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1

Draft Genome Sequence of Geobacillus sp. Strain FW23, Isolated from a Formation Water Sample  

PubMed Central

The thermophilic Geobacillus sp. strain FW23 was isolated from the Mehsana oil wells in Gujrat, India, during a screening for oil-degrading bacteria. Here, we report the draft genome sequence of Geobacillus sp. FW23, which may help reveal the genomic differences between this strain and the earlier reported species of the genus Geobacillus. PMID:24812215

Pore, Soham D.; Arora, Preeti

2014-01-01

2

Biotransformation of eugenol via protocatechuic acid by thermophilic Geobacillus sp. AY 946034 strain.  

PubMed

The metabolic pathway of eugenol degradation by thermophilic Geobacillus sp. AY 946034 strain was analyzed based on the lack of data about eugenol degradation by thermophiles. TLC, GC-MS, and biotransformation with resting cells showed that eugenol was oxidized through coniferyl alcohol, and ferulic and vanillic acids to protocatechuic acid before the aromatic ring was cleaved. The cell-free extract of Geobacillus sp. AY 946034 strain grown on eugenol showed a high activity of eugenol hydroxylase, feruloyl-CoA synthetase, vanillate-O-demethylase, and protocatechuate 3,4-dioxygenase. The key enzyme, protocatechuate 3,4- dioxygenase, which plays a crucial role in the degradation of various aromatic compounds, was purified 135-fold to homogeneity with a 34% overall recovery from Geobacillus sp. AY 946034. The relative molecular mass of the native enzyme was about 450 ± 10 kDa and was composed of the non-identical subunits. The pH and temperature optima for enzyme activity were 8 and 60°C, respectively. The half-life of protocatechuate 3,4-dioxygenase at the optimum temperature was 50 min. PMID:24375415

Giedraityte, Gražina; Kal?dien?, Lilija

2014-04-01

3

Crystallization and preliminary X-ray study of alpha-glucosidase from Geobacillus sp strain HTA-462, one of the deepest sea bacteria.  

PubMed

An alpha-glucosidase (EC 3.2.1.20) was purified from Geobacillus sp. strain HTA-462 cells and crystallized using the hanging-drop vapour-diffusion technique. The Geobacillus strain is a thermophilic and high-pressure-resistant bacterium found at the bottom of the Challenger Deep in the Mariana Trench. The crystal was characterized by X-ray diffraction and belongs to space group C2, with unit-cell parameters a = 104.0, b = 91.5, c = 72.9 A, beta = 109.4 degrees. Diffraction data to 2.5 A resolution were collected and processed. PMID:12832785

Shirai, Tsuyoshi; Hung, Vo Si; Akita, Masatake; Hatada, Yuji; Ito, Susumu; Horikoshi, Koki

2003-07-01

4

Gold nanoparticles synthesized by Geobacillus sp. strain ID17 a thermophilic bacterium isolated from Deception Island, Antarctica  

PubMed Central

Background The use of microorganisms in the synthesis of nanoparticles emerges as an eco-friendly and exciting approach, for production of nanoparticles due to its low energy requirement, environmental compatibility, reduced costs of manufacture, scalability, and nanoparticle stabilization compared with the chemical synthesis. Results The production of gold nanoparticles by the thermophilic bacterium Geobacillus sp. strain ID17 is reported in this study. Cells exposed to Au3+ turned from colourless into an intense purple colour. This change of colour indicates the accumulation of intracellular gold nanoparticles. Elemental analysis of particles composition was verified using TEM and EDX analysis. The intracellular localization and particles size were verified by TEM showing two different types of particles of predominant quasi-hexagonal shape with size ranging from 5–50 nm. The mayority of them were between 10?20 nm in size. FT-IR was utilized to characterize the chemical surface of gold nanoparticles. This assay supports the idea of a protein type of compound on the surface of biosynthesized gold nanoparticles. Reductase activity involved in the synthesis of gold nanoparticles has been previously reported to be present in others microorganisms. This reduction using NADH as substrate was tested in ID17. Crude extracts of the microorganism could catalyze the NADH-dependent Au3+ reduction. Conclusions Our results strongly suggest that the biosynthesis of gold nanoparticles by ID17 is mediated by enzymes and NADH as a cofactor for this biological transformation. PMID:23919572

2013-01-01

5

Isolation and Characterization of Novel Denitrifying Bacterium Geobacillus sp. SG-01 Strain from Wood Chips Composted with Swine Manure  

PubMed Central

Nitrate contamination in ground and surface water is an increasingly serious environmental problem and only a few bacterial strains have been identified that have the ability to remove nitrogen pollutants from wastewater under thermophilic conditions. We therefore isolated thermophilic facultative bacterial strains from wood chips that had been composted with swine manure under aerated high temperature conditions so as to identify strains with denitrifying ability. Nine different colonies were screened and 3 long rod-shaped bacterial strains designated as SG-01, SG-02, and SG-03 were selected. The strain SG-01 could be differentiated from SG-02 and SG-03 on the basis of the method that it used for sugar utilization. The 16S rRNA genes of this strain also had high sequence similarity with Geobacillus thermodenitrificans 465T (99.6%). The optimal growth temperatures (55°C), pH values (pH 7.0), and NaCl concentrations (1%) required for the growth of strain SG-01 were established. This strain reduced 1.18 mM nitrate and 1.45 mM nitrite in LB broth after 48 h of incubation. These results suggest that the G. thermodenitrificans SG-01 strain may be useful in the removal of nitrates and nitrites from wastewater generated as a result of livestock farming. PMID:25049754

Yang, Seung-Hak; Cho, Jin-Kook; Lee, Soon-Youl; Abanto, Oliver D.; Kim, Soo-Ki; Ghosh, Chiranjit; Lim, Joung-Soo; Hwang, Seong-Gu

2013-01-01

6

Draft Genome Sequence of Geobacillus thermopakistaniensis Strain MAS1  

PubMed Central

Geobacillus thermopakistaniensis strain MAS1 was isolated from a hot spring located in the Northern Areas of Pakistan. The draft genome sequence was 3.5 Mb and identified a number of genes of potential industrial importance, including genes encoding glycoside hydrolases, pullulanase, amylopullulanase, glycosidase, and alcohol dehydrogenases. PMID:24903880

Rashid, Naeem; Ayyampalayam, Saravanaraj

2014-01-01

7

A thermoalkaliphilic lipase of Geobacillus sp. T1.  

PubMed

A thermoalkaliphilic T1 lipase gene of Geobacillus sp. strain T1 was overexpressed in pGEX vector in the prokaryotic system. Removal of the signal peptide improved protein solubility and promoted the binding of GST moiety to the glutathione-Sepharose column. High-yield purification of T1 lipase was achieved through two-step affinity chromatography with a final specific activity and yield of 958.2 U/mg and 51.5%, respectively. The molecular mass of T1 lipase was determined to be approximately 43 kDa by gel filtration chromatography. T1 lipase had an optimum temperature and pH of 70 degrees C and pH 9, respectively. It was stable up to 65 degrees C with a half-life of 5 h 15 min at pH 9. It was stable in the presence of 1 mM metal ions Na(+), Ca(2+), Mn(2+), K(+) and Mg(2+ ), but inhibited by Cu(2+), Fe(3+) and Zn(2+). Tween 80 significantly enhanced T1 lipase activity. T1 lipase was active towards medium to long chain triacylglycerols (C10-C14) and various natural oils with a marked preference for trilaurin (C12) (triacylglycerol) and sunflower oil (natural oil). Serine and aspartate residues were involved in catalysis, as its activity was strongly inhibited by 5 mM PMSF and 1 mM Pepstatin. The T(m) for T1 lipase was around 72.2 degrees C, as revealed by denatured protein analysis of CD spectra. PMID:17426920

Leow, Thean Chor; Rahman, Raja Noor Zaliha Raja Abd; Basri, Mahiran; Salleh, Abu Bakar

2007-05-01

8

[Characterization of a thermophilic Geobacillus strain DM-2 degrading hydrocarbons].  

PubMed

A thermophilic Geobacillus strain DM-2 from a deep-subsurface oil reservoir was investigated on its capability of degrading crude oil under various conditions as well as its characters on degrading hydrocarbons in optimal conditions. The results showed that Geobacillus strain DM-2 was able to degrade crude oil under anoxic wide-range conditions with pH ranging from 4.0 to 10.0, high temperature in the range of 45-70 degrees C and saline concentration ranging from 0.2% to 3.0%. Furthermore, the optimal temperature and pH value for utilizing hydrocarbons by the strain were 60 degrees C and 7.0, respectively. Under such optimal conditions, the strain utilized liquid paraffine emulsified by itself as its carbon source for growth; further analysis by gas chromatography (GC) and infrared absorption spectroscopy demonstrated that it was able to degrade n-alkanes (C14-C30), branched-chain alkanes and aromatic hydrocarbons in crude oil and could also utilize long-chain n-alkanes from C16 to C36, among of which the degradation efficiency of C28 was the highest, up to 88.95%. One metabolite of the strain oxidizing alkanes is fatty acid.While utilizing C16 as carbon source for 5 d, only one fatty acid-acetic acid was detected by HPLC and MS as the product, with the amount of 0.312 g/L, which indicated that it degraded n-alkanes with pathway of inferior terminal oxidation,and then followed by a beta-oxidation pathway. Due to its characters of efficient emulsification, high-performance degradation of hydrocarbons and fatty-acid production under high temperature and anoxic condition, the strain DM-2 may be potentially applied to oil-waste treatment and microbial enhanced heavy oil recovery in extreme conditions. PMID:19256400

Liu, Qing-kun; Wang, Jun; Li, Guo-qiang; Ma, Ting; Liang, Feng-lai; Liu, Ru-lin

2008-12-01

9

Draft Genome Sequence of Geobacillus kaustophilus GBlys, a Lysogenic Strain with Bacteriophage ?OH2  

PubMed Central

Geobacillus kaustophilus strain GBlys was isolated along with the bacteriophage ?OH2, which infects G. kaustophilus NBRC 102445T. Here we present a draft sequence of this strain’s genome, which consists of 216 contigs for a total of 3,541,481 bp, 3,679 predicted coding sequences, and a G+C content of 52.1%. PMID:23950135

Mori, Kazuki; Martono, Hindra; Nagayoshi, Yuko; Fujino, Yasuhiro; Tashiro, Kosuke; Kuhara, Satoru; Ohshima, Toshihisa

2013-01-01

10

Experimental fossilisation of the thermophilic Gram-positive bacterium Geobacillus SP7A: a long duration preservation study.  

E-print Network

was monitored with the use of LIVE/DEAD staining to assess the structural integrity of the cells during, Geobacillus SP7A, LIVE/DEAD staining, microfossils, electron microscopy #12;Introduction Much progress has

Paris-Sud XI, Université de

11

Novel enzymatic activity of cell free extract from thermophilic Geobacillus sp. UZO 3 catalyzes reductive cleavage of diaryl ether bonds of 2,7-dichlorodibenzo- p-dioxin  

Microsoft Academic Search

We characterized the ability of the cell free extract from polychlorinated dibenzo-p-dioxins degrading bacterium Geobacillus sp. UZO 3 to reduce even highly chlorinated dibenzo-p-dioxins such as octachlorodibenzo-p-dioxins in incineration fly ash. The degradation of 2,7-dichlorodibenzo-p-dioxin (2,7-DCDD) as a model dioxin catalyzed by the cell free extract from this strain implicates that the ether bonds of 2,7-DCDD molecule undergo reductive cleavage,

Yuzoh Suzuki; Masaya Nakamura; Yuichiro Otsuka; Nao Suzuki; Keisuke Ohyama; Takeshi Kawakami; Kanna Sato; Shinya Kajita; Shojiro Hishiyama; Takeo Fujii; Atsushi Takahashi; Yoshihiro Katayama

2011-01-01

12

Identification of three Superoxide dismutase genes from a Geobacillus sp.  

PubMed

We report the characterization of three Superoxide dismutase (sod) genes isolated from a bacterium in the Geobacillus genus. We isolated the bacterium from high-temperature pond mud and used 16S rRNA gene sequence to confirm its identity in the Geobacillus genus. The three genes Mn-sod, Fe/Mn-sod, and Cu/Zn-sod were cloned and analyzed. Their open reading frames are Mn-sod: 615 bp encoding a 204 amino acid protein; Fe/Mn-sod: 1,236 bp encoding a 411 amino acid protein; Cu/Zn-sod: 522 bp encoding a 173 amino acid protein. When these sod genes were expressed in Escherichia coli, only Mn-SOD was able to be purified. The activity of the purified Mn-SOD we got was about 2,730 U/mg. Studies of this Mn-SOD showed that it was thermostable at 60°, had 70% activity at 80° after 2.5 h, and still had 30% activity at 90° after 2.5 h. Mn-SOD activity required the ion Mn²+. Based on gel electrophoresis, we deduced that this Mn-SOD was a homotetramer. No activity was detected after the other two genes (Fe/Mn-sod, Cu/Zn-sod) were expressed in Escherichia coli, but activities were detected when expressed in Pichia pastoris. PMID:21221750

Zou, Yuanyuan; Yang, Ling; Liu, Guoxian; Li, Yinv; Zhu, Yuexiong; Zhang, Zhifang

2011-01-01

13

Thermophilic fermentation of acetoin and 2,3-butanediol by a novel Geobacillus strain  

PubMed Central

Background Acetoin and 2,3-butanediol are two important biorefinery platform chemicals. They are currently fermented below 40°C using mesophilic strains, but the processes often suffer from bacterial contamination. Results This work reports the isolation and identification of a novel aerobic Geobacillus strain XT15 capable of producing both of these chemicals under elevated temperatures, thus reducing the risk of bacterial contamination. The optimum growth temperature was found to be between 45 and 55°C and the medium initial pH to be 8.0. In addition to glucose, galactose, mannitol, arabionose, and xylose were all acceptable substrates, enabling the potential use of cellulosic biomass as the feedstock. XT15 preferred organic nitrogen sources including corn steep liquor powder, a cheap by-product from corn wet-milling. At 55°C, 7.7?g/L of acetoin and 14.5?g/L of 2,3-butanediol could be obtained using corn steep liquor powder as a nitrogen source. Thirteen volatile products from the cultivation broth of XT15 were identified by gas chromatography–mass spectrometry. Acetoin, 2,3-butanediol, and their derivatives including a novel metabolite 2,3-dihydroxy-3-methylheptan-4-one, accounted for a total of about 96% of all the volatile products. In contrast, organic acids and other products were minor by-products. ?-Acetolactate decarboxylase and acetoin:2,6-dichlorophenolindophenol oxidoreductase in XT15, the two key enzymes in acetoin metabolic pathway, were found to be both moderately thermophilic with the identical optimum temperature of 45°C. Conclusions Geobacillus sp. XT15 is the first naturally occurring thermophile excreting acetoin and/or 2,3-butanediol. This work has demonstrated the attractive prospect of developing it as an industrial strain in the thermophilic fermentation of acetoin and 2,3-butanediol with improved anti-contamination performance. The novel metabolites and enzymes identified in XT15 also indicated its strong promise as a precious biological resource. Thermophilic fermentation also offers great prospect for improving its yields and efficiencies. This remains a core aim for future work. PMID:23217110

2012-01-01

14

Thermostable lipase from Geobacillus sp. Iso5: bioseparation, characterization and native structural studies.  

PubMed

The extracellular thermoalkaline lipase from Geobacillus sp. Iso5 was purified to homogeneity by ultrafiltration, 6% cross-linked agarose and Phenyl spehrose HIC column chromatography. The final purified lipase resulted in 8.7-fold with 6.2% yield. The relative molecular weight of the enzyme was determined to be a monomer of 47?kDa by SDS-PAGE and MALDI-TOF MS/MS spectroscopy. The purified enzyme exhibit optimum activity at 70?°C and pH 8.0. The enzyme retained above 90% activity at temperatures of 70?°C and about 35% activity at 85?°C for 2?h. However, the stability of the enzyme decreased at the temperature over 90?°C. The enzyme activity was promoted in the presence of Ca(2+) and Mg(2+) and strongly inhibited by HgCl2 , PMSF, DTT, K(+) , Co(2+) , and Zn (2+) . EDTA did not affect the enzyme activity. The secondary structure of purified lipase contains 36% ?-helix and 64% ?-sheet which was determined by Circular dichromism, FTIR, and Raman Spectroscopy. PMID:23775834

Mahadevan, Gurumurthy D; Neelagund, Shivayogeeswar E

2014-05-01

15

alpha-Glucosidase from a strain of deep-sea Geobacillus: a potential enzyme for the biosynthesis of complex carbohydrates.  

PubMed

An alpha-glucosidase from Geobacillus sp. strain HTA-462, one of the deepest sea bacteria isolated from the sediment of the Mariana Trench, was purified to homogeneity and estimated to be a 65-kDa protein by SDS-PAGE. At low ion strength, the enzyme exists in the homodimeric form (130 kDa). It is a thermo- and alkaline-stable enzyme with a half-life of 13.4 h and a maximum hydrolytic activity at 60 degrees C and pH 9.0 in 15 mM glycine-NaOH buffer. The enzyme exclusively hydrolyzed alpha-1,4-glycosidic linkages of oligosaccharides in an exo-type manner. The enzyme had an overwhelming transglycosylation activity and glycosylated various non-sugar molecules when maltose was used as a sugar donor. It converted maltose to isomaltose. The gene encoding the enzyme was cloned and sequenced. The recombinant enzyme could be extracellularly overproduced by Bacillus subtilis harboring its gene and preserved the primary properties of the native enzyme. Site-directed mutagenesis experiments showed that Asp98 is essential for the enzyme activity in addition to Asp199, Asp326, and Glu256. PMID:15940457

Hung, Vo Si; Hatada, Yuji; Goda, Saori; Lu, Jie; Hidaka, Yuko; Li, Zhijun; Akita, Masatake; Ohta, Yukari; Watanabe, Kenji; Matsui, Hirokazu; Ito, Susumu; Horikoshi, Koki

2005-10-01

16

Draft Genome Sequences of Geobacillus stearothermophilus Strains 22 and 53, Isolated from the Garga Hot Spring in the Barguzin River Valley of the Russian Federation  

PubMed Central

Geobacillus stearothermophilus strains 22 and 53 were isolated from sediment samples isolated from the Garga hot spring (72°C) located in the valley of the river Barguzin (the Baikal region, Russian Federation) (54°19?3.72?N, 110°59?38.4?E). PMID:25414504

Logacheva, Maria D.; Peltek, Sergey E.

2014-01-01

17

Draft Genome Sequence of Geobacillus icigianus Strain G1w1T Isolated from Hot Springs in the Valley of Geysers, Kamchatka (Russian Federation).  

PubMed

The Geobacillus icigianus G1w1(T) strain was isolated from sludge samples of unnamed vaporing hydrothermal (97°?) outlets situated in a geyser in the Troinoy region (Valley of Geysers, Kronotsky Nature Reserve, Kamchatka, Russian Federation; 54°25'51.40?N, 160°7'41.40?E). The sequenced and annotated genome is 3,457,810 bp and encodes 3,342 genes. PMID:25342695

Bryanskaya, Alla V; Rozanov, Aleksey S; Logacheva, Maria D; Kotenko, Anastasia V; Peltek, Sergey E

2014-01-01

18

Draft Genome Sequence of Geobacillus icigianus Strain G1w1T Isolated from Hot Springs in the Valley of Geysers, Kamchatka (Russian Federation)  

PubMed Central

The Geobacillus icigianus G1w1T strain was isolated from sludge samples of unnamed vaporing hydrothermal (97°?) outlets situated in a geyser in the Troinoy region (Valley of Geysers, Kronotsky Nature Reserve, Kamchatka, Russian Federation; 54°25?51.40?N, 160°7?41.40?E). The sequenced and annotated genome is 3,457,810 bp and encodes 3,342 genes. PMID:25342695

Bryanskaya, Alla V.; Logacheva, Maria D.; Kotenko, Anastasia V.; Peltek, Sergey E.

2014-01-01

19

Purification and characterization of intracellular and extracellular ?-glucosidases from Geobacillus toebii strain E134.  

PubMed

Two different ?-glucosidase-producing thermophilic E134 strains were isolated from a hot spring in Kozakli, Turkey. Based on the phenotypic, phylogenetic and chemotaxonomic evidence, the strain was proposed to be a species of G. toebii. Its thermostable exo-?-1,4-glucosidases also were characterized and compared, which were purified from the intracellular and extracellular fractions with estimated molecular weights of 65 and 45?kDa. The intracellular and extracellular ?-glucosidases showed optimal activity at 65?°C, pH 7·0, and at 70?°C, pH 6·8, with 3·65 and 0·83?Km values for the pNPG substrate, respectively. Both enzymes remained active over temperature and pH ranges of 35-70?°C and 4·5-11·0. They retained 82 and 84% of their activities when incubated at 60?°C for 5?h. Their relative activities were 45-75% and 45-60% at pH 4·5 and 11·0 values for 15?h at 35?°C. They could hydrolyse the ?-1,3 and ?-1,4 bonds on substrates in addition to a high transglycosylation activity, although the intracellular enzyme had more affinity to the substrates both in hydrolysis and transglycosylation reactions. Furthermore, although sodium dodecyl sulfate behaved as an activator for both of them at 60?°C, urea and ethanol only increased the activity of the extracellular ?-glucosidase. By this study, G. toebii E134 strain was introduced, which might have a potential in biotechnological processes when the conformational stability of its enzymes to heat, pH and denaturants were considered. Copyright © 2011 John Wiley & Sons, Ltd. PMID:22028281

Cihan, Arzu Coleri; Benli, Mehlika; Cokmus, Cumhur

2012-01-01

20

Enhancing the cellulose-degrading activity of cellulolytic bacteria CTL-6 (Clostridium thermocellum) by co-culture with non-cellulolytic bacteria W2-10 (Geobacillus sp.).  

PubMed

The effect of a non-cellulolytic bacterium W2-10 (Geobacillus sp.) on the cellulose-degrading activity of a cellulolytic bacterium CTL-6 (Clostridium thermocellum) was determined using cellulose materials (paper and straw) in peptone cellulose solution (PCS) medium under aerobic conditions. The results indicated that in the co-culture, addition of W2-10 resulted in a balanced medium pH, and may provide the required anaerobic environment for CTL-6. Overall, addition of W2-10 was beneficial to CTL-6 growth in the adverse environment of the PCS medium. In co-culture with W2-10, the CTL-6 cellulose degradation efficiency of filter paper and alkaline-treated wheat straw significantly increased up to 72.45 and 37.79 %, respectively. The CMCase activity and biomass of CTL-6 also increased from 0.23 U ml(-1) and 45.1 ?g ml(-1) (DNA content) up to 0.47 U ml(-1) and 112.2 ?g ml(-1), respectively. In addition, co-culture resulted in accumulation of acetate and propionate up to 4.26 and 2.76 mg ml(-1). This was a respective increase of 2.58 and 4.45 times, in comparison to the monoculture with CTL-6. PMID:23975281

Lü, Yucai; Li, Ning; Yuan, Xufeng; Hua, Binbin; Wang, Jungang; Ishii, Masaharu; Igarashi, Yasuo; Cui, Zongjun

2013-12-01

21

Characterisation of a new thermoalkaliphilic bacterium for the production of high-quality hemp fibres, Geobacillus thermoglucosidasius strain PB94A.  

PubMed

Novel thermophilic and alkaliphilic bacteria for the processing of bast fibres were isolated using hemp pectin as substrate. The strain PB94A, which showed the highest growth rate (micro = 0.5/h) was identified as Geobacillus thermoglucosidasius (DSM 21625). The strain grew optimally at 60 degrees C and pH 8.5. During growth on citrus pectin, the strain produced pectinolytic lyases, which were excreted into the medium. In contrast to the commercially available pectinase Bioprep 3000 L, the enzymes from G. thermoglucosidasius PB94A converted pectin isolated from hemp fibres. In addition to hemp pectin, the culture supernatant also degraded citrus, sugar beet and apple pectin and polygalacturonic acid. When hemp fibres were incubated with the cell-free fermentation broth of G. thermoglucosidasius PB94A, the fineness of the fibres increased. The strain did not produce any cellulases, which is important in order to avoid damaging the fibres during incubation. Therefore, these bacteria or their enzymes can be used to produce fine high-quality hemp fibres. PMID:19333594

Valladares Juárez, A G; Dreyer, J; Göpel, P K; Koschke, N; Frank, D; Märkl, H; Müller, R

2009-06-01

22

Analysis of Metabolic Pathways and Fluxes in a Newly Discovered Thermophilic and Ethanol-Tolerant Geobacillus Strain  

SciTech Connect

A recently discovered thermophilic bacterium, Geobacillus thermoglucosidasius M10EXG, ferments a range of C5 (e.g., xylose) and C6 sugars (e.g., glucose) and istolerant to high ethanol concentrations (10percent, v/v). We have investigated the central metabolism of this bacterium using both in vitro enzyme assays and 13C-based flux analysis to provide insights into the physiological properties of this extremophile and explore its metabolism for bio-ethanol or other bioprocess applications. Our findings show that glucose metabolism in G. thermoglucosidasius M10EXG proceeds via glycolysis, the pentose phosphate pathway, and the TCA cycle; the Entner?Doudoroff pathway and transhydrogenase activity were not detected. Anaplerotic reactions (including the glyoxylate shunt, pyruvate carboxylase, and phosphoenolpyruvate carboxykinase) were active, but fluxes through those pathways could not be accuratelydetermined using amino acid labeling. When growth conditions were switched from aerobic to micro-aerobic conditions, fluxes (based on a normalized glucose uptake rate of 100 units (g DCW)-1 h-1) through the TCA cycle and oxidative pentose phosphate pathway were reduced from 64+-3 to 25+-2 and from 30+-2 to 19+-2, respectively. The carbon flux under micro-aerobic growth was directed formate. Under fully anerobic conditions, G. thermoglucosidasius M10EXG used a mixed acid fermentation process and exhibited a maximum ethanol yield of 0.38+-0.07 mol mol-1 glucose. In silico flux balance modeling demonstrates that lactate and acetate production from G. thermoglucosidasius M10EXG reduces the maximum ethanol yieldby approximately threefold, thus indicating that both pathways should be modified to maximize ethanol production.

Tang, Yinjie J.; Sapra, Rajat; Joyner, Dominique; Hazen, Terry C.; Myers, Samuel; Reichmuth, David; Blanch, Harvey; Keasling, Jay D.

2009-01-20

23

Cadmium Ion Biosorption by the Thermophilic Bacteria Geobacillus stearothermophilus and G. thermocatenulatus  

PubMed Central

This study reports surface complexation models (SCMs) for quantifying metal ion adsorption by thermophilic microorganisms. In initial cadmium ion toxicity tests, members of the genus Geobacillus displayed the highest tolerance to CdCl2 (as high as 400 to 3,200 ?M). The thermophilic, gram-positive bacteria Geobacillus stearothermophilus and G. thermocatenulatus were selected for further electrophoretic mobility, potentiometric titration, and Cd2+ adsorption experiments to characterize Cd2+ complexation by functional groups within and on the cell wall. Distinct one-site SCMs described the extent of cadmium ion adsorption by both studied Geobacillus sp. strains over a range of pH values and metal/bacteria concentration ratios. The results indicate that a functional group with a deprotonation constant pK value of approximately 3.8 accounts for 66% and 80% of all titratable sites for G. thermocatenulatus and G. stearothermophilus, respectively, and is dominant in Cd2+ adsorption reactions. The results suggest a different type of functional group may be involved in cadmium biosorption for both thermophilic strains investigated here, compared to previous reports for mesophilic bacteria. PMID:16751511

Hetzer, Adrian; Daughney, Christopher J.; Morgan, Hugh W.

2006-01-01

24

Influence of Cations on Growth of Thermophilic Geobacillus spp. and Anoxybacillus flavithermus in Planktonic Culture  

PubMed Central

Free ions of Na+, K+, Ca2+, and Mg2+ influenced the optical density of planktonic cultures of thermophilic bacilli. Anoxybacillus flavithermus E16 and Geobacillus sp. strain F75 (milk powder manufacturing plant isolates) and A. flavithermus DSM 2641 and G. thermoleovorans DSM 5366 were studied. Ca2+ and Mg2+ were associated with increases in optical density more so than Na+ and K+. Overall, it appeared that Ca2+ and/or Mg2+ was required for the production of protein in thermophilic bacilli, as shown by results obtained with A. flavithermus E16, which was selected for further study. PMID:22287005

Palmer, Jon; Brooks, John; Smolinski, Edward; Lindsay, Denise; Flint, Steve

2012-01-01

25

Influence of cations on growth of thermophilic Geobacillus spp. and Anoxybacillus flavithermus in planktonic culture.  

