Yi-Han Hsu

Novosphingobium arabidopsis sp. nov., a DDT-resistant bacterium isolated from the rhizosphere of Arabidopsis thaliana

An aerobic, Gram-stain-negative, rod-shaped, DDT-resistant bacterium, designated strain CC-ALB-2(T), was isolated from the Arabidopsis thaliana rhizosphere. Strain CC-ALB-2(T) was able to grow at 25-37 °C, at pH 5.0-8.0, with 1.0% (w/v) NaCl and tolerate up to 200 mg l(-1) DDT. 16S rRNA gene sequence analysis of strain CC-ALB-2(T) showed highest sequence similarity to Novosphingobium stygium KCTC 2891(T) (97.1%) and Novosphingobium soli DSM 22821(T) (96.8%), and lower levels of similarity (<97.0%) to other species of the genus Novosphingobium. The major fatty acid profile consisted of C14 : 0 2-OH (13.1%), C16 : 0 (10.0%), C(15 : 0) iso 3-OH (5.8%), C(16: 1)ω7c/C(16 :1)ω6c (summed feature 3, 24.7%) and C(18 : 1)ω7c/C(18 : 1)ω6c (summed feature 8, 42.4%). The polar lipid profile constitutes sphingoglycolipid, glycolipid, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidyldimethylethanolamine, phosphatidylglycerol and phosphatidylcholine. The polyamine pattern showed a predominance of spermidine as the major polyamine. The predominant quinone system was ubiquinone (Q-10). The DNA G+C content was 68.9 ± 0.1 mol%. Based on the phylogenetic, phenotypic and chemotaxonomic features, strain CC-ALB-2(T) is proposed to represent a novel species of the genus Novosphingobium for which the name Novosphingobium arabidopsis sp. nov. is proposed. The type strain is CC-ALB-2(T) ( = BCRC 80571(T) = JCM 18896(T)).

Sphingomicrobium astaxanthinifaciens sp. nov., an astaxanthin-producing glycolipid-rich bacterium isolated from surface seawater and emended description of the genus Sphingomicrobium.

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)ω7c/C(18:1)ω6c (summed feature 8), C(16:1)ω7c/C(16:1)ω6c (summed feature 3), C(18:1) 2-OH, methyl C(18:1)ω7c, C(17:1)ω6c 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)).

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

A Gram-stain-negative, strictly aerobic, rod-shaped, non-flagellated, non-spore-forming and gliding marine bacterium, designated strain CC-AMZ-304(T), was isolated from coastal surface seawater near Taichung harbour, Taiwan. Strain CC-AMZ-304(T) predominantly synthesized zeaxanthin and thus formed yellow colonies on marine agar. The novel strain showed an 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 SC17(T) and Bizionia species (n = 7), respectively. The polar lipid profile of strain CC-AMZ-304(T) 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 iso-C15 : 0, iso-C15 : 1 G, iso-C17 : 0 3-OH, iso-C15 : 0 3-OH and C15 : 1ω5c. 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 (iso-C17 : 0 3-OH and iso-C15 : 0 3-OH) and a low amount of anteiso-C15 : 0, and several additional distinguishing biochemical features clearly discriminated strain CC-AMZ-304(T) from the type species of the genera Aestuariibaculum and Gaetbulibacter. Thus, based on data from the present polyphasic study, strain CC-AMZ-304(T) is considered to represent a novel species of a new genus within the family Flavobacteriaceae, for which the name Aquibacter zeaxanthinifaciens gen. nov., sp. nov. is proposed; the type strain of Aquibacter zeaxanthinifaciens is CC-AMZ-304(T) ( = JCM 18557(T) = BCRC 80463(T)). Emended descriptions of the genera Aestuariibaculum and Gaetbulibacter are also proposed.

Azospirillum fermentarium sp. nov., a nitrogen-fixing species isolated from a fermenter.

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 ω8c, C14 : 0 3-OH/C16 : 1 iso I, C16 : 1ω7c/C16 : 1ω6c and C18 : 1ω7c/C18 : 1ω6c. 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)).

Youngimonas vesicularis gen. nov., sp. nov., of the family Rhodobacteraceae, isolated from surface seawater, reclassification of Donghicola xiamenensis Tan et al. 2009 as Pseudodonghicola xiamenensis gen. nov., comb. nov. and emended description of the genus Donghicola Yoon et al. 2007.

