iso-C15:0, anteiso-C15:0, C16:1 ?6c and/or C16:1 ?7c and iso-C17:1 ?9c and/or C16:0 10-methyl. Polar lipids were found to include phosphatidylethanolamine, six unidentified lipids and three unidentified aminolipids. The DNA G+C content was determined to be 40.6 mol%. Menaquinone-6 was the sole respiratory quinone identified and triamine-sym-homospermidine was the predominant polyamine. Based on the polyphasic characteristics that are in line with those of Gramella species, in addition to distinguishing phylogenetic and phenotypic features, strain CC-AMWZ-3(T) appears to represent a novel species of the genus Gramella, for which the name Gramella planctonica sp. nov. (type strain CC-AMWZ-3(T) = JCM 18807(T) = BCRC 80553(T)) is proposed. In addition, emended descriptions of the species Gramella aestuarii and Gramella echinicola are also proposed.
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Impacts of industrial waste resources on maize (Zea mays L.) growth, yield, nutrients uptake and soil properties.
Waste Manag
PUBLISHED: 01-09-2014
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Discharging untreated highly acidic (pH<4.0), organic and nutrients rich monosodium glutamate wastewater (MW), and highly alkaline (pH>10.0) paper-mill wastewater (PW) causes environmental pollution. When acidity of MW neutralized (pH 6.5±0.1) with PW and lime (treatments represented as MW+PW and MW+Lime), then MW may be utilized as a potential source of nutrients and organic carbon for sustainable food production. Objectives of this study were to compare the effects of PW and lime neutralized MW and chemical fertilizers on maize (Zea mays L. cv. Snow Jean) plant growth, yield, nutrients uptake, soil organic matter and humic substances. The field experiment was carried out on maize using MW at 6000 L ha(-1). Impacts of the MW application on maize crop and soil properties were evaluated at different stages. At harvest, plant height, and plant N and K uptake were higher in MW treatment. Leaf area index at 60 days after sowing, plant dry matter accumulation at harvest, and kernels ear(-1) and 100-kernel weight were higher in MW+Lime treatment. Kernel N, P, K, Mn, Fe and Zn, and plant Zn uptake were highest in MW+Lime. Plant Fe uptake, and soil organic matter and humic substances were highest in MW+PW. The MW+PW and MW+Lime treatments exhibited comparable results with chemically fertilized treatment. The MW acidity neutralized with lime showed positive impacts on growth, yield and nutrients uptake; nevertheless, when MW pH neutralized with PW has an additional benefit on increase in soil organic matter and humic substances.
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Novosphingobium arabidopsis sp. nov., a novel DDT-resistant bacterium isolated from the Arabidopsis thaliana rhizosphere.
Int. J. Syst. Evol. Microbiol.
PUBLISHED: 10-24-2013
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An aerobic, Gram-stained-negative, rod-shaped, DDT-resistant bacterium (defined strain CC-ALB-2T) was isolated from the Arabidopsis thaliana rhizosphere. Strain CC-ALB-2T is able to grow at 25-37°C, pH 5.0-8.0, NaCl 1.0% (w/v) and tolerate DDT up to 200 mg l-1. The 16S rRNA gene sequence analysis of strain CC-ALB-2T showed highest sequence similarity to Novosphingobium stygium KCTC 2891T (97.1%) and Novosphingobium soli DSM 22821T (96.8%), and showed lower levels of similarity (<97.0%) to other Novosphingobium species. The major fatty acid profile consists of C14:0 2OH (13.1%), C16:0 (10.0%), C15:0 iso 3OH (5.8%), C16:1 ?7c / C16:1 ?6c (24.7%) and C18:1 ?7c / C18:1 ?6c (42.4%). The polar lipid profile constitutes sphingoglycolipid, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidyldimethylethanolamine, phosphatidylglycerol and phosphatidyl choline. The polyamine pattern showed predominance of spermidine as major polyamine. The predominant quinone system is ubiquinone (Q-10). The DNA G+C content is 68.9±0.1 mol%. Base on the phylogenetic, phenotypic and chemotaxonomic features, strain CC-ALB-2T is proposed to represent a novel species within the genus Novosphingobium for which the name Novosphingobium arabidopsis sp. nov. (=BCRC 80571T =JCM 18896T) is proposed.
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Robertkochia marina gen. nov., sp. nov., of the family Flavobacteriaceae isolated from surface seawater, and emended descriptions of the genera Joostella and Galbibacter.
Int. J. Syst. Evol. Microbiol.
PUBLISHED: 10-14-2013
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A Gram-staining-negative, orange-pigmented, strictly aerobic, carotenoid-producing, rod-shaped, non-flagellated, non-spore-forming bacterium motile by gliding designated strain CC-AMO-30DT was isolated from surface seawater collected near Taichung harbor, Taiwan. Strain CC-AMO-30DT shared pairwise 16S rRNA gene sequence similarities of 94.8, 93.7 and 92.5 % to the type species of the genera Joostella, Pustulibacterium and Galbibacter, respectively, and formed a distinct monophyletic lineage in phylogenetic trees. The major fatty acids (? 5 % of total fatty acids) were iso-C 15:1 G, iso-C15:0, iso-C17:0 3-OH, iso-C15:0 3-OH, iso-C16:0 and anteiso-C15:0. Polar lipid profile consisted of phosphatidylethanolamine, four unidentified lipids, two unidentified aminolipids and an unidentified phospholipid. The major polyamine was triamine sym-homospermidine. The DNA G + C content was 47.1 mol% and the predominant respiratory quinone was menaquinone-6 (MK-6). Based on the phylogenetic distinctiveness, and distinguishing phenotypic and chemotaxonomic characteristics, strain CC-AMO-30DT represents a novel genus and species of the family Flavobacteriaceae, for which the name Robertkochia marina gen. nov., sp. nov. is proposed; the type strain of the type species is CC-AMO-30DT (= JCM 18552T = BCRC 80469T). Emended descriptions of the genera Joostella and Galbibacter are also proposed.
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Chitinophaga taiwanensis sp. nov., a novel bacterium isolated from the Arabidopsis thaliana rhizosphere.
Int. J. Syst. Evol. Microbiol.
PUBLISHED: 10-04-2013
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An aerobic, Gram-negative, rod-shaped bacterium (strain CC-ALB-1T) was isolated from the Arabidopsis thaliana rhizosphere. Strain CC-ALB-1T is able to grow at 20-30 °C, pH 5.0-8.0 and NaCl 1.0% (w/v). The 16S rRNA gene sequence analysis of strain CC-ALB-1T showed highest sequence similarity to Chitinophaga ginsengisegetis KCTC 12654T (96.9%) and Chitinophaga niastensis JCM 15441T (96.7%), and other species showed lower levels of similarity (<97.0%) to all other Chitinophaga species. The fatty acid profile consists of C15:0 iso, C17:0 iso 3OH, C15:1 ?5c, C16:1 ?5c and C16:1 ?7c/C16:1 ?6c. The polar lipid profile constitutes phosphatidylethanolamine (PE), unidentified aminolipids (AL1-2) and unidentified lipids (L1-5). The predominant quinone system is menaquinone (MK-7). The DNA G+C content is 53.4±0.4 mol%. Based on the phylogenetic, phenotypic and chemotaxonomic features, strain CC-ALB-1T is proposed to represent a novel species within the genus Chitinophaga for which the name Chitinophaga taiwanensis sp. nov. (=BCRC 80570T =JCM 18895T) is proposed.
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Aquibacter zeaxanthinifaciens gen. nov., sp. nov., a zeaxanthin-producing bacterium of the family Flavobacteriaceae isolated from surface seawater, and emended descriptions of the genera Aestuariibaculum and Gaetbulibacter.
Int. J. Syst. Evol. Microbiol.
PUBLISHED: 09-18-2013
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A Gram-staining-negative, strictly aerobic, rod-shaped, non-flagellated, non-spore-forming and gliding marine bacterium designated strain CC-AMZ-304T was isolated from coastal surface seawater near Taichung harbor, Taiwan. Strain CC-AMZ-304T predominantly synthesized zeaxanthin and thus formed yellow-colored colonies on marine agar. The novel strain showed unstable phylogenetic position, although sharing high pairwise 16S rRNA gene sequence similarities of 95.9-94.9, 95.7 and 95.1-93.9 % with Gaetbulibacter species (n=4), Aestuariibaculum suncheonense SC17T and Bizionia species (n=7), respectively. The polar lipid profile of strain CC-AMZ-304T consisted of phosphatidylethanolamine, five unidentified lipids, one unidentified phospholipid, two unidentified aminolipids and one unidentified glycolipid. The major (> 5 % of the total) fatty acids were C15:0 iso, C15:1 iso G, C17:0 iso 3-OH, C15:0 iso 3-OH and C 15:1 ?5c. The DNA G + C content was 36.0 mol%. Menaquinone-6 (MK-6) was the sole respiratory quinone and the major polyamine was triamine sym-homospermidine. Phylogenetic distinctiveness, unique polar lipid composition, presence of significant amounts of branched hydroxyl fatty acids (C17:0 iso 3-OH and C15:0 iso 3-OH ) and of low amount of C15:0 anteiso, and several additional distinguishing biochemical features clearly discriminated strain CC-AMZ-304T from the type species of the genera Aestuariibaculum and Gaetbulibacter. Thus, based on the present polyphasic evidences, strain CC-AMZ-304T is proposed to represent a novel genus and species within the family Flavobacteriaceae, for which the name Aquibacter zeaxanthinifaciens gen. nov., sp. nov. proposed; the type strain is of the type species is CC-AMZ-304T (= JCM 18557T = BCRC 80463T). Emended descriptions of the genera Aestuariibaculum and Gaetbulibacter are also proposed.
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Lacibacterium aquatile gen. nov., sp. nov., a new member of the family Rhodospirillaceae isolated from a freshwater lake.
Int. J. Syst. Evol. Microbiol.
PUBLISHED: 09-03-2013
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A bacterial strain designated LTC-2(T) was isolated from a freshwater lake in Taiwan and characterized using a polyphasic taxonomic approach. Cells of strain LTC-2(T) were Gram-reaction-negative, facultatively anaerobic, poly-?-hydroxybutyrate-accumulating, motile by means of a monopolar flagellum, non-spore-forming, slightly curved rods surrounded by a thick capsule and formed creamy white colonies. Growth occurred at 10-37 °C (optimum, 20-30 °C), at pH 6.0-9.0 (optimum, pH 7.0-8.0) and with 0-1.0?% NaCl (optimum, 0?%). The predominant fatty acids were C18?:?1?7c, summed feature 3 (comprising C16?:?1?7c and/or C16?:?1?6c) and C16?:?0. The major isoprenoid quinone was Q-10 and the DNA G+C content was 58.5 mol%. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylmonomethylethanolamine, phosphatidyldimethylethanolamine, two uncharacterized phospholipids and two uncharacterized aminophospholipids. The major polyamines were putrescine, homospermidine and spermidine. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain LTC-2(T) forms a distinct lineage with respect to closely related genera in the family Rhodospirillaceae, most closely related to the genera Elstera and Dongia, and the levels of 16S rRNA gene sequence similarity with respect to the type species of related genera were less than 94?%. On the basis of the genotypic and phenotypic data, strain LTC-2(T) represents a novel genus and species of the family Rhodospirillaceae, for which the name Lacibacterium aquatile gen. nov., sp. nov. is proposed. The type strain is LTC-2(T) (?=?BCRC 80445(T)?=?LMG 26999(T)?=?KCTC 32017(T)).
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Kordia aquimaris sp. nov., a zeaxanthin-producing member of the family Flavobacteriaceae isolated from surface seawater, and emended description of the genus Kordia.
Int. J. Syst. Evol. Microbiol.
PUBLISHED: 08-30-2013
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A Gram-staining-negative, strictly aerobic, rod-shaped, non-flagellated, non-spore-forming and gliding marine bacterium designated strain CC-AMZ-301(T) was isolated from coastal surface seawater near Taichung harbour, Taiwan. Strain CC-AMZ-301(T) predominantly synthesized zeaxanthin and thus formed yellow colonies on marine agar. The novel strain showed high pairwise 16S rRNA gene sequence similarity to Kordia periserrulae IMCC1412(T) (95.0?%), K. algicida KCTC 8814P(T) (94.4?%) and K. antarctica IMCC3317(T) (94.2?%), and formed a phylogenetic lineage tightly associated with species of the genus Kordia. The polar lipid profile of strain CC-AMZ-301(T) consisted of three unidentified lipids, three unidentified aminolipids and one unidentified phospholipid. The major fatty acids (>5?% of total) were iso-C17?:?0 3-OH, iso-C15?:?0, summed feature 3 (C16?:?1?7c and/or C16?:?1?6c) and summed feature 9 (iso-C17?:?1?9c and/or 10-methyl C16?:?0). The DNA G+C content was 36.4 mol%. Menaquinone 6 (MK-6) was the predominant respiratory quinone. The major polyamine was the triamine sym-homospermidine. Based on evidence from the present polyphasic study, strain CC-AMZ-301(T) is proposed to represent a novel species of the genus Kordia, for which the name Kordia aquimaris sp. nov. is proposed; the type strain is CC-AMZ-301(T) (?=?JCM 18556(T)?=?BCRC 80464(T)). An emended description of the genus Kordia is also proposed.