PubMed

Free ions of Na(+), K(+), Ca(2+), and Mg(2+) influenced the optical density of planktonic cultures of thermophilic bacilli. Anoxybacillus flavithermus E16 and Geobacillus sp. strain F75 (milk powder manufacturing plant isolates) and A. flavithermus DSM 2641 and G. thermoleovorans DSM 5366 were studied. Ca(2+) and Mg(2+) were associated with increases in optical density more so than Na(+) and K(+). Overall, it appeared that Ca(2+) and/or Mg(2+) was required for the production of protein in thermophilic bacilli, as shown by results obtained with A. flavithermus E16, which was selected for further study. PMID:22287005

Somerton, Ben; Palmer, Jon; Brooks, John; Smolinski, Edward; Lindsay, Denise; Flint, Steve

2012-04-01

26

Calcium Carbonate Formation by Synechococcus sp. Strain PCC 8806 and Synechococcus sp. Strain PCC 8807  

SciTech Connect

Precipitation of CaCO3 catalyzed by the growth and physiology of cyanobacteria in the Genus Synechococcus represents a potential mechanism for sequestration of CO2 produced during the burning of coal for power generation. Microcosm experiments were performed in which Synechococcus sp. strain PCC 8806 and Synechococcus sp. strain PCC 8807 were tested for their ability to calcify when exposed to a fixed calcium concentration of 3.4 mM and bicarbonate concentrations of 0.5, 1.25 and 2.5 mM. Disappearance of soluble calcium was used as an indicator of CaCO3 formation; results from metabolically active microcosms were compared to controls with no cells or no carbonate added. Synechococcus sp. strain PCC 8806 removed calcium continuously over the duration of the experiment with approximately 18.6 mg of calcium in the solid phase. Calcium removal occurred over a two-day time period when Synechococcus sp. strain PCC 8807 was tested and only 8.9 mg of calcium was removed in the solid phase. The ability of the cyanobacteria to create an alkaline growth environment appeared to be the primary factor responsible for CaCO3 precipitation in these experiments. Removal of inorganic carbon by fixation into biomass was insignificant compared to the mass of inorganic carbon removed by incorporation into the growing CaCO3 solid.

Lee, Brady D.; William A. Apel; Michelle R. Walton

2006-12-01

27

Isolation and Characterization of a Geobacillus thermoleovorans Strain from an Ultra-Deep South African Gold Mine  

SciTech Connect

A thermophilic, facultative bacterium was isolated from a depth of 3.1 km below ground surface in an ultradeep gold mine in South Africa. This isolate, designated GE-7, was cultivated from pH 8.0, 600C fissure water. GE-7 grows optimally at 650C, pH 6.5 on a wide range of carbon substrates including GE-7 is a long rod-shaped bacterium (4-6 µm long x 0.5 wide) with terminal endospores and flagella, in addition to O2, can also utilize nitrate as an electron acceptor. Phylogenetic analysis of GE-7 16S rDNA sequence revealed high sequence similarity with G. thermoleovorans DSM 5366T (99.6%), however, certain phenotypic characteristics of GE-7 were distinct from this and other strains of G. thermoleovorans previously described.

Deflaun, Mary F.; Fredrickson, Jim K.; Dong, Hailiang; Pfiffner, Susan M.; Onstott, T. C.; Balkwill, David L.; Streger, Sheryl H.; Stackebrandt, E.; Knoessen, S.; van Heerden, E.

2007-03-08

28

Nitrogen Control of Atrazine Utilization in Pseudomonas sp. Strain ADP  

Microsoft Academic Search

Pseudomonas sp. strain ADP uses the herbicide atrazine as the sole nitrogen source. We have devised a simple atrazine degradation assay to determine the effect of other nitrogen sources on the atrazine degradation pathway. The atrazine degradation rate was greatly decreased in cells grown on nitrogen sources that support rapid growth of Pseudomonas sp. strain ADP compared to cells cultivated

V. Garcia-Gonzalez; Fernando Govantes; Liz J. Shaw; Richard G. Burns; Eduardo Santero

2003-01-01

29

Complete Genome Assembly of Corynebacterium sp. Strain ATCC 6931  

PubMed Central

The genus Corynebacterium is best known for the pathogen C. diphtheriae; however, it contains mostly commensal and nonpathogenic, as well as several opportunistic, pathogens. Here, we present the 2.47-Mb scaffolded assembly of the type strain, Corynebacterium sp. ATCC 6931 (NCTC 1914), as deposited into GenBank under accession number CP008913. PMID:25342684

Daligault, H. E.; Davenport, K. W.; Minogue, T. D.; Bishop-Lilly, K. A.; Bruce, D. C.; Chain, P. S.; Coyne, S. R.; Frey, K. G.; Jaissle, J.; Koroleva, G. I.; Ladner, J. T.; Li, P-E.; Meincke, L.; Munk, A. C.; Palacios, G. F.; Redden, C. L.

2014-01-01

30

Improvement of Thermal Stability via Outer-Loop Ion Pair Interaction of Mutated T1 Lipase from Geobacillus zalihae Strain T1  

PubMed Central

Mutant D311E and K344R were constructed using site-directed mutagenesis to introduce an additional ion pair at the inter-loop and the intra-loop, respectively, to determine the effect of ion pairs on the stability of T1 lipase isolated from Geobacillus zalihae. A series of purification steps was applied, and the pure lipases of T1, D311E and K344R were obtained. The wild-type and mutant lipases were analyzed using circular dichroism. The Tm for T1 lipase, D311E lipase and K344R lipase were approximately 68.52 °C, 70.59 °C and 68.54 °C, respectively. Mutation at D311 increases the stability of T1 lipase and exhibited higher Tm as compared to the wild-type and K344R. Based on the above, D311E lipase was chosen for further study. D311E lipase was successfully crystallized using the sitting drop vapor diffusion method. The crystal was diffracted at 2.1 Å using an in-house X-ray beam and belonged to the monoclinic space group C2 with the unit cell parameters a = 117.32 Å, b = 81.16 Å and c = 100.14 Å. Structural analysis showed the existence of an additional ion pair around E311 in the structure of D311E. The additional ion pair in D311E may regulate the stability of this mutant lipase at high temperatures as predicted in silico and spectroscopically. PMID:22312296

Ruslan, Rudzanna; Abd. Rahman, Raja Noor Zaliha Raja; Leow, Thean Chor; Ali, Mohd Shukuri Mohamad; Basri, Mahiran; Salleh, Abu Bakar

2012-01-01

31

Natural transformation of Thermotoga sp. strain RQ7  

PubMed Central

Background Thermotoga species are organisms of enormous interest from a biotechnological as well as evolutionary point of view. Genetic modifications of Thermotoga spp. are often desired in order to fully release their multifarious potentials. Effective transformation of recombinant DNA into these bacteria constitutes a critical step of such efforts. This study aims to establish natural competency in Thermotoga spp. and to provide a convenient method to transform these organisms. Results Foreign DNA was found to be relatively stable in the supernatant of a Thermotoga culture for up to 6 hours. Adding donor DNA to T. sp. strain RQ7 at its early exponential growth phase (OD600 0.18?~?0.20) resulted in direct acquisition of the DNA by the cells. Both T. neapolitana chromosomal DNA and Thermotoga-E. coli shuttle vectors effectively transformed T. sp. strain RQ7, rendering the cells resistance to kanamycin. The kan gene carried by the shuttle vector pDH10 was detected by PCR from the plasmid extract of the transformants, and the amplicons were verified by restriction digestions. A procedure for natural transformation of Thermotoga spp. was established and optimized. With the optimized method, T. sp. strain RQ7 sustained a transformation frequency in the order of 10-7 with both genomic and plasmid DNA. Conclusions T. sp. strain RQ7 cells are naturally transformable during their early exponential phase. They acquire DNA from both closely and distantly related species. Both chromosomal DNA and plasmid DNA serve as suitable substrates for transformation. Our findings lend a convenient technical tool for the genetic engineering of Thermotoga spp. PMID:24884561

2014-01-01

32

Integrative gene cloning and expression system for Streptomyces sp. US 24 and Streptomyces sp. TN 58 bioactive molecule producing strains.  

PubMed

Streptomyces sp. US 24 and Streptomyces sp. TN 58, two strains producing interesting bioactive molecules, were successfully transformed using E. coli ET12567 (pUZ8002), as a conjugal donor, carrying the integrative plasmid pSET152. For the Streptomyces sp. US 24 strain, two copies of this plasmid were tandemly integrated in the chromosome, whereas for Streptomyces sp. TN 58, the integration was in single copy at the attB site. Plasmid pSET152 was inherited every time for all analysed Streptomyces sp. US 24 and Streptomyces sp. TN 58 exconjugants under nonselective conditions. The growth, morphological differentiation, and active molecules production of all studied pSET152 integrated exconjugants were identical to those of wild type strains. Consequently, conjugal transfer using pSET152 integration system is a suitable means of genes transfer and expression for both studied strains. To validate the above gene transfer system, the glucose isomerase gene (xylA) from Streptomyces sp. SK was expressed in strain Streptomyces sp. TN 58. Obtained results indicated that heterologous glucose isomerase could be expressed and folded effectively. Glucose isomerase activity of the constructed TN 58 recombinant strain is of about eighteenfold higher than that of the Streptomyces sp. SK strain. Such results are certainly of importance due to the potential use of improved strains in biotechnological process for the production of high-fructose syrup from starch. PMID:19547659

Sioud, Samiha; Aigle, Bertrand; Karray-Rebai, Ines; Smaoui, Slim; Bejar, Samir; Mellouli, Lotfi

2009-01-01

33

Effect of salt stress on the physiology of Frankia sp strain CcI6.  

PubMed

Actinorhizal plants are able to overcome saline soils and reclaim land. Frankia sp strain CcI6 was isolated from nodules of Casuarina cunninghamiana found in Egypt. Phylogenetic analysis of Frankia sp. strain CcI6 revealed that the strain is closely related to Frankia sp. strain CcI3. The strain displays an elevated level of NaCl tolerance. Vesicle production and nitrogenase activity were also influenced by NaCl. PMID:24287648

Oshone, Rediet; Mansour, Samira R; Tisa, Louis S

2013-11-01

34

Complete Genome Sequence of an Alkane Degrader, Alcanivorax sp. Strain NBRC 101098  

PubMed Central

Alcanivorax sp. strain NBRC 101098 was isolated from seawater in Japan. Strain NBRC 101098 is able to degrade various types of n-alkanes. Here, we report the complete genome of strain NBRC 101098. PMID:25125640

Miura, Takamasa; Tsuchikane, Keiko; Numata, Mitsuru; Hashimoto, Maiko; Hosoyama, Akira; Ohji, Shoko; Yamazoe, Atsushi

2014-01-01

35

Anaerobic phototrophic nitrite oxidation by Thiocapsa sp. strain KS1 and Rhodopseudomonas sp. strain LQ17.  

PubMed

In anaerobic enrichment cultures for phototrophic nitrite-oxidizing bacteria from different freshwater sites, two different cell types, i.e. non-motile cocci and motile, rod-shaped bacteria, always outnumbered all other bacteria. Most-probable-number (MPN) dilution series with samples from two freshwater sites yielded only low numbers (strain KS1 and the purple nonsulfur bacterium strain LQ17, both of which were isolated from activated sludge collected from the municipal sewage treatment plant in Konstanz, Germany. Strain KS1 converted 1 mM nitrite stoichiometrically to nitrate with concomitant formation of cell matter within 2-3 days, whereas strain LQ17 oxidized only up to 60 % of the given nitrite to nitrate within several months with the concomitant formation of cell biomass. Nitrite oxidation to nitrate was strictly light-dependent and required the presence of molybdenum in the medium. Nitrite was oxidized in both the presence and absence of oxygen. Nitrite inhibited growth at concentrations higher than 2 mM. Hydroxylamine and hydrazine were found to be toxic to the phototrophs in the range 5-50 muM and did not stimulate phototrophic growth. Based on morphology, substrate-utilization pattern, in vivo absorption spectra, and 16S rRNA gene sequence similarity, strain KS1 was assigned to the genus Thiocapsa and strain LQ17 to the genus Rhodopseudomonas. Also, Thiocapsa roseopersicina strains DSM 217 and DSM 221 were found to oxidize nitrite to nitrate with concomitant growth. We conclude that the ability to use nitrite phototrophically as electron donor is widespread in nature, but low MPN counts indicate that its contribution to nitrite oxidation in the studied habitats is rather limited. PMID:20447994

Schott, Joachim; Griffin, Benjamin M; Schink, Bernhard

2010-08-01

36

Complete genome sequence of Paenibacillus sp. strain JDR-2  

SciTech Connect

Paenibacillus sp. strain JDR-2, an aggressively xylanolytic bacterium isolated from sweetgum (Liquidambar styraciflua) wood, is able to efficiently depolymerize, assimilate and metabolize 4-O-methylglucuronoxylan, the predominant structural component of hardwood hemicelluloses. A basis for this capability was first supported by the identification of genes and characterization of encoded enzymes and has been further defined by the sequencing and annotation of the complete genome, which we describe. In addition to genes implicated in the utilization of -1,4-xylan, genes have also been identified for the utilization of other hemicellulosic polysaccharides. The genome of Paenibacillus sp. JDR-2 contains 7,184,930 bp in a single replicon with 6,288 protein-coding and 122 RNA genes. Uniquely prominent are 874 genes encoding proteins involved in carbohydrate transport and metabolism. The prevalence and organization of these genes support a metabolic potential for bioprocessing of hemicellulose fractions derived from lignocellulosic resources.

Chow, Virginia [University of Florida; Nong, Guang [University of Florida; St. John, Franz J. [US Forest Service, Forest Products Laboratory, Madison, Wisconsin, USA; Dickstein, Ellen [University of Florida; Chertkov, Olga [Los Alamos National Laboratory (LANL); Bruce, David [Los Alamos National Laboratory (LANL); Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Brettin, Thomas S [ORNL; Han, James [U.S. Department of Energy, Joint Genome Institute; Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute; Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Nolan, Matt [U.S. Department of Energy, Joint Genome Institute; Pati, Amrita [U.S. Department of Energy, Joint Genome Institute; Martin, Joel [U.S. Department of Energy, Joint Genome Institute; Copeland, A [U.S. Department of Energy, Joint Genome Institute; Land, Miriam L [ORNL; Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Jones, Jeffrey B. [University of Florida; Ingram, Lonnie O. [University of Florida; Shanmugam, Keelnathan T. [University of Florida; Preston, James F. [University of Florida

2012-01-01

37

Complete genome sequence of Paenibacillus sp. strain JDR-2  

PubMed Central

Paenibacillus sp. strain JDR-2, an aggressively xylanolytic bacterium isolated from sweetgum (Liquidambar styraciflua) wood, is able to efficiently depolymerize, assimilate and metabolize 4-O-methylglucuronoxylan, the predominant structural component of hardwood hemicelluloses. A basis for this capability was first supported by the identification of genes and characterization of encoded enzymes and has been further defined by the sequencing and annotation of the complete genome, which we describe. In addition to genes implicated in the utilization of ?-1,4-xylan, genes have also been identified for the utilization of other hemicellulosic polysaccharides. The genome of Paenibacillus sp. JDR-2 contains 7,184,930 bp in a single replicon with 6,288 protein-coding and 122 RNA genes. Uniquely prominent are 874 genes encoding proteins involved in carbohydrate transport and metabolism. The prevalence and organization of these genes support a metabolic potential for bioprocessing of hemicellulose fractions derived from lignocellulosic resources. PMID:22675593

Chow, Virginia; Nong, Guang; St. John, Franz J.; Rice, John D.; Dickstein, Ellen; Chertkov, Olga; Bruce, David; Detter, Chris; Brettin, Thomas; Han, James; Woyke, Tanja; Pitluck, Sam; Nolan, Matt; Pati, Amrita; Martin, Joel; Copeland, Alex; Land, Miriam L.; Goodwin, Lynne; Jones, Jeffrey B.; Ingram, Lonnie O.; Shanmugam, Keelnathan T.; Preston, James F.

2012-01-01

38

Monocyclic aromatic hydrocarbon degradation by Rhodococcus sp. strain DK17.  

PubMed

Rhodococcus sp. strain DK17 was isolated from soil and analyzed for the ability to grow on o-xylene as the sole carbon and energy source. Although DK17 cannot grow on m- and p-xylene, it is capable of growth on benzene, phenol, toluene, ethylbenzene, isopropylbenzene, and other alkylbenzene isomers. One UV-generated mutant strain, DK176, simultaneously lost the ability to grow on o-xylene, ethylbenzene, isopropylbenzene, toluene, and benzene, although it could still grow on phenol. The mutant strain was also unable to oxidize indole to indigo following growth in the presence of o-xylene. This observation suggests the loss of an oxygenase that is involved in the initial oxidation of the (alkyl)benzenes tested. Another mutant strain, DK180, isolated for the inability to grow on o-xylene, retained the ability to grow on benzene but was unable to grow on alkylbenzenes due to loss of a meta-cleavage dioxygenase needed for metabolism of methyl-substituted catechols. Further experiments showed that DK180 as well as the wild-type strain DK17 have an ortho-cleavage pathway which is specifically induced by benzene but not by o-xylene. These results indicate that DK17 possesses two different ring-cleavage pathways for the degradation of aromatic compounds, although the initial oxidation reactions may be catalyzed by a common oxygenase. Gas chromatography-mass spectrometry and 300-MHz proton nuclear magnetic resonance spectrometry clearly show that DK180 accumulates 3,4-dimethylcatechol from o-xylene and both 3- and 4-methylcatechol from toluene. This means that there are two initial routes of oxidation of toluene by the strain. Pulsed-field gel electrophoresis analysis demonstrated the presence of two large megaplasmids in the wild-type strain DK17, one of which (pDK2) was lost in the mutant strain DK176. Since several other independently derived mutant strains unable to grow on alkylbenzenes are also missing pDK2, the genes encoding the initial steps in alkylbenzene metabolism (but not phenol metabolism) appear to be present on this approximately 330-kb plasmid. PMID:12089003

Kim, Dockyu; Kim, Young-Soo; Kim, Seong-Ki; Kim, Si Wouk; Zylstra, Gerben J; Kim, Young Min; Kim, Eungbin

2002-07-01

39

Biodegradation of malathion by Brevibacillus sp. strain KB2 and Bacillus cereus strain PU.  

PubMed

We report here the degradation of a pesticide, malathion, by Brevibacillus sp. strain KB2 and Bacillus cereus strain PU, isolated from soil samples collected from malathion contaminated field and an army firing range respectively. Both the strains were cultured in the presence of malathion under aerobic and energy-limiting conditions. Both strains grew well in the medium having malathion concentration up to 0.15%. Reverse phase HPLC-UV analysis indicated that Strain KB2 was able to degrade 72.20% of malaoxon (an analogue of malathion) and 36.22% of malathion, while strain PU degraded 87.40% of malaoxon and 49.31% of malathion, after 7 days of incubation. The metabolites mal-monocarboxylic acid and mal-dicarboxylic acid were identified by Gas chromatography/mass spectrometry. The factors affecting biodegradation efficiency were investigated and effect of malathion concentration on degradation rate was also determined. The strain was analyzed for carboxylesterase activity and maximum activity 210 ± 2.5 U ml(-1) and 270 U ± 2.7 ml(-1) was observed for strains KB2 and PU, respectively. Cloning and sequencing of putative malathion degrading carboxylesterase gene was done using primers based PCR approach. PMID:22805834

Singh, Baljinder; Kaur, Jagdeep; Singh, Kashmir

2012-03-01

40

Decolorization of sulfonated azo dye Metanil Yellow by newly isolated bacterial strains: Bacillus sp. strain AK1 and Lysinibacillus sp. strain AK2.  

PubMed

Two different bacterial strains capable of decolorizing a highly water soluble azo dye Metanil Yellow were isolated from dye contaminated soil sample collected from Atul Dyeing Industry, Bellary, India. The individual bacterial strains Bacillus sp. AK1 and Lysinibacillus sp. AK2 decolorized Metanil Yellow (200 mg L(-1)) completely within 27 and 12h respectively. Various parameters like pH, temperature, NaCl and initial dye concentrations were optimized to develop an economically feasible decolorization process. The maximum concentration of Metanil Yellow (1000 mg L(-1)) was decolorized by strains AK2 and AK1 within 78 and 84 h respectively. These strains could decolorize Metanil Yellow over a broad pH range 5.5-9.0; the optimum pH was 7.2. The decolorization of Metanil Yellow was most efficient at 40°C and confirmed by UV-visible spectroscopy, TLC, HPLC and GC/MS analysis. Further, both the strains showed the involvement of azoreductase in the decolorization process. Phytotoxicity studies of catabolic products of Metanil Yellow on the seeds of chick pea and pigeon pea revealed much reduction in the toxicity of metabolites as compared to the parent dye. These results indicating the effectiveness of strains AK1 and AK2 for the treatment of textile effluents containing azo dyes. PMID:21470774

Anjaneya, O; Souche, S Yogesh; Santoshkumar, M; Karegoudar, T B

2011-06-15

41

Draft Genome Sequence of the Antarctic Polyextremophile Nesterenkonia sp. Strain AN1.  

PubMed

Nesterenkonia sp. strain AN1 was isolated from Antarctic soil and is a polyextremophile, being tolerant of low temperatures, high salt concentrations, and high alkalinity. Here we report the draft genome sequence of this strain. PMID:24675854

Aliyu, Habibu; De Maayer, Pieter; Rees, Jasper; Tuffin, Marla; Cowan, Don A

2014-01-01

42

Draft Genome Sequence of the Brazilian Cyanobium sp. Strain CACIAM 14  

PubMed Central

Given the scarcity of data pertaining to whole-genome sequences of cyanobacterial strains isolated in Brazil, we hereby present the draft genome sequence of the Cyanobium sp. strain CACIAM 14, isolated in southeastern Amazonia. PMID:25013140

Siqueira, Andrei Santos; dos Santos, Bruno Garcia Simoes; da Silva, Fabio Daniel Florencio; Lima, Clayton Pereira; Cardoso, Jedson Ferreira; Vianez Junior, Joao Lidio da Silva Goncalves; Dall'Agnol, Leonardo Teixeira; McCulloch, John Anthony; Nunes, Marcio Roberto Teixeira; Goncalves, Evonnildo Costa

2014-01-01

43

Complete genome sequence of Arthrobacter sp. strain FB24  

SciTech Connect

Arthrobacter sp. strain FB24 is a species in the genus Arthrobacter Conn and Dimmick 1947, in the family Micrococcaceae and class Actinobacteria. A number of Arthrobacter genome sequences have been completed because of their important role in soil, especially bioremediation. This isolate is of special interest because it is tolerant to multiple metals and it is extremely resistant to elevated concentrations of chromate. The genome consists of a 4,698,945 bp circular chromosome and three plasmids (96,488, 115,507, and 159,536 bp, a total of 5,070,478 bp), coding 4,536 proteins of which 1,257 are without known function. This genome was sequenced as part of the DOE Joint Genome Institute Program.

Nakatsu, C. H.; Barabote, Ravi; Thompson, Sue; Bruce, David; Detter, Chris; Brettin, T.; Han, Cliff F.; Beasley, Federico; Chen, Weimin; Konopka, Allan; Xie, Gary

2013-09-30

44

Draft Genome Sequence of Brevibacillus sp. Strain BAB-2500, a Strain That Might Play an Important Role in Agriculture  

PubMed Central

A Gram-positive bacterium, Brevibacillus sp. strain BAB-2500, was isolated as a lab contaminant in Gandhinagar, Gujarat, India. The draft genome (5.3 Mb) of the strain possesses genes for the reduction of arsenate and aluminum. These findings might provide insights into the utilization of this strain for improving crop production. PMID:23472223

Joshi, M. N.; Sharma, A.; Pandit, A. S.; Pandya, R. V.; Saxena, A. K.

2013-01-01

45

Draft Genome Sequences of Devosia sp. Strain 17-2-E-8 and Devosia riboflavina Strain IFO13584  

PubMed Central

Here we report the draft genome of Devosia sp. strain 17-2-E-8, isolated from Ontario agricultural soil (Canada) with promising deoxynivalenol biotransformation capabilities. In addition, we report the draft genome of Devosia riboflavina strain IFO13584, used as a control strain in our studies aimed at highlighting unique gene clusters involved in deoxynivalenol epimerization. PMID:25278537

Hassan, Yousef I.; Lepp, Dion; He, Jianwei

2014-01-01

46

Draft Genome Sequence of Brevibacillus sp. Strain BAB-2500, a Strain That Might Play an Important Role in Agriculture.  

PubMed

A Gram-positive bacterium, Brevibacillus sp. strain BAB-2500, was isolated as a lab contaminant in Gandhinagar, Gujarat, India. The draft genome (5.3 Mb) of the strain possesses genes for the reduction of arsenate and aluminum. These findings might provide insights into the utilization of this strain for improving crop production. PMID:23472223

Joshi, M N; Sharma, A; Pandit, A S; Pandya, R V; Saxena, A K; Bagatharia, S B

2013-01-01

47

Induction of nitrate-dependent Fe(II) oxidation by Fe(II) in Dechloromonas sp. strain UWNR4 and Acidovorax sp. strain 2AN.  

PubMed

We evaluated the inducibility of nitrate-dependent Fe(II)-EDTA oxidation (NDFO) in non-growth, chloramphenicol-amended, resting-cell suspensions of Dechloromonas sp. strain UWNR4 and Acidovorax sp. strain 2AN. Cells previously incubated with Fe(II)-EDTA oxidized ca. 6-fold more Fe(II)-EDTA than cells previously incubated with Fe(III)-EDTA. This is the first report of induction of NDFO by Fe(II). PMID:23144134

Chakraborty, Anirban; Picardal, Flynn

2013-01-01

48

Induction of Nitrate-Dependent Fe(II) Oxidation by Fe(II) in Dechloromonas sp. Strain UWNR4 and Acidovorax sp. Strain 2AN  

PubMed Central

We evaluated the inducibility of nitrate-dependent Fe(II)-EDTA oxidation (NDFO) in non-growth, chloramphenicol-amended, resting-cell suspensions of Dechloromonas sp. strain UWNR4 and Acidovorax sp. strain 2AN. Cells previously incubated with Fe(II)-EDTA oxidized ca. 6-fold more Fe(II)-EDTA than cells previously incubated with Fe(III)-EDTA. This is the first report of induction of NDFO by Fe(II). PMID:23144134

Chakraborty, Anirban

2013-01-01

49

Mechanism of algal aggregation by Bacillus sp. strain RP1137.  

PubMed

Alga-derived biofuels are one of the best alternatives for economically replacing liquid fossil fuels with a fungible renewable energy source. Production of fuel from algae is technically feasible but not yet economically viable. Harvest of dilute algal biomass from the surrounding water remains one of the largest barriers to economic production of algal biofuel. We identified Bacillus sp. strain RP1137 in a previous study and showed that this strain can rapidly aggregate several biofuel-producing algae in a pH- and divalent-cation-dependent manner. In this study, we further characterized the mechanism of algal aggregation by RP1137. We show that aggregation of both algae and bacteria is optimal in the exponential phase of growth and that the density of ionizable residues on the RP1137 cell surface changes with growth stage. Aggregation likely occurs via charge neutralization with calcium ions at the cell surface of both algae and bacteria. We show that charge neutralization occurs at least in part through binding of calcium to negatively charged teichoic acid residues. The addition of calcium also renders both algae and bacteria more able to bind to hydrophobic beads, suggesting that aggregation may occur through hydrophobic interactions. Knowledge of the aggregation mechanism may enable engineering of RP1137 to obtain more efficient algal harvesting. PMID:24771029

Powell, Ryan J; Hill, Russell T

2014-07-01

50

Co-metabolic degradation of tetrabromobisphenol A by novel strains of Pseudomonas sp. and Streptococcus sp.  

PubMed

Three strains capable of rapidly degrading TBBPA by co-metabolism and utilizing formate as the carbon source, named as J-F-01, J-F-02, and J-F-03, respectively, were isolated from enrichment cultures, which have been treated with 0.5mg/L TBBPA for 240d. Based on morphology and 16S rRNA gene sequence analysis, both J-F-01 and J-F-02 were determined to Pseudomonas sp., while J-F-03 was identified as Streptococcus sp. A shorter half-life (6.1d) of TBBPA was observed in pure culture of J-F-03 when compared with J-F-01 (22.5d) and J-F-02 (13.6d). Surprisingly, the degradation of TBBPA was significantly enhanced by the mixed culture of J-F-02 and J-F-03. The optimal degradation conditions for the mixed cultures were determined. Under the optimal conditions, TBBPA (0.5mg/L) was completely metabolized by the mixed culture within ten days. Moreover, bromide and the metabolisms were detected, and a possible metabolic pathway was deduced from the detection of metabolite production patterns. PMID:25062538

Peng, Xingxing; Qu, Xiangdong; Luo, Weishi; Jia, Xiaoshan

2014-10-01

51

Draft Genome Sequence of the Agar-Degrading Bacterium Catenovulum sp. Strain DS-2, Isolated from Intestines of Haliotis diversicolor  

PubMed Central

Catenovulum sp. strain DS-2, isolated from intestines of Haliotis diversicolor, is able to degrade agar and produce agaro-oligosaccharides. Here, we report the draft genome sequence of Catenovulum sp. strain DS-2. PMID:24604650

Shan, Dapeng; Li, Xu; Gu, Zheng; Wei, Guangshan; Gao, Zheng

2014-01-01

52

Methylammonium uptake by Rhizobium sp. strain 32H1.  

