Asif Hameed

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)).

Kordia aquimaris sp. nov., a zeaxanthin-producing member of the family Flavobacteriaceae isolated from surface seawater, and emended description of the genus Kordia.

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 : 1ω7c and/or C16 : 1ω6c) and summed feature 9 (iso-C17 : 1ω9c 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.

Siansivirga zeaxanthinifaciens gen. nov., sp. nov., a novel zeaxanthin-producing member of the family Flavobacteriaceae isolated from coastal seawater of Taiwan

A strictly aerobic, Gram-negative, rod-shaped bacterium (strain CC-SAMT-1(T)) showing gliding motility was isolated from coastal seawater of China Sea, Taiwan. Strain CC-SAMT-1(T) synthesizes all-trans-zeaxanthin (6.5 ± 0.5 mg g(-1) dry biomass) as a predominant xanthophyll carotenoid. As determined by 16S rRNA gene analysis, strain CC-SAMT-1(T) shared very high sequence similarity to the members of the genera Mariniflexile (96.1-95.3%) and Gaetbulibacter (96.0-95.9%); however, it formed a distinct phyletic lineage distantly associated with Mariniflexile species. Polar lipid profile constitutes phosphatidylethanolamine, four unidentified aminolipids, four unidentified lipids, and an unidentified glycolipid. Strain CC-SAMT-1(T) contains excessive unidentified aminolipid lipid (AL2-4) and glycolipid contents, and therefore clearly distinct from Mariniflexile species. Major fatty acids (> 5% of total fatty acids) were iso-C(15:0) (14.8%), iso-C(17:0) 3-OH (11.8%), iso-C(15:1) G (10.6%), anteiso-C(15:0) (9.7%), C(16:0) (8.1%), iso-C(16:0) 3-OH (7.9%), iso-C(15:0) 3-OH (7.5%), and summed feature 3 (containing C(16:1) ω6c and/or C(16:1) ω7c) (7.5%). Menaquinone-6 (MK-6) was major respiratory quinone. DNA G+C content was 33.7 mol%. Based on polyphasic taxonomy, strain CC-SAMT-1(T) represents a novel genus and species in the family Flavobacteriaceae for which the name Siansivirga zeaxanthinifaciens gen. nov., sp. nov. is proposed. The type strain is CC-SAMT-1(T) (= BCRC 80315(T) = JCM 17682(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.

Phosphate-solubilizing soil yeast Meyerozyma guilliermondii CC1 improves maize (Zea mays L.) productivity and minimizes requisite chemical fertilization

AimPhosphate-solubilizing yeasts have been under-exploited in eco-friendly maize cultivation. In this regard, soil yeasts Meyerozyma guilliermondii CC1, Rhodotorula mucilaginosa CC2 and M. caribbica CC3 were investigated for their plant growth-promoting (PGP) activities.MethodsSoil yeasts were isolated and characterized. Maize (Zea mays L. cv. Tainong No.1) and Chinese cabbage (Brassica rapa L. cv. Pekinensis) were used for seed bioassay. Growth-promoting effects of yeasts under greenhouse conditions were evaluated using maize and lettuce (Lactuca sativa L. cvs. Capitata and Taiwan sword leaf). Ultimately, M. guilliermondii CC1 was tested on field-grown maize; treatments included full-dose chemical fertilizers (CF), yeast (CC1), half-dose chemical fertilizers (½CF), CC1 + ½CF and control. Nutrient uptake, growth, and yield of maize and rhizospheric soil microbes were estimated.ResultsStrain M. guilliermondii CC1 exhibited better seed vigor index in maize and Chinese cabbage. CC1 + ½CF significantly improved the dry-weights, and nutrient uptakes of maize and sword leaf lettuce under greenhouse conditions. In field, CC1 + ½CF application exerted a pronounced effect on growth of maize, cob yield, nutrient-uptake and rhizospheric soil microbial counts.ConclusionOur results validated superior biochemical potency and PGP traits of M. guilliermondii CC1 that reduced requisite chemical fertilizer application without affecting the optimal productivity in maize.

Supercritical carbon dioxide micronization of zeaxanthin from moderately thermophilic bacteria Muricauda lutaonensis CC-HSB-11T.

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 μm. 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.

Gramella oceani sp. nov., a zeaxanthin-producing bacterium of the family Flavobacteriaceae isolated from marine sediment.

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)ω6c and/or C(16 : 1)ω7c and iso-C(17 : 1)ω9c 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)).