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Luteibaculum oceani gen. nov., sp. nov., a carotenoid-producing, lipolytic bacterium isolated from surface seawater, and emended description of the genus Owenweeksia Lau et al. 2005.
Int. J. Syst. Evol. Microbiol.
PUBLISHED: 08-29-2013
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A yellow-pigmented, Gram-staining-negative, strictly aerobic, rod-shaped, non-flagellated, non-spore-forming, lipolytic and gliding marine bacterium designated strain CC-AMWY-103B(T) was isolated from surface seawater collected at Kending, Taiwan. The strain shared the highest 16S rRNA gene sequence similarity of 89.4?% with Owenweeksia hongkongensis JCM 12287(T) and Brumimicrobium mesophilum YH207(T), and established a distinct phyletic lineage associated with the members of the family Cryomorphaceae. The polar lipid profile of strain CC-AMWY-103B(T) consisted of phosphatidylethanolamine, ten unidentified lipids and four unidentified aminolipids. The major fatty acids (>5?% of the total) were iso-C15?:?0, iso-C15?:?1 G, C15?:?1?5c, iso-C17?:?0 3-OH and C15?:?1?8c. The DNA G+C content was 44.2±0.3 mol%. The predominant respiratory quinone was menaquinone-6 (MK-6) and the major polyamine was spermidine. Based on its genetic, phylogenetic, phenotypic and chemotaxonomic distinctiveness, strain CC-AMWY-103B(T) is proposed to represent a distinct member of the family Cryomorphaceae, for which the name Luteibaculum oceani gen. nov., sp. nov. is proposed; the type strain of Luteibaculum oceani is CC-AMWY-103B(T) (?=?JCM 18817(T)?=?BCRC 80551(T)). An emended description of the genus Owenweeksia is also proposed.
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Pseudomonas guguanensis sp. nov., a gammaproteobacterium isolated from a hot spring.
Int. J. Syst. Evol. Microbiol.
PUBLISHED: 08-05-2013
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An aerobic, Gram-stain-negative, rod-shaped bacterium (designated strain CC-G9A(T)), motile by a polar-flagellum, was isolated from a hot spring water sample in Taiwan. Strain CC-G9A(T) could grow at 20-42 °C, pH 6.0-10.0 and tolerate up to 7?% (w/v) NaCl. The 16S rRNA gene sequence analysis of strain CC-G9A(T) showed pairwise sequence similarity to Pseudomonas mendocina LMG 1223(T) (97.7?%), Pseudomonas alcaligenes ATCC 14909(T) (97.8?%), Pseudomonas alcaliphila DSM 17744(T) (97.8?%), Pseudomonas toyotomiensis JCM 15604(T) (97.6?%), Pseudomonas oleovorans subsp. lubricantis DSM 21016(T) (97.6?%) and Pseudomonas argentinensis BCRC 17807(T) (97.5?%), and lower sequence similarity to other species of the genus Pseudomonas. According to DNA-DNA association analysis, the relatedness of strain CC-G9A(T) to P. mendocina BCRC 10458(T), P. alcaliphila DSM 17744(T), P. alcaligenes BCRC 11893(T), P. oleovorans subsp. lubricantis DSM 21016(T), P. argentinensis BCRC 17807(T) and P. oleovorans subsp. oleovorans BCRC 11902 was 55.1±3.1, 13.7±1.5, 14.1±1.8, 58.5±1.1, 28.9±2.0 and 28.6±1.8?%, respectively. The evolutionary trees reconstructed based on 16S rRNA, gyrB and rpoB gene sequences revealed varying phylogenetic neighbourhoods of strain CC-G9A(T) with regard to the most closely related type strains. The predominant quinone system was ubiquinone (Q-9) and the DNA G+C content was 64.3±1.3 mol%. The major fatty acids were C10?:?0 3-OH, C12?:?0, C12?:?0 3-OH, C16?:?0 and summed features 3 and 8 consisting of C16?:?1?7c/C16?:?1?6c and C18?:?1?7c/C18?:?1?6c, respectively. The major polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine and phosphatidylglycerol. According to distinct phylogenetic, phenotypic and chemotaxonomic features, strain CC-G9A(T) is proposed to represent a novel species within the genus Pseudomonas for which the name Pseudomonas guguanensis sp. nov. is proposed. The type strain is CC-G9A(T) (?=?BCRC 80438(T)?=?JCM 18416(T)).
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Shimia biformata sp. nov., isolated from surface seawater, and emended description of the genus Shimia Choi and Cho 2006.
Int. J. Syst. Evol. Microbiol.
PUBLISHED: 08-01-2013
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A novel, Gram-staining-negative, non-flagellated, oval or short-rod-shaped, strictly aerobic and non-spore-forming marine bacterium, designated strain CC-AMW-C(T), was isolated from coastal surface seawater in Kending County, Taiwan. Cells of strain CC-AMW-C(T) displayed unusual morphology and formed colourless or beige colonies on marine agar. The isolate shared pairwise 16S rRNA gene sequence similarities of 97.2 and 97.1?% with Shimia marina BCRC 80068(T) and Shimia isoporae BCRC 80085(T), respectively, and established a discrete phyletic lineage closely associated with the members of the genus Shimia. DNA-DNA hybridization values indicated <18.2?% genomic relatedness with species of the genus Shimia. The polar lipid profile of strain CC-AMW-C(T) comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, two unidentified aminolipids, four unidentified lipids and an unidentified phospholipid. The predominant fatty acids were C18?:?1?7c and/or C18?:?1?6c (summed feature 8; 75.5?%). The DNA G+C content was 61.2 mol%. The predominant respiratory quinone was ubiquinone Q-10 and the major polyamine was cadaverine. The chemotaxonomic evidence, including extraordinary amounts of C18?:?1?7c and/or C18?:?1?6c, major polar lipids, polyamine, quinone and DNA G+C contents of CC-AMW-C(T), was in line with that of the members of the genus Shimia. Thus, strain CC-AMW-C(T) should be classified as a novel species of the genus Shimia, for which the name Shimia biformata sp. nov. is proposed. The type strain is CC-AMW-C(T) (?=?JCM 18818(T)?=?BCRC 80548(T)). An emended description of the genus Shimia is also proposed.
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Sphingomicrobium marinum sp. nov. and Sphingomicrobium flavum sp. nov., isolated from surface seawater, and emended description of the genus Sphingomicrobium.
Int. J. Syst. Evol. Microbiol.
PUBLISHED: 07-16-2013
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Two Gram-staining-negative, yellow-pigmented, rod-shaped, strictly aerobic, non-flagellated and non-spore-forming amylolytic marine bacterial strains, designated CC-AMZ-30M(T) and CC-AMZ-30N(T), were isolated from coastal surface seawater in Taiwan. Strain CC-AMZ-30M(T) shared pairwise 16S rRNA gene sequence similarities of 95.8, 95.0 and <94.0?% to Sphingomicrobium lutaoense CC-TBT-3(T), Sphingomicrobium astaxanthinifaciens CC-AMO-30B(T) and other sphingomonads, respectively. Strain CC-AMZ-30N(T) shared 97.0, 96.7, 95.0 and <95.1?% similarities to strain CC-AMZ-30M(T), Sphingomicrobium lutaoense CC-TBT-3(T), Sphingomicrobium astaxanthinifaciens CC-AMO-30B(T) and other sphingomonads, respectively. The common polar lipids of the two strains include a signature glycolipid (GL2), diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and sphingoglycolipid in major amounts besides moderate-to-trace amounts of an unidentified aminolipid and several unidentified glycolipids. Both strains contained C18?:?1?7c/C18?:?1?6c, C16?:?1?7c/C16?:?1?6c, C16?:?0 and C18?:?1 2-OH as major (>5?% of the total) fatty acids. Strains CC-AMZ-30M(T) and CC-AMZ-30N(T) had DNA G+C contents of 64.2 and 65.2 mol%, respectively. The major polyamine was spermidine in strain CC-AMZ-30M(T) and triamine sym-homospermidine in strain CC-AMZ-30N(T). Both strains contained ubiquinone Q-10 as the predominant respiratory quinone. Differential phylogenetic and chemotaxonomic evidence including the presence of characteristic GL2, C18?:?1 2-OH and several other phenotypic features supported the classification of strains CC-AMZ-30M(T) and CC-AMZ-30N(T) as two novel species of the genus Sphingomicrobium, for which we propose the names Sphingomicrobium marinum sp. nov. and Sphingomicrobium flavum sp. nov., respectively; corresponding type strains are Sphingomicrobium marinum CC-AMZ-30M(T) (?=?JCM 18554(T)?=?BCRC 80466(T)) and Sphingomicrobium flavum CC-AMZ-30N(T) (?=?JCM 18555(T)?=?BCRC 80467(T)). An emended description of the genus Sphingomicrobium is also proposed.
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Zeaxanthin production by novel marine isolates from coastal sand of India and its antioxidant properties.
Appl. Biochem. Biotechnol.
PUBLISHED: 07-08-2013
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Zeaxanthin carotenoids are class of commercially important natural products and diverse biomolecules produced by plants and many microorganisms. Bacteria often produce a cocktail of polar and nonpolar carotenoids limiting their industrial applications. Marine members of the family Flavobacteriaceae are known to produce potential carotenoids such as astaxanthin and zeaxanthin. A few bacterial species have been reported for the predominant production zeaxanthin. Here, we report the molecular identification of the zeaxanthin as a major carotenoid produced by two novel bacteria (YUAB-SO-11 and YUAB-SO-45) isolated from sandy beaches of South West Coast of India and the effect of carbon sources on the production of zeaxanthin. The strains were identified based on the 16S rRNA gene sequencing as a member of genus Muricauda. The closest relatives of YUAB-SO-11 and YUAB-SO-45 were Muricauda aquimarina (JCM 11811(T)) (98.9 %) and Muricauda olearia (JCM 15563(T)) (99.2 %), respectively, indicating that both of these strains might represent a novel species. The highest level of zeaxanthin production was achieved (YUAB-SO-11, 1.20 ± 0.11 mg g(-1)) and (YUAB-SO-45, 1.02 ± 0.13 mg g(-1)) when cultivated in marine broth supplemented with 2 % NaCl (pH 7) and incubated at 30 °C. Addition of 0.1 M glutamic acid, an intermediate of citric acid cycle, enhanced the zeaxanthin production as 18 and 14 % by the strains YUAB-SO-11 and YUAB-SO-45 respectively. The zeaxanthin showed in vitro nitric oxide scavenging, inhibition of lipid peroxidation, and 2,2-diphenyl-1-picryl hydrazyl scavenging activities higher than the commercial zeaxanthin. The results of this study suggest that two novel strains YUAB-SO-11 and YUAB-SO-45 belonging to genus Muricauda produce zeaxanthin as a predominant carotenoid, and higher production of zeaxanthin was achieved on glutamic acid supplementation. The pigment showed good in vitro antioxidant activity, which can be exploited further for commercial applications.
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Description of Noviherbaspirillum malthae gen. nov., sp. nov., isolated from an oil-contaminated soil, and proposal to reclassify Herbaspirillum soli, Herbaspirillum aurantiacum, Herbaspirillum canariense and Herbaspirillum psychrotolerans as Noviherbaspi
Int. J. Syst. Evol. Microbiol.