PubMed Central

We present evidence that methylammonium is transported into cowpea Rhizobium sp. strain 32H1 cells by a membrane carrier whose natural substrate is ammonium. After growth in low (0.2%) oxygen, which is necessary for nitrogen fixation by these cells, respiring rhizobial cells took up [14C]methylammonium to high intracellular levels. Cells grown in atmospheric (21%) oxygen did not take up methylammonium. Uptake (transport plus metabolism) was maximal in cells harvested in the early stationary phase of batch culture and had a distinct pH optimum of 6.5 to 7.0. Uptake was inhibited by metabolic poisons that dissipate the proton motive force or inhibit ATP synthesis. Inhibition of uptake by ammonium and the counterflow phenomenon indicated that ammonium and methylammonium share a transport carrier. Of the methylammonium taken up, about 15% was accumulated to intracellular levels 20 times higher than those in the medium; most of the methylammonium was metabolized to gamma-N-methylglutamine. PMID:6826521

Gober, J W; Kashket, E R

1983-01-01

53

Complete Genome Sequence of Paenibacillus strain Y4.12MC10, a Novel Paenibacillus lautus strain Isolated from Obsidian Hot Spring in Yellowstone National Park  

SciTech Connect

Paenibacillus speciesY412MC10 was one of a number of organisms initially isolated from Obsidian Hot Spring, Yellowstone National Park, Montana, USA. The isolate Y412MC10 was initially classified as a Geobacillus sp. based on its isolation conditions and similarity to other organisms isolated from hot springs at Yellowstone National Park. Comparison of 16 S rRNA sequences within the Bacillales indicated that Geobacillus sp.Y412MC10 clustered with Paenibacillus species and not Geobacillus; the 16S rRNA analysis indicated the organism was a strain of Paenibacillus lautus. Lucigen Corp. prepared genomic DNA and the genome was sequenced, assembled, and annotated by the DOE Joint Genome Institute. The genome of Paenibacillus lautus strain Y412MC10 consists of one circular chromosome of 7,121,665 bp with an average G+C content of 51.2%. The Paenibacillus sp.Y412MC10 genome sequence was deposited at the NCBI in October 2009 (NC{_}013406). Comparison to other Paenibacillus species shows the organism lacks nitrogen fixation, antibiotic production and social interaction genes reported in other Paenibacilli. Over 25% of the proteins predicted by the Y412MC10 genome share no identity with the closest sequenced Paenibacillus species; most of these are predicted hypothetical proteins and their specific function in the environment is unknown.

Mead, David [University of Wisconsin, Madison; Lucas, Susan [U.S. Department of Energy, Joint Genome Institute; Copeland, A [U.S. Department of Energy, Joint Genome Institute; Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute; Cheng, Jan-Fang [U.S. Department of Energy, Joint Genome Institute; Bruce, David [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Chertkov, Olga [Los Alamos National Laboratory (LANL); Zhang, Xiaojing [Los Alamos National Laboratory (LANL); Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Han, Cliff [Los Alamos National Laboratory (LANL); Tapia, Roxanne [Los Alamos National Laboratory (LANL); Land, Miriam L [ORNL; Hauser, Loren John [ORNL; Chang, Yun-Juan [ORNL; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Ovchinnikova, Galina [U.S. Department of Energy, Joint Genome Institute; Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute; Brumm, Catherine [United States Department of Energy Joint Genome Institute; Hochstein, Rebecca [Lucigen Corporation, Middleton, Wisconsin; Schoenfeld, Thomas [Lucigen Corporation, Middleton, Wisconsin; Brumm, Phillip [University of Wisconsin, Madison

2012-01-01

54

Draft Genome Sequence of Ristocetin-Producing Strain Amycolatopsis sp. Strain MJM2582 Isolated in South Korea  

PubMed Central

The draft genome sequence of a ristocetin-producing Amycolatopsis strain (sp. MJM2582) isolated in South Korea is reported here. This strain has a genome of approximately 8.9 Mb containing 7,933 predicted genes, including the ristocetin cluster and 32 additional predicted secondary metabolite biosynthesis clusters. PMID:25359910

Kwun, Min Jung; Cheng, Jinhua; Yang, Seung Hwan; Lee, Dong-Ryung; Suh, Joo-Won

2014-01-01

55

Genome Sequence of Gluconacetobacter sp. Strain SXCC-1, Isolated from Chinese Vinegar Fermentation Starter?  

PubMed Central

Gluconacetobacter strains are prominent bacteria during traditional vinegar fermentation. Here, we report a draft genome sequence of Gluconacetobacter sp. strain SXCC-1. This strain was isolated from a fermentation starter (Daqu) used for commercial production of Shanxi vinegar, the best-known vinegar of China. PMID:21551293

Du, Xin-jun; Jia, Shi-ru; Yang, Yue; Wang, Shuo

2011-01-01

56

The cloned 1-aminocyclopropane-1-carboxylate (ACC) deaminase gene from Sinorhizobium sp. strain BL3 in Rhizobium sp. strain TAL1145 promotes nodulation and growth of Leucaena leucocephala  

Microsoft Academic Search

The objective of this study was to determine the role of 1-aminocyclopropane-1-carboxylate (ACC) deaminase of symbionts in nodulation and growth of Leucaena leucocephala. The acdS genes encoding ACC deaminase were cloned from Rhizobium sp. strain TAL1145 and Sinorhizobium sp. BL3 in multicopy plasmids, and transferred to TAL1145. The BL3-acdS gene greatly enhanced ACC deaminase activity in TAL1145 compared to the

Panlada Tittabutr; Jonathan D. Awaya; Qing X. Li; Dulal Borthakur

2008-01-01

57

Gliding motility of Cytophaga sp. strain U67.  

PubMed Central

Video techniques were used to analyze the motion of the gliding bacterium Cytophaga sp. strain U67. Cells moved singly on glass along the long axis at a speed of about 2 micrometers/s, advancing, retreating, stopping, pivoting about a pole, or flipping over. They did not flex or roll. Cells of different lengths moved at about the same speed. Cells sometimes spun continuously about a pole at a frequency of about 2 HZ, the body moving in a plane parallel to that of the glass or on the surface of a cone having either a large or a small solid angle. Polystyrene latex spheres moved to and fro on the surfaces of cells, also at a speed of about 2 micrometers/s. They moved in the same fashion whether a cell was in suspension, gliding, or at rest on the glass. Two spheres on the same cell often moved in opposite directions, passing by one another in close proximity. Small and large spheres and aggregates of spheres all moved at about the same speed. An aggregate moved down the side of a cell with a fixed orientation, even when only one sphere was in contact with the cell. Spheres occasionally left one cell and were picked up by another. Cell pretreated with small spheres did not adhere to glass. When the cells were deprived of oxygen, they stopped gliding, and the spheres stopped moving on their surfaces. The spheres became completely immobilized; they no longer moved from cell to cell or exhibited Brownian movement. Cytophaga spp. are known to have a typical gram-negative cell envelope: an inner (cytoplasmic) membrane, a thin peptidoglycan layer, and an outer (lipopolysaccharide) membrane. Our data are consistent with a model for gliding in which sites to which glass and polystyrene strongly adsorb move within the fluid outer membrane along tracks fixed to the rigid peptidoglycan framework. Images PMID:7085564

Lapidus, I R; Berg, H C

1982-01-01

58

Reclassification of Gluconacetobacter hansenii strains and proposals of Gluconacetobacter saccharivorans sp. nov. and Gluconacetobacter nataicola sp. nov.  

PubMed

Ten strains previously assigned to Acetobacter hansenii (=Gluconacetobacter hansenii), Acetobacter pasteurianus LMG 1584 and eight reference strains of the genus Gluconacetobacter were reclassified by 16S rRNA gene sequencing, DNA-DNA similarity, DNA base composition and phenotypic characteristics. The A. hansenii strains and A. pasteurianus LMG 1584 were included in the cluster of acetic acid bacteria (family Acetobacteraceae) by 16S rRNA gene sequences. Further, they were separated into seven distinct groups by DNA-DNA similarity. DNA-DNA similarity group I was identified as G. hansenii. DNA-DNA similarity group II was retained as Gluconacetobacter sp., because DNA-DNA similarity between the strain and Gluconacetobacter entanii LTH 4560(T) could not be determined. This was due to a lack of availability of the type strain from any source. DNA-DNA similarity group III was regarded as a novel species, for which the name Gluconacetobacter saccharivorans sp. nov. (type strain, LMG 1582(T)=NRIC 0614(T)) is proposed. DNA-DNA similarity group IV included the type strains of Gluconacetobacter oboediens and Gluconacetobacter intermedius, and three A. hansenii strains. This group was identified as G. oboediens because high values of DNA-DNA similarity were obtained between the type strains and G. oboediens has priority over G. intermedius. DNA-DNA similarity group V was identified as Gluconacetobacter europaeus. DNA-DNA similarity group VI was regarded as a novel species, for which the name Gluconacetobacter nataicola sp. nov. (type strain, LMG 1536(T)=NRIC 0616(T)) is proposed. DNA-DNA similarity group VII was reclassified as Gluconacetobacter xylinus. The description of G. hansenii is emended. PMID:16957106

Lisdiyanti, Puspita; Navarro, Richard R; Uchimura, Tai; Komagata, Kazuo

2006-09-01

59

Growth in Coculture Stimulates Metabolism of the Phenylurea Herbicide Isoproturon by Sphingomonas sp. Strain SRS2  

PubMed Central

Metabolism of the phenylurea herbicide isoproturon by Sphingomonas sp. strain SRS2 was significantly enhanced when the strain was grown in coculture with a soil bacterium (designated strain SRS1). Both members of this consortium were isolated from a highly enriched isoproturon-degrading culture derived from an agricultural soil previously treated regularly with the herbicide. Based on analysis of the 16S rRNA gene, strain SRS1 was assigned to the ?-subdivision of the proteobacteria and probably represents a new genus. Strain SRS1 was unable to degrade either isoproturon or its known metabolites 3-(4-isopropylphenyl)-1-methylurea, 3-(4-isopropylphenyl)-urea, or 4-isopropyl-aniline. Pure culture studies indicate that Sphingomonas sp. SRS2 is auxotrophic and requires components supplied by association with other soil bacteria. A specific mixture of amino acids appeared to meet these requirements, and it was shown that methionine was essential for Sphingomonas sp. SRS2. This suggests that strain SRS1 supplies amino acids to Sphingomonas sp. SRS2, thereby leading to rapid metabolism of 14C-labeled isoproturon to 14CO2 and corresponding growth of strain SRS2. Proliferation of strain SRS1 suggests that isoproturon metabolism by Sphingomonas sp. SRS2 provides unknown metabolites or cell debris that supports growth of strain SRS1. The role of strain SRS1 in the consortium was not ubiquitous among soil bacteria; however, the indigenous soil microflora and some strains from culture collections also stimulate isoproturon metabolism by Sphingomonas sp. strain SRS2 to a similar extent. PMID:12089031

S?rensen, Sebastian R.; Ronen, Zeev; Aamand, Jens

2002-01-01

60

Genome Sequence of the Microsporidian Species Nematocida sp1 Strain ERTm6 (ATCC PRA-372)  

PubMed Central

Microsporidia comprise a phylum of obligate intracellular pathogens related to fungi. Microsporidia Nematocida sp1 strain ERTm6 was isolated from wild-caught Caenorhabditis briggsae and causes a lethal intestinal infection in Caenorhabditis nematodes. We report the genome sequence of N. sp1 ERTm6, which will facilitate study of the Nematocida genus and other Microsporidia. PMID:25237020

Bakowski, Malina A.; Priest, Margaret; Young, Sarah

2014-01-01

61

Draft Genome Sequence of the Shellfish Bacterial Pathogen Vibrio sp. Strain B183  

PubMed Central

We report the draft genome sequence of Vibrio sp. strain B183, a Gram-negative marine bacterium isolated from shellfish that causes mortality in larval mariculture. The availability of this genome sequence will facilitate the study of its virulence mechanisms and add to our knowledge of Vibrio sp. diversity and evolution. PMID:25237023

Schott, Eric J.

2014-01-01

62

Draft Genome Sequence of Hawaiian Sea Slug Symbiont Vibrio sp. Strain ER1A  

PubMed Central

Bacteria belonging to the genus Vibrio are prevalent in the marine environment and are known for forming symbiotic relationships with hosts. Vibrio sp. strain ER1A is a dominant symbiont of the Hawaiian sea slug, Elysia rufescens. Here we report the draft genome sequence of Vibrio sp. ER1A. PMID:25146136

Davis, Jeanette

2014-01-01

63

Draft Genome Sequence of Hawaiian Sea Slug Symbiont Vibrio sp. Strain ER1A.  

PubMed

Bacteria belonging to the genus Vibrio are prevalent in the marine environment and are known for forming symbiotic relationships with hosts. Vibrio sp. strain ER1A is a dominant symbiont of the Hawaiian sea slug, Elysia rufescens. Here we report the draft genome sequence of Vibrio sp. ER1A. PMID:25146136

Davis, Jeanette; Hill, Russell T

2014-01-01

64

Antibiofilm Activity of the Marine Bacterium Pseudoalteromonas sp. Strain 3J6?  

PubMed Central

Biofilm formation results in medical threats or economic losses and is therefore a major concern in a variety of domains. In two-species biofilms of marine bacteria grown under dynamic conditions, Pseudoalteromonas sp. strain 3J6 formed mixed biofilms with Bacillus sp. strain 4J6 but was largely predominant over Paracoccus sp. strain 4M6 and Vibrio sp. strain D01. The supernatant of Pseudoalteromonas sp. 3J6 liquid culture (SN3J6) was devoid of antibacterial activity against free-living Paracoccus sp. 4M6 and Vibrio sp. D01 cells, but it impaired their ability to grow as single-species biofilms and led to higher percentages of nonviable cells in 48-h biofilms. Antibiofilm molecules of SN3J6 were able to coat the glass surfaces used to grow biofilms and reduced bacterial attachment about 2-fold, which might partly explain the biofilm formation defect but not the loss of cell viability. SN3J6 had a wide spectrum of activity since it affected all Gram-negative marine strains tested except other Pseudoalteromonas strains. Biofilm biovolumes of the sensitive strains were reduced 3- to 530-fold, and the percentages of nonviable cells were increased 3- to 225-fold. Interestingly, SN3J6 also impaired biofilm formation by three strains belonging to the human-pathogenic species Pseudomonas aeruginosa, Salmonella enterica, and Escherichia coli. Such an antibiofilm activity is original and opens up a variety of applications for Pseudoalteromonas sp. 3J6 and/or its active exoproducts in biofilm prevention strategies. PMID:20363799

Dheilly, Alexandra; Soum-Soutera, Emmanuelle; Klein, Geraldine L.; Bazire, Alexis; Compere, Chantal; Haras, Dominique; Dufour, Alain

2010-01-01

65

Expression of small RNAs by Bacillus sp. strain PS3 and B. subtilis cells during sporulation  

Microsoft Academic Search

A small RNA sequence identified in an rRNA-tRNA cluster from the thermophilic Bacillus sp. strain PS3 was examined. An oligonucleotide probe specific for the RNA bound to multiple restriction fragments in Bacillus sp. strain PS3 DNA, thus several copies of this sequence occur in its genome. Similar findings were observed using DNA from B. subtilis, B. stearothermophilus, Escherichia coli, Staphylococcus

Pamela S Fink; Armando Soto; G. Scott Jenkins; Kathleen S Rupert

1997-01-01

66

Heterologous exopolysaccharide production in Rhizobium sp. strain NGR234 and consequences for nodule development.  

PubMed Central

Rhizobium sp. strain NGR234 produces large amounts of acidic exopolysaccharide. Mutants that fail to synthesize this exopolysaccharide are also unable to nodulate the host plant Leucaena leucocephala. A hybrid strain of Rhizobium sp. strain NGR234 containing exo genes from Rhizobium meliloti was constructed. The background genetics and nod genes of Rhizobium sp. strain NGR234 are retained, but the cluster of genes involved in exopolysaccharide biosynthesis was deleted. These exo genes were replaced with genes required for the synthesis of succinoglycan exopolysaccharide from R. meliloti. As a result of the genetic manipulation, the ability of these hybrids to synthesize exopolysaccharide was restored, but the structure was that of succinoglycan and not that of Rhizobium sp. strain NGR234. The replacement genes were contained on a cosmid which encoded the entire known R. meliloti exo gene cluster, with the exception of exoB. Cosmids containing smaller portions of this exo gene cluster did not restore exopolysaccharide production. The presence of succinoglycan was indicated by staining with the fluorescent dye Calcofluor, proton nuclear magnetic resonance spectroscopy, and monosaccharide analysis. Although an NGR234 exoY mutant containing the R. meliloti exo genes produced multimers of the succinoglycan repeat unit, as does the wild-type R. meliloti, the deletion mutant of Rhizobium sp. strain NGR234 containing the R. meliloti exo genes produced only the monomer. The deletion mutant therefore appeared to lack a function that affects the multiplicity of succinoglycan produced in the Rhizobium sp. strain NGR234 background. Although these hybrid strains produced succinoglycan, they were still able to induce the development of an organized nodule structure on L. leucocephala. The resulting nodules did not fix nitrogen, but they did contain infection threads and bacteroids within plant cells. This clearly demonstrated that a heterologous acidic exopolysaccharide structure was sufficient to enable nodule development to proceed beyond the developmental barrier imposed on mutants of Rhizobium sp. strain NGR234 that are unable to synthesize any acidic exopolysaccharide. Images PMID:2022612

Gray, J X; Zhan, H J; Levery, S B; Battisti, L; Rolfe, B G; Leigh, J A

1991-01-01

67

Culture Independent Detection of Sphingomonas sp. EPA 505 Related Strains in Soils Contaminated with Polycyclic Aromatic Hydrocarbons (PAHs)  

Microsoft Academic Search

The Sphingomonas genus hosts many interesting pollutant-degrading strains. Sphingomonas sp. EPA505 is the best studied polycyclic aromatic hydrocarbon (PAH)-degrading Sphingomonas strain. Based on 16S rRNA gene sequence analysis, Sphingomonas sp. strain EPA505 forms a separate branch in the Sphingomonas phylogenetic tree grouping exclusively PAH-degrading isolates. For specific PCR detection and monitoring of Sphingomonas sp. EPA505 and related strains in PAH-contaminated

N. M. Leys; A. Ryngaert; L. Bastiaens; E. M. Top; W. Verstraete; D. Springael

2005-01-01

68

Specificity of monoclonal antibodies to strains of Dickeya sp. that cause bacterial heart rot of pineapple.  

PubMed

During a severe outbreak of bacterial heart rot that occurred in pineapple plantations on Oahu, Hawaii, in 2003 and years following, 43 bacterial strains were isolated from diseased plants or irrigation water and identified as Erwinia chrysanthemi (now Dickeya sp.) by phenotypic, molecular, and pathogenicity assays. Rep-PCR fingerprint patterns grouped strains from pineapple plants and irrigation water into five genotypes (A-E) that differed from representatives of other Dickeya species, Pectobacterium carotovorum and other enteric saprophytes isolated from pineapple. Monoclonal antibodies produced following immunization of mice with virulent type C Dickeya sp. showed only two specificities. MAb Pine-1 (2D11G1, IgG1 with kappa light chain) reacted to all 43 pineapple/water strains and some reference strains (D. dianthicola, D. chrysanthemi, D. paradisiaca, some D. dadantii, and uncharacterized Dickeya sp.) but did not react to reference strains of D. dieffenbachiae, D. zeae, or one of the two Malaysian pineapple strains. MAb Pine-2 (2A7F2, IgG3 with kappa light chain) reacted to all type B, C, and D strains but not to any A or E strains or any reference strains except Dickeya sp. isolated from Malaysian pineapple. Pathogenicity tests showed that type C strains were more aggressive than type A strains when inoculated during cool months. Therefore, MAb Pine-2 distinguishes the more virulent type C strains from less virulent type A pineapple strains and type E water strains. MAbs with these two specificities enable development of rapid diagnostic tests that will distinguish the systemic heart rot pathogen from opportunistic bacteria associated with rotted tissues. Use of the two MAbs in field assays also permits the monitoring of a known subpopulation and provides additional decision tools for disease containment and management practices. PMID:21050038

Peckham, Gabriel D; Kaneshiro, Wendy S; Luu, Van; Berestecky, John M; Alvarez, Anne M

2010-10-01

69

Complete genome sequence of Kosakonia sacchari type strain SP1(T.).  

PubMed

Kosakonia sacchari sp. nov. is a new species within the new genus Kosakonia, which was included in the genus Enterobacter. K sacchari is a nitrogen-fixing bacterium named for its association with sugarcane (Saccharum officinarum L.). K sacchari bacteria are Gram-negative, aerobic, non-spore-forming, motile rods. Strain SP1(T) (=CGMCC1.12102(T)=LMG 26783(T)) is the type strain of the K sacchari sp. nov and is able to colonize and fix N2 in association with sugarcane plants, thus promoting plant growth. Here we summarize the features of strain SP1(T) and describe its complete genome sequence. The genome contains a single chromosome and no plasmids, 4,902,024 nucleotides with 53.7% GC content, 4,460 protein-coding genes and 105 RNA genes including 22 rRNA genes, 82 tRNA genes, and 1 ncRNA gene. PMID:25197499

Chen, Mingyue; Zhu, Bo; Lin, Li; Yang, Litao; Li, Yangrui; An, Qianli

2014-06-15

70

Complete Genome Sequence of Exiguobacterium sp. Strain MH3, Isolated from Rhizosphere of Lemna minor.  

PubMed

We report the complete genome sequence of Exiguobacterium sp. strain MH3, isolated from the rhizosphere of duckweed. The genome assembly is 3.16 Mb, with a G+C content of 47.24%, and it may provide useful information about plant-microbe interactions and the genetic basis for the tolerance of the strain to various environmental stresses. PMID:24356831

Tang, Jie; Zhang, Ying; Meng, Hao; Xue, Zhiquan; Ma, Jiong

2013-01-01

71

Complete Genome Sequence of Exiguobacterium sp. Strain MH3, Isolated from Rhizosphere of Lemna minor  

PubMed Central

We report the complete genome sequence of Exiguobacterium sp. strain MH3, isolated from the rhizosphere of duckweed. The genome assembly is 3.16 Mb, with a G+C content of 47.24%, and it may provide useful information about plant-microbe interactions and the genetic basis for the tolerance of the strain to various environmental stresses. PMID:24356831

Tang, Jie; Zhang, Ying; Meng, Hao; Xue, Zhiquan

2013-01-01

72

Inducamides A-C, Chlorinated Alkaloids from an RNA Polymerase Mutant Strain of Streptomyces sp.  

PubMed

Inducamides A-C (1-3), three new chlorinated alkaloids featuring an amide skeleton generated by a tryptophan fragment and a 6-methylsalicylic acid unit, were isolated from a chemically induced mutant strain of Streptomyces sp. with the inducamides only being produced in the mutant strain. Their structures, including stereochemistry, were determined by spectroscopic analysis, Marfey's method, and CD spectroscopy. PMID:25338006

Fu, Peng; Jamison, Matthew; La, Scott; MacMillan, John B

2014-11-01

73

Draft Genome Sequence of the Filamentous Cyanobacterium Leptolyngbya sp. Strain Heron Island J, Exhibiting Chromatic Acclimation  

PubMed Central

Leptolyngbya sp. strain Heron Island is a cyanobacterium exhibiting chromatic acclimation. However, this strain has strong interactions with other bacteria, making it impossible to obtain axenic cultures for sequencing. A protocol involving an analysis of tetranucleotide frequencies, G+C content, and BLAST searches has been described for separating the cyanobacterial scaffolds from those of its cooccurring bacteria. PMID:24503993

Paul, Robin; Jinkerson, Robert E.; Buss, Kristina; Steel, Jason; Mohr, Remus; Hess, Wolfgang R.; Chen, Min

2014-01-01

74

Genome sequence of Methanobrevibacter sp. strain jh1, isolated from rumen of Korean native cattle.  

PubMed

The Methanobrevibacter sp. strain JH1 was isolated from the rumen of Korean native cattle (HanWoo; Bos taurus coreanae). Here, we provide a 2.06-Mb draft genome sequence of strain JH1 that might provide more information about the lifestyle of rumen methanogens and about the genes and proteins that can be targeted to curb methane emissions. PMID:23469331

Lee, Jong-Hwan; Rhee, Moon-Soo; Kumar, Sanjay; Lee, Geun-Hye; Chang, Dong-Ho; Kim, Dae-Soo; Choi, Sang-Haeng; Lee, Dong-Woo; Yoon, Min-Ho; Kim, Byoung-Chan

2013-01-01

75

Draft Genome Sequence of Pseudomonas sp. Strain JMM, a Sediment-Hosted Environmental Isolate  

PubMed Central

Pseudomonas sp. strain JMM was isolated from the sediments of a natural water reservoir (pH, 6 to 7) located at Chambyal village in Samba district of Jammu and Kashmir, India. Here we report the annotated draft genome sequence of strain JMM having 52 contigs with 5,884 genes and an average G+C content of 66.5%. PMID:25189587

Grewal, Simmi; Vakhlu, Jyoti; Gupta, Vipin; Sangwan, Naseer; Kohli, Puneet; Nayyar, Namita; Rani, Pooja; Sance, Shivani Singh

2014-01-01

76

Secondary substrate ultilization of methylene chloride by an isolated strain of Pseudomonas sp  

Microsoft Academic Search

Secondary substrate utilization of methylene chloride was analyzed by using Pseudomonas sp. strain LP. Both batch and continuously fed reactors demonstrated that this strain was capable of simultaneously consuming two substrates at different concentrations: the primary substrate at the higher concentration (milligrams per liter) and the secondary substrate at the lower concentration (micrograms per liter). The rate of methylene chloride

L. T. Lapat-Polasko; P. L. McCarty; A. J. B. Zehnder

1984-01-01

77

3-Nitrotoluene dioxygenase from Diaphorobacter sp. strains: cloning, sequencing and evolutionary studies.  

PubMed

The first step in the degradation of 3-nitrotoluene by Diaphorobacter sp. strain DS2 is the dihydroxylation of the benzene ring with the concomitant removal of nitro group. This is catalyzed by a dioxygenase enzyme system. We report here the cloning and sequencing of the complete dioxygenase gene with its putative regulatory sequence from the genomic DNA of Diaphorobacter sp. strains DS1, DS2 and DS3. Analysis of the 5 kb DNA stretch that was cloned, revealed five complete open reading frames (ORFs) encoding for a reductase, a ferredoxin and two dioxygenase subunits with predicted molecular weights (MW) of 35, 12, 50 and 23 kDa respectively. A regulatory protein was also divergently transcribed from the reductase subunit and has a predicated MW of 34 kDa. Presence of parts of two functional ORFs in between the reductase and the ferredoxin subunits reveals an evolutionary route from a naphthalene dioxygenase like system of Ralstonia sp. strain U2. Further a 100 % identity of its ferredoxin subunit reveals its evolution via dinitrotoluene dioxygenase like system present in Burkholderia cepacia strain R34. A modeled structure of oxygenase3NT from strain DS2 was generated using nitrobenzene dioxygenase as a template. The modeled structure only showed minor changes at its active site. Comparison of growth patterns of strains DS1, DS2 and DS3 revealed that Diaphorobacter sp. strain DS1 has been evolved to degrade 4-nitrotoluene better by an oxidative route amongst all three strains. PMID:24217981

Singh, Deepak; Kumari, Archana; Ramanathan, Gurunath

2014-07-01

78

Draft Genome Sequences of Type Strain Sediminibacterium salmoneum NJ-44 and Sediminibacterium sp. Strain C3, a Novel Strain Isolated from Activated Sludge  

PubMed Central

The genus Sediminibacterium comprises species present in diverse natural and engineered environments. Here, we report for the first time the genome sequences of the type strain Sediminibacterium salmoneum NJ-44 (NBRC 103935) and Sediminibacterium sp. strain C3 (BNM541), isolated from activated sludge, a valuable model for the study of substrate-dependent autoaggregation. PMID:24435857

Ayarza, Joaquín M.; Figuerola, Eva L. M.

2014-01-01

79

Study of cellulases from a newly isolated thermophilic and cellulolytic Brevibacillus sp. strain JXL  

Microsoft Academic Search

A potentially novel aerobic, thermophilic, and cellulolytic bacterium designated as Brevibacillus sp. strain JXL was isolated from swine waste. Strain JXL can utilize a broad range of carbohydrates including: cellulose,\\u000a carboxymethylcellulose (CMC), xylan, cellobiose, glucose, and xylose. In two different media supplemented with crystalline\\u000a cellulose and CMC at 57°C under aeration, strain JXL produced a basal level of cellulases as

Yanna Liang; Jemil Yesuf; Steve Schmitt; Kelly Bender; John Bozzola

2009-01-01

80

Complete Genome Sequence of the Polycyclic Aromatic Hydrocarbon-Degrading Bacterium Alteromonas sp. Strain SN2?  