A Gram-staining-negative, non-pigmented, strictly aerobic, rod-shaped, non-spore-forming, non-motile bacterium, devoid of bacteriochlorophyll, designated strain CC-AMW-E(T), was isolated from surface seawater off the coast at Kending, Taiwan. Strain CC-AMW-E(T) shared 95.7 and 93.9% 16S rRNA gene sequence similarity, respectively, with the type strains of the type species of the genera Donghicola (Donghicola eburneus SW-277(T)) and Roseovarius (Roseovarius tolerans EL-172(T)). The predominant (>75% of the total) fatty acid was summed feature 8 (C(18 : 1)ω6c and/or C(18 : 1)ω7c). The polar lipid profile included major amounts of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine and an unidentified aminolipid. In addition, moderate amounts of an unidentified lipid and trace amounts of an unidentified phospholipid were detected. The DNA G+C content was 67.9 mol%. Ubiquinone Q-10 was the sole respiratory quinone. Based on its phylogenetic distinctiveness and distinguishing phenotypic characteristics (in particular its polar lipid pattern), we conclude that strain CC-AMW-E(T) represents a novel genus and species of the family Rhodobacteraceae, for which the name Youngimonas vesicularis gen. nov., sp. nov. is proposed. The type strain of Youngimonas vesicularis is CC-AMW-E(T) ( = JCM 18819(T) = BCRC 80549(T)). In addition, an emended description of the genus Donghicola Yoon et al. 2007 and the reclassification of Donghicola xiamenensis Tan et al. 2009 as Pseudodonghicola xiamenensis gen. nov., comb. nov. (type strain Y-2(T) = MCCC 1A00107(T) = LMG 24574(T) = CGMCC 1.7081(T)) are proposed.

Pseudomonas sagittaria sp. nov., a siderophore-producing bacterium isolated from oil-contaminated soil.

An aerobic, Gram-stain-negative, rod-shaped bacterium with a single polar flagellum, designated CC-OPY-1(T), was isolated from an oil-contaminated site in Taiwan. CC-OPY-1(T) produces siderophores, and can grow at temperatures of 25-37 °C and pH 5.0-9.0 and tolerate <5 % (w/v) NaCl. The 16S rRNA gene sequence analysis of CC-OPY-1(T) showed high pairwise sequence similarity to Pseudomonas alcaligenes BCRC 11893(T) (97.1 %), Pseudomonas. alcaliphila DSM 17744(T) (97.1 %), Pseudomonas tuomuerensis JCM 14085(T) (97.1 %), Pseudomonas toyotomiensis JCM 15604(T) (96.9 %) and lower sequence similarity to remaining species of the genus Pseudomonas. The phylogenetic trees reconstructed based on gyrB and rpoB gene sequences supported the classification of CC-OPY-1(T) as a novel member of the genus Pseudomonas. The predominant quinone system of strain CC-OPY-1T was ubiquinone (Q-9) and the DNA G+C content was 68.4 ± 0.3 mol%. The major fatty acids were C12 : 0, C16 : 0, C17 : 0 cyclo and summed features 3 and 8 consisting of C16 : 1ω7c/C16 : 1ω6c and C18 : 1ω7c/C18 : 1ω6c, respectively. The major polar lipids were phosphatidylethanolamine (PE), phosphatidylglycerol (PG), diphosphatidylglycerol (DPG), phosphatidylcholine (PC) and two unknown phospholipids (PL1-2). Due to distinct phylogenetic, phenotypic and chemotaxonomic features, CC-OPY-1(T) is proposed to represent a novel species within the genus Pseudomonas for which the name Pseudomonas sagittaria sp. nov. is proposed. The type strain is CC-OPY-1(T) ( = BCRC 80399(T) = JCM 18195(T)).

Shimia biformata sp. nov., isolated from surface seawater, and emended description of the genus Shimia Choi and Cho 2006.

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 : 1ω7c and/or C18 : 1ω6c (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 : 1ω7c and/or C18 : 1ω6c, 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.

Nocardioides echinoideorum sp. nov., isolated from sea urchins (Tripneustes gratilla).

A Gram-stain-positive, aerobic, non-motile, rod-shaped, yellow-pigment-producing bacterium, (designated strain CC-CZW004T), was isolated from seafood samples (sea urchins) at Penghu Island in Taiwan. Strain CC-CZW004T grew optimally at pH 7.0 and 30 °C in the presence of 3 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA genes revealed a distinct taxonomic position attained by strain CC-CZW004T with respect to other members of the genus Nocardioides. The novel strain shared highest 16S rRNA gene sequence similarities to Nocardioides daejeonensis JCM 16922T (96.4 %), Nocardioides pacificus JCM 19260T (96.3 %), and Marmoricola scoriae JCM 17444T (96.2 %). The major fatty acids of strain CC-CZW004T consisted of C17:0, C16:1ω5c, C17:1ω8c`, iso-C16:0 and C19:1ω11c/C19:1ω9c (summed feature 6). The diagnostic diamino acid in the cell wall was ll-2,6-diaminopimelic acid. The polar lipid profile was composed of major amounts of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and aminophospholipid. The DNA G+C content was 73.3 mol%. The predominant quinone system was menaquinone (MK-8). On the basis of polyphasic taxonomic evidences presented here, strain CC-CZW004T represents a novel species of the genus Nocardioides, for which the name Nocardioides echinoideorum sp. nov. is proposed. The type strain is CC-CZW004T ( = BCRC 16974T = JCM 30276T).

Pseudomonas formosensis sp. nov., a gamma-proteobacteria isolated from food-waste compost in Taiwan.

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 ω8c and summed features 3 and 8 consisting of C(16:1)ω7c/C(16:1)ω6c and C(18:1)ω7c/C(18:1)ω6c, 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.

Pseudomonas guguanensis sp. nov., a gammaproteobacterium isolated from a hot spring

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 : 1ω7c/C16 : 1ω6c and C18 : 1ω7c/C18 : 1ω6c, 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)).