PUBLISHED: 06-07-2013
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An aerobic, Gram-negative, rod-shaped bacterium with polar flagella, strain CC-AFH3(T), was isolated from an oil-contaminated site located in Kaohsiung county, Taiwan. Strain CC-AFH3(T) grew at 20-40 °C, pH 5.0-10.0 and <2?% (w/v) NaCl. 16S rRNA gene sequence analysis indicated that strain CC-AFH3(T) showed the greatest degree of similarity to Herbaspirillum soli SUEMI10(T) (96.5?%), H. aurantiacum SUEMI08(T) (96.3?%), H. canariense SUEMI03(T) (96.0?%), H. psychrotolerans PB1(T) (95.4?%) and members of other Herbaspirillum species (94.1-95.2?%), and lower similarity to members of other genera (<94?%). Phylogenetic analyses also positioned the novel strain in the genus Herbaspirillum as an independent lineage. The major fatty acids in strain CC-AFH3(T) were C10?:?0 3-OH, C12?:?0, C14?:?0 2-OH, C16?:?0, iso-C15?:?0 3-OH, C17?:?0 cyclo, C16?:?1?7c/C16?:?1?6c and C18?:?1?7c/C18?:?1?6c. The major polar lipids of strain CC-AFH3(T) were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylcholine. The predominant quinone was ubiquinone 8 (Q-8) and the DNA G+C content was 63.4 mol%. On the basis of 16S rRNA gene sequence analysis in combination with physiological and chemotaxonomic data, strain CC-AFH3(T) represents a novel species in a new genus, for which we propose the name Noviherbaspirillum malthae gen. nov., sp. nov.; the type strain of Noviherbaspirillum malthae is CC-AFH3(T) (?=?BCRC 80516(T)?=?JCM 18414(T)). We also propose the reclassification of Herbaspirillum soli, Herbaspirillum aurantiacum, Herbaspirillum canariense and Herbaspirillum psychrotolerans as Noviherbaspirillum soli comb. nov. (type strain SUEMI10(T)?=?LMG 26149(T)?=?CECT 7840(T)), Noviherbaspirillum aurantiacum comb. nov. (type strain SUEMI08(T)?=?LMG 26150(T)?=?CECT 7839(T)), Noviherbaspirillum canariense comb. nov. (type strain SUEMI03(T)?=?LMG 26151(T)?=?CECT 7838(T)) and Noviherbaspirillum psychrotolerans comb. nov. (type strain PB1(T)?=?DSM 26001(T)?=?LMG 27282(T)), respectively. An emended description of Herbaspirillum seropedicae is also presented.
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Azoarcus olearius sp. nov., a nitrogen-fixing bacterium isolated from oil-contaminated soil.
Int. J. Syst. Evol. Microbiol.
PUBLISHED: 05-03-2013
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A novel nitrogen-fixing strain, designated DQS-4(T), was isolated from oil-contaminated soil in Taiwan and was characterized using a polyphasic taxonomic approach. Cells of strain DQS-4(T) stained Gram-negative, contained poly-?-hydroxybutyrate granules and were motile rods, surrounded by a thin capsule. Cells displayed a strictly aerobic type of metabolism and fixed nitrogen microaerobically. Growth occurred at 10-45 °C (optimum, 35-40 °C), at pH 7.0-8.0 (optimum, pH 7.0) and with 0-2?% NaCl (optimum, 0.5-1?%). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain DQS-4(T) belonged to the genus Azoarcus, and its closest neighbours were Azoarcus indigens VB32(T) and Azoarcus communis SWub3(T), with sequence similarities of 97.4 and 96.4?%, respectively. The major cellular fatty acids of strain DQS-4(T) were summed feature 3 (comprising C16?:?1?7c and/or C16?:?1?6c), C16?:?0 and C18?:?1?7c. The major cellular hydroxy fatty acid was C10?:?0 3-OH. The DNA G+C content was 64.5 mol%. The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and several uncharacterized aminophospholipids and phospholipids. The mean level of DNA-DNA relatedness between strain DQS-4(T) and A. indigens LMG 9092(T) was 27.4?%. On the basis of the genotypic and phenotypic data, strain DQS-4(T) represents a novel species in the genus Azoarcus, for which the name Azoarcus olearius sp. nov. is proposed. The type strain is DQS-4(T) (?=?BCRC 80407(T)?=?KCTC 23918(T)?=?LMG 26893(T)).
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Azospirillum fermentarium sp. nov., a nitrogen-fixing species isolated from a fermenter.
Int. J. Syst. Evol. Microbiol.
PUBLISHED: 05-03-2013
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An aerobic, Gram-stain-negative, spiral or rod-shaped, non-spore-forming, diazotrophic bacterium (strain CC-LY743(T)) was isolated from a fermentative tank in Taiwan. Strain CC-LY743(T) was able to grow at 20-37 °C and pH 6.0-8.0 and tolerated up to 3.0?% (w/v) NaCl. It was positive for nitrogen fixation, with activity of 10.6 nmol ethylene h(-1). 16S rRNA gene sequence analysis of strain CC-LY743(T) showed highest similarity to Azospirillum picis DSM 19922(T) (96.1?%), Azospirillum oryzae JCM 21588(T) (96.0?%) and Azospirillum rugosum DSM 19657(T) (96.0?%) and lower similarity (<96.0?%) to all other Azospirillum species. Highest nifH gene sequence similarities were obtained with Azospirillum brasilense BCRC 12270(T) (92.0?%), Azospirillum formosense BCRC 80273(T) (92.3?%) and A. rugosum DSM 19657(T) (91.8?%). It was positive in the rapid identification by a genus-specific primer set. The predominant quinone system was ubiquinone 10 (Q-10) and the DNA G+C content was 69.6±0.1 mol%. The major fatty acids found in strain CC-LY743(T) were n-C16?:?0, C19?:?0 cyclo ?8c, C14?:?0 3-OH/C16?:?1 iso I, C16?:?1?7c/C16?:?1?6c and C18?:?1?7c/C18?:?1?6c. Based on its phylogenetic, phenotypic and chemotaxonomic features, strain CC-LY743(T) is considered to represent a novel species within the genus Azospirillum for which the name Azospirillum fermentarium sp. nov. is proposed. The type strain is CC-LY743(T) (?=?BCRC 80505(T)?=?JCM 18688(T)?=?LMG 27264(T)).
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Sphingomicrobium astaxanthinifaciens sp. nov., an astaxanthin-producing glycolipid-rich bacterium isolated from surface seawater and emended description of the genus Sphingomicrobium.
Int. J. Syst. Evol. Microbiol.
PUBLISHED: 03-22-2013
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A Gram-stain-negative, rod-shaped, strictly aerobic, flagellated and non-spore-forming marine bacterium designated strain CC-AMO-30B(T) was isolated from coastal surface seawater, Taiwan. Strain CC-AMO-30B(T) synthesized astaxanthin [40 µg (g dry weight)(-1)] and formed reddish-orange-coloured colonies on marine agar (Difco 2216). The strain showed highest pairwise 16S rRNA gene sequence similarity to Sphingomicrobium lutaoense CC-TBT-3(T) (96.4%) followed by other members of the family Sphingomonadaceae (<94%) and established a discrete phyletic lineage associated with the former. The polar lipid profile constituted a remarkable number of unidentified glycolipids (GL1-8), in addition to diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, sphingoglycolipid and two unidentified lipids (L1-2). The major fatty acids (>5% of total fatty acids) were C(18:1)?7c/C(18:1)?6c (summed feature 8), C(16:1)?7c/C(16:1)?6c (summed feature 3), C(18:1) 2-OH, methyl C(18:1)?7c, C(17:1)?6c and C(16?:?0). DNA G+C content was 70.6%; major respiratory quinone was ubiquinone Q-10; predominant polyamine was the triamine sym-homospermidine. Chemotaxonomic evidence including characteristic glycolipid profile, presence of significant amounts of C(18:1) 2-OH and absence of typical hydroxylated fatty acids such as C(14:0) 2-OH, C(15:0) 2-OH and C(16:0) 2-OH in considerable amounts, accompanied by phylogenetic distinctiveness and several other phenotypic features support the classification of strain CC-AMO-30B(T) as a representative of a novel species within the genus Sphingomicrobium for which the name Sphingomicrobium astaxanthinifaciens sp. nov. is proposed; the type strain is CC-AMO-30B(T) (?=JCM 18551(T)?=BCRC 80465(T)).
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Chiayiivirga flava gen. nov., sp. nov., a novel bacterium of the family Xanthomonadaceae isolated from an agricultural soil, and emended description of the genus Dokdonella.
Int. J. Syst. Evol. Microbiol.
PUBLISHED: 03-08-2013
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A novel Gram-reaction-negative, yellow-pigmented, aerobic, non-motile and rod-shaped bacterium designated strain CC-YHH031(T) was isolated from an agricultural soil collected at Chiayi County, Taiwan. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain CC-YHH031(T) formed a discrete monophyletic lineage in the family Xanthomonadaceae, sharing high pairwise sequence similarity of 93.5-95.2 and 94.8% with species of the genus Dokdonella (94.9% similarity to the type strain of the type species) and Aquimonas voraii GPTSA 20(T), respectively. The genomic DNA G+C content of strain CC-YHH031(T) was 68.6 ± 0.7 mol% and the predominant respiratory quinone was ubiquinone Q-8. Spermidine was the principal polyamine, with minor amounts of putrescine. Major fatty acids (>5% of total fatty acids) were iso-C(16:00, iso-C(15:0), C(16:1)?7c and/or C(16:1)?6c (summed feature 3), iso-C(17:1)?9c, iso-C(14:0), iso-C(11:0) and iso-C(11:0) 3-OH. The polar lipid profile of strain CC-YHH031(T) included phosphatidylethanolamine, phosphatidylmonomethylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, two unidentified aminophospholipids (APL1-2) and four unidentified phospholipids (PL1-4). Strain CC-YHH031(T) was distinguished particularly from the type species of the genus Dokdonella (Dokdonella koreensis) by the presence of major amounts of iso-C(14:0) and summed feature 3 and minor amounts of iso-C(17:0) and by the complete absence of anteiso-C(17:0), the presence of PL1-3 and APL1-2, the absence of APL3 and the presence of putrescine in the former. On the basis of distinguishing genotypic and phenotypic evidence, strain CC-YHH031(T) is proposed to represent a novel genus and species within the family Xanthomonadaceae, for which the name Chiayiivirga flava gen. nov., sp. nov. is proposed. The type strain of Chiayiivirga flava is CC-YHH031(T) (?=BCRC 80273(T)?=DSM 24163(T)).
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Low density supercritical fluids precipitation of 9-cis and all trans-?-carotenes enriched particulates from Dunaliella salina.
J Chromatogr A
PUBLISHED: 03-06-2013
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In this study, supercritical anti-solvent (SAS) pulverization coupled with reverse phase elution chromatography was employed to isolate 9-cis and trans-?-carotenes from Dunaliella salina. Total concentration of 9-cis (134.7mg/g) and trans-?-carotene (204.2mg/g) was increased from 338.9mg/g of the ultrasonic extract to 859.7mg/g (338.9 for 9-cis and 520.8 for trans) of the elution fraction. The SAS pulverization of the collected fraction further produced submicron-sized particulates containing 932.1mg/g (355.6 for 9-cis and 576.5 for trans) of total ?-carotenes with a recovery of 86.3% (83.9% for cis and 87.8% for trans). Effects of two SAS operational conditions on the purity, recovery of total ?-carotenes, mean size and morphology of the precipitates were obtained from an experimentally designed method. Generation of micronized particulates enriched with 9-cis and trans-?-carotenes by low-density SAS was proved to be feasible and environmental benign.
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Pseudomonas formosensis sp. nov., a gamma-proteobacteria isolated from food-waste compost in Taiwan.
Int. J. Syst. Evol. Microbiol.
PUBLISHED: 02-22-2013
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A taxonomic study was carried out on a novel aerobic bacterial strain, designated CC-CY503(T), isolated from food-waste compost in Taiwan. Cells were Gram-stain-negative short rods, motile by means of a monopolar flagellum. Strain CC-CY503(T) was able to grow at 20-50 °C and pH 6.0-10.0 and to tolerate <6% NaCl (w/v). Phylogenetic analysis of 16S rRNA gene sequences showed that this bacterium belonged to the genus Pseudomonas, with Pseudomonas pertucinogena ATCC 190(T) as the closest neighbour, sharing a sequence similarity of 97.9%. The DNA-DNA relatedness value of strain CC-CY503(T) with P. pertucinogena ATCC 190(T) was 37.8 ± 2.3%. The phylogenetic trees reconstructed based on gyrB and rpoB gene sequences supported the classification of strain CC-CY503(T) as a novel member of the genus Pseudomonas. The predominant quinone system was ubiquinone (Q-9) and the DNA G+C content was 63.1 ± 0.4 mol%. The major fatty acids were C(12:0), C(16:0), C(17:0) cyclo, C(19:0) cyclo ?8c and summed features 3 and 8 consisting of C(16:1)?7c/C(16:1)?6c and C(18:1)?7c/C(18:1)?6c, respectively. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and phosphatidylcholine. On the basis of its distinct phylogenetic, phenotypic and chemotaxonomic features, strain CC-CY503(T) (?=BCRC 80437(T)?=JCM 18415(T)) is proposed to represent a novel species within the genus Pseudomonas, for which the name Pseudomonas formosensis sp. nov. is proposed.