PubMed Central

Alteromonas sp. strain SN2, able to metabolize polycyclic aromatic hydrocarbons, was isolated from a crude oil-contaminated sea-tidal flat. Here we report the complete 4.97-Mb genome sequence and annotation of strain SN2. These will advance the understanding of strain SN2's adaptation to the sea-tidal flat ecosystem and its pollutant metabolic versatility. PMID:21705606

Jin, Hyun Mi; Jeong, Haeyoung; Moon, Eun-Joung; Math, Renukaradhya K.; Lee, Kangseok; Kim, Hae-Jin; Jeon, Che Ok; Oh, Tae Kwang; Kim, Jihyun F.

2011-01-01

81

Growth in Coculture Stimulates Metabolism of the Phenylurea Herbicide Isoproturon by Sphingomonas sp. Strain SRS2  

Microsoft Academic Search

Metabolism of the phenylurea herbicide isoproturon by Sphingomonas sp. strain SRS2 was significantly enhanced when the strain was grown in coculture with a soil bacterium (designated strain SRS1). Both members of this consortium were isolated from a highly enriched isoproturon-degrading culture derived from an agricultural soil previously treated regularly with the herbicide. Based on analysis of the 16S rRNA gene,

S. R. Sorensen; Zeev Ronen; Jens Aamand

2002-01-01

82

Metabolism of hydroxydibenzofurans, methoxydibenzofurans, acetoxydibenzofurans, and nitrodibenzofurans by Sphingomonas sp. strain HH69  

Microsoft Academic Search

The metabolism of 11 substituted dibenzofurans by the dibenzofuran-degrading Sphingomonas sp. strain HH69 was investigated. Strain HH69 utilizes 2-, 3-, and 4-acetoxydibenzofuran as well as 2-, 3-, and 4-hydroxydibenzofuran as sole sources of carbon and energy. The degradation of acetoxydibenzofurans is initiated by hydrolysis of the ester bonds, yielding the corresponding hydroxydibenzofurans and acetate. Strain HH69 grew on 2-methoxydibenzofuran only

H. Harms; R. M. Wittich; P. Fortnagel

1995-01-01

83

Genome characteristics of facultatively symbiotic Frankia sp. strains reflect host range and host plant biogeography  

PubMed Central

Soil bacteria that also form mutualistic symbioses in plants encounter two major levels of selection. One occurs during adaptation to and survival in soil, and the other occurs in concert with host plant speciation and adaptation. Actinobacteria from the genus Frankia are facultative symbionts that form N2-fixing root nodules on diverse and globally distributed angiosperms in the “actinorhizal” symbioses. Three closely related clades of Frankia sp. strains are recognized; members of each clade infect a subset of plants from among eight angiosperm families. We sequenced the genomes from three strains; their sizes varied from 5.43 Mbp for a narrow host range strain (Frankia sp. strain HFPCcI3) to 7.50 Mbp for a medium host range strain (Frankia alni strain ACN14a) to 9.04 Mbp for a broad host range strain (Frankia sp. strain EAN1pec.) This size divergence is the largest yet reported for such closely related soil bacteria (97.8%–98.9% identity of 16S rRNA genes). The extent of gene deletion, duplication, and acquisition is in concert with the biogeographic history of the symbioses and host plant speciation. Host plant isolation favored genome contraction, whereas host plant diversification favored genome expansion. The results support the idea that major genome expansions as well as reductions can occur in facultative symbiotic soil bacteria as they respond to new environments in the context of their symbioses. PMID:17151343

Normand, Philippe; Lapierre, Pascal; Tisa, Louis S.; Gogarten, Johann Peter; Alloisio, Nicole; Bagnarol, Emilie; Bassi, Carla A.; Berry, Alison M.; Bickhart, Derek M.; Choisne, Nathalie; Couloux, Arnaud; Cournoyer, Benoit; Cruveiller, Stephane; Daubin, Vincent; Demange, Nadia; Francino, Maria Pilar; Goltsman, Eugene; Huang, Ying; Kopp, Olga R.; Labarre, Laurent; Lapidus, Alla; Lavire, Celine; Marechal, Joelle; Martinez, Michele; Mastronunzio, Juliana E.; Mullin, Beth C.; Niemann, James; Pujic, Pierre; Rawnsley, Tania; Rouy, Zoe; Schenowitz, Chantal; Sellstedt, Anita; Tavares, Fernando; Tomkins, Jeffrey P.; Vallenet, David; Valverde, Claudio; Wall, Luis G.; Wang, Ying; Medigue, Claudine; Benson, David R.

2007-01-01

84

Identification of Acetobacter strains isolated from Indonesian sources, and proposals of Acetobacter syzygii sp. nov., Acetobacter cibinongensis sp. nov., and Acetobacter orientalis sp. nov.  

PubMed

Forty-six strains of acetic acid bacteria newly isolated from flowers, fruits, and fermented foods collected in Indonesia were taxonomically studied. They were Gram-negative rods, produced acetic acid from ethanol, oxidized acetate and lactate to CO(2) and H(2)O, and had Q-9 as the major ubiquinone system. On the basis of DNA-DNA similarity, all strains studied, including type strains and reference strains of the genus Acetobacter, were separated into eleven groups (Groups I to XI). Of the 46 isolates, two isolates were included in Group II and identified as Acetobacter pasteurianus, five in Group IV as A. orleanensis, 16 in Group V as A. lovaniensis, five in Group VII as A. indonesiensis, and three in Group VIII as A. tropicalis. The remaining 15 isolates constituted three new groups based on DNA-DNA similarity; four isolates were included in Group IX, two in Group X, and nine in Group XI. No isolates were identified as A. aceti (Group I), A. peroxydans (Group III), and A. estunensis (Group VI). Phylogenetic analysis based on 16S rDNA sequences of representative strains of the Groups indicated belonging to the strains of the genus Acetobacter. On the basis of DNA base composition, DNA-DNA similarity, and 16S rDNA sequences, three new species of the genus Acetobacter are proposed: Acetobacter syzygii sp. nov. for Group IX, Acetobacter cibinongensis sp. nov. for Group X, and Acetobacter orientalis sp. nov. for Group XI. The distribution of Acetobacter strains in Indonesia is discussed in light of isolation sources. PMID:12483554

Lisdiyanti, Puspita; Kawasaki, Hiroko; Seki, Tatsuji; Yamada, Yuzo; Uchimura, Tai; Komagata, Kazuo

2001-06-01

85

Draft Genome Sequence of the Antitrypanosomally Active Sponge-Associated Bacterium Actinokineospora sp. Strain EG49  

PubMed Central

The marine sponge-associated bacterium Actinokineospora sp. strain EG49 produces the antitrypanosomal angucycline-like compound actinosporin A. The draft genome of Actinokineospora sp. EG49 has a size of 7.5 megabases and a GC content of 72.8% and contains 6,629 protein-coding sequences (CDS). antiSMASH predicted 996 genes residing in 36 secondary metabolite gene clusters. PMID:24604655

Harjes, Janno; Ryu, Taewoo; Abdelmohsen, Usama Ramadan; Moitinho-Silva, Lucas; Horn, Hannes; Ravasi, Timothy

2014-01-01

86

Identification of metabolites from the degradation of fluoranthene by Mycobacterium sp. strain PYR-1  

SciTech Connect

Polycyclic aromatic hydrocarbons (PAHs) such as flouranthene are widespread environmental pollutants shown to be cytotoxic, mutagenic, and carcinogenic. Mycobacterium sp. strain PYR-1 substancially mineralizes fluoranthene in pure culture and in sediments. In this report, additional metabolites of fluoranthene are identified and its possible modes of degradation by Mycobacterium sp. strain PYR-1 are discussed. The experimental results identify metabolites with the intact fluorene configuration and an initial oxygenated metabolite in which the single benzene ring has been attacked. Several metabolic pathways, operating simultaneously, are involved in the degradation of fluoranthen by Mycobacterium sp. strain PYR-1. The low concentrations of metabolites, the rapid evolution of carbon dioxide, and the rapid disappearance of fluoranthene from the medium provide concrete evidence of the usefulness of this Mycobacterium for bioremediation of some PAHs.

Kelley, I.; Freeman, J.P.; Evans, F.E.; Cerniglia, C.E. (Food and Drug Administration, Jefferson, AR (United States))

1993-03-01

87

Hypervariable Pili and Flagella Genes Provide Suitable New Targets for DNA High-Resolution Melt-Based Genotyping of Dairy Geobacillus spp.  

PubMed

Although nonpathogenic in nature, spores of Geobacillus are able to attach to surfaces, germinate, and form biofilms, allowing rapid multiplication and persistence within milk powder processing plants, causing final product contamination, and eventually leading to a loss of revenue in terms of downgraded product quality. As a result, Geobacillus spp. have been found to be common contaminants of milk powder worldwide. Genotyping methods can help in gaining insight into the ecology and transmission of these thermophilic bacteria within and between dairy processing plants. The objective of this study was to use the assembled draft genomes of two Geobacillus spp. to identify and test new hypervariable genotyping targets for differentiating closely related dairy Geobacillus isolates. The two Geobacillus spp. strains obtained from high spore count powders were obtained in 2010 (isolate 7E) and in 1995 (isolate 126) and were previously shown to be of same genotype based on a variable number tandem repeat genotyping method. Significant nucleotide sequence variation was found in genes encoding pili and flagella, which were further investigated as suitable loci for a new high-resolution melt analysis (HRMA)-based genotyping method. Three genes encoding pulG (containing prepilin-type N-terminal cleavage domain), pilT (pili retraction protein), and fliW (flagellar assembly protein) were selected as targets for the new pili/flagella gene (PilFla) HRMA genotyping method. The three-gene-based PilFla-HRMA genotyping method differentiated 35 milk powder Geobacillus spp. isolates into 19 different genotype groups (D = 0.93), which compared favorably to the previous method (which used four variable number tandem repeat loci) that generated 16 different genotype groups (D = 0.90). In conclusion, through comparative genomics of two closely related dairy Geobacillus strains, we have identified new hypervariable regions that prove to be useful targets for highly discriminatory genotyping. PMID:25285488

Chauhan, Kanika; Seale, R Brent; Deeth, Hilton C; Turner, Mark S

2014-10-01

88

Metabolism of Bismuth Subsalicylate and Intracellular Accumulation of Bismuth by Fusarium sp. Strain BI  

PubMed Central

Enrichment cultures were conducted using bismuth subsalicylate as the sole source of carbon and activated sludge as the inoculum. A pure culture was obtained and identified as a Fusarium sp. based on spore morphology and partial sequences of 18S rRNA, translation elongation factor 1-?, and ?-tubulin genes. The isolate, named Fusarium sp. strain BI, grew to equivalent densities when using salicylate or bismuth subsalicylate as carbon sources. Bismuth nitrate at concentrations of up to 200 ?M did not limit growth of this organism on glucose. The concentration of soluble bismuth in suspensions of bismuth subsalicylate decreased during growth of Fusarium sp. strain BI. Transmission electron microscopy and energy-dispersive spectroscopy revealed that the accumulated bismuth was localized in phosphorus-rich granules distributed in the cytoplasm and vacuoles. Long-chain polyphosphates were extracted from fresh biomass grown on bismuth subsalicylate, and inductively coupled plasma optical emission spectrometry showed that these fractions also contained high concentrations of bismuth. Enzyme activity assays of crude extracts of Fusarium sp. strain BI showed that salicylate hydroxylase and catechol 1,2-dioxygenase were induced during growth on salicylate, indicating that this organism degrades salicylate by conversion of salicylate to catechol, followed by ortho cleavage of the aromatic ring. Catechol 2,3-dioxygenase activity was not detected. Fusarium sp. strain BI grew with several other aromatic acids as carbon sources: benzoate, 3-hydroxybenzoate, 4-hydroxybenzoate, gentisate, d-mandelate, l-phenylalanine, l-tyrosine, phenylacetate, 3-hydroxyphenylacetate, 4-hydroxyphenylacetate, and phenylpropionate. PMID:15691943

Dodge, Anthony G.; Wackett, Lawrence P.

2005-01-01

89

Preliminary characterization of the probiotic properties of Candida famata and Geobacillus thermoleovorans  

PubMed Central

Background and Objective Probiotics are live microbial feed supplements which beneficially affect the host animal by improving its intestinal microbial balance, producing metabolites which inhibit the colonization or growth of other microorganisms or by competing with them for resources such as nutrients or space. The aim of this study was to investigate the probiotic properties of Candida famata and Geobacillus thermoleovorans. Material and Methods In this study, yeast and bacterial strains isolated from pure oil waste were identified using Api 50 CHB and Api Candida Systems and their probiotic properties were studied through antimicrobial activity, biofilm production, adherence assay and enzymatic characterization. Results and Conclusion According to biochemical analyses, these strains corresponded to Geobacillus thermoleovorans and Candida famata. Antagonism assay results showed that the tested strains have an inhibitory effect against tested pathogenic bacteria. The yeast Candida famata was unable to produce biofilm on Congo Red Agar (CRA), while the bacterial strain was a slime producer. Adherence assays to abiotic surfaces revealed that the investigated strains were fairly adhesive to polystyrene with values ranging from 0.18 to 0.34 at 595 nm. The enzymatic characterization revealed that the tested strains expressed enzymes such as phosphatase alkaline, esterase lipase (C8), amylase, lipase, lecitenase and caseinase. The obtained results may allow the isolated strains to be considered as having the potential to be candidate probiotics. PMID:22347595

Mahdhi, A; Hmila, Z; Behi, A; Bakhrouf, A

2011-01-01

90

Bio sorption of strontium from aqueous solution by New Strain Bacillus sp. GTG-83  

SciTech Connect

Attempt was made to isolate bacterial strains capable of removing Sr biologically. In this study we collected ten different water samples from naturally radioactive spring Neydasht in Iran and bacterial strains samples isolated. Initial screening of a total of 50 bacterial isolates resulted in selection of one strain. The strain showed maximum adsorption capacity with 55 mg Sr/g dry wt. It was tentatively identified as Bacillus sp. according to morphological and biochemical properties and called strain GTG-83. Studies indicated that Bacillus sp. GTG-83 was able to grow aerobically in the presence of 50 mM SrCl{sub 2} but showed severe growth inhibition at levels above that concentration. The bio-sorption capacity of Bacillus sp. GTG-83 strongly depends on solution pH, and the maximum Sr sorption capacity of Bacillus sp. GTG-83 were obtained at pH 10 independent of the absence or the presence of increasing concentrations of salt (MgCl{sub 2}). Sr-salt bio-sorption studies were also performed at this pH values. Equilibrium uptakes of Sr increased with increasing Sr concentrations up to 250 mg/l for Bacillus sp. GTG-83. Maximum bio-sorption of Sr was obtained at temperatures in the range of 30-35 deg. C. Bacillus sp. GTG-83 bio-sorbed 97 mg Sr/g dry wt at 100 mg/l initial Sr concentration without salt medium (MgCl{sub 2}). When salt concentration (MgCl{sub 2}) increased to 15% (w/v), these values dropped to 23.6 mg Sr/g dry wt at the same conditions. Uptake of Sr within 5 min of incubation was relatively rapid and the absorption continued slowly thereafter. (authors)

Tajer Mohammad Ghazvini, P.; Ghorbanzadeh Mashkani, S.; Ghafourian, H. [Nuclear Research Center, Atomic Energy, Organization of Iran, Dept. of Nuclear Biotechnology, North Karegar St., Tehran (Iran, Islamic Republic of)

2007-07-01

91

Studies on Biodegradation of Nicotine by Arthrobacter sp. Strain HF2  

Microsoft Academic Search

A nicotine-degrading bacterium, strain HF-2, was isolated from tobacco waste-contaminated soil and identified as a member of Arthrobacter sp. based on morphology, physiological tests, 16S rDNA sequence and phylogenetic characteristics. At thermal denaturation test indicated that the G + C mol% of strain HF-1 was 63.5. The relationship between the growth of the isolate and the nicotine degradation suggested that

AIDONG RUAN; HANG MIN; WEI ZHU

2006-01-01

92

Optimization of manganese peroxidase production by the white rot fungus Bjerkandera sp. strain BOS55  

Microsoft Academic Search

Manganese dependent peroxidase (MnP) is the most ubiquitous peroxidase produced by white rot fungi. MnP is known to be involved in lignin degradation, biobleaching and in the oxidation of hazardous organopollutants. Bjerkandera sp. strain BOS55 is a nitrogen-unregulated white rot fungus which produces high amounts of MnP in the excess of N-nutrients due to increased biomass yield. Therefore, the strain

Tünde Mester; Jim A. Field

1997-01-01

93

Discovery of Rare and Highly Toxic Microcystins from Lichen-Associated Cyanobacterium Nostoc sp. Strain IO-102-I  

PubMed Central

The production of hepatotoxic cyclic heptapeptides, microcystins, is almost exclusively reported from planktonic cyanobacteria. Here we show that a terrestrial cyanobacterium Nostoc sp. strain IO-102-I isolated from a lichen association produces six different microcystins. Microcystins were identified with liquid chromatography-UV mass spectrometry by their retention times, UV spectra, mass fragmentation, and comparison to microcystins from the aquatic Nostoc sp. strain 152. The dominant microcystin produced by Nostoc sp. strain IO-102-I was the highly toxic [ADMAdda5]microcystin-LR, which accounted for ca. 80% of the total microcystins. We assigned a structure of [DMAdda5]microcystin-LR and [d-Asp3,ADMAdda5]microcystin-LR and a partial structure of three new [ADMAdda5]-XR type of microcystin variants. Interestingly, Nostoc spp. strains IO-102-I and 152 synthesized only the rare ADMAdda and DMAdda subfamilies of microcystin variants. Phylogenetic analyses demonstrated congruence between genes involved directly in microcystin biosynthesis and the 16S rRNA and rpoC1 genes of Nostoc sp. strain IO-102-I. Nostoc sp. strain 152 and the Nostoc sp. strain IO-102-I are distantly related, revealing a sporadic distribution of toxin production in the genus Nostoc. Nostoc sp. strain IO-102-I is closely related to Nostoc punctiforme PCC 73102 and other symbiotic Nostoc strains and most likely belongs to this species. Together, this suggests that other terrestrial and aquatic strains of the genus Nostoc may have retained the genes necessary for microcystin biosynthesis. PMID:15466511

Oksanen, Ilona; Jokela, Jouni; Fewer, David P.; Wahlsten, Matti; Rikkinen, Jouko; Sivonen, Kaarina

2004-01-01

94

Draft Genome Sequence of the Nitrate- and Phosphate-Accumulating Bacillus sp. Strain MCC0008  

PubMed Central

Here, we report the draft genome sequence of the nitrate- and phosphate-accumulating Bacillus sp. strain MCC0008, isolated from a consortium enriched from municipal sewage in nitrate broth (HiMedia M439). The total size of the genome is 5,609,456 bp, with a G+C content of 35.1%. PMID:23409265

DebRoy, Shreya; Bhattacharjee, Amrita; Thakur, Ashoke Ranjan

2013-01-01

95

Draft Genome Sequence of the Halophilic Bacterium Halobacillus sp. Strain BAB-2008  

PubMed Central

The Halobacillus sp. strain BAB-2008 is a moderately halophilic, rod-shaped, Gram-positive, orange-pigmented, carotenoid-producing bacterium isolated from saline soil near Zazam-Solar Park Road, Gujarat, India. Here we present the 3.7-Mb genome sequence to provide insights into its functional genomics and potential applications for carotenoid and enzyme production. PMID:23469348

Joshi, M. N.; Pandit, A. S.; Sharma, A.; Pandya, R. V.; Saxena, A. K.

2013-01-01

96

Draft Genome Sequence of Kocuria sp. Strain UCD-OTCP (Phylum Actinobacteria)  

PubMed Central

Here, we present the draft genome of Kocuria sp. strain UCD-OTCP, a member of the phylum Actinobacteria, isolated from a restaurant chair cushion. The assembly contains 3,791,485 bp (G+C content of 73%) and is contained in 68 scaffolds. PMID:23661474

Coil, David A.; Doctor, Jessica I.; Lang, Jenna M.; Darling, Aaron E.

2013-01-01

97

Draft Genome Sequence of the Oyster Larval Probiotic Bacterium Vibrio sp. Strain OY15.  

PubMed

We report the draft genome sequence of Vibrio sp. strain OY15, a Gram-negative marine bacterium isolated from an oyster (Crassostrea virginica) digestive tract and shown to possess probiotic activity. The availability of this genome sequence will facilitate the study of the mechanisms of probiotic activity as well as virulence capacity. PMID:25278542

Schreier, Harold J; Schott, Eric J

2014-01-01

98

Draft Genome Sequence of the Oyster Larval Probiotic Bacterium Vibrio sp. Strain OY15  

PubMed Central

We report the draft genome sequence of Vibrio sp. strain OY15, a Gram-negative marine bacterium isolated from an oyster (Crassostrea virginica) digestive tract and shown to possess probiotic activity. The availability of this genome sequence will facilitate the study of the mechanisms of probiotic activity as well as virulence capacity. PMID:25278542

Schott, Eric J.

2014-01-01

99

Genome Sequence of the Aerobic Arsenate-Reducing Bacterium Pantoea sp. Strain IMH  

PubMed Central

We here report the draft assembly for the genome of Pantoea sp. strain IMH, isolated from arsenic-contaminated soil in Inner Mongolia, China, with the ability to aerobically reduce arsenate to arsenite. The genome sequence will allow for the characterization of the molecular mechanisms of arsenate reduction. PMID:24723713

Tian, Haixia

2014-01-01

100

Genome Sequence of Amycolatopsis sp Strain ATCC 39116, a Plant Biomass-Degrading Actinomycete  

SciTech Connect

We announce the availability of a high-quality draft of the genome sequence of Amycolatopsis sp. strain 39116, one of few bacterial species that are known to consume the lignin component of plant biomass. This genome sequence will further ongoing efforts to use microorganisms for the conversion of plant biomass into fuels and high-value chemicals.

Davis, Jennifer R. [Brown University; Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute; Teshima, Hazuki [Los Alamos National Laboratory (LANL); Bruce, David [Los Alamos National Laboratory (LANL); Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Tapia, Roxanne [Los Alamos National Laboratory (LANL); Han, Shunsheng [Los Alamos National Laboratory (LANL); Han, James [U.S. Department of Energy, Joint Genome Institute; Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Nolan, Matt [U.S. Department of Energy, Joint Genome Institute; Mikhailova, Natalia [U.S. Department of Energy, Joint Genome Institute; Land, Miriam L [ORNL; Sello, Jason K. [Brown University

2012-01-01

101

Draft Genome Sequence of the Naphthalene Degrader Herbaspirillum sp. Strain RV1423  

PubMed Central

Herbaspirillum sp. strain RV1423 was isolated from a site contaminated with alkanes and aromatic compounds and harbors the complete pathway for naphthalene degradation. The new features found in RV1423 increase considerably the versatility and the catabolic potential of a genus of bacteria previously considered mainly to be diazotrophic endophytes to plants. PMID:24652979

Jauregui, Ruy; Rodelas, Belén; Geffers, Robert; Boon, Nico; Pieper, Dietmar H.

2014-01-01

102

Genome Sequence of the Sulfitobacter sp. Strain 2047-Infecting Lytic Phage ?CB2047-B  

PubMed Central

We announce the complete genome sequence of a lytic podovirus, ?CB2047-B, which infects the bacterium Sulfitobacter sp. strain 2047, a member of the Roseobacter clade. Genome analysis revealed ?CB2047-B to be an N4-like phage, with its genome having high nucleotide similarity to other N4-like roseophage genomes. PMID:24435853

Ankrah, Nana Y. D.; Budinoff, Charles R.; Wilson, William H.; Wilhelm, Steven W.

2014-01-01

103

Properties of Mutants of Synechocystis sp. Strain PCC 6803 Lacking Inorganic Carbon Sequestration Systems  

E-print Network

Properties of Mutants of Synechocystis sp. Strain PCC 6803 Lacking Inorganic Carbon SequestrationA is the only active inorganic carbon sequestration system showed low activity of HCO3 ­ uptake and grew under the significance of carbon sequestration in dissipating excess light energy. Keywords: CO2 and HCO3 � uptake -- CO2

Roegner, Matthias

104

Draft Genome Sequence of Hoeflea sp. Strain BAL378, a Potential Producer of Bioactive Compounds  

PubMed Central

Some phytoplankton-associated marine bacteria produce bioactive compounds. Members of the genus Hoeflea may be examples of such bacteria; however, data describing their metabolisms are scarce. Here, we report the draft genome sequence of Hoeflea sp. strain BAL378, a putative producer of bacteriocins, polyketides, and auxins, as demonstrated by genome mining. PMID:25414510

Riemann, Lasse; Gram, Lone

2014-01-01

105

Draft Genome Sequence of the Lignin-Degrading Burkholderia sp. Strain LIG30, Isolated from Wet Tropical Forest Soil.  

PubMed

Burkholderia species are common soil Betaproteobacteria capable of degrading recalcitrant aromatic compounds and xenobiotics. Burkholderia sp. strain LIG30 was isolated from wet tropical forest soil and is capable of utilizing lignin as a sole carbon source. Here we report the draft genome sequence of Burkholderia sp. strain LIG30. PMID:24948777

Woo, Hannah L; Utturkar, Sagar; Klingeman, Dawn; Simmons, Blake A; DeAngelis, Kristen M; Brown, Steven D; Hazen, Terry C

2014-01-01

106

Draft Genome Sequence of the Lignin-Degrading Burkholderia sp. Strain LIG30, Isolated from Wet Tropical Forest Soil  

PubMed Central

Burkholderia species are common soil Betaproteobacteria capable of degrading recalcitrant aromatic compounds and xenobiotics. Burkholderia sp. strain LIG30 was isolated from wet tropical forest soil and is capable of utilizing lignin as a sole carbon source. Here we report the draft genome sequence of Burkholderia sp. strain LIG30. PMID:24948777

Woo, Hannah L.; Utturkar, Sagar; Klingeman, Dawn; Simmons, Blake A.; DeAngelis, Kristen M.; Brown, Steven D.

2014-01-01

107

Transformation of carbon tetrachloride by Pseudomonas sp. strain KC under denitrification conditions.  

PubMed Central

A denitrifying Pseudomonas sp. (strain KC) capable of transforming carbon tetrachloride (CT) was isolated from groundwater aquifer solids. Major products of the transformation of 14C-labeled CT by Pseudomonas strain KC under denitrification conditions were 14CO2 and an unidentified water-soluble fraction. Little or no chloroform was produced. Addition of dissolved trace metals, notably, ferrous iron and cobalt, to the growth medium appeared to enhance growth of Pseudomonas strain KC while inhibiting transformation of CT. It is hypothesized that transformation of CT by this organism is associated with the mechanism of trace-metal scavenging. PMID:2268146

Criddle, C S; DeWitt, J T; Grbic-Galic, D; McCarty, P L

1990-01-01

108

Multilocus sequence analysis of putative Vibrio mediterranei strains and description of Vibrio thalassae sp. nov.  