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Vogesella fluminis sp. nov., isolated from a freshwater river, and emended description of the genus Vogesella.
Int. J. Syst. Evol. Microbiol.
PUBLISHED: 02-08-2013
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A bacterial strain designated Npb-07(T) was isolated from a freshwater river in Taiwan and characterized using a polyphasic taxonomic approach. Strain Npb-07(T) was Gram-negative, aerobic, rod-shaped and motile by means of a single polar flagellum. Growth occurred at 10-37 °C (optimum, 20-30 °C), at pH 6.0-9.0 (optimum, pH 6.0-7.0) and with 0-1 % NaCl (optimum, 0.5 %). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain Npb-07(T) belonged to the genus Vogesella and its most closely related neighbour was Vogesella indigofera ATCC 19706(T) with sequence similarity of 98.4 %. The major fatty acids were summed feature 3 (comprising C16 : 1?7c and/or C16 : 1?6c, 44.4 %) and C16 : 0 (31.9 %). The major respiratory quinone was Q-8. The DNA G+C content of the genomic DNA was 65.3 mol%. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, two uncharacterized aminophospholipids and an uncharacterized phospholipid. The DNA-DNA relatedness of strain Npb-07(T) with respect to V. indigofera ATCC 19706(T) was less than 70 %. On the basis of the genotypic, chemotaxonomic and phenotypic data, strain Npb-07(T) represents a novel species in the genus Vogesella, for which the name Vogesella fluminis sp. nov. is proposed. The type strain is Npb-07(T) ( = LMG 26669(T) = BCRC 80377(T) = KCTC 23713(T)).
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Cohnella formosensis sp. nov., a xylanolytic bacterium isolated from the rhizosphere of Medicago sativa L.
Int. J. Syst. Evol. Microbiol.
PUBLISHED: 01-11-2013
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A Gram-positive, spore-forming, aerobic, rod-shaped, xylanolytic bacterium designated strain CC-Alfalfa-35(T) was isolated from the rhizosphere of Medicago sativa L. in Taiwan. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain CC-Alfalfa-35(T) was affiliated to the genus Cohnella. Strain CC-Alfalfa-35(T) shared 95.3 % pairwise 16S rRNA gene sequence similarity to the type strain of the type species of the genus Cohnella (Cohnella thermotolerans DSM 17683(T)) besides showing a similarity of 97.4-93.6 % with other recognized species of the genus Cohnella. The DNA-DNA hybridization value between CC-Alfalfa-35(T) and Cohnella thailandensis KCTC 22296(T) was 37.7 % ± 1.7 % (reciprocal value, 55.7 % ± 3.0 %). Predominant cellular fatty acids were iso-C16 : 0 and anteiso-C15 : 0. The polar lipid profile constituted diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, lysyl-phosphatidylglycerol, three unidentified phospholipids and three unidentified aminophospholipids. The major respiratory quinone was MK-7 and the DNA G+C content was 58.3 mol%. Strain CC-Alfalfa-35(T) contained meso-diaminopimelic acid as the major diamino acid in the cell-wall peptidoglycan. Based on the polar lipid and fatty acid profiles, which were in line with those of C. thermotolerans DSM 17683(T), coupled with additional distinguishing genotypic, phenotypic and chemotaxonomic features, strain CC-Alfalfa-35(T) is proposed to represent a novel species within the genus Cohnella, for which the name Cohnella formosensis sp. nov. is proposed. The type strain is CC-Alfalfa-35(T) ( = JCM 18405(T) = BCRC 80428(T)).
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Microbulbifer taiwanensis sp. nov., isolated from coastal soil.
Int. J. Syst. Evol. Microbiol.
PUBLISHED: 12-09-2011
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A Gram-negative, non-spore-forming rod (CC-LN1-12(T)) was isolated from coastal soil samples of Lutao Island (Green Island), Taiwan, and its taxonomic position was studied. 16S rRNA gene sequence analysis showed that isolate CC-LN1-12(T) was grouped into the Microbulbifer cluster, with the highest similarities to Microbulbifer okinawensis ABABA23(T) (97.9?%), Microbulbifer maritimus TF-17(T) (97.7?%) and Microbulbifer donghaiensis CN85(T) (97.7?%), similarities to all other species of the genus Microbulbifer were lower than 96.8?%. The polyamine pattern contained the major compounds spermidine and cadaverine. The fatty acid profile, comprising the major fatty acids iso-C(15?:?0), iso-C(17?:?1)?9c, C(18?:?1)?7c and iso-C(11?:?0) 3-OH as the major hydroxylated fatty acid, supported the affiliation of strain CC-LN1-12(T) to the genus Microbulbifer. DNA-DNA hybridizations between strain CC-LN1-12(T) and Microbulbifer okinawensis ABABA23(T), M. donghaiensis CN85(T) and M. maritimus JCM 12187(T) resulted in relatedness values of 21.5?% (14.3?%, reciprocal analysis), 35.9?% (48.5?%, reciprocal analysis) and 48.1?% (52.1?%, reciprocal analysis), respectively. From these data, as well as from physiological and biochemical tests, strain CC-LN1-12(T) could be clearly differentiated from the most closely related species of the genus Microbulbifer. It is concluded that strain CC-LN1-12(T) represents a novel species, for which the name Microbulbifer taiwanensis sp. nov. is proposed. The type strain is CC-LN1-12(T) (?=?LMG 26125(T)?=?CCM 7856(T)).
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Sphingomonas formosensis sp. nov., a polycyclic aromatic hydrocarbon-degrading bacterium isolated from agricultural soil.
Int. J. Syst. Evol. Microbiol.
PUBLISHED: 08-26-2011
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In the present study, a yellow-pigmented, Gram-negative, short rod-shaped novel bacterium that was capable of degrading a wide range of polycyclic aromatic hydrocarbons (naphthalene, phenanthrene and pyrene) was isolated from agricultural soil located in Yunlin County, Taiwan. Comparative 16S rRNA gene sequence analysis positioned the novel strain in the genus Sphingomonas as an independent lineage adjacent to a subclade containing Sphingomonas fennica K101(T), Sphingomonas histidinilytica UM2(T), Sphingomonas wittichii RW1(T) and Sphingomonas haloaromaticamans A175(T). 16S rRNA gene sequence analysis of strain CC-Nfb-2(T) showed highest sequence similarity to S. fennica K101(T) (96.2%), S. histidinilytica UM2(T) (96.1%), S. wittichii RW1(T) (95.9%), S. haloaromaticamans A175(T) (95.7%), and Sphingobium ummariense RL-3(T) (94.7%); lower sequence similarities were observed with strains of all other Sphingomonas species. The strain contained phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, sphingoglycolipid and diphosphatidylglycerol. The predominant fatty acids were summed feature 8 (C(18:1)?7c and/or C(18:1)?6c) C(16:0) and 11-methyl C(18:1)?7c; C(14:0) 2-OH was the major 2-hydroxy fatty acid. Previously, these lipids have been found to be characteristic of members of the genus Sphingomonas. The serine palmitoyl transferase gene (spt) was also detected and sphingolipid synthesis was confirmed. The predominant isoprenoid quinone system was ubiquinone (Q-10) and the isolate contained sym-homospermidine as the major polyamine. The DNA G+C content of the isolate was 62.8±0.8 mol%. On the basis of chemotaxonomic, phenotypic and phylogenetic data, strain CC-Nfb-2(T) represents a novel species within the genus Sphingomonas, for which the name Sphingomonas formosensis sp. nov. is proposed; the type strain is CC-Nfb-2(T) (=BCRC 80272(T)=DSM 24164(T)).
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Sphingomicrobium lutaoense gen. nov., sp. nov., isolated from a coastal hot spring.
Int. J. Syst. Evol. Microbiol.
PUBLISHED: 07-29-2011
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A yellowish pigmented, Gram-negative, rod-shaped, non-spore-forming bacterium (strain CC-TBT-3(T)), was isolated on marine agar 2216 from a coastal hot spring of Green Island (Lutao), located off Taituang, Taiwan. 16S rRNA gene sequence analysis of strain CC-TBT-3(T) showed a relatively low similarity (<95.5 %) to representatives of the genera Novosphingobium, Sphingosinicella and Sphingomonas of the Sphingomonadaceae, with the most related strain being the type strain of Novosphingobium soli. In addition to the relatively low 16S rRNA gene sequence similarity to members of established species, the isolate also showed some unique chemotaxonomic features, including the presence of some glycolipids with unusual chromatographic behaviour. The major components of the polar lipid profile were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, sphingoglycolipid and three unidentified glycolipids. The major respiratory quinone was ubiquinone Q-10. The polyamine pattern was characterized by the triamine sym-homospermidine as a major component. Although the predominant fatty acids were C(18:1)?7c and summed feature 3 (C(16:1)?7c and/or iso-C(15:0) 2-OH), the isolate did not show the typical hydroxyl fatty acids, such as C(14:0) 2-OH, C(15:0) 2-OH and C(16:0) 2-OH, found in members of the genera Novosphingobium, Sphingomonas and Sphingosinicella, but showed instead high amounts of C(18:1) 2-OH (12.0 %). The DNA G+C content of strain CC-TBT-3(T) was 63.4 mol%. 16S rRNA gene sequence, chemotaxonomic and physiological analyses revealed that strain CC-TBT-3(T) represents a novel species in a new genus in the family Sphingomonadaceae for which the name Sphingomicrobium lutaoense gen. nov., sp. nov. is proposed; the type strain is of the type species S. lutoaense, CC-TBT-3(T) ( = DSM 24194(T) = CCM 7794(T)).
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Azospirillum formosense sp. nov., a diazotroph from agricultural soil.
Int. J. Syst. Evol. Microbiol.
PUBLISHED: 07-08-2011
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A gram-negative, spiral or rod-shaped, non-spore-forming diazotrophic bacterium, designated CC-Nfb-7(T), was isolated from agricultural soil in Yunlin County, Taiwan. 16S rRNA gene sequence analysis showed that strain CC-Nfb-7(T) was most closely related to Azospirillum brasilense DSM 1690(T) (97.4?% 16S rRNA gene sequence similarity), Azospirillum rugosum IMMIB AFH-6(T) (96.8?%) and Azospirillum oryzae JCM 21588(T) (96.6?%); <96.5?% 16S rRNA gene sequence similarity was found with all other members of the genus Azospirillum. DNA-DNA relatedness between strain CC-Nfb-7(T) and A. brasilense DSM 1690(T), A. rugosum DSM 19657(T) and A. oryzae JCM 21588(T) was 38.9, 30.1 and 31.8?%, respectively. The respiratory quinone was ubiquinone Q-10. The major fatty acids were summed feature 8 (consisting of C(18?:?1)?7c and/or C(18?:?1)?6c), summed feature 3 (consisting of C(16?:?1)?7c and/or C(16?:?1)?6c), summed feature 2 (consisting of C(14?:?0) 3-OH and/or iso-C(16?:?1) I), C(16?:?0), C(18?:?0) 2-OH and C(16?:?0) 3-OH. The polar lipids consisted mainly of phosphatidylglycerol, phosphatidylcholine and one unidentified phospholipid. Furthermore, moderate amounts of phosphatidylethanolamine, phosphatidyldimethylethanolamine and one unidentified aminophospholipid were also detected. Strain CC-Nfb-7(T) could be distinguished from members of phylogenetically related species by differences in phenotypic properties. On the basis of morphological, chemotaxonomic and phylogenetic data, strain CC-Nfb-7(T) represents a novel species within the genus Azospirillum, for which we propose the name Azospirillum formosense sp. nov. The type strain is CC-Nfb-7(T) (?=?BCRC 80273(T)?=?JCM 17639(T)?=?DSM 24137(T)).
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Inhella fonticola sp. nov., isolated from spring water, and emended description of the genus Inhella.
Int. J. Syst. Evol. Microbiol.