PubMed

A multilocus sequence analysis based on partial gyrB, mreB, rpoD and pyrH genes was undertaken with 61 putative Vibrio mediterranei/V. shilonii strains from different hosts (mussels, oysters, clams, coral, fish and plankton) or habitat (seawater and sediment) and geographical origins (Mediterranean, Atlantic and Pacific). A consistent grouping was obtained with individual and concatenated gene sequences, and the clade, comprising 54 strains, was split into three subclades by all methods: subclade A (40 strains, including AK1, the former type strain of Vibrio shilonii), subclade B (8 strains) corresponding to the species V. mediterranei, and subclade C (six strains) representing a new species, V. thalassae sp. nov., with strain MD16(T) (=CECT 8203(T)=KCTC 32373(T)) as the proposed type strain. Average nucleotide identity (ANI) values, determined as a measure of genomic similarity, confirmed these assignments, and supported that strains in subclade C were a different species from V. mediterranei, with ANIb and ANIm figures lower than 90.0%. The synonymy of V. shilonii and V. mediterranei was also stressed by both MLSA and ANI determinations (97.0% between both type strains). No connection was found between geographic origin or sample type and MLSA grouping. PMID:24935234

Tarazona, Eva; Lucena, Teresa; Arahal, David R; Macián, M Carmen; Ruvira, María A; Pujalte, María J

2014-07-01

109

Cesium Accumulation and Growth Characteristics of Rhodococcus erythropolis CS98 and Rhodococcus sp. Strain CS402  

PubMed Central

Growth and cesium accumulation characteristics of two cesium-accumulating bacteria isolated from soils were investigated. Rhodococcus erythropolis CS98 and Rhodococcus sp. strain CS402 accumulated high levels of cesium (approximately 690 and 380 ?mol/g [dry weight] of cells or 92 and 52 mg/g [dry weight] of cells, respectively) after 24 h of incubation in the presence of 0.5 mM cesium. The optimum pH for cesium uptake by both Rhodococcus strains was 8.5. Rubidium and cesium assumed part of the role of potassium in the growth of both Rhodococcus strains. Potassium and rubidium inhibited cesium accumulation by these Rhodococcus strains. It is likely that both Rhodococcus strains accumulated cesium through a potassium transport system. PMID:16349312

Tomioka, Noriko; Uchiyama, Hiroo; Yagi, Osami

1994-01-01

110

Strategy for improving extracellular lipolytic activities by a novel thermotolerant Staphylococcus sp. strain  

PubMed Central

Background Extracellular bacterial lipases received much attention for their substrate specificity and their ability to function under extreme environments (pH, temperature...). Many staphylococci produced lipases which were released into the culture medium. Reports of extracellular thermostable lipases from Staphylococcus sp. and active in alkaline conditions are not previously described. Results This study focused on novel strategies to increase extracellular lipolytic enzyme production by a novel Staphylococcus sp. strain ESW. The microorganism needed neutral or alkaline pH values between 7.0 and 12.0 for growth. For pH values outside this range, cell growth seemed to be significantly inhibited. Staphylococcus sp. culture was able to grow within a wide temperature range (from 30 to 55°C). The presence of oils in the culture medium leaded to improvements in cells growth and lipolytic enzyme activity. On the other hand, although chemical surfactants leaded to an almost complete inhibition of growth and lipolytic enzyme production, their addition along the culture could affect the location of the enzyme. In addition, our results showed that this novel Staphylococcus sp. strain produced biosurfactants simultaneously with lipolytic activity, when soapstock (The main co-product of the vegetable oil refining industry), was used as the sole carbon source. Conclusion A simultaneous biosurfactant and extracellular lipolytic enzymes produced bacterial strain with potential application in soap stock treatment PMID:22078466

2011-01-01

111

Draft Genome Sequence of the Organophosphorus-Degrading Bacterium Pseudomonas sp. Strain 1-7, Isolated from Organophosphorus-Polluted Sludge  

PubMed Central

Pseudomonas sp. strain 1-7, isolated from organophosphorus-polluted sludge, is able to degrade many organophosphorus compounds. Here, we report the draft genome sequence of Pseudomonas sp. strain 1-7. PMID:25278536

Tian, Jian; Xu, Li; Zhang, Shuangyu; Sun, Wen; Chu, Xiaoyu

2014-01-01

112

Transmission Dynamics of Bartonella sp. Strain OE 1-1 in Sundevall's Jirds (Meriones crassus)  

PubMed Central

A high prevalence of Bartonella infection is found in many natural systems; however, the transmission dynamics leading to observations of these infections is not fully understood. The capability of Xenopsylla ramesis fleas to serve as competent vectors of Bartonella sp. OE 1-1 (a strain closely related to the zoonotic Bartonella elizabethae) to Meriones crassus jirds was investigated. Naïve X. ramesis fleas were placed for 72 h on naïve jirds or jirds that were either experimentally or naturally infected with Bartonella sp. strain OE 1-1, after which they were placed on naïve jirds. Postfeeding, 69 to 100% of the fleas collected from each Bartonella-positive jird contained Bartonella DNA, and all naïve jirds became positive for Bartonella sp. OE 1-1 after infestation with the infected fleas. In addition, maternal transmission of Bartonella sp. OE 1-1 in jirds was tested by mating 5 Bartonella-positive and 5 naïve female jirds with 10 naïve male jirds in the absence of fleas. Fifteen offspring were delivered by each group. Cultures of blood drawn from all offspring on days 35 and 47 postdelivery were found to be negative for Bartonella. A single spleen sample from the offspring of a Bartonella-positive mother was found molecularly positive for Bartonella sp. OE 1-1. This study demonstrates that X. ramesis fleas are competent vectors of Bartonella sp. OE 1-1 to M. crassus jirds and indicates that maternal transmission is probably not the major transmission route from female jirds to their offspring. We suggest that the dynamics of Bartonella sp. OE 1-1 in the M. crassus jird population in nature is mostly dependent on its vectors. PMID:23241972

Morick, Danny; Krasnov, Boris R.; Khokhlova, Irina S.; Gottlieb, Yuval

2013-01-01

113

Studies on biodegradation of nicotine by Arthrobacter sp. strain HF-2.  

PubMed

A nicotine-degrading bacterium, strain HF-2, was isolated from tobacco waste-contaminated soil and identified as a member of Arthrobacter sp. based on morphology, physiological tests, 16S rDNA sequence and phylogenetic characteristics. At thermal denaturation test indicated that the G + C mol% of strain HF-1 was 63.5. The relationship between the growth of the isolate and the nicotine degradation suggested that strain HF-2 could utilize nicotine as sole sources of carbon, nitrogen and energy. Blue pigment was observed during the nicotine degradation by strain HF-2. The isolate grew well at 20 to 33 degrees C, initial pH 6.5 to 8.0 and 0.5 to 2.0 g L-1 of nicotine concentration in the nicotine inorganic salt media. The maximum growth and nicotine degradation occurred at 30 degrees C, initial pH 7.0 and 0.7 g.L-1 of nicotine concentration in media under natural incubation condition. Strain HF-2 could degrade 100% of nicotine under the optimized incubation conditions for 43 h. The concentrations of nicotine were monitored by high performance liquid chromatography. This study demonstrates Arthrobacter sp. strain HF-2 had a great ability to degrade nicotine, and it may be available for the application to the bioremediation of environments contaminated by tobacco waste. PMID:16923598

Ruan, Aidong; Min, Hang; Zhu, Wei

2006-01-01

114

A promising strain of Streptomyces sp. with agricultural traits for growth promotion and disease management.  

PubMed

A bacterial strain, Streptomyces sp. CIMAP- A1 was isolated from Geranium rhizosphere and identified by morphological, physiological, biochemical and molecular characters (16S rDNA gene sequence). Phylogenetically, it was found most closely related to S. vinacendrappus, strain NRRL-2363 with 99% sequence similarity. The strain had potential antagonistic activity (in vitro) against wide range of phytopathogenic fungi like Stemphylium sp., Botrytis cinerea, Sclerotinia sclerotiorum, Colletotrichum spp., Curvularia spp., Corynespora cassicola and Thielavia basicola. The extracellular secondary metabolites produced by the strain in the culture filtrates significantly inhibited the spore germination, growth of germ tube of the germinated spores and radial growth of Alternaria alternata, Colletotrichum acutatum, Curvularia andropogonis and Fusarium moniliforme. The extraction of culture filtrate with solvents and purification by following VLC and PTLC methods always yielded a 10th fraction antifungal compound showing activity against wide range of phytopathogenic fungi. The strain was able to produce siderophores and indole-3-acetic acid. The strain was found to enhance the growth and biomass production of Geranium. It increased 11.3% fresh shoot biomass of Geranium and 21.7% essential oil yield. PMID:23016493

Alam, Mansoor; Dharni, Seema; Abdul-Khaliq; Srivastava, Santosh Kumar; Samad, Abdul; Gupta, Mahesh Kumar

2012-08-01

115

Isolation and characterization of an isoproturon mineralizing Sphingomonas sp. strain SH from a French agricultural soil.  

PubMed

The phenylurea herbicide isoproturon, 3-(4-isopropylphenyl)-1,1-dimethylurea (IPU), was found to be rapidly mineralized in an agricultural soil in France that had been periodically exposed to IPU. Enrichment cultures from samples of this soil isolated a bacterial strain able to mineralize IPU. 16S rRNA sequence analysis showed that this strain belonged to the phylogeny of the genus Sphingomonas (96% similarity with Sphingomonas sp. JEM-14, AB219361) and was designated Sphingomonas sp. strain SH. From this strain, a partial sequence of a 1,2-dioxygenase (catA) gene coding for an enzyme degrading catechol putatively formed during IPU mineralization was amplified. Phylogenetic analysis revealed that the catA sequence was related to Sphingomonas spp. and showed a lack of congruence between the catA and 16S rRNA based phylogenies, implying horizontal gene transfer of the catA gene cluster between soil microbiota. The IPU degrading ability of strain SH was strongly influenced by pH with maximum degradation taking place at pH 7.5. SH was only able to mineralize IPU and its known metabolites including 4-isopropylaniline and it could not degrade other structurally related phenylurea herbicides such as diuron, linuron, monolinuron and chlorotoluron or their aniline derivatives. These observations suggest that the catabolic abilities of the strain SH are highly specific to the metabolism of IPU. PMID:21110068

Hussain, Sabir; Devers-Lamrani, Marion; El Azhari, Najoi; Martin-Laurent, Fabrice

2011-06-01

116

Genetic and biochemical analyses of chlorobenzene degradation gene clusters in Pandoraea sp. strain MCB032.  

PubMed

Pandoraea sp. strain MCB032 was isolated as an emerging chlorobenzene degrader from a functionally stable bioreactor where species succession had occurred. In this study, two gene clusters encoding chlorobenzene metabolic functions have been cloned. Within the cbs gene cluster, CbsA and CbsB are similar to the chlorobenzene dioxygenase and the cis-chlorobenzene dihydrodiol dehydrogenase in Ralstonia sp. JS705 and shown to transform chlorobenzene to 3-chlorocatechol. The clc gene cluster shows strong similarity to the clc genes of Ralstonia sp. JS705 and encodes chlorocatechol 1,2-dioxygenase (ClcA) and other enzymes, which catalyze the conversion of chlorocatechol to 3-oxoadipate. The Michaelis constants (K (m)) values of ClcA for catechol, 3-methylcatechol and 3-chlorocatechol were determined as 10.0, 8.9 and 3.4 muM, respectively. CbsX, a putative transport protein present in the cbs cluster of strain MCB032 but not in those of other chlorobenzene degraders, shows 76 and 53% identities to two previously identified transport proteins involved in toluene degradation, TbuX from Ralstonia pickettii PKO1 and TodX from Pseudomonas putida F1. The presence of the transport protein in strain MCB032 likely provides a mechanistic explanation for its higher chlorobenzene affinity and may well be the basis for the competitive advantage of this strain in the bioreactor. PMID:19365620

Jiang, Xi-Wen; Liu, Hong; Xu, Ying; Wang, Shu-Jun; Leak, David J; Zhou, Ning-Yi

2009-06-01

117

Pseudomonas arsenicoxydans sp nov., an arsenite-oxidizing strain isolated from the Atacama desert.  

PubMed

A Gram-negative, arsenite-oxidizing bacterial strain, designated VC-1, was isolated from sediment samples from the Camarones Valley in the Atacama Desert, Chile. Strain VC-1 was strictly aerobic, oxidase and catalase positive, rod shaped, of about 5.5 microm in length and 0.5-1.0 microm in diameter. It was motile by means of multiple polar flagella. The phylogenetic reconstruction of the 16S rRNA gene sequence, an MLSA study by concatenating six genes, and DDH studies indicated that the strain differed genotypically from its closest relatives and was therefore recognized as a new species within the genus Pseudomonas. Phenotypic analysis combining metabolic tests, fatty acid profiles and MALDI-TOF profiles of total cell extracts supported the classification of the new species for which we propose the designation Pseudomonas arsenicoxydans sp. nov. The type strain is accessible under the culture collection numbers CCUG 58201(T) and CECT 7543(T). PMID:20409659

Campos, Victor L; Valenzuela, Cristian; Yarza, Pablo; Kämpfer, Peter; Vidal, Roberto; Zaror, C; Mondaca, Maria-Angelica; Lopez-Lopez, Arantxa; Rosselló-Móra, Ramon

2010-06-01

118

Benzoate Catabolite Repression of the Phthalate Degradation Pathway in Rhodococcus sp. Strain DK17?  

PubMed Central

Rhodococcus sp. strain DK17 exhibits a catabolite repression-like response when provided simultaneously with benzoate and phthalate as carbon and energy sources. Benzoate in the medium is depleted to detection limits before the utilization of phthalate begins. The transcription of the genes encoding benzoate and phthalate dioxygenase paralleled the substrate utilization profile. Two mutant strains with defective benzoate dioxygenases were unable to utilize phthalate in the presence of benzoate, although they grew normally on phthalate in the absence of benzoate. PMID:17158614

Choi, Ki Young; Zylstra, Gerben J.; Kim, Eungbin

2007-01-01

119

Isolation and characterization of Pseudomonas sp. strain HF-1, capable of degrading nicotine.  

PubMed

A nicotine-degrading bacterium, strain HF-1, was isolated from tobacco waste-contaminated soil and identified as a member of Pseudomonas sp. based on morphology, physiological tests, Vitek system (GN+), Biolog GN, 16S rDNA sequence and phylogenetic characteristics. The thermal denaturation test indicated that the G+C content of the DNA of HF-1 was 62.7 mol%. The relationship between growth and nicotine degradation of the isolate suggested that strain HF-1 could utilize nicotine as sole source of carbon, nitrogen and energy. Viridescent pigment was observed during nicotine degradation by strain HF-1. The isolate grew optimally at 30 degrees C, initial pH 6.5-7.5 and 1.3 g l(-1) of nicotine concentration in the nicotine inorganic salt medium, which is basically consistent with degradation of nicotine by the isolate. Strain HF-1 could degrade 99.6% of nicotine under the optimized incubation conditions for 25 h monitored by high-performance liquid chromatography. This study demonstrates that Pseudomonas sp. strain HF-1 had strong ability to degrade nicotine, and may be useful for bioremediation of environments contaminated by tobacco waste. PMID:15921891

Ruan, Aidong; Min, Hang; Peng, Xiaohui; Huang, Zheng

2005-01-01

120

Exploring the function of alcohol dehydrogenases during the endophytic life of Azoarcus Sp. strain BH72.  

PubMed

The endophytic bacterium Azoarcus sp. strain BH72 is capable of colonizing the interior of rice roots, where it finds suitable physicochemical properties for multiplying and fixing nitrogen. Because these properties are poorly understood, a microtiter-plate-based screening of a transcriptional gfp (green fluorescent protein) fusion library of Azoarcus sp. grown under different conditions was performed. Monitoring of the GFP activity allowed the identification of a gene highly expressed in medium supplemented with ethanol. Sequence analysis revealed that this gene encodes a pyrrolo-quinoline quinone-dependent alcohol dehydrogenase (ADH). Inspection of the complete genome sequence of the Azoarcus sp. strain BH72 identified seven additional genes encoding putative ADH, indicating that BH72 is well equipped to survive in different environmental conditions offering various alcohols as carbon source. Analyses of these eight putative ADH showed that expression of three was induced by ethanol, of which two were also expressed inside rice roots. The fact that waterlogged plants such as rice accumulate ethanol suggests that ethanol occurs in sufficiently high concentration within the root to induce expression of bacterial ADH. Disruption of these two ADH evoked a reduced competitiveness to the wild type in colonizing rice roots internally. Thus, it is likely that ethanol is an important carbon source for the endophytic life of Azoarcus sp. PMID:21848400

Krause, Andrea; Bischoff, Birte; Miché, Lucie; Battistoni, Federico; Reinhold-Hurek, Barbara

2011-11-01

121

Isolation and characterization of Pseudomonas sp. strain HF1, capable of degrading nicotine  

Microsoft Academic Search

A nicotine-degrading bacterium, strain HF-1, was isolated from tobacco waste-contaminated soil and identified as a member of Pseudomonas sp. based on morphology, physiological tests, Vitek system (GN+), Biolog GN, 16S rDNA sequence and phylogenetic characteristics. The thermal denaturation test indicated that the G+C content of the DNA of HF-1 was 62.7 mol%. The relationship between growth and nicotine degradation of

Aidong Ruan; Hang Min; Xiaohui Peng; Zheng Huang

2005-01-01

122

Tetrahydrofuran degradation by a newly isolated culture of Pseudonocardia sp. strain K1  

Microsoft Academic Search

An organism capable to grow aerobically on tetrahydrofuran as sole source of carbon and energy was isolated from a waste water treatment plant. The organism designated as strain K1 was identified as Pseudonocardia sp. by chemotaxonomic and morphological characteristics as well as analysis of the gene encoding the 16S rRNA. The highest binary sequence similarity value of 99.0% was obtained

Ulrike Kohlweyer; Barbara Thiemer; Thomas Schräder; Jan R Andreesen

2000-01-01

123

Two-step process for ketocarotenoid production by a green alga, Chlorococcum sp. strain MA1  

Microsoft Academic Search

The production of ketocarotenoids (KCs) from Chlorococcum sp. strain MA-1was investigated by a two-step process. In the first step, 18 g biomass l-1 was achieved by feeding glucose to the heterotrophic cultures; in the second step, the high-density cultures were treated with light illumination or chemical stress in dark, respectively, to induce KC synthesis. Light-treated cultures could produce 103 mg

D.-H. Zhang; Y.-K. Lee

2001-01-01

124

Construction of the astaxanthin biosynthetic pathway in a methanotrophic bacterium Methylomonas sp. strain 16a  

Microsoft Academic Search

Methylomonas sp. strain 16a is an obligate methanotrophic bacterium that uses methane or methanol as the sole carbon source. An effort\\u000a was made to engineer this organism for astaxanthin production. Upon expressing the canthaxanthin gene cluster under the control\\u000a of the native hps promoter in the chromosome, canthaxanthin was produced as the main carotenoid. Further conversion to astaxanthin was carried

Rick W. Ye; Henry Yao; Kristen Stead; Tao Wang; Luan Tao; Qiong Cheng; Pamela L. Sharpe; Wonchul Suh; Eva Nagel; Dennis Arcilla; Dominic Dragotta; Edward S. Miller

2007-01-01

125

Synthesis in vitro of very long chain fatty acids in Vibrio sp. strain ABE1  

Microsoft Academic Search

The activity of fatty acid synthetase (FAS) from Vibrio sp. strain ABE-1 required the presence of acyl carrier protein and was completely inhibited by thiolactomycin, an inhibitor specific for a type II FAS. These observations indicate that this enzyme is a type II FAS. Analysis by gas-liquid chromotography of the reaction products synthesized in vitro from [2-14C]malonyl-CoA by the partially

Naoki Morita; Nobuhiro Okajima; Masaru Gotoh; Hideyuki Hayashi; Hidetoshi Okuyama; Shoji Sasaki

1992-01-01

126

Genetic and Functional Analysis of the Styrene Catabolic Cluster of Pseudomonas sp. Strain Y2  

Microsoft Academic Search

The chromosomal region of Pseudomonas sp. strain Y2 involved in the conversion of styrene to phenylacetate (upper catabolic pathway) has been cloned and sequenced. Four catabolic genes, styABCD, and two regulatory genes, stySR, were identified. This gene cluster when transferred to Escherichia coli W confers to this pheny- lacetate-degrading host the ability to grow on styrene as the sole carbon

ANA VELASCO; SERGIO ALONSO; J. PERERA; EDUARDO DIAZ

1998-01-01

127

Identification of novel regulatory mechanisms controlling heterocyst development in Anabaena Sp. strain PCC 7120  

E-print Network

. (August 2008) Maria Ramona Aldea, B.S., Babes-Bolyai University; M.S., Babes-Bolyai University Chair of Advisory Commite: Dr. James W. Golden The regulatory mechanisms that govern heterocyst development in Anabaena sp. strain PC 7120 have been... formation and maintenance...................... 18 The patS gene is required for de novo patern formation... 18 The hetN gene is required for maintenance of the heterocyst patern.............................. 23 Other predicted cel...

Aldea, Maria Ramona

2009-05-15

128

Production of amylase by newly isolated moderate halophile, Halobacillus sp. strain MA2  

Microsoft Academic Search

Production of extracellular amylase was demonstrated under stress conditions of high temperature and high salinity in aerobically cultivated culture of a newly isolated moderately halophilic bacterium of spore-forming Halobacillus sp. strain MA-2 in medium containing starch, peptone, beef extract, and NaCl. The maximum amylase production was secreted in the presence of 15% (w\\/v) Na2SO4 (3.2 U ml?1). The isolate was

M. A Amoozegar; F Malekzadeh; Khursheed A Malik

2003-01-01

129

Characterization of Synechocystis sp. strain PCC 6803 and ? nbl mutants under nitrogen-deficient conditions  

Microsoft Academic Search

The impact of nitrogen deficiency on the unicellular cyanobacterium Synechocystis sp. strain PCC 6803 and three nbl (non-bleaching) mutants ((nblA1, (nblA2 and (nblB) was investigated. The (nblA mutants entered a non-dividing, dormant state soon after the initiation of nitrogen starvation. The cells became larger, the membrane system was disorganized, and ribosomes were found near the membranes much less frequently. Photosystem

Hong Li; Louis A. Sherman

2002-01-01

130

Novelties of Heat Shock Response in the Nitrogen-Fixing Cyanobacterium Anabaena Sp. Strain L-31  

Microsoft Academic Search

A b s t r a c t Studies on heat shock response in the nitrogen-fixing cyanobacterium, Anabaena sp. strain L-31 revealed the synthesis of several Hsps, many of which were similar to those observed in Escherichia coli in terms of molecular mass. Of the several Hsps synthesised, the 59 and 61 kDa GroEL proteins, which act as molecular chaperones,

Hema Rajaram; Shree Kumar Apte

131

Light-dependent expression of superoxide dismutase from cyanobacterium Synechocystis sp. strain PCC 6803  

Microsoft Academic Search

The oxygenic phototrophic cyanobacterium Synechocystis sp. strain PCC 6803 inevitably evolves superoxide during photosynthesis. Synechocystis 6803 contains only one type of superoxide dismutase, designated as SodB; therefore, this protein plays an important role in preventing oxidative damages caused by light. Because there was no direct evidence that SodB in Synechocystis 6803 could be regulated by light, the relationship between SodB

Jae-Hyun Kim; Kyong Hoon Suh

2005-01-01

132

Polycyclic aromatic hydrocarbon degradation by the white rot fungus Bjerkandera sp. strain BOS55  

Microsoft Academic Search

Outline of this thesis<\\/strong>In this thesis the conditions for optimal PAH oxidation by the white rot fungus Bjerkandera sp. strain BOS55 were evaluated. In Chapter 2, culture conditions like aeration and cosubstrate concentrations, which influenced the oxidation of the PAH compound anthracene and the ligninolytic indicator dye Poly R-478 by the white rot fungus, were studied. Two parameters were identified

M. J. J. Kotterman

1998-01-01

133

Draft Genome Sequence of Root-Colonizing Bacterium Bacillus sp. Strain PTS-394  

PubMed Central

Here, we report the high-quality draft genome sequence of Bacillus sp. strain PTS-394, isolated from the rhizosphere of tomatoes grown on Putuo Mountain (Xiamen, Fujian province, China), which exhibited excellent colonization ability on plant roots. The 4.0-Mb genome uncovered the mechanism for its potential root colonization ability and may provide novel insights into plant-bacterium interactions. PMID:24526631

Qiao, Junqing; Liang, Xuejie; Hu, Yonghong; Du, Yan

2014-01-01

134

An unexpected gene cluster for downstream degradation of alkylphenols in Sphingomonas sp. strain TTNP3  

Microsoft Academic Search

In silico analysis of nucleotide sequences flanking the recently found hydroquinone dioxygenase in Sphingomonas sp. strain TTNP3 revealed a gene cluster that encodes a hydroquinone catabolic pathway. In addition to the two open-reading\\u000a frames encoding the recently characterized hydroquinone dioxygenase, the cluster consisted of six open-reading frames. We\\u000a were able to express the three open-reading frames, hqdC, hqdD, and hqdE,

Boris A. Kolvenbach; Hyazinth Dobrowinski; Jan Fousek; Cestmir Vlcek; Andreas Schäffer; Frederic L. P. Gabriel; Hans-Peter E. Kohler; Philippe F. X. Corvini

135

Aromatic hydroxylation of indan by o-xylene-degrading Rhodococcus sp. strain DK17.  

PubMed

The metabolically versatile Rhodococcus sp. strain DK17 utilizes indan as a growth substrate via the o-xylene pathway. Metabolite and reverse transcription-PCR analyses indicate that o-xylene dioxygenase hydroxylates indan at the 4,5 position of the aromatic moiety to form cis-indan-4,5-dihydrodiol, which is dehydrogenated to 4,5-indandiol by a dehydrogenase. 4,5-indandiol undergoes ring cleavage by a meta-cleavage dioxygenase. PMID:19880642

Kim, Dockyu; Lee, Choong Hwan; Choi, Jung Nam; Choi, Ki Young; Zylstra, Gerben J; Kim, Eungbin

2010-01-01

136

Draft Genome Sequence of Plant Growth-Promoting Rhizobacterium Pantoea sp. Strain AS-PWVM4  

PubMed Central

Nonpathogenic Pantoea spp. have been shown to confer biofertilizer and biocontrol activities, indicating their potential for increasing crop yield. Herein, we provide the high-quality genome sequence of Pantoea sp. strain AS-PWVM4, a Gram-negative motile plant growth-promoting rhizobacterium isolated from a pomegranate plant. The 4.9-Mb genome contains genes related to plant growth promotion and the synthesis of siderophores. PMID:24309733

Khatri, Indu; Kaur, Sukhvir; Devi, Usha; Kumar, Navinder; Sharma, Deepak

2013-01-01

137

Genome Sequence of the Agar-Degrading Marine Bacterium Alteromonadaceae sp. Strain G7  

PubMed Central

Here, we present the high-quality draft genome sequence of the agar-degrading marine gammaproteobacterium Alteromonadaceae sp. strain G7, which was isolated from coastal seawater to be utilized as a bioresource for production of agar-derived biofuels. The 3.91-Mb genome contains a number of genes encoding algal polysaccharide-degrading enzymes such as agarases and sulfatases. PMID:23209220

Kwak, Min-Jung; Song, Ju Yeon; Kim, Byung Kwon; Chi, Won-Jae; Kwon, Soon-Kyeong; Choi, Soobeom; Chang, Yong-Keun

2012-01-01

138

Application of a recN sequence similarity analysis to the identification of species within the bacterial genus Geobacillus.  

PubMed

Full-length recN and 16S rRNA gene sequences were determined for a collection of 68 strains from the thermophilic Gram-positive genus Geobacillus, members of which have been isolated from geographically and ecologically diverse locations. Phylogenetic treeing methods clustered the isolates into nine sequence similarity groups, regardless of which gene was used for analysis. Several of these groups corresponded unambiguously to known Geobacillus species, whereas others contained two or more type strains from species with validly published names, highlighting a need for a re-assessment of the taxonomy for this genus. For taxonomic analysis of bacteria related at a genus, species or subspecies level, recN sequence comparisons had a resolving power nearly an order or magnitude greater than 16S rRNA gene comparisons. Mutational saturation rendered recN comparisons much less powerful than 16S rRNA gene comparisons for analysis of higher taxa, however. Analysis of recN sequences should prove a powerful tool for assigning strains to species within Geobacillus, and perhaps within other genera as well. PMID:15879251

Zeigler, Daniel R

2005-05-01

139

Plant compounds that induce polychlorinated biphenyl biodegradation by Arthrobacter sp. strain B1B.  

PubMed Central

Plant compounds that induced Arthrobacter sp. strain B1B to cometabolize polychlorinated biphenyls (PCBs) were identified by a screening assay based on the formation of a 4,4'-dichlorobiphenyl ring fission product. A chemical component of spearmint (Mentha spicata), l-carvone, induced Arthrobacter sp. strain B1B to cometabolize Aroclor 1242, resulting in significant degradation of 26 peaks in the mixture, including selected tetra- and pentachlorobiphenyls. Evidence for PCB biodegradation included peak disappearance, formation of a phenylhexdienoate ring fission product, and chlorobenzoate accumulation in the culture supernatant. Carvone was not utilized as a growth substrate and was toxic at concentrations of greater than 500 mg liter-1. Several compounds structurally related to l-carvone, including limonene, p-cymene, and isoprene, also induced cometabolism of PCBs by Arthrobacter sp. strain B1B. A structure-activity analysis showed that chemicals with an unsaturated p-menthane structural motif promoted the strongest cometabolism activity. These data suggest that certain plant-derived terpenoids may be useful for promoting enhanced rates of PCB biodegradation by soil bacteria. PMID:9143124

Gilbert, E S; Crowley, D E

1997-01-01

140

Photoacclimation of Prochlorococcus sp. (Prochlorophyta) Strains Isolated from the North Atlantic and the Mediterranean Sea.  