PUBLISHED: 06-17-2011
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A yellow-pigmented bacterial strain designated TNR-25(T) was isolated from spring water in Taiwan and was characterized using a polyphasic taxonomic approach. Strain TNR-25(T) was gram-negative, obligately aerobic, rod-shaped, non-motile and non-spore-forming. Growth occurred at 15-40 °C (optimum, 25 °C), at pH 6.0-10.0 (optimum, pH 7.0) and with 0-0.5?% NaCl (optimum, 0?%). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain TNR-25(T) belonged to the genus Inhella and its closest neighbour was Inhella inkyongensis IMCC1713(T) with 98.1?% sequence similarity. The major fatty acids (>10?%) of strain TNR-25(T) were summed feature 3 (comprising C(16?:?1)?7c and/or C(16?:?1)?6c) and C(16?:?0). The major cellular hydroxy fatty acids were C(10?:?0) 3-OH and C(12?:?0) 3-OH. The isoprenoid quinone was Q-8 and the DNA G+C content was 69.6 mol%. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylserine, diphosphatidylglycerol and several uncharacterized phospholipids. The DNA-DNA relatedness between strain TNR-25(T) and I. inkyongensis IMCC1713(T) was about 30.6-35.5?%. On the basis of the genotypic and phenotypic data, strain TNR-25(T) represents a novel species in the genus Inhella, for which the name Inhella fonticola sp. nov. is proposed; the type strain is TNR-25(T) (?=?BCRC 80211(T)?=?LMG 25721(T)).
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Aquabacterium limnoticum sp. nov., isolated from a freshwater spring.
Int. J. Syst. Evol. Microbiol.
PUBLISHED: 05-06-2011
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A Gram-negative, facultatively anaerobic, short-rod-shaped, non-motile and non-spore-forming bacterial strain, designated ABP-4(T), was isolated from a freshwater spring in Taiwan and was characterized using the polyphasic taxonomy approach. Growth occurred at 20-40 °C (optimum, 30-37 °C), at pH 7.0-10.0 (optimum, pH 7.0-9.0) and with 0-3% NaCl (optimum, 0%). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain ABP-4(T), together with Aquabacterium fontiphilum CS-6(T) (96.4% sequence similarity), Aquabacterium commune B8(T) (96.1%), Aquabacterium citratiphilum B4(T) (95.5%) and Aquabacterium parvum B6(T) (94.7%), formed a deep line within the order Burkholderiales. Strain ABP-4(T) contained summed feature 3 (comprising C(16:1) ?7c and/or C(16:1) ?6c), C(18:1) ?7c and C(16:0) as predominant fatty acids. The major cellular hydroxy fatty acid was C(10:0) 3-OH. The major isoprenoid quinone was Q-8 and the DNA G+C content was 68.6 mol%. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylserine, diphosphatidylglycerol and several uncharacterized phospholipids. The DNA-DNA relatedness of strain ABP-4(T) with respect to recognized species of the genus Aquabacterium was less than 70%. On the basis of the genotypic, chemotaxonomic and phenotypic data, strain ABP-4(T) represents a novel species in the genus Aquabacterium, for which the name Aquabacterium limnoticum sp. nov. is proposed. The type strain is ABP-4(T) (=BCRC 80167(T)=KCTC 23306(T)).
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Identification of N-acyl-l-homoserine lactones produced by non-pigmented Chromobacterium aquaticum CC-SEYA-1(T) and pigmented Chromobacterium subtsugae PRAA4-1(T).
3 Biotech
PUBLISHED: 04-28-2011
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Many members of the genus Chromobacterium produce violacein, a characteristic purple pigment which is induced by small diffusible N-acyl homoserine lactones (AHL) quorum-sensing molecules. In this study, the production of AHL of the non-pigmented C. aquaticum CC-SEYA-1(T) and the pigmented C. subtsugae PRAA4-1(T) were determined by using a CV026 biosensor assay. The profile of AHL was identified from the extracts of stationary phase cultures using gas chromatography-mass spectroscopy (GC-MS) and thin layer chromatography (TLC). CV026 biosensor assay revealed that both the non-pigmented C. aquaticum CC-SEYA-1(T) and the pigmented C. subtsugae PRAA4-1(T) produced AHL molecules, which were identified, respectively, as N-octanoyl homoserine lactone (OHL) [also known as C-8 homoserine lactone (C8-HSL)] and N-hexanoyl homoserine lactone (HHL) [also known as C-6 homoserine lactone (C6-HSL)]. The pigment produced by C. subtsugae PRAA4-1(T) was similar to that of Chromobacterium violaceum ATCC12472(T) but no characteristic visible spectral peaks of the pigment were observed in the extracts of C. aquaticum CC-SEYA-1(T). In addition, C. aquaticum CC-SEYA-1(T) and C. subtsugae PRAA4-1(T) showed hemolytic activities.
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Stappia aquimarina sp. nov., isolated from seawater.
Int. J. Syst. Evol. Microbiol.
PUBLISHED: 03-23-2011
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A light-yellow pigmented bacterial strain designated SPIO-19(T) was isolated from seawater in Taiwan and was characterized using the polyphasic taxonomy approach. Strain SPIO-19(T) was Gram-negative, obligately aerobic, rod-shaped, motile by means of one polar flagellum and non-spore forming. Growth occurred at 15-42°C (optimum, 30-40°C), at pH 5.0-9.0 (optimum, pH 8.0) and with 0.5-9.0% NaCl (optimum, 1.0-5.0%). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain SPIO-19(T) belonged to the genus Stappia and its closest neighbours were Stappia indica B106(T) and Stappia stellulata IAM 12621(T) with sequence similarities of 98.0% and 97.9%, respectively. Strain SPIO-19(T) contained C(18:1)?7c as predominant fatty acid. The major isoprenoid quinone was Q-10 and the DNA G+C content was 64.5 mol%. The polar lipid profile consisted of a mixture of phosphatidylglycerol (PG), diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), phosphatidylmonomethylethanolamine (PMME), phosphatidylcholine (PC), an uncharacterized aminolipid (AL) and an uncharacterized phospholipid (PL). The level of DNA-DNA relatedness of strain SPIO-19(T) to Stappia indica B106(T) and to Stappia stellulata IAM 12621(T) was 22.6 ± 2.8 % and 38.9 ± 3.8 %, respectively. On the basis of the genotypic and phenotypic data, strain SPIO-19(T) represents a new species in the genus Stappia, for which the name Stappia aquimarina sp. nov. is proposed. The type strain is SPIO-19(T) (=BCRC 80170(T) =LMG 25532(T)).
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Supercritical carbon dioxide micronization of zeaxanthin from moderately thermophilic bacteria Muricauda lutaonensis CC-HSB-11T.
J. Agric. Food Chem.
PUBLISHED: 03-18-2011
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Moderately thermophilic bacterial strain CC-HSB-11(T) (Muricauda lutaonensis), which was described recently from a coastal hot spring of Green Island, Taiwan, has been identified to produce zeaxanthin as a predominant xanthophyll by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Cell culture in bioreactor produced 3.12 ± 0.18 mg zeaxanthin L(-1) of culture. Micronization of zeaxanthin was achieved through supercritical carbon dioxide antisolvent precipitation method. Yield of zeaxanthin after the process was 53.4%. Dynamic light scattering assay determined the polydisperse existence of micronized particles of size 3 nm to 2 ?m. Field emission scanning electron microscopy revealed distinct morphology and size distribution heterogeneity of particles. Integrity of zeaxanthin after the antisolvent process was assessed by LC-MS/MS. The technique capitalizes on the inherent ability of CC-HSB-11(T) to synthesize zeaxanthin and the work demonstrated feasibility of antisolvent precipitation method to produce microparticles exploiting a bacterial strain.
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Evaluation of the optimal strategy for ex situ bioremediation of diesel oil-contaminated soil.
Environ Sci Pollut Res Int
PUBLISHED: 03-07-2011
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Bioaugmentation and biostimulation have been widely applied in the remediation of oil contamination. However, ambiguous results have been reported. It is important to reveal the controlling factors on the field for optimal selection of remediation strategy. In this study, an integrated field landfarming technique was carried out to assess the relative effectiveness of five biological approaches on diesel degradation. The limiting factors during the degradation process were discussed.
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Rapid detection and identification of the free-living nitrogen fixing genus Azospirillum by 16S rRNA-gene-targeted genus-specific primers.
Antonie Van Leeuwenhoek
PUBLISHED: 01-24-2011
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The modern agricultural practice utilizing plant growth promoting rhizobacteria (PGPR) has brought great benefits in the promotion of crop growth. Among PGPR, Azospirillum is considered as an important genus which is not only closely-associated with plants but also shows potential in the degradation of organic contaminants. However, lack of media for selective isolation or techniques for specific detection or identification limit the exploration of these rhizobacteria. This motivated us to design a genus-specific oligonucleotide primer pair which could assist in rapid detection of species of the genus Azospirillum by means of PCR-specific amplification. The sensitivity and specificity of the newly designed primer pair Azo494-F/Azo756-R were tested against 12 Azospirillum type strains and other closely-related genera. The Azospirillum-specific 16S rRNA gene fragment (263 bp) was successfully amplified for all the reference Azospirillum species with the designed primer pair. No amplification was noted for closely-related species from other genera. The genus specificity was validated with 18 strains including environmental isolates. Interestingly, two strains assigned earlier as Azospirillum amazonense (DSM 2787(T)) and Azospirillum irakense (DSM 11586(T)) failed to produce an Azospirillum-specific fragment with this primer pair. Further phylogenetic analysis of these two isolates based on 16S rRNA gene sequences shows that these two strains might belong to other genera rather than Azospirillum. Preliminary screening of isolates and soil samples with the Azospirillum-specific primers was successful in terms of the rapid detection of Azospirillum isolates. By using real-time PCR analysis the minimum limit of Azospirillum detection was 10(2) CFU g(-1) in the seeded soil sample. The newly designed primers can be used to study the diversity of Azospirillum in ecosystems and aid in the exploration of novel species.
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The flexibility of UV-inducible mutation in Deinococcus ficus as evidenced by the existence of the imuB-dnaE2 gene cassette and generation of superior feather degrading bacteria.
Microbiol. Res.
PUBLISHED: 01-12-2011
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The lexA-imuB-dnaE2 gene cassette contributing to the TLS (translesion synthesis) polymerase activity and can easily cause mutation after DNA damage in many bacteria. But it was previously thought that TLS polymerase activity was unlikely to exist in the radio-resistant genus Deinococcus. In our preliminary studies, the lexA-imuB-dnaE2 gene cassette was found in a newly isolated feather-degrading Deinococcus ficus. Here we have attempted to determine the imuB gene sequence from another Deinococcus species namely D. grandis, by using the newly designed primers. The destroying of either imuB or dnaE2 gene in D. ficus leads to the increase in UV sensitivity and decrease in UV-induced mutations, which demonstrated the existence of TLS polymerase activity in D. ficus. In the presence of lexA-imuB-dnaE2, it is possible to obtain mutants with various keratinolytic activities after UV exposure. The keratinolytic activity of mutant strain CC-ZG207 increased by approximately twofold during growth in liquid feather medium. In contrast, the mutant strain CC-ZG227 showed only half of the keratinolytic activity compared with the wild type strain. By utilizing SDS-PAGE and zymogram profile analysis, the change in the protease activity was observed. We have proposed that the superior mutants of D. ficus can be created under UV stress, which is mediated by the lexA-imuB-dnaE2 gene cassette.
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Rheinheimera aquatica sp. nov., an antimicrobial activity producing bacterium isolated from freshwater culture pond.
J. Microbiol. Biotechnol.
PUBLISHED: 10-30-2010
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A bacterial strain designated GR5(T) was isolated from freshwater culture pond in Taiwan during the screening of bacteria for antimicrobial compounds and characterized using the polyphasic taxonomic approach. Strain GR5(T) was Gram-negative, aerobic, greenish-yellow colored, rod-shaped, and motile by means of a polar single flagellum. Growth occurred at 10-40 degrees C (optimum, 35 degrees C), at pH 7.0-8.0 (optimum pH 8.0) and with 0-2.0% NaCl (optimum, 0.5-1.0%). The major fatty acids were C(16:1) omega7c (36.3%), C(16:0) (16.6%), C(12:0) 3-OH (12.5%) and C(18:1) omega7c (9.1%). The major respiratory quinone was Q-8. The DNA G+C content of the genomic DNA was 51.9 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain GR5(T) belonged to the genus Rheinheimera and its most closely neighbours were Rheinheimera texasensis A62-14B(T) and Rheinheimera tangshanensis JA3-B52(T) with sequence similarities of 98.1 and 97.5%, respectively. The sequence similarities to any other recognized species within Gammaproteobacteria were less than 96.5%. The mean level of DNA-DNA relatedness between strain GR5(T) and R. texasensis A62-14B(T), the strain most closely related to the isolate, was 26.5 +/- 7.6 %. On the basis of the phylogenetic and phenotypic data, strain GR5(T) should be classified as representing a novel species, for which the name Rheinheimera aquatica sp. nov. is proposed. The type strain is GR5(T) (= BCRC 80081(T) = LMG 25379(T)).