PubMed Central

Two Atlantic (SARG and NATL1) strains and one Mediterranean (MED) strain of Prochlorococcus sp., a recently discovered marine, free-living prochlorophyte, were grown over a range of "white" irradiances (lg) and under low blue light to examine their photoacclimation capacity. All three strains contained divinyl (DV) chlorophylls (Chl) a and b, both distinguishable from "normal" Chls by their red-shifted blue absorption maximum, a Chl c-like pigment at low concentration, zeaxanthin, and [alpha]-carotene. The presence of two phaeophytin b peaks in acidified extracts from both Atlantic strains grown at high lg suggests that these strains also had a normal Chl b-like pigment. In these strains, the total Chl b to DV-Chl a molar ratio decreased from about 1 at 7.5 [mu]mol quanta m-2 s-1 to 0.4 to 0.5 at 133 [mu]mol quanta m-2 s-1. In contrast, the MED strain always had a low DV-Chl b to DV-Chl a molar ratio, ranging between 0.13 at low lg and 0.08 at high lg. The discrepancies between the Atlantic and MED strains could result from differences either in the number of light-harvesting complexes (LHC) II per photosystem II or in the Chl b-binding capacity of the apoproteins constituting LHC II. Photosynthesis was saturated at approximately 5 fg C(fg Chl)-1 h-1 or 6 fg C cell-1 h-1, and growth was saturated at approximately 0.45 d-1 for both MED and SARG strains at 18[deg]C, but saturating irradiances differed between strains. Atlantic strains exhibited increased light-saturated rates and quantum yield for carbon fixation under blue light. PMID:12231684

Partensky, F.; Hoepffner, N.; Li, WKW.; Ulloa, O.; Vaulot, D.

1993-01-01

141

Alkane inducible proteins in Geobacillus thermoleovorans B23  

PubMed Central

Background Initial step of ?-oxidation is catalyzed by acyl-CoA dehydrogenase in prokaryotes and mitochondria, while acyl-CoA oxidase primarily functions in the peroxisomes of eukaryotes. Oxidase reaction accompanies emission of toxic by-product reactive oxygen molecules including superoxide anion, and superoxide dismutase and catalase activities are essential to detoxify them in the peroxisomes. Although there is an argument about whether primitive life was born and evolved under high temperature conditions, thermophilic archaea apparently share living systems with both bacteria and eukaryotes. We hypothesized that alkane degradation pathways in thermophilic microorganisms could be premature and useful to understand their evolution. Results An extremely thermophilic and alkane degrading Geobacillus thermoleovorans B23 was previously isolated from a deep subsurface oil reservoir in Japan. In the present study, we identified novel membrane proteins (P16, P21) and superoxide dismutase (P24) whose production levels were significantly increased upon alkane degradation. Unlike other bacteria acyl-CoA oxidase and catalase activities were also increased in strain B23 by addition of alkane. Conclusion We first suggested that peroxisomal ?-oxidation system exists in bacteria. This eukaryotic-type alkane degradation pathway in thermophilic bacterial cells might be a vestige of primitive living cell systems that had evolved into eukaryotes. PMID:19320977

2009-01-01

142

Monooxygenase-Mediated 1,2-Dichloroethane Degradation by Pseudomonas sp. Strain DCA1  

PubMed Central

A bacterial strain, designated Pseudomonas sp. strain DCA1, was isolated from a 1,2-dichloroethane (DCA)-degrading biofilm. Strain DCA1 utilizes DCA as the sole carbon and energy source and does not require additional organic nutrients, such as vitamins, for optimal growth. The affinity of strain DCA1 for DCA is very high, with a Km value below the detection limit of 0.5 ?M. Instead of a hydrolytic dehalogenation, as in other DCA utilizers, the first step in DCA degradation in strain DCA1 is an oxidation reaction. Oxygen and NAD(P)H are required for this initial step. Propene was converted to 1,2-epoxypropane by DCA-grown cells and competitively inhibited DCA degradation. We concluded that a monooxygenase is responsible for the first step in DCA degradation in strain DCA1. Oxidation of DCA probably results in the formation of the unstable intermediate 1,2-dichloroethanol, which spontaneously releases chloride, yielding chloroacetaldehyde. The DCA degradation pathway in strain DCA1 proceeds from chloroacetaldehyde via chloroacetic acid and presumably glycolic acid, which is similar to degradation routes observed in other DCA-utilizing bacteria. PMID:10347028

Hage, Jacobus C.; Hartmans, Sybe

1999-01-01

143

Dynamic Metabolic and Transcriptional Profiling of Rhodococcus sp. Strain YYL during the Degradation of Tetrahydrofuran  

PubMed Central

Although tetrahydrofuran-degrading Rhodococcus sp. strain YYL possesses tetrahydrofuran (THF) degradation genes similar to those of other tetrahydrofuran-degrading bacteria, a much higher degradation efficiency has been observed in strain YYL. In this study, nuclear magnetic resonance (NMR)-based metabolomics analyses were performed to explore the metabolic profiling response of strain YYL to exposure to THF. Exposure to THF slightly influenced the metabolome of strain YYL when yeast extract was present in the medium. The metabolic profile of strain YYL over time was also investigated using THF as the sole carbon source to identify the metabolites associated with high-efficiency THF degradation. Lactate, alanine, glutarate, glutamate, glutamine, succinate, lysine, trehalose, trimethylamine-N-oxide (TMAO), NAD+, and CTP were significantly altered over time in strain YYL grown in 20 mM THF. Real-time quantitative PCR (RT-qPCR) revealed changes in the transcriptional expression levels of 15 genes involved in THF degradation, suggesting that strain YYL could accumulate several disturbances in osmoregulation (trehalose, glutamate, glutamine, etc.), with reduced glycolysis levels, an accelerated tricarboxylic acid cycle, and enhanced protein synthesis. The findings obtained through 1H NMR metabolomics analyses and the transcriptional expression of the corresponding genes are complementary for exploring the dynamic metabolic profile in organisms. PMID:24532074

He, Zhixing; Yao, Yanlai

2014-01-01

144

Monooxygenase-mediated 1,2-dichloroethane degradation by Pseudomonas sp. strain DCA1  

SciTech Connect

A bacterial strain, designated Pseudomonas sp. strain DCA1, was isolated from a 1,2-dichloroethane (DCA)-degrading biofilm. Strain DCA1 utilizes DCA as the sole carbon and energy source and does not require additional organic nutrients, such as vitamins, for optimal growth. The affinity of strain DCA1 for DCA is very high, with a K{sub m} value below the detection limit of 0.5 {micro}M. Instead of a hydrolytic dehalogenation, as in other DCA utilizers, the first step in DCA degradation in strain DCA1 is an oxidation reaction. Oxygen and NAD(P)H are required for this initial step. Propene was converted to 1,2-epoxypropane by DCA-grown cells and competitively inhibited DCA degradation. The authors concluded that a monooxygenase is responsible for the first step in DCA degradation in strain DCA1. Oxidation of DCA probably results in the formation of the unstable intermediate 1,2-dichloroethanol, which spontaneously releases chloride, yielding chloroacetaldehyde. The DCA degradation pathway is strain DCA1 proceeds from chloroacetaldehyde via chloroacetic acid and presumably glycolic acid, which is similar to degradation routes observed in other DCA-utilizing bacteria.

Hage, J.C.; Hartmans, S. [Wageningen Univ. (Netherlands)

1999-06-01

145

Draft Genome Sequence of Paenibacillus sp. Strain MSt1 with Broad Antimicrobial Activity, Isolated from Malaysian Tropical Peat Swamp Soil  

PubMed Central

We report the draft genome sequence of Paenibacillus sp. strain MSt1, which has broad-range antimicrobial activity, isolated from tropical peat swamp soil. Genes involved in antimicrobial biosynthesis are found to be present in this genome. PMID:25301658

Ong, Kuan Shion; Yule, Catherine M.; Gan, Han Ming; Lee, Sui Mae

2014-01-01

146

Augmentation of tribenuron methyl removal from polluted soil with Bacillus sp. strain BS2 and indigenous earthworms.  

PubMed

Tribenuron methyl (TBM) is a member of the sulfonylurea herbicide family and is widely used worldwide. In this study, TBM-degrading bacteria were enriched with TBM as potential carbon, nitrogen or sulfur source, and 44 bacterial isolates were obtained. These isolates were phylogenetically diverse, and were grouped into 25 operational taxonomic units and 14 currently known genera. Three representatives, Bacillus sp. strain BS2, Microbacterium sp. strain BS3, and Cellulosimicrobium sp. strain BS11, were selected, and their growth and TBM removal from culture broth were investigated. In addition, indigenous earthworms were collected and applied to augment TBM degradation in lab-scale soil column experiments. Results demonstrated that Bacillus sp. strain BS2 and earthworms significantly increased TBM removal during soil column experiments. PMID:23513692

Tang, Qiang; Zhao, Zhiping; Liu, Yajun; Wang, Nanxi; Wang, Baojun; Wang, Yanan; Zhou, Ningyi; Liu, Shuangjiang

2012-01-01

147

Identification, Purification and Characterization of Laterosporulin, a Novel Bacteriocin Produced by Brevibacillus sp. Strain GI-9  

PubMed Central

Background Bacteriocins are antimicrobial peptides that are produced by bacteria as a defense mechanism in complex environments. Identification and characterization of novel bacteriocins in novel strains of bacteria is one of the important fields in bacteriology. Methodology/Findings The strain GI-9 was identified as Brevibacillus sp. by 16 S rRNA gene sequence analysis. The bacteriocin produced by strain GI-9, namely, laterosporulin was purified from supernatant of the culture grown under optimal conditions using hydrophobic interaction chromatography and reverse-phase HPLC. The bacteriocin was active against a wide range of Gram-positive and Gram-negative bacteria. MALDI-TOF experiments determined the precise molecular mass of the peptide to be of 5.6 kDa and N-terminal sequencing of the thermo-stable peptide revealed low similarity with existing antimicrobial peptides. The putative open reading frame (ORF) encoding laterosporulin and its surrounding genomic region was fished out from the draft genome sequence of GI-9. Sequence analysis of the putative bacteriocin gene did not show significant similarity to any reported bacteriocin producing genes in database. Conclusions We have identified a bacteriocin producing strain GI-9, belonging to the genus Brevibacillus sp. Biochemical and genomic characterization of laterosporulin suggests it as a novel bacteriocin with broad spectrum antibacterial activity. PMID:22403615

Singh, Pradip Kumar; Chittpurna; Ashish; Sharma, Vikas; Patil, Prabhu B.; Korpole, Suresh

2012-01-01

148

TNT and nitroaromatic compounds are chemoattractants for Burkholderia cepacia R34 and Burkholderia sp. strain DNT.  

PubMed

Nitroaromatic compounds are toxic and potential carcinogens. In this study, a drop assay was used to detect chemotaxis toward nitroaromatic compounds for wild-type Burkholderia cepacia R34, wild-type Burkholderia sp. strain DNT, and a 2,4-dinitrotoluene (2,4-DNT) dioxygenase mutant strain (S5). The three strains are chemotactic toward 2,4,6-trinitrotoluene (TNT), 2,3-DNT, 2,4-DNT, 2,5-DNT, 2-nitrotoluene (NT), 4NT, and 4-methyl-5-nitrocatechol (4M5NC), but not toward 2,6-DNT. Of these, only 2,4-DNT is a carbon and energy source for B. cepacia R34 and Burkholderia sp. strain DNT, and 4M5NC is an intermediate in the 2,4-DNT degradation pathway. It was determined that the 2,4-DNT dioxygenase genes are not required for the chemotaxis for these nitroaromatic compounds because the DNT DDO mutant S5 has a chemotactic response toward 2,4-DNT although 2,4-DNT is not metabolized by S5; hence, 2,4-DNT itself is the chemoattractant. This is the first report of chemotaxis toward TNT, 2,3-DNT, 2,4-DNT, 2,5-DNT, 2NT, 4NT, and 4M5NC. PMID:15856226

Leungsakul, Thammajun; Keenan, Brendan G; Smets, Barth F; Wood, Thomas K

2005-12-01

149

Purification and characterization of hydroquinone dioxygenase from Sphingomonas sp. strain TTNP3  

PubMed Central

Hydroquinone-1,2-dioxygenase, an enzyme involved in the degradation of alkylphenols in Sphingomonas sp. strain TTNP3 was purified to apparent homogeneity. The extradiol dioxygenase catalyzed the ring fission of hydroquinone to 4-hydroxymuconic semialdehyde and the degradation of chlorinated and several alkylated hydroquinones. The activity of 1 mg of the purified enzyme with unsubstituted hydroquinone was 6.1 ?mol per minute, the apparent Km 2.2 ?M. ICP-MS analysis revealed an iron content of 1.4 moles per mole enzyme. The enzyme lost activity upon exposure to oxygen, but could be reactivated by Fe(II) in presence of ascorbate. SDS-PAGE analysis of the purified enzyme yielded two bands of an apparent size of 38 kDa and 19 kDa, respectively. Data from MALDI-TOF analyses of peptides of the respective bands matched with the deduced amino acid sequences of two neighboring open reading frames found in genomic DNA of Sphingomonas sp strain TTNP3. The deduced amino acid sequences showed 62% and 47% identity to the large and small subunit of hydroquinone dioxygenase from Pseudomonas fluorescens strain ACB, respectively. This heterotetrameric enzyme is the first of its kind found in a strain of the genus Sphingomonas sensu latu. PMID:21906340

2011-01-01

150

Efficient production of laccases by Trametes sp. AH28-2 in cocultivation with a Trichoderma strain  

Microsoft Academic Search

A biocontrol fungus isolated from rotting wood was identified as a Trichoderma strain (named as Trichoderma sp. ZH1) by internal transcribed spacer (ITS) sequences of rRNA genes. The laccase yield of Trametes sp. AH28-2 in cocultivation with Trichoderma sp. ZH1 reached 6,210 U l?1, approximately identical to those induced by toxic aromatic inducers. Cocultures maintained 60–70 % of their highest laccase

H. Zhang; Y. Z. Hong; Y. Z. Xiao; J. Yuan; X. M. Tu; X. Q. Zhang

2006-01-01

151

Molecular detection of Rickettsia bellii and Rickettsia sp. strain Colombianensi in ticks from Cordoba, Colombia.  

PubMed

The purpose of this study was to provide molecular evidence of Rickettsia spp. in ticks collected from 2 sites of Cordoba. From May to June 2009, 1069 Amblyomma cajennense ticks were removed from 40 capybaras (Hydrochoerus hydrochaeris) in a rural locality of Monteria. Furthermore, 458 Amblyomma sp. larvae and 20 Amblyomma sp. nymphs were collected in a rural locality of Los Cordobas (Cordoba) by drag sampling on vegetation (n=1547). Ticks were grouped into pools and tested for rickettsial infection by real-time PCR targeting the rickettsial gene gltA. Subsequently, PCR targeting for gltA, ompA, ompB, and 16S rRNA, sequencing, and phylogenetic analyses were undertaken. Rickettsial DNA was detected in 10 (4.6%) out of 214 pools of ticks by RT-PCR. Five (33%) of free-living Amblyomma sp. larval pools were positive, as well as 5 (2.6%) pools from A. cajennense. Only the gltA gene was amplified from 5 pools of free-living larvae. The nucleotide sequences were 100% identical to R. bellii by BLAST. Only one pool from A. cajennense was positive for gltA, ompA, ompB, and 16S rRNA. The partial nucleotide sequences of these genes were 100% identical to nucleotide sequences of the same genes of a new proposed species Candidatus Rickettsia sp. strain Colombianensi. This is the first report of R. bellii in ticks in Colombia and the second report of detection of Candidatus Rickettsia sp. strain Colombianensi. These Rickettsia species are still considered of unknown pathogenicity. Further studies are needed to characterize the ecological and potential pathogenic role of these 2 Rickettsia species found in Cordoba. PMID:24378078

Miranda, Jorge; Mattar, Salim

2014-03-01

152

Gene Transfer in Leptolyngbya sp. Strain BL0902, a Cyanobacterium Suitable for Production of Biomass and Bioproducts  

Microsoft Academic Search

Current cyanobacterial model organisms were not selected for their growth traits or potential for the production of renewable biomass, biofuels, or other products. The cyanobacterium strain BL0902 emerged from a search for strains with superior growth traits. Morphology and 16S rRNA sequence placed strain BL0902 in the genus Leptolyngbya. Leptolyngbya sp. strain BL0902 (hereafter Leptolyngbya BL0902) showed robust growth at

Arnaud Taton; Ewa Lis; Dawn M. Adin; Guogang Dong; Scott Cookson; Steve A. Kay; Susan S. Golden; James W. Golden

2012-01-01

153

The cloned 1-aminocyclopropane-1-carboxylate (ACC) deaminase gene from Sinorhizobium sp. strain BL3 in Rhizobium sp. strain TAL1145 promotes nodulation and growth of Leucaena leucocephala.  

PubMed

The objective of this study was to determine the role of 1-aminocyclopropane-1-carboxylate (ACC) deaminase of symbionts in nodulation and growth of Leucaena leucocephala. The acdS genes encoding ACC deaminase were cloned from Rhizobium sp. strain TAL1145 and Sinorhizobium sp. BL3 in multicopy plasmids, and transferred to TAL1145. The BL3-acdS gene greatly enhanced ACC deaminase activity in TAL1145 compared to the native acdS gene. The transconjugants of TAL1145 containing the native or BL3 acdS gene could grow in minimal media containing 1.5mM ACC, whereas BL3 could tolerate up to 3mM ACC. The TAL1145 acdS gene was inducible by mimosine and not by ACC, while the BL3 acdS gene was highly inducible by ACC and not by mimosine. The transconjugants of TAL1145 containing the native- and BL3-acdS genes formed nodules with greater number and sizes, and produced higher root mass on L. leucocephala than by TAL1145. This study shows that the introduction of multiple copies of the acdS gene increased ACC deaminase activities of TAL1145 and enhanced its symbiotic efficiency on L. leucocephala. PMID:18406559

Tittabutr, Panlada; Awaya, Jonathan D; Li, Qing X; Borthakur, Dulal

2008-06-01

154

Draft Genome Sequence of Salimicrobium sp. Strain MJ3, Isolated from Myulchi-Jeot, Korean Fermented Seafood  

PubMed Central

Salimicrobium sp. strain MJ3 was isolated from myulchi-jeot, traditional fermented seafood made from anchovy in South Korea. Here we announce the draft genome sequence of Salimicrobium sp. MJ3 with 2,717,782 bp, which consists of 45 contigs (>500 bp in size), and provide a description of their annotation. PMID:23144427

Lee, Se Hee; Jung, Ji Young

2012-01-01

155

Draft Genome Sequence of Blastomonas sp. Strain CACIA 14H2, a Heterotrophic Bacterium Associated with Cyanobacteria  

PubMed Central

With the new methods for assembling sequence data from metagenomic samples, the genomic study of heterotrophic bacterium-cyanobacterium associations can now be improved. In this work, the draft genome sequence of Blastomonas sp. strain CACIA 14H2, obtained from a nonaxenic culture of a Cyanobium sp., is presented. PMID:24435876

Siqueira, Andrei Santos; dos Santos, Bruno Garcia Simoes; da Silva, Fabio Daniel Florencio; Lima, Clayton Pereira; Cardoso, Jedson Ferreira; Vianez-Junior, Joao Lidio S. G.; Nunes, Marcio Roberto Teixeira; Goncalves, Evonnildo Costa

2014-01-01

156

Novel Antiphytopathogenic Compound 2-Heptyl-5-Hexylfuran-3-Carboxylic Acid, Produced by Newly Isolated Pseudomonas sp. Strain SJT25 ?†  

PubMed Central

Pseudomonas sp. strain SJT25, which strongly antagonizes plant pathogens, was isolated from rice rhizosphere soil by a bioactivity-guided approach. A novel antiphytopathogenic compound was isolated from the fermentation broth of Pseudomonas sp. SJT25 and identified as 2-heptyl-5-hexylfuran-3-carboxylic acid. This compound showed antimicrobial activities both in vitro and in vivo. PMID:21742907

Wang, Xiao-Ying; Xu, Yu-Quan; Lin, Shuang-Jun; Liu, Zhen-Zhen; Zhong, Jian-Jiang

2011-01-01

157

Initial Reactions in Anaerobic Oxidation of m-Xylene by the Denitrifying Bacterium Azoarcus sp. Strain T  

Microsoft Academic Search

The initial enzymatic steps in anaerobic m-xylene oxidation were studied in Azoarcus sp. strain T, a denitrifying bacterium capable of mineralizing m-xylene via 3-methylbenzoate. Permeabilized cells of m-xylene- grown Azoarcus sp. strain T catalyzed the addition of m-xylene to fumarate to form (3-methylbenzyl)succinate. In the presence of succinyl coenzyme A (CoA) and nitrate, (3-methylbenzyl)succinate was oxidized to E-(3- methylphenyl)itaconate (or

CYNTHIA J. KRIEGER; HARRY R. BELLER; MARTIN REINHARD; ALFRED M. SPORMANN

1999-01-01

158

Toxicological Effects of Selective Herbicides on Plant Growth Promoting Activities of Phosphate Solubilizing Klebsiella sp . Strain PS19  

Microsoft Academic Search

This study examines the effect of four herbicides, quizalafop-p-ethyl, clodinafop, metribuzin and glyphosate, on plant growth promoting activities like phosphate solubilization, siderophores,\\u000a indole acetic acid, exo-polysaccharides, hydrogen cyanide and ammonia production by herbicide tolerant Klebsiella sp. strain PS19. The strain was isolated from mustard rhizosphere. The selected herbicides were applied two to three times\\u000a at the recommended rates. Klebsiella sp.

Munees Ahemad

2011-01-01

159

Heat-shock response and its contribution to thermotolerance of the nitrogen-fixing cyanobacterium Anabaena sp. strain L-31  

Microsoft Academic Search

Compared to Escherichia coli, the nitrogen-fixing soil cyanobacterium Anabaena sp. strain L-31 exhibited significantly superior abilities to survive prolonged and continuous heat stress and recover therefrom. Temperature upshift induced the synthesis of heat-shock proteins of similar molecular mass in the two microbes. However, in Anabaena sp. strain L-31 the heat-shock proteins (particularly the GroEL proteins) were synthesised throughout the stress

Hema Rajaram; Shree Kumar Apte

2003-01-01

160

Aerobic Mineralization of Hexachlorobenzene by Newly Isolated Pentachloronitrobenzene-Degrading Nocardioides sp. Strain PD653 ?  

PubMed Central

A novel aerobic pentachloronitrobenzene-degrading bacterium, Nocardioides sp. strain PD653, was isolated from an enrichment culture in a soil-charcoal perfusion system. The bacterium also degraded hexachlorobenzene, a highly recalcitrant environmental pollutant, accompanying the generation of chloride ions. Liberation of 14CO2 from [U-ring-14C]hexachlorobenzene was detected in a culture of the bacterium and indicates that strain PD653 is able to mineralize hexachlorobenzene under aerobic conditions. The metabolic pathway of hexachlorobenzene is initiated by oxidative dechlorination to produce pentachlorophenol. As further intermediate metabolites, tetrachlorohydroquinone and 2,6-dichlorohydroquinone have been detected. Strain PD653 is the first naturally occurring aerobic bacteria capable of mineralizing hexachlorobenzene. PMID:19429557

Takagi, Kazuhiro; Iwasaki, Akio; Kamei, Ichiro; Satsuma, Koji; Yoshioka, Yuichi; Harada, Naoki

2009-01-01

161

The sll1951 Gene Encodes the Surface Layer Protein of Synechocystis sp. Strain PCC 6803  

PubMed Central

Sll1951 is the surface layer (S-layer) protein of the cyanobacterium Synechocystis sp. strain PCC 6803. This large, hemolysin-like protein was found in the supernatant of a strain that was deficient in S-layer attachment. An sll1951 deletion mutation was introduced into Synechocystis and was easily segregated to homozygosity under laboratory conditions. By thin-section and negative-stain transmission electron microscopy, a ?30-nm-wide S-layer lattice covering the cell surface was readily visible in wild-type cells but was absent in the ?sll1951 strain. Instead, the ?sll1951 strain displayed a smooth lipopolysaccharide surface as its most peripheral layer. In the presence of chaotropic agents, the wild type released a large (>150-kDa) protein into the medium that was identified as Sll1951 by mass spectrometry of trypsin fragments; this protein was missing in the ?sll1951 strain. In addition, Sll1951 was prominent in crude extracts of the wild type, indicating that it is an abundant protein. The carotenoid composition of the cell wall fraction of the ?sll1951 strain was similar to that of the wild type, suggesting that the S-layer does not contribute to carotenoid binding. Although the photoautotrophic growth rate of the ?sll1951 strain was similar to that of the wild-type strain, the viability of the ?sll1951 strain was reduced upon exposure to lysozyme treatment and hypo-osmotic stress, indicating a contribution of the S-layer to the integrity of the Synechocystis cell wall. This work identifies the S-layer protein in Synechocystis and shows that, at least under laboratory conditions, this very abundant, large protein has a supportive but not a critical role in the function of the cyanobacterium. PMID:24078613

Trautner, Christoph

2013-01-01

162

Biodegradation of 3-nitrotoluene by Rhodococcus sp. strain ZWL3NT.  

PubMed

A pure bacterial culture was isolated by its ability to utilize 3-nitrotoluene (3NT) as the sole source of carbon, nitrogen, and energy for growth. Analysis of its 16S rRNA gene showed that the organism (strain ZWL3NT) belongs to the genus Rhodococcus. A rapid disappearance of 3NT with concomitant release of nitrite was observed when strain ZWL3NT was grown on 3NT. The isolate also grew on 2-nitrotoluene, 3-methylcatechol and catechol. Two metabolites, 3-methylcatechol and 2-methyl-cis,cis-muconate, in the reaction mixture were detected after incubation of cells of strain ZWL3NT with 3NT. Enzyme assays showed the presence of both catechol 1,2-dioxygenase and catechol 2,3-dioxygenase in strain ZWL3NT. In addition, a catechol degradation gene cluster (catRABC cluster) for catechol ortho-cleavage pathway was cloned from this strain and cell extracts of Escherichia coli expressing CatA and CatB exhibited catechol 1,2-dioxygenase activity and cis,cis-muconate cycloisomerase activity, respectively. These experimental evidences suggest a novel pathway for 3NT degradation with 3-methylcatechol as a key metabolite by Rhodococcus sp. strain ZWL3NT. PMID:23250222

Tian, Xiao-Jun; Liu, Xiao-Yang; Liu, Hong; Wang, Shu-Jun; Zhou, Ning-Yi

2013-10-01

163

Survival of the anaerobic fungus Orpinomyces sp. strain C1A after prolonged air exposure  

PubMed Central

Anaerobic fungi are efficient plant biomass degraders and represent promising agents for a variety of biotechnological applications. We evaluated the tolerance of an anaerobic fungal isolate, Orpinomyces sp. strain C1A, to air exposure in liquid media using soluble (cellobiose) and insoluble (dried switchgrass) substrates. Strain C1A grown on cellobiose survived for 11, and 13.5?hours following air exposure when grown under planktonic, and immobilized conditions, respectively. When grown on switchgrass media, strain C1A exhibited significantly enhanced air tolerance and survived for 168?hours. The genome of strain C1A lacked a catalase gene, but contained superoxide dismutase and glutathione peroxidase genes. Real time PCR analysis indicated that superoxide dismutase, but not glutathione peroxidase, exhibits a transient increase in expression level post aeration. Interestingly, the C1A superoxide dismutase gene of strain C1A appears to be most closely related to bacterial SODs, which implies its acquisition from a bacterial donor via cross kingdom horizontal gene transfer during Neocallimastigomycota evolution. We conclude that strain C1A utilizes multiple mechanisms to minimize the deleterious effects of air exposure such as physical protection and the production of oxidative stress enzymes. PMID:25367149

Struchtemeyer, Christopher G.; Ranganathan, Abhaya; Couger, M. B.; Liggenstoffer, Audra S.; Youssef, Noha H.; Elshahed, Mostafa S.

2014-01-01

164

Agroinfiltration by Cytokinin-Producing Agrobacterium sp. Strain GV3101 Primes Defense Responses in Nicotiana tabacum.  

PubMed

Transient infiltrations in tobacco are commonly used in plant studies, but the host response to different disarmed Agrobacterium strains is not fully understood. The present study shows that pretreatment with disarmed Agrobacterium tumefaciens GV3101 primes the defense response to subsequent infection by Pseudomonas syringae in Nicotiana tabacum. The presence of a trans-zeatin synthase (tzs) gene in strain GV3101 may be partly responsible for the priming response, as the tzs-deficient Agrobacterium sp. strain LBA4404 only weakly imparts such responses. Besides inducing the expression of defense-related genes like PR-1 and NHL10, GV3101 pretreatment increased the expression of tobacco mitogen-activated protein kinase (MAPK) pathway genes like MEK2, WIPK (wound-induced protein kinase), and SIPK (salicylic acid-induced protein kinase). Furthermore, the GV3101 strain showed a stronger effect than the LBA4404 strain in activating phosphorylation of the tobacco MAPK, WIPK and SIPK, which presumably prime the plant immune machinery. Lower doses of exogenously applied cytokinins increased the activation of MAPK, while higher doses decreased the activation, suggesting a balanced level of cytokinins is required to generate defense response in planta. The current study serves as a cautionary warning for plant researchers over the choice of Agrobacterium strains and their possible consequences on subsequent pathogen-related studies. PMID:25054409

Sheikh, Arsheed Hussain; Raghuram, Badmi; Eschen-Lippold, Lennart; Scheel, Dierk; Lee, Justin; Sinha, Alok Krishna

2014-11-01

165

Isolation, identification and computational studies on Pseudomonas aeruginosa sp. strain MPC1 in tannery effluent.  

PubMed

A study about isolation, identification and analysis of bacteria in waste water. Here the tannery effluent used as a sample for the entire analysis. A bacterial strain, designated MPC1 was isolated from a waste water sample collected from tannery effluent, Trichy, India and identified using a molecular approach. On the basis of the bacterial 16s rRNA gene sequence phylogeny and comparison of this gene sequence with sequence in RNA sequence database, it is considered that isolate is closely related to members of the Pseudomonas aeruginosa Sp. Phylogenetic and molecular evolutionary analyses were conducted using MEGA. Identification of regulatory elements and Transcription Factor with their binding sites in 16S rRNA gene of Pseudomonas aeruginosa mpc1 was performed using BPROM tool. The sequence of 16s rRNA (Pseudomonas aeruginosa sp MPC 1) is submitted to Genbank in NCBI database (Ac.No-JF708077). PMID:21738311

Senthil, Renganathan; Angel, Kanagamani Jini; Malathi, Ravi; Venkatesan, Dhanapal

2011-01-01

166

Expression, purification and substrate specificities of 3-nitrotoluene dioxygenase from Diaphorobacter sp. strain DS2.  

PubMed

3-Nitotoluene dioxygenase (3-NTDO) is the first enzyme in the degradation pathway of 3-nitrotoluene (3-NT) by Diaphorobacter sp. strain DS2. The complete gene sequences of 3-NTDO were PCR amplified from genomic DNA of Diaphorobacter sp., cloned, sequenced and expressed. The 3-NTDO gene revealed a multi component structure having a reductase, a ferredoxin and two oxygenase subunits. Clones expressing the different subunits were constructed in pET21a expression vector system and overexpressed in E. coli BL21(DE3) host. Each subunit was individually purified separately to homogeneity. The active recombinant enzyme was reconstituted in vitro by mixing all three purified subunits. The reconstituted recombinant enzyme could catalyse biotransformations on a variety of organic aromatics. PMID:24491551

Singh, Deepak; Kumari, Archana; Ramaswamy, S; Ramanathan, Gurunath

2014-02-28

167

Short Chain N-acyl Homoserine Lactone Production by Soil Isolate Burkholderia sp. Strain A9  

PubMed Central

In the bacteria kingdom, quorum sensing (QS) is a cell-to-cell communication that relies on the production of and response to specific signaling molecules. In proteobacteria, N-acylhomoserine lactones (AHLs) are the well-studied signaling molecules. The present study aimed to characterize the production of AHL of a bacterial strain A9 isolated from a Malaysian tropical soil. Strain A9 was identified as Burkholderia sp. using matrix-assisted laser desorption ionization-time-of-flight mass spectrometry and 16S rDNA nucleotide sequence analysis. AHL production by A9 was detected with two biosensors, namely Chromobacterium violaceum CV026 and Escherichia coli [pSB401]. Thin layer chromatography results showed N–hexanoylhomoserine lactone (C6-HSL) and N–octanoylhomoserine lactone (C8-HSL) production. Unequivocal identification of C6-HSL and C8-HSL was achieved by high resolution triple quadrupole liquid chromatography-mass spectrometry analysis. We have demonstrated that Burkholderia sp. strain A9 produces AHLs that are known to be produced by other Burkholderia spp. with CepI/CepR homologs. PMID:24084115

Chen, Jian Woon; Koh, Chong-Lek; Sam, Choon-Kook; Yin, Wai-Fong; Chan, Kok-Gan

2013-01-01

168

Minimal Streptomyces sp. strain C5 daunorubicin polyketide biosynthesis genes required for aklanonic acid biosynthesis.  

PubMed

The structure of the Streptomyces sp. strain C5 daunorubicin type II polyketide synthase (PKS) gene region is different from that of other known type II PKS gene clusters. Directly downstream of the genes encoding ketoacylsynthase alpha and beta (KS alpha, KS beta) are two genes (dpsC, dpsD) encoding proteins of unproven function, both absent from other type II PKS gene clusters. Also in contrast to other type II PKS clusters, the gene encoding the acyl carrier protein (ACP), dpsG, is located about 6.8 kbp upstream of the genes encoding the daunorubicin KS alpha and KS beta. In this work, we demonstrate that the minimal genes required to produce aklanonic acid in heterologous hosts are dpsG (ACP), dauI (regulatory activator), dpsA (KS alpha), dpsB (KS beta), dpsF (aromatase), dpsE (polyketide reductase), and dauG (putative deoxyaklanonic acid oxygenase). The two unusual open reading frames, dpsC (KASIII homolog lacking a known active site) and dpsD (acyltransferase homolog), are not required to synthesize aklanonic acid. Additionally, replacement of dpsD or dpsCD in Streptomyces sp. strain C5 with a neomycin resistance gene (aphI) results in mutant strains that still produced anthracyclines. PMID:9098068

Rajgarhia, V B; Strohl, W R

1997-04-01

169

Hexavalent Chromium Removal by a Paecilomyces sp. Fungal Strain Isolated from Environment  

PubMed Central

A resistant and capable fungal strain in removing hexavalent chromium was isolated from an environment near of Chemical Science Faculty, located in the city of San Luis Potosí, Mexico. The strain was identified as Paecilomyces sp., by macro- and microscopic characteristics. Strain resistance of the strain to high Cr (VI) concentrations and its ability to reduce chromium were studied. When it was incubated in minimal medium with glucose, another inexpensive commercial carbon source like unrefined and brown sugar or glycerol, in the presence of 50?mg/L of Cr (VI), the strain caused complete disappearance of Cr (VI), with the concomitant production of Cr (III) in the growth medium after 7 days of incubation, at 28°C, pH 4.0, 100?rpm, and an inoculum of 38?mg of dry weight. Decrease of Cr (VI) levels from industrial wastes was also induced by Paecilomyces biomass. These results indicate that reducing capacity of chromate resistant filamentous fungus Cr (VI) could be useful for the removal of Cr (VI) pollution. PMID:20634988

Cardenas-Gonzalez, Juan F.; Acosta-Rodriguez, Ismael

2010-01-01

170

Genome Sequence of the Polyphosphate-Accumulating Organism Arthrobacter sp. Strain PAO19 Isolated from Maize Rhizosphere Soil  

PubMed Central

Arthrobacter sp. strain PAO19 is a polyphosphate-accumulating organism isolated from maize rhizosphere soil. Here we report its genome sequence, which may shed light on its role in phosphate removal from water bodies. To our knowledge, this is the first genome announcement of a polyphosphate-accumulating strain of the genus Arthrobacter. PMID:23908294

Li, Xiaolong; Yang, Jinshui; Li, Baozhen

2013-01-01

171

Draft Genome Sequence of Streptomyces sp. Strain Wigar10, Isolated from a Surface-Sterilized Garlic Bulb  

PubMed Central

Streptomyces sp. strain Wigar10 was isolated from a surface-sterilized garlic bulb (Allium sativum var. Purple Stripe). Its genome encodes several novel secondary metabolite biosynthetic gene clusters and provides a genetic basis for further investigation of this strain's chemical biology and potential for interaction with its garlic host. PMID:22123757

Klassen, Jonathan L.; Adams, Sandye M.; Bramhacharya, Shanti; Giles, Steven S.; Goodwin, Lynne A.; Woyke, Tanja; Currie, Cameron R.

2011-01-01

172

Genome Sequence of Martelella sp. Strain AD-3, a Moderately Halophilic Polycyclic Aromatic Hydrocarbon-Degrading Bacterium  

PubMed Central

Martelella sp. strain AD-3, enriched from a petroleum-contaminated site with high salinity, can efficiently degrade polycyclic aromatic hydrocarbons. Here, we report the 4.75-Mb genome sequence of strain AD-3 with its genetic feature of helping to remediate environmental organic pollutants. PMID:24435873

Cui, Changzheng; Li, Pengpeng; Liu, Gao; Lin, Kuangfei; Luo, Qishi; Liu, Shanshan; Xu, Ping

2014-01-01

173

Draft genome sequence of Frankia sp. strain CN3, an atypical, noninfective (Nod-) ineffective (Fix-) isolate from Coriaria nepalensis.  

PubMed

We report here the genome sequence of Frankia sp. strain CN3, which was isolated from Coriaria nepalensis. This genome sequence is the first from the fourth lineage of Frankia, strains of which are unable to reinfect actinorhizal plants. At 10 Mb, it represents the largest Frankia genome sequenced to date. PMID:23516212

Ghodhbane-Gtari, Faten; Beauchemin, Nicholas; Bruce, David; Chain, Patrick; Chen, Amy; Walston Davenport, Karen; Deshpande, Shweta; Detter, Chris; Furnholm, Teal; Goodwin, Lynne; Gtari, Maher; Han, Cliff; Han, James; Huntemann, Marcel; Ivanova, Natalia; Kyrpides, Nikos; Land, Miriam L; Markowitz, Victor; Mavrommatis, Kostas; Nolan, Matt; Nouioui, Imen; Pagani, Ioanna; Pati, Amrita; Pitluck, Sam; Santos, Catarina L; Sen, Arnab; Sur, Saubashya; Szeto, Ernest; Tavares, Fernando; Teshima, Hazuki; Thakur, Subarna; Wall, Luis; Woyke, Tanja; Tisa, Louis S

2013-01-01

174

Draft Genome Sequence of Cupriavidus sp. Strain SK-3, a 4-Chlorobiphenyl- and 4-Clorobenzoic Acid-Degrading Bacterium  

PubMed Central

We report the draft genome sequence of Cupriavidus sp. strain SK-3, which can use 4-chlorobiphenyl and 4-clorobenzoic acid as the sole carbon source for growth. The draft genome sequence allowed the study of the polychlorinated biphenyl degradation mechanism and the recharacterization of the strain SK-3 as a Cupriavidus species. PMID:24994805

Vilo, Claudia; Benedik, Michael J.; Ilori, Matthew

2014-01-01

175

The Draft Genome Sequence of Nocardioides sp. Strain CF8 Reveals the Scope of Its Metabolic Capabilities  

PubMed Central

Nocardioides sp. strain CF8 was isolated from a soil sample collected at the Hanford Department of Energy site, Richland, WA. The strain was identified in microcosms based on its ability to grow on butane and has been characterized for its potential applications in the biodegradation of halogenated hydrocarbons. Here, the draft genome sequence is reported. PMID:23833136

Kimbrel, Jeffrey A.; Chang, Jeff; Arp, Daniel J.

2013-01-01

176

Draft Genome Sequence of the Aquatic Phosphorus-Solubilizing and -Mineralizing Bacterium Bacillus sp. Strain CPSM8  

PubMed Central

Bacillus sp. strain CPSM8 is an efficient solubilizer and mineralizer of phosphorus. Here, we present the 4.39-Mb draft genome sequence of the strain, providing insight into the phosphorus-releasing genes related to productivity in aquatic habitats. PMID:24482525

Maitra, Nilanjan; Whitman, William B.; Ayyampalayam, Saravanaraj; Samanta, Srikanta; Sarkar, Keka; Bandopadhyay, Chinmay; Aftabuddin, M.; Sharma, Anil P.

2014-01-01

177

Draft Genome Sequence of Tatumella sp. Strain UCD-D_suzukii (Phylum Proteobacteria) Isolated from Drosophila suzukii Larvae  

PubMed Central

Here we present the draft genome of Tatumella sp. strain UCD-D_suzukii, the first member of this genus to be sequenced. The genome contains 3,602,931 bp in 72 scaffolds. This strain was isolated from Drosophila suzukii larvae as part of a larger project to study the microbiota of D. suzukii. PMID:24762940

Dunitz, Madison I.; James, Pamela M.; Jospin, Guillaume; Coil, David A.; Chandler, James Angus

2014-01-01

178

Draft Genome Sequence of Tatumella sp. Strain UCD-D_suzukii (Phylum Proteobacteria) Isolated from Drosophila suzukii Larvae.  

PubMed

Here we present the draft genome of Tatumella sp. strain UCD-D_suzukii, the first member of this genus to be sequenced. The genome contains 3,602,931 bp in 72 scaffolds. This strain was isolated from Drosophila suzukii larvae as part of a larger project to study the microbiota of D. suzukii. PMID:24762940

Dunitz, Madison I; James, Pamela M; Jospin, Guillaume; Eisen, Jonathan A; Coil, David A; Chandler, James Angus

2014-01-01

179

The Draft Genome Sequence of Nocardioides sp. Strain CF8 Reveals the Scope of Its Metabolic Capabilities.  

PubMed

Nocardioides sp. strain CF8 was isolated from a soil sample collected at the Hanford Department of Energy site, Richland, WA. The strain was identified in microcosms based on its ability to grow on butane and has been characterized for its potential applications in the biodegradation of halogenated hydrocarbons. Here, the draft genome sequence is reported. PMID:23833136

Kimbrel, Jeffrey A; Chang, Jeff; Arp, Daniel J; Sayavedra-Soto, Luis A

2013-01-01

180

[Bioflocculant producing capability by two strains of Bacillus sp. in diversified carbon sources].  

PubMed

Two strains of Bacillus sp. F2 and F6 could produce bioflocculants with high flocculating effects by pure culture and mixed culture. Many kinds of carbon sources could be utilized. Organic compound which molecular weight under 200 such as saccharide, alcoholic aldehyde, ester and organic acid were favorable for producing bioflocculant. And some low-cost biomass scrap could be used as good carbon sources for industrialized production of bioflocculants, such as waste beet molasses, cellulose's fermentation residue and sewage of hydrogen producing reactor. PMID:16366489

Zhu, Yan-Bin; Ma, Fang; Ren, Nan-Qi; Huang, Jun-Li; Wang, Ai-Jie

2005-09-01

181

Novel cyclopentenone derivatives produced by a rare actinobacterial strain Actinoalloteichus nanshanensis sp. nov. NEAU 119.  

PubMed

Four novel cyclopentenone derivatives (1-4), characterising a cyclopentenone ring conjugated with a 1,8-dioxadecalin, were isolated from rare actinobacterial strain Actinoalloteichus nanshanensis sp. nov. NEAU 119. The structures of these compounds were elucidated on the basis of extensive spectroscopic analysis. Bioassays indicated that compounds 1-4 showed low cytotoxicities against human leukaemia cell line K562 and human renal carcinoma cell line ACHN. To the best of our knowledge, this is the first example of isolation of C11 cyclopentenones from actinomycetes. PMID:23432091

Wang, Xiang-Jing; Zhang, Ji; Wang, Ji-Dong; Qian, Ping-Ting; Liu, Chong-Xi; Xiang, Wen-Sheng

2013-10-01

182

Two New Antibiotic Pyridones Produced by a Marine Fungus, Trichoderma sp. Strain MF106  

PubMed Central

Two unusual pyridones, trichodin A (1) and trichodin B (2), together with the known compound, pyridoxatin (3), were extracted from mycelia and culture broth of the marine fungus, Trichoderma sp. strain MF106 isolated from the Greenland Seas. The structures of the new compounds were characterized as an intramolecular cyclization of a pyridine basic backbone with a phenyl group. The structure and relative configuration of the new compounds were established by spectroscopic means. The new compound 1 and the known compound 3 showed antibiotic activities against the clinically relevant microorganism, Staphylococcus epidermidis, with IC50 values of 24 ?M and 4 ?M, respectively. PMID:24663111

Wu, Bin; Oesker, Vanessa; Wiese, Jutta; Schmaljohann, Rolf; Imhoff, Johannes F.

2014-01-01

183

Complete genome sequence of Mycobacterium sp. strain (Spyr1) and reclassification to Mycobacterium gilvum Spyr1  

PubMed Central

Mycobacterium sp.Spyr1 is a newly isolated strain that occurs in a creosote contaminated site in Greece. It was isolated by an enrichment method using pyrene as sole carbon and energy source and is capable of degrading a wide range of PAH substrates including pyrene, fluoranthene, fluorene, anthracene and acenapthene. Here we describe the genomic features of this organism, together with the complete sequence and annotation. The genome consists of a 5,547,747 bp chromosome and two plasmids, a larger and a smaller one with sizes of 211,864 and 23,681 bp, respectively. In total, 5,588 genes were predicted and annotated. PMID:22180818

Kallimanis, Aristeidis; Karabika, Eugenia; Mavromatis, Kostantinos; Lapidus, Alla; LaButti, Kurt M.; Liolios, Konstantinos; Ivanova, Natalia; Goodwin, Lynne; Woyke, Tanja; Velentzas, Athanasios D.; Perisynakis, Angelos; Ouzounis, Christos C.; Kyrpides, Nikos C.; Koukkou, Anna I.; Drainas, Constantin

2011-01-01

184

Characterization of Transcriptional Regulatory Genes for Biphenyl Degradation in Rhodococcus sp. Strain RHA1  

Microsoft Academic Search

Transcription of the bphA1A2A3A4C1B genes, which are responsible for the conversion of biphenyl and polychlorinated biphenyl to the meta-cleavage products in Rhodococcus sp. strain RHA1, was examined. The bphA1 promoter (PbphA1) was identified and was shown to promote transcription induction by biphenyl and ethylbenzene. An 8.8-kb HindIII fragment that promotes transcription induction of PbphA1 in Rhodococcus erythropolis IAM1399 was isolated

Hisashi Takeda; Akihiro Yamada; Keisuke Miyauchi; Eiji Masai; Masao Fukuda

2004-01-01

185

Physiological Adaptations Involved in Alkane Assimilation at a Low Temperature by Rhodococcus sp. Strain Q15†  

PubMed Central

We examined physiological adaptations which allow the psychrotroph Rhodococcus sp. strain Q15 to assimilate alkanes at a low temperature (alkanes are contaminants which are generally insoluble and/or solid at low temperatures). During growth at 5°C on hexadecane or diesel fuel, strain Q15 produced a cell surface-associated biosurfactant(s) and, compared to glucose-acetate-grown cells, exhibited increased cell surface hydrophobicity. A transmission electron microscopy examination of strain Q15 grown at 5°C revealed the presence of intracellular electron-transparent inclusions and flocs of cells connected by an extracellular polymeric substance (EPS) when cells were grown on a hydrocarbon and morphological differences between the EPS of glucose-acetate-grown and diesel fuel-grown cells. A lectin binding analysis performed by using confocal scanning laser microscopy (CSLM) showed that the EPS contained a complex mixture of glycoconjugates, depending on both the growth temperature and the carbon source. Two glycoconjugates [?-d-Gal-(1-3)-d-GlcNAc and ?-l-fucose] were detected only on the surfaces of cells grown on diesel fuel at 5°C. Using scanning electron microscopy, we observed strain Q15 cells on the surfaces of octacosane crystals, and using CSLM, we observed strain Q15 cells covering the surfaces of diesel fuel microdroplets; these findings indicate that this organism assimilates both solid and liquid alkane substrates at a low temperature by adhering to the alkane phase. Membrane fatty acid analysis demonstrated that strain Q15 adapted to growth at a low temperature by decreasing the degree of saturation of membrane lipid fatty acids, but it did so to a lesser extent when it was grown on hydrocarbons at 5°C; these findings suggest that strain Q15 modulates membrane fluidity in response to the counteracting influences of low temperature and hydrocarbon toxicity. PMID:10388690

Whyte, L. G.; Slagman, S. J.; Pietrantonio, F.; Bourbonnière, L.; Koval, S. F.; Lawrence, J. R.; Inniss, W. E.; Greer, C. W.

1999-01-01

186

Effect of pesticides on plant growth promoting traits of greengram-symbiont, Bradyrhizobium sp. strain MRM6.  

PubMed

The aim of this study was to investigate the toxicity of herbicides (metribuzin and glyphosate), insecticides (imidacloprid and thiamethoxam) and fungicides (hexaconazole, metalaxyl and kitazin) at the recommended and the higher dose rates on plant growth promoting activities of Bradyrhizobium sp. under in vitro conditions. The Bradyrhizobium sp. strain MRM6 was isolated from nodules of greengram plants. Pesticide-concentration dependent progressive-decline was observed in plant growth promoting traits of the strain MRM6 apart from exo-polysaccharides which increased consistently on increasing pesticide concentrations. Generally, the highest toxicity to plant growth promoting characteristics of the Bradyrhizobium sp. strain MRM6 was observed when the strain MRM6 was grown with three times the recommended field rates of glyphosate, imidacloprid and hexaconazole. PMID:21359648

Ahemad, Munees; Khan, Mohammad Saghir

2011-04-01

187

Role of heterotrophic bacteria in complete mineralization of trichloroethylene by Methylocystis sp. strain M.  

PubMed Central

Biodegradation experiments with radioactively labeled trichloroethylene showed that 32% of the radioactive carbon was converted to glyoxylic acid, dichloroacetic acid and trichloroacetic acid and that the same percentage was converted to CO2 and CO after 140 h of incubation by a pure culture of a type II methane-utilizing bacterium, Methylocystis sp. strain M, isolated from a mixed culture, MU-81, in our laboratory. In contrast, these water-soluble (14C)trichloroethylene degradation products were completely or partially degraded further and converted to CO2 by the MU-81 mixed culture. This phenomenon was attributed to the presence of a heterotrophic bacterium (strain DA4), which was identified as Xanthobacter autotrophicus, in the MU-81 culture. The results indicate that the heterotrophic bacteria play an important role in complete trichloroethylene degradation by methanotrophs. PMID:1444420

Uchiyama, H; Nakajima, T; Yagi, O; Nakahara, T

1992-01-01

188

Global proteomic analysis of the chromate response in Arthrobacter sp. strain FB24.  

PubMed

A global proteomic evaluation of the response of Arthrobacter sp. strain FB24 to 5 and 20 mM Cr(VI) was conducted using both two-dimensional gel electrophoresis (2-DGE) and liquid chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS). The changes in protein expression found with 2-DGE indicate alterations in central metabolism and amino acid synthesis. Proteome coverage increased from 22% with 2-DGE to 71% with LC/LC-MS/MS. The proteins exhibiting the highest levels of expression under Cr(VI) stress suggest intracellular sulfur limitation, which could be driven by competition for the sulfate (SO4(2-)) transporter by the chromate (CrO4(2-)) ion. These results are consistent with the growth defects seen with strain FB24 when Cr(VI) concentrations exceeded 5 mM. PMID:19231868

Henne, Kristene L; Turse, Joshua E; Nicora, Carrie D; Lipton, Mary S; Tollaksen, Sandra L; Lindberg, Carl; Babnigg, Gyorgy; Giometti, Carol S; Nakatsu, Cindy H; Thompson, Dorothea K; Konopka, Allan E

2009-04-01

189

Global Proteomic Analysis of the Chromate Response in Arthrobacter sp strain FB24  

SciTech Connect

A global proteomic evaluation of the response of Arthrobacter sp. strain FB24 to 5 mM and 20 mM Cr(VI) was conducted using both two-dimensional gel electrophoresis (2-DGE) and liquid chromatography coupled to tandem mass spectrometry (LC/LC-MS/MS). The changes in protein expression found with 2-DGE indicate alterations in central metabolism and amino acid synthesis. Proteome coverage increased from 22% with 2-DGE to 71% with LC/LC-MS/MS. The proteins exhibiting the highest levels of expression under Cr(VI) stress suggest intracellular sulfur limitation, which could be driven by competition for the sulfate (SO42-) transporter by the chromate (CrO42-) ion. These results are consistent with the growth defects seen with strain FB24 when Cr(VI) concentrations exceed 5 mM.

Henne, Kristene L.; Turse, Joshua E.; Nicora, Carrie D.; Lipton, Mary S.; Tollaksen, Sandra L.; Lindberg, Carl; Babbnig, Gyorgy; Giometti, Carol S.; Nakatsu, Cindy N.; Thompson, Dorothea K.; Konopka, Allan

2009-04-01

190

Global proteomic analysis of the chromate response in Arthrobacter sp strain FB24.  

SciTech Connect

A global proteomic evaluation of the response of Arthrobacter sp. strain FB24 to 5 and 20 mM Cr(VI) was conducted using both two-dimensional gel electrophoresis (2-DGE) and liquid chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS). The changes in protein expression found with 2-DGE indicate alterations in central metabolism and amino acid synthesis. Proteome coverage increased from 22% with 2-DGE to 71% with LC/LC-MS/MS. The proteins exhibiting the highest levels of expression under Cr(VI) stress suggest intracellular sulfur limitation, which could be driven by competition for the sulfate (SO{sub 4}{sup 2-}) transporter by the chromate (CrO{sub 4}{sup 2-}) ion. These results are consistent with the growth defects seen with strain FB24 when Cr(VI) concentrations exceeded 5 mM.

Henne, K. L.; Turse, J. E.; Nicora, C. D.; Lipton, M. S.; Tollaksen, S. L.; Lindberg, C.; Babnigg, G.; Giometti, C. S.; Nakatsu, C. H.; Thompson, D. K.; Konopka, A. E.; Biosciences Division; Purdue Univ.; PNNL

2009-04-01

191

The Biosynthetic Pathway for Myxol-2? Fucoside (Myxoxanthophyll) in the Cyanobacterium Synechococcus sp. Strain PCC 7002? †  

PubMed Central

Synechococcus sp. strain PCC 7002 produces a variety of carotenoids, which comprise predominantly dicylic ?-carotene and two dicyclic xanthophylls, zeaxanthin and synechoxanthin. However, this cyanobacterium also produces a monocyclic myxoxanthophyll, which was identified as myxol-2? fucoside. Compared to the carotenoid glycosides produced by diverse microorganisms, cyanobacterial myxoxanthophyll and closely related compounds are unusual because they are glycosylated on the 2?-OH rather than on the 1?-OH position of the ? end of the molecule. In this study, the genes encoding two enzymes that modify the ? end of myxoxanthophyll in Synechococcus sp. strain PCC 7002 were identified. Mutational and biochemical studies showed that open reading frame SynPCC7002_A2032, renamed cruF, encodes a 1?-hydroxylase and that open reading frame SynPCC7002_A2031, renamed cruG, encodes a 2?-O-glycosyltransferase. The enzymatic activity of CruF was verified by chemical characterization of the carotenoid products synthesized when cruF was expressed in a lycopene-producing strain of Escherichia coli. Database searches showed that homologs of cruF and cruG occur in the genomes of all sequenced cyanobacterial strains that are known to produce myxol or the acylic xanthophyll oscillaxanthin. The genomes of many other bacteria that produce hydroxylated carotenoids but do not contain crtC homologs also contain cruF orthologs. Based upon observable intermediates, a complete biosynthetic pathway for myxoxanthophyll is proposed. This study expands the suite of enzymes available for metabolic engineering of carotenoid biosynthetic pathways for biotechnological applications. PMID:19304845

Graham, Joel E.; Bryant, Donald A.

2009-01-01

192

Isolation of Pseudomonas sp. strain HB01 which degrades the persistent brominated flame retardant gamma-hexabromocyclododecane.  

PubMed

In this study, we isolated Pseudomonas sp. strain HB01 from a soil sample contaminated with brominated pollutants, and found that it degraded gamma-hexabromocyclododecane (gamma-HBCD). The strain degraded 81% of 1 mM gamma-HBCD within 5 d of culture. Furthermore, it demonstrated biodegradation of structurally related (bromo) alkanes. To the best of our knowledge, this is the first report that outlines the isolation of a bacterial strain that degrades gamma-HBCD. PMID:19584526

Yamada, Takashi; Takahama, Yuhki; Yamada, Yasuhiro

2009-07-01

193

Aerobic and anaerobic toluene degradation by a newly isolated denitrifying bacterium, Thauera sp. strain DNT-1.  

PubMed

A newly isolated denitrifying bacterium, Thauera sp. strain DNT-1, grew on toluene as the sole carbon and energy source under both aerobic and anaerobic conditions. When this strain was cultivated under oxygen-limiting conditions with nitrate, first toluene was degraded as oxygen was consumed, while later toluene was degraded as nitrate was reduced. Biochemical observations indicated that initial degradation of toluene occurred through a dioxygenase-mediated pathway and the benzylsuccinate pathway under aerobic and denitrifying conditions, respectively. Homologous genes for toluene dioxygenase (tod) and benzylsuccinate synthase (bss), which are the key enzymes in aerobic and anaerobic toluene degradation, respectively, were cloned from genomic DNA of strain DNT-1. The results of Northern blot analyses and real-time quantitative reverse transcriptase PCR suggested that transcription of both sets of genes was induced by toluene. In addition, the tod genes were induced under aerobic conditions, whereas the bss genes were induced under both aerobic and anaerobic conditions. On the basis of these results, it is concluded that strain DNT-1 modulates the expression of two different initial pathways of toluene degradation according to the availability of oxygen in the environment. PMID:15006757

Shinoda, Yoshifumi; Sakai, Yasuyoshi; Uenishi, Hiroshi; Uchihashi, Yasumitsu; Hiraishi, Akira; Yukawa, Hideaki; Yurimoto, Hiroya; Kato, Nobuo

2004-03-01

194

Metabolism of dibenzofuran by pseudomonas sp. strain HH69 and the mixed culture HH27  

SciTech Connect

A Pseudomonas sp. strain, HH69, and a mixed culture, designated HH27, were isolated by selective enrichment from soil samples. The pure strain and the mixed culture grew aerobically on dibenzofuran as the sole source of carbon and energy. Degradation proceeded via salicylic acid which was branched into the gentisic acid and the catechol pathway. Both salicylic acid and gentisic acid accumulated in the culture medium of strain HH69. The acids were slowly metabolized after growth ceased. The enzymes responsible for their metabolism showed relatively low activities. Besides the above-mentioned acids, 2-hydroxyacetophenone, benzopyran-4-one (chrome), several 2-substituted chroman-4-ones, and traces of the four isomeric monohydroxydibenzofurans were identified in the culture medium. 2,2{prime},3-Trihydroxybiphenyl was isolated from the medium of a dibenzofuran-converting mutant derived from parent strain HH69, which can no longer grow on dibenzofuran. This gives evidence for a novel type of dioxygenases responsible for the attack on the biarylether structure of the dibenzofuran molecule. A meta-fission mechanism for cleavage of the dihydroxylated aromatic nucleus of 2,2{prime},3-trihydroxybiphenyl is suggested as the next enzymatic step in the degradative pathway.