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Salinicoccus sesuvii sp. nov., isolated from the rhizosphere of Sesuvium portulacastrum.
Int. J. Syst. Evol. Microbiol.
PUBLISHED: 10-29-2010
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A Gram-staining-positive coccus, designated CC-SPL15-2(T), was isolated from the rhizosphere of Sesuvium portulacastrum. By 16S rRNA gene sequence analysis, it was shown that strain CC-SPL15-2(T) belonged to the genus Salinicoccus. The isolate was most closely related to Salinicoccus hispanicus DSM 5352(T) (98.3?% 16S rRNA gene sequence similarity) and Salinicoccus roseus DSM 5351(T) (96.7?%); similarities to all other members of the genus Salinicoccus were <96.5?%. In accordance with characteristics of the genus Salinicoccus, the quinone system was mainly composed of menaquinone MK-6. The polar lipid profile exhibited the major components diphosphatidylglycerol, phosphatidylglycerol and an unidentified glycolipid. In the polyamine pattern, spermidine was the predominant compound. The fatty acids were anteiso-C(15?:?0), iso-C(15?:?0), iso-C(16?:?0) and anteiso-C(17?:?0), which supported the affiliation of strain CC-SPL15-2(T) to the genus Salinicoccus. DNA-DNA relatedness between strain CC-SPL15-2(T) and S. hispanicus CCUG 43288(T) was 42 and 32?% (reciprocal analysis). From these data as well as from physiological and biochemical tests, a clear differentiation of strain CC-SPL15-2(T) from S. hispanicus and other members of the genus Salinicoccus was possible. We propose that strain CC-SPL15-2(T) be assigned to a novel species, with the name Salinicoccus sesuvii sp. nov. The type strain is CC-SPL15-2(T) (?=?DSM 23267(T) ?=?CCM 7756(T)).
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Pseudoteredinibacter isoporae gen. nov., sp. nov., a marine bacterium isolated from the reef-building coral Isopora palifera.
Int. J. Syst. Evol. Microbiol.
PUBLISHED: 09-10-2010
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A Gram-negative, heterotrophic, marine bacterium, designated strain SW-11(T), was isolated from the reef-building coral Isopora palifera in Kenting, Taiwan. Cells were rods and were motile by a single polar flagellum. The strain grew at 10-45 °C (optimum, 30-35 °C), at pH 7.0-8.0 (optimum, pH 7.5) and with 2.0-4.0 % NaCl (optimum, 2.5-3.0 %). The polar lipids comprised phosphatidylethanolamine, phosphatidylglycerol, phosphatidylserine, diphosphatidylglycerol and four unknown phospholipids. Isoprenoid quinones consisted of ubiquinone 9 (78.8 %) and ubiquinone 8 (21.1 %). Major cellular fatty acids were summed feature 3 (C(16 : 1)?7c and/or C(16 : 1)?6c; 22.3 %), C(17 : 1)?8c (13.4 %), summed feature 8 (C(18 : 1)?6c and/or C(18 : 1)?7c; 13.1 %), C(16 : 0) (10.3 %) and anteiso-C(17 : 1)?9c (10.0 %). The DNA G+C content was 51.6 mol%. 16S rRNA gene sequence analysis indicated that strain SW-11(T) belongs to the class Gammaproteobacteria and is a member of the order Alteromonadales. Strain SW-11(T) shared 93.2 % 16S rRNA gene sequence similarity with Teredinibacter turnerae T7902(T) and 92.1 % with Saccharophagus degradans 2-40(T), and can be further distinguished from these two related strains by distinct patterns of fatty acid content and differences in the polar lipid profile, the ability to utilize different compounds as carbon sources, the ability to degrade various compounds and differences in enzyme activities. The phylogenetic data and those from physiological, morphological and chemotaxonomic characterizations indicate that strain SW-11(T) represents a novel species and genus, for which the name Pseudoteredinibacter isoporae gen. nov., sp. nov. is proposed. The type strain of Pseudoteredinibacter isoporae is SW-11(T) (?= BCRC 17935(T) ?= LMG 25246(T)).
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Microbacterium arthrosphaerae sp. nov., isolated from the faeces of the pill millipede Arthrosphaera magna Attems.
Int. J. Syst. Evol. Microbiol.
PUBLISHED: 07-23-2010
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A Gram-reaction-positive, rod-shaped bacterium, designated strain CC-VM-Y(T), was isolated from the faeces of the pill millipede Arthrosphaera magna Attems from India and was subsequently studied to determine its taxonomic position. Based on16S rRNA gene sequence similarities, the isolate clearly grouped with members of the genus Microbacterium. On the basis of pairwise comparisons of the 16S rRNA gene sequences, strain CC-VM-Y(T) was most closely related to Microbacterium insulae DS-66(T) (98 %), Microbacterium hydrocarbonoxydans DSM 160809(T) (97.8 %) and Microbacterium hominis NBRC 15708(T) (97.9 %). The peptidoglycan contained the amino acids ornithine (Orn), alanine (Ala), glycine (Gly), homoserine (Hsr) and glutamic acid (Glu) in an approximate molar ratio of 1.0 : 0.8 : 2.2 : 0.8 : 0.3. In addition, substantial amounts of threo-3-hydroxy glutamic acid (Hyg) were detected, which is characteristic of peptidoglycan type B2?. The acyl type of the peptidoglycan was glycolyl. The menaquinones of strain CC-VM-Y(T) were MK-13 (72 %), MK-12 (25 %) and MK-11 (3 %). The polar lipids consisted of phosphatidylglycerol, diphosphatidylglycerol, one unknown phospholipid and one unknown glycolipid. The fatty acid profile comprised anteiso-C(15 : 0), iso-C(16 : 0) and anteiso-C(17 : 0) as the major fatty acids, which was congruent with fatty acid profiles of other members of the genus Microbacterium. The results of physiological and biochemical tests as well as DNA-DNA hybridizations with the most closely related species, M. insulae, M. hydrocarbonoxydans and M. hominis, revealed clear phenotypic and genotypic differences between strain CC-VM-Y(T) and other members of the genus Microbacterium. Based on these results, strain CC-VM-Y(T) (?=?DSM 22421(T) ?=?CCM 7681(T)) represents a new species of the genus Microbacterium, for which the name Microbacterium arthrosphaerae sp. nov. is proposed.
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Jhaorihella thermophila gen. nov., sp. nov., a moderately thermophilic bacterium isolated from a coastal hot spring.
Int. J. Syst. Evol. Microbiol.
PUBLISHED: 07-23-2010
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A beige-coloured, gram-staining negative, aerobic, non-motile, moderately thermophilic, rod-shaped bacterium, CC-MHSW-1(T), was isolated on Marine Agar 2216 from a water sample from a coastal hot spring on Green Island (Lutao), located off Taituang, Taiwan. 16S rRNA gene sequence analysis demonstrated that the novel strain shared <94?% sequence similarity with members of the genera Lutimaribacter, Maritimibacter and Oceanicola. Ubiquinone (Q-10) was the major respiratory quinone and C(18?:?1)?7c was the predominant fatty acid. The predominant polar lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol and unidentified phospholipids and aminolipids. The DNA G+C content of strain CC-MHSW-1(T) was 64.7 mol%. On the basis of 16S rRNA gene sequence analysis and the chemotaxonomic and physiological data, strain CC-MHSW-1(T) represents a new genus and species in the family Rhodobacteraceae for which the name Jhaorihella thermophila gen. nov., sp. nov., is proposed. The type strain of the type species is CC-MHSW-1(T) (?=?JCM 15068(T)?=?CCM 7767(T)).
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Flavobacterium macrobrachii sp. nov., isolated from a freshwater shrimp culture pond.
Int. J. Syst. Evol. Microbiol.
PUBLISHED: 07-02-2010
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A bacterial strain, designated an-8(T), was isolated from a freshwater shrimp culture pond in Taiwan and characterized using a polyphasic taxonomic approach. Cells of strain an-8(T) were Gram-reaction-negative, aerobic, rod-shaped and non-motile, formed yellow-pigmented colonies and grew at 15-30 °C (optimum 25 °C), pH 7-8 (optimum pH 8.0) and in 0-1 % (w/v) NaCl (optimum 0 %). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain an-8(T) belonged to the genus Flavobacterium and its most closely related neighbours were Flavobacterium terrigena DS-20(T) and Flavobacterium terrae R2A1-13(T) with sequence similarities of 95.1 and 94.9 %, respectively. Strain an-8(T) contained iso-C(15 : 0), summed feature 3 (C(16 : 1)?6c and/or C(16 : 1)?7c), iso-C(16 : 0) 3-OH, iso-C(15 : 0) 3-OH, iso-C(17 : 0) 3-OH and iso-C(15 : 1) as the major fatty acids. The major isoprenoid quinone was MK-6. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidyldimethylethanolamine, phosphatidylserine and several unidentified polar lipids. The G+C content of the genomic DNA was 39.8 mol%. On the basis of the phylogenetic and phenotypic data, strain an-8(T) represents a novel species of the genus Flavobacterium, for which the name Flavobacterium macrobrachii sp. nov. is proposed. The type strain is an-8(T) (?=?BCRC 17965(T) ?=?LMG 25203(T)).
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Allobacillus halotolerans gen. nov., sp. nov. isolated from shrimp paste.
Int. J. Syst. Evol. Microbiol.
PUBLISHED: 05-28-2010
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A novel bacterial strain designated B3A(T), isolated from shrimp paste, was investigated by a polyphasic taxonomic approach. Cells stained Gram-positive and were aerobic, non-pigmented, sporulating and rod-shaped with a polar flagellum. 16S rRNA gene sequence analysis indicated that strain B3A(T) belonged to the class Bacilli and was a member of the family Bacillaceae. Strain B3A(T) shared low levels of 16S rRNA gene sequence similarity (<94.0 %) with members of other genera in the family Bacillaceae and was most closely related to Halalkalibacillus halophilus BH2(T) (93.8 % sequence similarity). The isolate was able to grow at 20-45 °C, with 0.5-15 % NaCl and at pH 6-9. Menaquinone with seven isoprene units (MK-7) was the major respiratory quinone and 16 : 0 iso, 15 : 0 anteiso and 14 : 0 iso were the major fatty acids. The major polar lipids were diphosphatidylglycerol and phosphatidylglycerol. The characteristic diamino acid of the peptidoglycan was meso-diaminopimelic acid. The DNA G+C content was 45.3 mol%. On the basis of 16S rRNA gene sequence analysis in combination with chemotaxonomic and physiological data, strain B3A(T) represents a novel genus and species in the family Bacillaceae for which the name Allobacillus halotolerans gen. nov., sp. nov. is proposed. The type strain of Allobacillus halotolerans is B3A(T) (?=?BCRC 17939(T) ?=?LMG 24826(T)).
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Novosphingobium soli sp. nov., isolated from soil.
Int. J. Syst. Evol. Microbiol.
PUBLISHED: 03-05-2010
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A yellow-pigmented, Gram-negative, rod-shaped, non-spore-forming bacterium, strain CC-TPE-1(T), was isolated from oil-contaminated soil near an oil refinery located in Kaohsiung County, Taiwan. 16S rRNA gene sequence analysis of strain CC-TPE-1(T) showed highest sequence similarity to Novosphingobium naphthalenivorans TUT562(T) (98.1?%), N. panipatense SM16(T) (97.9?%) and N. mathurense SM117(T) (97.6?%) and lower (<97?%) sequence similarity to all other Novosphingobium species. DNA-DNA hybridizations of strain CC-TPE-1(T) with N. naphthalenivorans DSM 18518(T), N. panipatense SM16(T) and N. mathurense SM117(T) showed low relatedness of 30?% (reciprocal 35?%), 29.1?% (reciprocal 30.6?%) and 35?% (reciprocal 23.6?%), respectively. The major respiratory quinone was ubiquinone Q-10, the predominant fatty acid was C(18?:?1)?7c (49.9?%) and three 2-hydroxy fatty acids, C(14?:?0) 2-OH (8.2?%), C(15?:?0) 2-OH (2.45?%) and C(16?:?0) 2-OH (1.05?%), were detected. Polar lipids consisted mainly of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, phosphatidyldimethylethanolamine, two sphingoglycolipids, phosphatidylmonomethylethanolamine and several unidentified lipids, and a yellow pigment was also detected. The polyamine pattern contained the single major compound spermidine. Characterization by 16S rRNA gene sequence analysis, physiological parameters, pigment analysis and polyamine, ubiquinone, polar lipid and fatty acid compositions revealed that strain CC-TPE-1(T) represents a novel species of the genus Novosphingobium, for which we propose the name Novosphingobium soli sp. nov., with the type strain CC-TPE-1(T) (=DSM 22821(T) =CCM 7706(T) =CCUG 58493(T)).
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Gordonia humi sp. nov., isolated from soil.
Int. J. Syst. Evol. Microbiol.
PUBLISHED: 02-12-2010
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A Gram-stain-positive, non-endospore-forming actinobacterium (CC-12301(T)) was isolated from soil attached to a spawn used in the laboratory to grow the edible mushroom Agaricus brasiliensis. Based on 16S rRNA gene sequence similarities, strain CC-12301(T) was shown to belong to the genus Gordonia and was most closely related to the type strains of Gordonia hydrophobica (97.6?% similarity), Gordonia terrae (97.5?%), Gordonia amarae (97.5?%) and Gordonia malaquae (97.4?%). The quinone system was determined to consist predominantly of menaquinone MK-9(H(2)), minor amounts of MK-8(H(2)) and MK-7(H(2)). The polar lipid profile consisted of the major compounds diphosphatidylglycerol and phosphatidylethanolamine, moderate amounts of two phosphatidylinositol mannosides and phosphatidylinositol and minor amounts of phosphatidylglycerol, three unidentified glycolipids, two phosphoglycolipids and a phospholipid. Mycolic acids were present. These chemotaxonomic traits and the major fatty acids, which were C(16?:?1) cis9, C(16?:?0), C(18?:?1) and tuberculostearic acid (10-methyl C(18?:?0)), supported the affiliation of strain CC-12301(T) to the genus Gordonia. The results of physiological and biochemical tests allowed clear phenotypic differentiation of strain CC-12301(T) from the most closely related Gordonia species. Strain CC-12301(T) therefore represents a novel species, for which the name Gordonia humi sp. nov. is proposed, with the type strain CC-12301(T) (=DSM 45298(T) =CCM 7727(T)).
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Arcicella aurantiaca sp. nov., isolated from stream water.
Int. J. Syst. Evol. Microbiol.
PUBLISHED: 01-29-2010
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A bacterial strain designated TNR-18(T) was isolated from stream water in southern Taiwan and characterized using a polyphasic taxonomic approach. Cells of strain TNR-18(T) were Gram-stain-negative, strictly aerobic, non-motile and vibrioid, and the strain formed orange colonies. Growth occurred at 10-30°C, with 0-0.2?% NaCl and at pH6.0-10.0. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain TNR-18(T) belonged to the genus Arcicella; its closest neighbours were Arcicella rosea TW5(T) and Arcicella aquatica NO-502(T), with respective sequence similarities of 97.9 and 97.8?%. Predominant cellular fatty acids (>10?%) were summed feature 3 (C(16?:?1)?7c/C(16?:?1)?6c; 37.7?%), C(16?:?1)?5c (13.0?%) and iso-C(15?:?0) (11.1?%). The major respiratory quinone was MK-7. The polar lipid profile contained phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and several uncharacterized polar lipids. The DNA G+C content was 39.9 mol%. On the basis of the phylogenetic and phenotypic data, strain TNR-18(T) should be classified as representing a novel species, for which the name Arcicella aurantiaca sp. nov. is proposed. The type strain is TNR-18(T) (=LMG 25207(T) =BCRC 17969(T)).
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Molecular detection and phylogenetic analysis of the alkane 1-monooxygenase gene from Gordonia spp.
Syst. Appl. Microbiol.
PUBLISHED: 01-04-2010
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The alkB gene encodes for alkane 1-monooxygenase, which is a key enzyme responsible for the initial oxidation of inactivated alkanes. This functional gene can be used as a marker to assess the catabolic potential of bacteria in bioremediation. In the present study, a pair of primers was designed based on the conserved regions of the AlkB amino acid sequences of Actinobacteria, for amplifying the alkB gene from the genus Gordonia (20 Gordonia strains representing 13 species). The amplified alkB genes were then sequenced and analyzed. In the phylogenetic tree based on the translated AlkB amino acid sequences, all the Gordonia segregated clearly from other closely related genera. The sequence identity of the alkB gene in Gordonia ranged from 58.8% to 99.1%, which showed higher sequence variation at the inter-species level compared with other molecular markers, such as the 16S rRNA gene (93.1-99.8%), gyrB gene (77.5-97.3%) or catA gene (72.4-99.5%). The genetic diversity of four selected loci also showed that the alkB gene might have evolved faster than rrn operons, as well as the gyrB or catA genes, in Gordonia. All the available actinobacterial alkB gene sequences derived from the whole genome shotgun sequencing projects are phylogenetically characterized here for the first time, and they exclude the possibility of horizontal gene transfer of the alkB gene in these bacterial groups.
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Agaricicola taiwanensis gen. nov., sp. nov., an alphaproteobacterium isolated from the edible mushroom Agaricus blazei.
Int. J. Syst. Evol. Microbiol.
PUBLISHED: 10-09-2009
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A Gram-negative, beige-pigmented, aerobic, motile, club-shaped bacterium, designated strain CC-SBABM117(T), was isolated from the stipe of the edible mushroom Agaricus blazei Murrill. 16S rRNA gene sequence analysis demonstrated that the strain shared <93 % similarity with the type strains of species in the genera Pannonibacter, Methylopila, Nesiotobacter and Stappia. The organism was unable to produce acid from carbohydrates, but utilized a number of organic acids and amino acids. Ubiquinone 10 (Q-10) was the major respiratory quinone and C(18 : 1) ? 7c, C(19 : 0) cyclo ? 8c, C(16 : 0) and C(18 : 0) were the predominant fatty acids. The predominant polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol and phosphatidylethanolamine. The DNA G+C content of strain CC-SBABM117(T) was 62.7 mol%. On the basis of 16S rRNA gene sequence analysis and chemotaxonomic and physiological data, strain CC-SBABM117(T) is considered to represent a novel species of a new genus, for which the name Agaricicola taiwanensis gen. nov., sp. nov. is proposed. The type strain of Agaricicola taiwanensis is CC-SBABM117(T) (=BCRC 17964(T) =CCM 7684(T)).
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Fontibacter flavus gen. nov., sp. nov., a member of the family Cyclobacteriaceae, isolated from a hot spring.
Int. J. Syst. Evol. Microbiol.
PUBLISHED: 10-09-2009
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The taxonomic position of a bright orange-pigmented bacterial strain, designated CC-GZM-130(T), isolated from a water sample of the Guan-zing-ling hot spring, southern Taiwan, was studied. The strain was able to grow on nutrient agar at 25-40 degrees C and in the presence of 1-3 % (w/v) NaCl. Comparative analyses of the 16S rRNA gene sequence showed that the isolate was grouped in the vicinity of the genus Aquiflexum with the highest sequence similarity of 92.1 % to the type strain of Aquiflexum balticum, followed by sequence similarities of 92.0, 91.6 and 91.5 % to the type strains of Algoriphagus ornithinivorans, Algoriphagus hitonicola and Belliella baltica, respectively. The polyamine pattern showed that the major compound was sym-homospermidine. The quinone system was menaquinone MK-7. The polar lipid profile was composed predominantly of phosphatidylethanolamine, three polar lipids and one aminolipid. Minor amounts of other lipids were also detectable. The main characteristics of the fatty acid profiles of strain CC-GZM-130(T), B. baltica and Aquiflexum balticum were similar, with iso-C(15 : 0), iso-C(17 : 1)? 9c and iso-C(17 : 0) 3-OH as the major fatty acids, but some qualitative and quantitative differences were observed. The DNA G+C content of the novel strain was 53.2 mol%. The isolate clearly differed genotypically and phenotypically from representatives of the most closely related genera. On the basis of these differences, a novel species in a new genus, Fontibacter flavus gen. nov., sp. nov., is proposed with CC-GZM-130(T) (=CCUG 57694(T)=CCM 7650(T)) as the type strain of the type species.
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Influence of gamma-radiation on the nutritional and functional qualities of lotus seed flour.
J. Agric. Food Chem.
PUBLISHED: 09-26-2009
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In the present study, we investigated the physicochemical and functional properties of lotus seed flour exposed to low and high doses of gamma-radiation (0-30 kGy; the dose recommended for quarantine and hygienic purposes). The results indicated raw seed flour to be rich in nutrients with minimal quantities of antinutritional factors. Irradiation resulted in a dose-dependent increase in some of the proximal constituents. The raw and gamma-irradiated seeds meet the Food and Agricultural Organization-World Health Organization recommended pattern of essential amino acids. Some of the antinutritional factors (phytic acid, total phenolics, and tannins) were lowered with gamma-irradiation, while the seed flours were devoid of lectins, L-3,4-dihydroxyphenylalanine, and polonium-210. The functional properties of the seed flour were significantly improved with gamma-radiation. gamma-radiation selectively preserved or improved the desired nutritional and functional traits of lotus seeds, thus ensuring a safe production of appropriate nutraceutically valued products.
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Chitinibacter alvei sp. nov., isolated from stream water.
Int. J. Syst. Evol. Microbiol.
PUBLISHED: 09-11-2009
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A Gram-negative, aerobic bacterium, designated strain TNR-14T, was isolated from water of a stream located in southern Taiwan. Cells were rod-shaped and motile by means of a polar flagellum. The isolate exhibited optimum growth at 20 degrees C, at pH 7.0 and in the absence of NaCl. Phylogenetic analyses based on 16S rRNA gene sequences showed that the strain belonged to the genus Chitinibacter and was related most closely to the type strain of Chitinibacter tainanensis (96.0% similarity). The predominant cellular fatty acids were summed feature 3 (C16:1omega7c and/or C16:1omega6c; 54.03%) and C16:0 (27.22%). The DNA G+C content of strain TNR-14T was 57.5 mol%. The results of physiological and biochemical tests and chemotaxonomic data allowed the clear phenotypic differentiation of the new isolate from Chitinibacter tainanensis. Strain TNR-14T is therefore considered to represent a novel species of the genus Chitinibacter, for which the name Chitinibacter alvei sp. nov. is proposed. The type strain is TNR-14T (=LMG 25206T =DSM 22217T =BCRC 17968T).
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Chryseobacterium arthrosphaerae sp. nov., isolated from the faeces of the pill millipede Arthrosphaera magna Attems.
Int. J. Syst. Evol. Microbiol.
PUBLISHED: 09-11-2009
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A bacterial strain (CC-VM-7T), isolated from the faeces of the pill millipede Arthrosphaera magna Attems collected in India, was studied to determine its taxonomic allocation. Cells stained Gram-negative and were rod-shaped. Comparative analyses of the 16S rRNA gene sequence of the strain with those of the most closely related species clearly suggested allocation to the genus Chryseobacterium, with the highest sequence similarities of 99.2% to Chryseobacterium gleum CCUG 14555T, 98.6% to Chryseobacterium indologenes CCUG 14556T and 98.4% to Chryseobacterium aquifrigidense KCTC 12894T. 16S rRNA gene sequence similarities to all other species of the genus Chryseobacterium were below 98%. The major whole-cell fatty acids were iso-C15:0 and iso-C17:1omega9c. DNA-DNA hybridization resulted in relatedness values of only 29.6% (reciprocal 31.3%) to Chryseobacterium gleum CCUG 14555T, 41.2% (reciprocal 38.8%) to C. indologenes CCUG 14556T and 35.4% (reciprocal 38.5%) to C. aquifrigidense KCTC 12894T. DNA-DNA relatedness, biochemical and chemotaxonomic properties clearly show that strain CC-VM-7T represents a novel species, for which the name Chryseobacterium arthrosphaerae sp. nov. is proposed. The type strain is CC-VM-7T (=CCUG 57618T =CCM 7645T).
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Microlunatus soli sp. nov., isolated from soil.
Int. J. Syst. Evol. Microbiol.
PUBLISHED: 08-06-2009
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A Gram-stain-positive, coccoid, non-endospore-forming actinobacterium (strain CC-12602(T)) was isolated from a spawn used for growing the edible mushroom Agaricus brasiliensis in the laboratory. On the basis of 16S rRNA gene sequence analysis, strain CC-12602(T) was shown to belong to the genus Microlunatus and was related most closely to the type strains of Microlunatus ginsengisoli (96.1 % similarity), M. phosphovorus (95.9 %), M. panaciterrae (95.8 %) and M. aurantiacus (95.5 %). The quinone system comprised menaquinone MK-9(H4) as the major component and the polyamine pattern consisted of spermidine and spermine as major compounds. The predominant polar lipids were phosphatidylglycerol and unknown phospholipid PL3. Moderate amounts of diphosphatidylglycerol, an unknown glycolipid and three unknown phospholipids and minor amounts of an unknown phospholipid and a polar lipid were detected. The peptidoglycan type was A3gamma, based on LL-2,6-diaminopimelic acid with an interpeptide bridge consisting of a single glycine residue and a second glycine residue at position 1 of the peptide subunit. Peptidoglycan structure and major fatty acids (anteiso-C(15 : 0), iso-C(16 : 0) and iso-C(15 : 0)) supported the affiliation of strain CC-12602(T) to the genus Microlunatus. The results of physiological and biochemical tests allowed strain CC-12602(T) to be differentiated phenotypically from recognized Microlunatus species. Strain CC-12602(T) is therefore considered to represent a novel species of the genus Microlunatus, for which the name Microlunatus soli sp. nov. is proposed. The type strain is CC-12602(T) (=DSM 21800(T) =CCM 7685( T)).
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Algoriphagus olei sp. nov., isolated from oil-contaminated soil.
Int. J. Syst. Evol. Microbiol.
PUBLISHED: 07-23-2009
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A motile, Gram-negative, pinkish red-pigmented bacterium (strain CC-Hsuan-617(T)) was isolated from an oil-contaminated soil near an oil refinery located in Kaohsiung County, Taiwan. 16S rRNA gene sequence analysis showed that strain CC-Hsuan-617(T) clustered with Algoriphagus mannitolivorans (97.5 % sequence similarity), Algoriphagus aquatilis (98.0 %) and Algoriphagus boritolerans (97.5 %), followed by Algoriphagus ornithinivorans (97.1 %) and Algoriphagus alkaliphilus (97.1 %). The fatty acid profile of the novel strain was slightly different from those reported for recognized Algoriphagus species. The quinone system contained menaquinone MK-7 as the predominant component. The major polar lipids were phosphatidylethanolamine, an unknown polar lipid, an unknown phospholipid and an unknown aminophospholipid. The main cell polyamine was sym-homospermidine; lesser amounts of spermine and spermidine were also found. The results of DNA-DNA hybridization, and physiological and biochemical tests allowed the genotypic and phenotypic differentiation of strain CC-Hsuan-617(T) from recognized Algoriphagus species. Strain CC-Hsuan-617(T) is thus considered to represent a novel species of the genus Algoriphagus, for which the name Algoriphagus olei sp. nov. is proposed. The type strain is CC-Hsuan-617(T) (=BCRC 17886(T)=CCUG 57471(T)).
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Vogesella lacus sp. nov., isolated from a soft-shell turtle culture pond.
Int. J. Syst. Evol. Microbiol.
PUBLISHED: 07-22-2009
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A non-pigmented, Gram-negative, aerobic, rod-shaped bacterium, strain GR13(T), was isolated using nutrient agar from a water sample from a pond used for the culture of soft-shell turtles (Trionyx sinensis), Pingtung County, Taiwan. 16S rRNA gene sequence studies indicated that the novel strain formed a monophyletic branch at the periphery of the evolutionary radiation occupied by the genus Vogesella. Its closest neighbours were Vogesella indigofera ATCC 19706(T) and Vogesella perlucida DS-28(T) (both with 97.4 % gene sequence similarity). The novel isolate could be distinguished from these species by several phenotypic characteristics. The predominant fatty acids were summed feature 3 (C(16 : 1)omega7c and/or C(15 : 0) iso 2-OH; 60 %), C(16 : 0) (13.6 %) and C(18 : 1)omega7c (12.5 %). The DNA G+C content of strain GR13(T) was 63 mol%. The DNA-DNA hybridization values for the novel strain with V. indigofera and V. perlucida were <25 %. On the basis of the 16S rRNA gene sequence analysis and the chemotaxonomic and physiological data, it is concluded that strain GR13(T) represents a novel species in the genus Vogesella, for which the name Vogesella lacus sp. nov. is proposed. The type strain is GR13(T) (=BCRC 17836(T)=LMG 24504(T)).
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Muricauda lutaonensis sp. nov., a moderate thermophile isolated from a coastal hot spring.
Int. J. Syst. Evol. Microbiol.
PUBLISHED: 07-22-2009
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A yellow-pigmented, Gram-staining-negative, aerobic, non-motile, moderately thermophilic, rod-shaped bacterium, designated strain CC-HSB-11(T), was isolated from a coastal hot spring of Green Island (Lutao), located off Taituang, Taiwan. 16S rRNA gene sequence analysis demonstrated that it shared <94.4 % sequence similarity with Muricauda species. Menaquinone with six isoprene units (MK-6) was the major respiratory quinone and iso-C(15 : 0), iso-C(15 : 1) G, iso-C(15 : 0) 3-OH, iso-C(16 : 0) 3-OH, iso-C(17 : 0) 3-OH and summed feature 3 (comprising iso-C(15 : 0) 2-OH and/or C(16 : 1)omega7c/t) were the predominant fatty acids. The predominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. Six unidentified phospholipids and glycolipids also occurred as minor components. The DNA G+C content of strain CC-HSB-11(T) was 46.4+/-1 mol%. On the basis of 16S rRNA gene sequence similarities with other Muricauda species and differentiating fatty acid compositions and other phenotypic data, strain CC-HSB-11(T) represents a novel species in the genus Muricauda, for which the name Muricauda lutaonensis sp. nov. is proposed. The type strain is CC-HSB-11(T) (=BCRC 17850(T) =KCTC 22339(T)).
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Andreprevotia lacus sp. nov., isolated from a fish-culture pond.
Int. J. Syst. Evol. Microbiol.
PUBLISHED: 07-21-2009
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A bacterial strain designated GFC-1(T) was isolated from a fish-culture pond in Taiwan and was characterized by using the polyphasic taxonomic approach. Strain GFC-1(T) was Gram-negative, aerobic, rod-shaped, motile and non-spore-forming. Phylogenetic analyses based on 16S rRNA gene sequences showed that the strain belonged to the genus Andreprevotia of the family Neisseriaceae and its closest neighbour was Andreprevotia chitinilytica JS11-7(T) (97.0 % sequence similarity). The results of physiological and biochemical tests allowed clear phenotypic differentiation of isolate GFC-1(T) from A. chitinilytica JS11-7(T). The major fatty acids were summed feature 3 (C(16 : 1)omega7c and/or iso-C(15 : 0) 2-OH), C(16 : 0) and C(18 : 1)omega7c. The DNA G+C content was 63.0 mol%. On the basis of 16S rRNA gene sequence analysis and chemotaxonomic and physiological data, strain GFC-1(T) should be classified as representing a novel species and a second member of the genus Andreprevotia, for which the name Andreprevotia lacus sp. nov. is proposed. The type strain is GFC-1(T) (=BCRC 17832(T)=LMG 24502(T)).
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Flectobacillus roseus sp. nov., isolated from freshwater in Taiwan.
Int. J. Syst. Evol. Microbiol.
PUBLISHED: 07-21-2009
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Two Gram-negative, aerobic, pale pink/rose-coloured, rod-shaped, non-motile bacterial strains, designated GFA-11(T) and RG-4, were isolated from a freshwater fish culture pond and a freshwater spring sample, respectively. Based on characterization by using a polyphasic approach, the two strains showed highly similar phenotypic, physiological and genetic characteristics. They shared 99.9 % 16S rRNA gene sequence similarity and 89-94 % DNA-DNA relatedness, suggesting that they represent a single genomic species. Phylogenetic analysis based on 16S rRNA gene sequences showed that strains GFA-11(T) and RG-4 formed a monophyletic branch at the periphery of the evolutionary radiation occupied by the genus Flectobacillus within the family Flexibacteraceae. Their closest neighbours were Flectobacillus major DSM 103(T) (97.7 % 16S rRNA gene sequence similarity) and Flectobacillus lacus CL-GP79(T) (95.9 %). Levels of DNA-DNA relatedness between the two novel strains and the type strains of F. major and F. lacus were less than 70 %. The results of physiological and biochemical tests allowed clear phenotypic differentiation of strains GFA-11(T) and RG-4 from recognized members of the genus Flectobacillus. The predominant fatty acid constituents of strain GFA-11(T) were C(16 : 1)omega5c (40.2 % of the total) and iso-C(15 : 0) (15.0 %). The DNA G+C content of strain GFA-11(T) was 39.7 mol%. On the basis of 16S rRNA gene sequence analysis and chemotaxonomic and physiological data, strains GFA-11(T) and RG-4 are considered to represent a novel species of the genus Flectobacillus, for which the name Flectobacillus roseus sp. nov. is proposed. The type strain is GFA-11(T) (=BCRC 17834(T)=LMG 24501(T)).
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Belliella pelovolcani sp. nov., isolated from a mud-volcano in Taiwan.
Int. J. Syst. Evol. Microbiol.
PUBLISHED: 07-21-2009
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Strain CC-SAL-25(T), a non-motile, Gram-negative, red-pigmented bacterium, was isolated from a rare mud-volcano, located in Wandan, Pingtung County, Taiwan. Studies based on 16S rRNA gene sequences showed that the strain clustered closely with Belliella baltica BA143(T) (95.4 % sequence similarity). A menaquinone with seven isoprene units (MK-7) was the major respiratory quinone. The fatty acid profile was slightly different from that of B. baltica BA143(T). The results of the physiological and biochemical tests showed that strain CC-SAL-25(T) could be clearly differentiated from recognized Belliella species based on phenotypic properties. It was evident from the genotypic and phenotypic data that strain CC-SAL-25(T) should be classified as representing a second novel species in the genus Belliella. The name proposed for this taxon is Belliella pelovolcani sp. nov., and the type strain is CC-SAL-25(T) (=BCRC 17883(T)=KCTC 13248(T)).
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Lutaonella thermophila gen. nov., sp. nov., a moderately thermophilic member of the family Flavobacteriaceae isolated from a coastal hot spring.
Int. J. Syst. Evol. Microbiol.
PUBLISHED: 07-15-2009
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A yellow-pigmented, Gram-staining-negative, aerobic, non-motile, moderately thermophilic, rod-shaped bacterium, CC-MHSW-2T, was isolated from a coastal hot spring of Green Island (Lutao), located off Taituang, Taiwan. The 16S rRNA gene sequence analysis demonstrated that it shared <93.2% sequence similarity with Aquimarina species. The organism was unable to produce acid from carbohydrates, but it could utilize a number of organic acids and amino acids. Menaquinone 6 (MK-6) was the major respiratory quinone and iso-C15:0, iso-C17:0 3-OH and summed feature 3 (comprising C16:1omega7c and/or C16:1omega6c) were the predominant fatty acids. This fatty acid profile distinguished the isolate from members of the genera Aquimarina, Tamlana, Zhouia, Leeuwenhoekiella and Cellulophaga. The DNA G+C content of strain CC-MHSW-2T was 39.7+/-1 mol%. On the basis of the 16S rRNA gene sequence analysis and the chemotaxonomic and physiological data, strain CC-MHSW-2T represents a novel genus and species in the family Flavobacteriaceae, for which the name Lutaonella thermophila gen. nov., sp. nov. is proposed. The type strain is CC-MHSW-2T (=KCTC 22538T=JCM 15069T).
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Molecular detection and phylogenetic analysis of the catechol 1,2-dioxygenase gene from Gordonia spp.
Syst. Appl. Microbiol.
PUBLISHED: 05-09-2009
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The C12O gene (catA gene) encodes for catechol 1,2-dioxygenase, which is a key enzyme involved in the first step catalysis of the aromatic ring in the ortho-cleavage pathway. This functional gene can be used as a marker to assess the catabolic potential of bacteria in bioremediation. C12OF and C12OR primers were designed based on the conserved regions of the CatA amino acid sequence of Actinobacteria for amplifying the catA gene from the genus Gordonia (16 Gordonia representing 11 species). The amplified catA genes (382bp) were sequenced and analyzed. In the phylogenetic tree based on the translated catA amino acid sequences, all the Gordonia segregated clearly from other closely related genera. The sequence similarity of the catA gene in Gordonia ranged from 72.4% to 99.5%, indicating that the catA gene might have evolved faster than rrn operons or the gyrB gene at the inter-species level. A single nucleotide deletion of the catA gene was observed in Gordonia amicalis CC-MJ-2a, Gordonia rhizosphera and Gordonia sputi at nucleotide position 349. This deletion led to an encoding frame shift downstream of 11 amino acid residues, from WPSVAARAPAP to GHPWRPAHLHL, which was similar to most of the non-Gordonia Actinobacteria. Such variations might influence the catabolic activities or substrate utilization patterns of catechol 1,2-dioxygenase among Gordonia.
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