Fortnagel, P.; Harms, H.; Wittich, R.M. (Institut fuer Allgemeine Botanik, Ohnhorststrasse (Germany, F.R.)); Krohn, S.; Meyer, H.; Sinnwell, V.; Wilkes, H.; Francke, W. (Universitaet Hamburg (Germany, F.R.))

1990-04-01

195

Composition of the carbohydrate granules of the cyanobacterium, Cyanothece sp. strain ATCC 51142  

NASA Technical Reports Server (NTRS)

Cyanothece sp. strain ATCC 51142 is an aerobic, unicellular, diazotrophic cyanobacterium that temporally separates O2-sensitive N2 fixation from oxygenic photosynthesis. The energy and reducing power needed for N2 fixation appears to be generated by an active respiratory apparatus that utilizes the contents of large interthylakoidal carbohydrate granules. We report here on the carbohydrate and protein composition of the granules of Cyanothece sp. strain ATCC 51142. The carbohydrate component is a glucose homopolymer with branches every nine residues and is chemically identical to glycogen. Granule-associated protein fractions showed temporal changes in the number of proteins and their abundance during the metabolic oscillations observed under diazotrophic conditions. There also were temporal changes in the protein pattern of the granule-depleted supernatant fractions from diazotrophic cultures. None of the granule-associated proteins crossreacted with antisera directed against several glycogen-metabolizing enzymes or nitrogenase, although these proteins were tentatively identified in supernatant fractions. It is suggested that the granule-associated proteins are structural proteins required to maintain a complex granule architecture.

Schneegurt, M. A.; Sherman, D. M.; Sherman, L. A.; Mitchell, C. A. (Principal Investigator)

1997-01-01

196

17-Hydroxysteroid dehydrogenases of Mycobacterium sp. VKM Ac-1815D mutant strain.  

PubMed

Whole cells and crude extract of Mycobacterium sp. VKM Ac-1815D mutant strain Et1 were shown to carry out 17beta-reduction, 17beta-dehydrogenation and 1(2)-reduction of 3-keto-C(19)-steroids. Two 17-hydroxy steroid dehydrogenases (17-OH SDH) were partially purified from the strain by ammonium sulfate fractionation, ion-exchange chromatography on DEAE-sephacel and gel-filtration on Bio-Gel A. The enzymes differed in chromatographic properties and specific activities. One enzyme--17-OH SDH (2) (tetramer, M(r) approximately 210,000) was found to be responsible for bi-directional reduction-oxidation of steroids at C 17, whereas the other one--17-OH SDH (1) (monomer, M(r) approximately 68,000) specifically catalysed 17beta-dehydrogenation of 17-hydroxysteroids (testosterone and 1(2)-dehydro testosterone). The 17beta-reduction of 1-ene-17-ketosteroids was accompanied by 1(2)-reduction. A role of 1-ene-reductase as a steroid-binding protein associated with 17-OH SDH (2) in Mycobacterium sp. is discussed. PMID:12163139

Egorova, O V; Nikolayeva, V M; Donova, M V

2002-07-01

197

Phenotypic characterization of 10 methanol oxidation mutant classes in Methylobacterium sp. strain AM1.  

PubMed Central

Twenty-five methanol oxidation mutants of the facultative methylotroph Methylobacterium sp. strain AM1 have been characterized by complementation analysis and assigned to 10 complementation groups, Mox A1, A2, A3, and B through H (D. N. Nunn and M. E. Lidstrom, J. Bacteriol. 166:582-591, 1986). In this study we have characterized each of the mutants belonging to the 10 Mox complementation groups for the following criteria: phenazine methosulfate-dichlorophenolindophenol dye-linked methanol dehydrogenase activity; methanol-dependent whole-cell oxygen consumption; the presence or absence of methanol dehydrogenase protein by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and Western blotting; the absorption spectra of purified mutant methanol dehydrogenase proteins; and the presence or absence of the soluble cytochrome c proteins of Methylobacterium sp. strain AM1, as determined by reduced-oxidized difference spectra and sodium dodecyl sulfate-polyacrylamide gel electrophoresis. With this information, we have proposed functions for each of the genes deficient in the mutants of the 10 Mox complementation groups. These proposed gene functions include two linked genes that encode the methanol dehydrogenase structural protein and the soluble cytochrome cL, a gene encoding a secretion function essential for the synthesis and export of methanol dehydrogenase and cytochrome cL, three gene functions responsible for the proper association of the pyrrolo-quinoline quinone prosthetic group with the methanol dehydrogenase apoprotein, and four positive regulatory gene functions controlling the expression of the ability to oxidize methanol. Images PMID:3009412

Nunn, D N; Lidstrom, M E

1986-01-01

198

Host range susceptibility of Enterococcus sp. strains isolated from diseased turbot: possible routes of infection.  

PubMed Central

Experiments were conducted to assess the pathogenicity of Enterococcus sp. strains isolated from diseased turbot for several fish species (turbot, salmon, trout, and seabream), as well as for mice. The intraperitoneal injection assays indicated that the tested strains showed host specificity for turbot, with a high degree of virulence (50% lethal dose of 10(4) cells per g of fish). The Spanish Enterococcus sp. isolates were nonpathogenic for the other fish species studied and for mice. The possible routes of infection were determined by bath exposure (with and without prior abrasion of the skin) and by intragastric inoculations with food and feces contaminated with the pathogen. The bath challenges indicated that the Enterococcus isolates were able to overcome the defense mechanisms present on the surface of the turbot only if the skin was abraded prior to the exposure. The antibacterial activities of components of a glycoprotein nature present in the turbot skin mucus are probably responsible in part for the resistance in noninjured fish to infection. On the other hand, we demonstrated the capacity of this pathogen to overcome adverse conditions in the stomachs of fish when associated with food or fecal material, since it is able to establish an infective state and to produce mortalities after 16 to 20 days postingestion. From all of these findings, we can conclude that horizontal transmissions through water and the fecal-oral route are the main avenues of infection of turbot streptococcosis. PMID:8593061

Romalde, J L; Magarinos, B; Nunez, S; Barja, J L; Toranzo, A E

1996-01-01

199

Rapid aggregation of biofuel-producing algae by the bacterium Bacillus sp. strain RP1137.  

PubMed

Algal biofuels represent one of the most promising means of sustainably replacing liquid fuels. However, significant challenges remain before alga-based fuels become competitive with fossil fuels. One of the largest challenges is the ability to harvest the algae in an economical and low-energy manner. In this article, we describe the isolation of a bacterial strain, Bacillus sp. strain RP1137, which can rapidly aggregate several algae that are candidates for biofuel production, including a Nannochloropsis sp. This bacterium aggregates algae in a pH-dependent and reversible manner and retains its aggregation ability after paraformaldehyde fixation, opening the possibility for reuse of the cells. The optimal ratio of bacteria to algae is described, as is the robustness of aggregation at different salinities and temperatures. Aggregation is dependent on the presence of calcium or magnesium ions. The efficiency of aggregation of Nannochloropsis oceanica IMET1 is between 70 and 95% and is comparable to that obtained by other means of harvest; however, the rate of harvest is fast, with aggregates forming in 30 s. PMID:23892750

Powell, Ryan J; Hill, Russell T

2013-10-01

200

Phenotypic characterization of 10 methanol oxidation mutant classes in Methylobacterium sp. strain AM1  

SciTech Connect

Twenty-five methanol oxidation mutants of the facultative methylotroph Methylobacterium sp. strain AM1 have been characterized by complementation analysis and assigned to 10 complementation groups, Mox A1, A2, A3, and B through H. In this study we have characterized each of the mutants belonging to the 10 Mox complementation groups for the following criteria: (i) phenazine methosulfate-dichlorophenolindophenol dye-linked methanol dehydrogenase activity; (ii) methanol-dependent whole-cell oxygen consumption; (iii) the presence or absence of methanol dehydrogenase protein by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and Western blotting; (iv) the absorption spectra of purified mutant methanol dehydrogenase proteins; and (v) the presence or absence of the soluble cytochrome c proteins of Methylobacterium sp. strain AM1, as determined by reduced-oxidized difference spectra and sodium dodecyl sulfate-polyacrylamide gel electrophoresis. With this information, we have proposed functions for each of the genes deficient in the mutants of the 10 Mox complementation groups. These proposed gene functions include two linked genes that encode the methanol dehydrogenase structural protein and the soluble cytochrome c/sub L/, a gene encoding a secretion function essential for the synthesis and export of methanol dehydrogenase and cytochrome c/sub L/, three gene functions responsible for the proper association of the pyrrolo-quinoline quinone prosthetic group with the methanol dehydrogenase apoprotein, and four positive regulatory gene functions controlling the expression of the ability to oxidize methanol.

Nunn, D.N.; Lidstrom, M.E.

1986-05-01

201

Growth of Acinetobacter sp. strain HO1-N on n-hexadecanol: physiological and ultrastructural characteristics.  

PubMed Central

The growth of Acinetobacter sp. strain HO1-N on hexadecanol results in the formation of intracytoplasmic membranes and intracellular rectangular inclusions containing one of the end products of hexadecanol metabolism, hexadecyl palmitate. The intracellular inclusions were purified and characterized as "wax ester inclusions" consisting of 85.6% hexadecyl palmitate, 4.8% hexadecanol, and 9.6% phospholipid, with a phospholipid-to-protein ratio of 0.42 mumol of lipid phosphate per mg of inclusion protein. The cellular lipids consisted of 69.8% hexadecyl palmitate, 22.8% phospholipid, 1.9% triglyceride, 4.7% mono- and diglyceride, 0.1% free fatty acid, and 0.8% hexadecanol, as compared with 98% hexadecyl palmitate and 1.9% triglyceride, which comprised the extracellular lipids. Cell-associated hexadecanol represented 0.05% of the exogenously supplied hexadecanol, with hexadecyl palmitate accounting for 14.7% of the total cellular dry weight. Acinetobacter sp. strain HO1-N possesses a mechanism for the intracellular packaging of hexadecyl palmitate in wax ester inclusions, which differ in structure and chemical composition from "hydrocarbon inclusions" isolated from hexadecane-grown cells. Images PMID:2984172

Singer, M E; Tyler, S M; Finnerty, W R

1985-01-01

202

Plasmid Localization and Organization of Melamine Degradation Genes in Rhodococcus sp. Strain Mel  

PubMed Central

Rhodococcus sp. strain Mel was isolated from soil by enrichment and grew in minimal medium with melamine as the sole N source with a doubling time of 3.5 h. Stoichiometry studies showed that all six nitrogen atoms of melamine were assimilated. The genome was sequenced by Roche 454 pyrosequencing to 13× coverage, and a 22.3-kb DNA region was found to contain a homolog to the melamine deaminase gene trzA. Mutagenesis studies showed that the cyanuric acid hydrolase and biuret hydrolase genes were clustered together on a different 17.9-kb contig. Curing and gene transfer studies indicated that 4 of 6 genes required for the complete degradation of melamine were located on an ?265-kb self-transmissible linear plasmid (pMel2), but this plasmid was not required for ammeline deamination. The Rhodococcus sp. strain Mel melamine metabolic pathway genes were located in at least three noncontiguous regions of the genome, and the plasmid-borne genes encoding enzymes for melamine metabolism were likely recently acquired. PMID:22210223

Dodge, Anthony G.; Wackett, Lawrence P.

2012-01-01

203

Glycogen production for biofuels by the euryhaline cyanobacteria Synechococcus sp. strain PCC 7002 from an oceanic environment  

PubMed Central

Background Oxygenic photosynthetic microorganisms such as cyanobacteria and microalgae have attracted attention as an alternative carbon source for the next generation of biofuels. Glycogen abundantly accumulated in cyanobacteria is a promising feedstock which can be converted to ethanol through saccharification and fermentation processes. In addition, the utilization of marine cyanobacteria as a glycogen producer can eliminate the need for a freshwater supply. Synechococcus sp. strain PCC 7002 is a fast-growing marine coastal euryhaline cyanobacteria, however, the glycogen yield has not yet been determined. In the present study, the effects of light intensity, CO2 concentration, and salinity on the cell growth and glycogen content were investigated in order to maximize glycogen production in Synechococcus sp. strain PCC 7002. Results The optimal culture conditions for glycogen production in Synechococcus sp. strain PCC 7002 were investigated. The maximum glycogen production of 3.5 g L?1 for 7 days (a glycogen productivity of 0.5 g L?1 d?1) was obtained under a high light intensity, a high CO2 level, and a nitrogen-depleted condition in brackish water. The glycogen production performance in Synechococcus sp. strain PCC 7002 was the best ever reported in the ?-polyglucan (glycogen or starch) production of cyanobacteria and microalgae. In addition, the robustness of glycogen production in Synechococcus sp. strain PCC 7002 to salinity was evaluated in seawater and freshwater. The peak of glycogen production of Synechococcus sp. strain PCC 7002 in seawater and freshwater were 3.0 and 1.8 g L?1 in 7 days, respectively. Glycogen production in Synechococcus sp. strain PCC 7002 maintained the same level in seawater and half of the level in freshwater compared with the optimal result obtained in brackish water. Conclusions We conclude that Synechococcus sp. strain PCC 7002 has high glycogen production activity and glycogen can be provided from coastal water accompanied by a fluctuation of salinity. This work supports Synechococcus sp. strain PCC 7002 as a promising carbohydrate source for biofuel production. PMID:24959200

2014-01-01

204

High-Level Chromate Resistance in Arthrobacter sp. strain FB24 Requires Previously Uncharacterized Accessory Genes  

SciTech Connect

The annotated genome sequence of Arthrobacter sp. strain FB24 revealed a chromate resistance determinant (CRD): a cluster of 8 genes located on a 10.6 kb fragment of a 96 kb plasmid. The CRD includes chrA, which encodes a putative chromate efflux protein, and three genes with amino acid similarities to the amino and carboxy termini of ChrB, a putative regulatory protein. There are also three novel genes that have not been previously associated with chromate resistance in other bacteria; they encode an oxidoreductase (most similar to malate:quinone oxidoreductase), a functionally unknown protein with a WD40 repeat domain and a lipoprotein. A chromate-sensitive mutant (strain D11) was generated by curing FB24 of its 96-kb plasmid. Elemental analysis indicated that chromate-exposed cells of strain D11 accumulated three times more chromium than strain FB24. Introduction of the CRD into strain D11 conferred chromate resistance comparable to wild-type levels, whereas deletion of specific regions of the CRD led to decreased resistance. Using real-time reverse transcriptase PCR, we show that expression of each gene within the CRD is specifically induced in response to chromate but not by lead, hydrogen peroxide or arsenate. Higher levels of chrA expression were achieved when the chrB orthologs and the WD40 repeat domain genes were present, suggesting their regulatory roles. Collectively, our findings indicate that chromate resistance in strain FB24 is primarily achieved by plasmid-mediated chromate efflux with the contribution of previously unrecognized accessory genes.

Henne, Kristene L.; Nakatsu, Cindy N.; Thompson, Dorothea K.; Konopka, Allan

2009-09-24

205

Multiple pathways for toluene degradation in Burkholderia sp. strain JS150.  

PubMed Central

Burkholderia (Pseudomonas) sp. strain JS150 uses multiple pathways for the metabolism of catechols that result from degradation of aromatic compounds. This suggests that the strain also uses multiple upstream pathways for the initial hydroxylation of aromatic substrates. Two distinct DNA fragments that allowed Pseudomonas aeruginosa PAO1c to grow with benzene as a sole carbon source were cloned from strain JS150. One of the recombinant plasmids containing the initial steps for the degradative pathway contained a 14-kb DNA insert and was designated pRO2016. We have previously shown that the DNA insert originated from a plasmid carried by strain JS150 and contained genes encoding a multicomponent toluene-2-monooxygenase (tbmABCDEF) as well as the cognate regulatory protein (tbmR) that controls expression of the 2-monooxygenase (G. R. Johnson and R. H. Olsen, Appl. Environ. Microbiol. 61:3336-3346, 1995). Subsequently, we have identified an additional region on this DNA fragment that encodes toluene-4-monooxygenase activity. The toluene-4-monooxygenase activity was also regulated by the tbmR gene product. A second DNA fragment that allowed P. aeruginosa to grow with benzene was obtained as a 20-kb insert on a recombinant plasmid designated pRO2015. The DNA insert contained genes encoding toluene-4-monooxygenase activity but no toluene-2-monooxygenase activity. The pRO2015 insert originated from the chromosome of strain JS150, unlike the region cloned in pRO2016. Southern blots and restriction map comparisons showed that the genes for the individual 4-monooxygenases were distinct from one another. Thus, strain JS150 has been shown to have at least three toluene/benzene monooxygenases to initiate toluene metabolism in addition to the toluene dioxygenase reported previously by others. PMID:9327568

Johnson, G R; Olsen, R H

1997-01-01

206

Reduction of Mo(VI) by the bacterium Serratia sp. strain DRY5.  

PubMed

The need to isolate efficient heavy metal reducers for cost effective bioremediation strategy have resulted in the isolation of a potent molybdenum-reducing bacterium. The isolate was tentatively identified as Serratia sp. strain DRY5 based on the Biolog GN carbon utilization profiles and partial 16S rDNA molecular phylogeny. Strain DRY5 produced 2.3 times the amount of Mo-blue than S. marcescens strain Dr.Y6, 23 times more than E. coli K12 and 7 times more than E. cloacae strain 48. Strain DRY5 required 37 degrees C and pH 7.0 for optimum molybdenum reduction. Carbon sources such as sucrose, maltose, glucose and glycerol, supported cellular growth and molybdate reduction after 24 hr of static incubation. The most optimum carbon source that supported reduction was sucrose at 1.0% (w/v). Ammonium sulphate, ammonium chloride, glutamic acid, cysteine, and valine supported growth and molybdate reduction with ammonium sulphate as the optimum nitrogen source at 0. 2% (w/v). Molybdate reduction was optimally supported by 30 mM molybdate. The optimum concentration of phosphate for molybdate reduction was 5 mM when molybdate concentration was fixed at 30 mM and molybdate reduction was totally inhibited at 100 mM phosphate. Mo-blue produced by this strain shows a unique characteristic absorption profile with a maximum peak at 865 nm and a shoulder at 700 nm, Dialysis tubing experiment showed that 95.42% of Mo-blue was found in the dialysis tubing suggesting that the molybdate reduction seen in this bacterium was catalyzed by enzyme(s). The characteristics of isolate DRY5 suggest that it would be useful in the bioremediation ofmolybdenum-containing waste. PMID:20112865

Rahman, M F A; Shukor, M Y; Suhaili, Z; Mustafa, S; Shamaan, N A; Syed, M A

2009-01-01

207

Response of Nitrosospira sp. Strain AF-Like Ammonia Oxidizers to Changes in Temperature, Soil Moisture Content, and Fertilizer Concentration?  

PubMed Central

Very little is known regarding the ecology of Nitrosospira sp. strain AF-like bacteria, a unique group of ammonia oxidizers within the Betaproteobacteria. We studied the response of Nitrosospira sp. strain AF-like ammonia oxidizers to changing environmental conditions by applying molecular methods and physiological measurements to Californian grassland soil manipulated in the laboratory. This soil is naturally high in Nitrosospira sp. strain AF-like bacteria relative to the much-better-studied Nitrosospira multiformis-like ammonia-oxidizing bacteria. Increases in temperature, soil moisture, and fertilizer interacted to reduce the relative abundance of Nitrosospira sp. strain AF-like bacteria, although they remained numerically dominant. The overall abundance of ammonia-oxidizing bacteria increased with increasing soil moisture and decreased with increasing temperature. Potential nitrification activity was altered by interactions among temperature, soil moisture, and fertilizer, with activity tending to be higher when soil moisture and temperature were increased. The increase in potential nitrification activity with increased temperature was surprising, given that the overall abundance of ammonia-oxidizing bacteria decreased significantly under these conditions. This observation suggests that (i) Nitrosospira sp. strain AF-like bacteria may respond to increased temperature with an increase in activity, despite a decrease in abundance, or (ii) that potential nitrification activity in these soils may be due to organisms other than bacteria (e.g., archaeal ammonia oxidizers), at least under conditions of increased temperature. PMID:17158615

Avrahami, Sharon; Bohannan, Brendan J. M.

2007-01-01

208

Isolation and characterization of a gene cluster involved in PAH degradation in Mycobacterium sp. strain SNP11: Expression in Mycobacterium smegmatis mc 2155  

Microsoft Academic Search

Mycobacterium sp. strain SNP11 is able to grow with pyrene, fluoranthene, phenanthrene and fluorene the sole carbon and energy sources. A probe based on the previously described gene pdoA2, which encodes the ? subunit of a PAH ring-hydroxylating dioxygenase in Mycobacterium sp. strain 6PY1 [S. Krivobok et al., Identification of pyrene-induced proteins in Mycobacterium sp. strain 6PY1: evidence for two ring-hydroxylating

Christophe Pagnout; Gilles Frache; Pascal Poupin; Benoît Maunit; Jean-François Muller; Jean-François Férard

2007-01-01

209

New metabolites in the degradation of fluorene by Arthrobacter sp. strain F101.  

PubMed Central

Identification of new metabolites and demonstration of key enzyme activities support and extend the pathways previously reported for fluorene metabolism by Arthrobacter sp. strain F101. Washed-cell suspensions of strain F101 with fluorene accumulated 9-fluorenone, 4-hydroxy-9-fluorenone, 3-hydroxy-1-indanone, 1-indanone, 2-indanone, 3-(2-hydroxyphenyl) propionate, and a compound tentatively identified as a formyl indanone. Incubations with 2-indanone produced 3-isochromanone. The growth yield with fluorene as a sole source of carbon and energy corresponded to an assimilation of about 34% of fluorene carbon. About 7.4% was transformed into 9-fluorenol, 9-fluorenone, and 4-hydroxy-9-fluorenone. Crude extracts from fluorene-induced cells showed 3,4-dihydrocoumarin hydrolase and catechol 2,3-dioxygenase activities. These results and biodegradation experiments with the identified metabolites indicate that metabolism of fluorene by Arthrobacter sp. strain F101 proceeds through three independent pathways. Two productive routes are initiated by dioxygenation at positions 1,2 and 3,4, respectively. meta cleavage followed by an aldolase reaction and loss of C-1 yield the detected indanones. Subsequent biological Baeyer-Villiger reactions produce the aromatic lactones 3,4-dihydrocoumarin and 3-isochromanone. Enzymatic hydrolysis of the former gives 3-(2-hydroxyphenyl) propionate, which could be a substrate for a beta oxidation cycle, to give salicylate. Further oxidation of the latter via catechol and 2-hydroxymuconic semialdehyde connects with the central metabolism, allowing the utilization of all fluorene carbons. Identification of 4-hydroxy-9-fluorenone is consistent with an alternative pathway initiated by monooxygenation at C-9 to give 9-fluorenol and then 9-fluorenone. Although dioxygenation at 3,4 positions of the ketone apparently occurs, this reaction fails to furnish a subsequent productive oxidation of this compound. PMID:9055403

Casellas, M; Grifoll, M; Bayona, J M; Solanas, A M

1997-01-01

210

Toxicological effects of selective herbicides on plant growth promoting activities of phosphate solubilizing Klebsiella sp. strain PS19.  

PubMed

This study examines the effect of four herbicides, quizalafop-p-ethyl, clodinafop, metribuzin and glyphosate, on plant growth promoting activities like phosphate solubilization, siderophores, indole acetic acid, exo-polysaccharides, hydrogen cyanide and ammonia production by herbicide tolerant Klebsiella sp. strain PS19. The strain was isolated from mustard rhizosphere. The selected herbicides were applied two to three times at the recommended rates. Klebsiella sp. strain PS19 tolerated a concentration of 1600 ?g/ml each of quizalafop-p-ethyl and clodinafop, and 3200 and 2800 ?g/ml of metribuzin and glyphosate, respectively. The activities of Klebsiella sp. strain PS19 observed under in vitro environment were persistent in the presence of all herbicides at lower rates. The plant growth promoting activities even-though decreased regularly, but was not lost completely, as the concentration of each herbicide was increased from the recommended to three times of higher doses. Among all herbicides, quizalafop-p-ethyl, generally, showed maximum toxicity to plant growth promoting activities of Klebsiella sp. strain PS19. As an example, 40, 80 and 120 ?g/l of quizalafop-p-ethyl added to liquid culture Pikovskaya medium, decreased phosphate solubilizing activity of strain PS19 by 93, 95 and 97%, respectively over untreated control. The study revealed that the higher rates of herbicides though decreased the plant growth promoting activity but it did not completely inhibit the metabolic activities of strain PS19. The herbicide tolerance together with growth promoting activities observed under herbicide stress suggests that Klebsiella sp. strain PS19 could be used as bacterial preparation for facilitating the growth and yields of crops even in soils polluted with herbicides. PMID:20721665

Ahemad, Munees; Saghir Khan, Md

2011-02-01

211

Degradation of 1,2-Dibromoethane by Mycobacterium sp. Strain GP1  

PubMed Central

The newly isolated bacterial strain GP1 can utilize 1,2-dibromoethane as the sole carbon and energy source. On the basis of 16S rRNA gene sequence analysis, the organism was identified as a member of the subgroup which contains the fast-growing mycobacteria. The first step in 1,2-dibromoethane metabolism is catalyzed by a hydrolytic haloalkane dehalogenase. The resulting 2-bromoethanol is rapidly converted to ethylene oxide by a haloalcohol dehalogenase, in this way preventing the accumulation of 2-bromoethanol and 2-bromoacetaldehyde as toxic intermediates. Ethylene oxide can serve as a growth substrate for strain GP1, but the pathway(s) by which it is further metabolized is still unclear. Strain GP1 can also utilize 1-chloropropane, 1-bromopropane, 2-bromoethanol, and 2-chloroethanol as growth substrates. 2-Chloroethanol and 2-bromoethanol are metabolized via ethylene oxide, which for both haloalcohols is a novel way to remove the halide without going through the corresponding acetaldehyde intermediate. The haloalkane dehalogenase gene was cloned and sequenced. The dehalogenase (DhaAf) encoded by this gene is identical to the haloalkane dehalogenase (DhaA) of Rhodococcus rhodochrous NCIMB 13064, except for three amino acid substitutions and a 14-amino-acid extension at the C terminus. Alignments of the complete dehalogenase gene region of strain GP1 with DNA sequences in different databases showed that a large part of a dhaA gene region, which is also present in R. rhodochrous NCIMB 13064, was fused to a fragment of a haloalcohol dehalogenase gene that was identical to the last 42 nucleotides of the hheB gene found in Corynebacterium sp. strain N-1074. PMID:10094681

Poelarends, Gerrit J.; van Hylckama Vlieg, Johan E. T.; Marchesi, Julian R.; Freitas Dos Santos, Luisa M.; Janssen, Dick B.

1999-01-01

212

Hydrolytic potential of Trichoderma sp. strains evaluated by microplate-based screening followed by switchgrass saccharification.  

PubMed

Bioconversion of lignocellulosic biomass to fuel requires a hydrolysis step to obtain fermentable sugars, generally accomplished by fungal enzymes. Large-scale screening of different microbial strains would provide optimal enzyme cocktails for any target feedstock. The aim of this study was to screen a large collection of Trichoderma sp. strains for the hydrolytic potential towards switchgrass (Panicum virgatum L.). Strains were cultivated in a small-scale system and assayed in micro-plates for xylanase and cellulase activities. The population distributions of these traits are reported after growth on switchgrass in comparison with cellulose. The distribution profiles suggest that the growth on switchgrass strongly promotes xylanase production. The IK4 strain displayed the highest xylanase activity after growth on switchgrass (133U/mL). Enzymes (10FPU/g substrate) from IK4 were compared with those from 2 cellulolytic Trichoderma strains and a commercial enzyme in saccharification time-course experiments on untreated and pretreated switchgrass and on an artificial substrate. Samples were analysed by DNS assay and by an oxygraphic method for sugar equivalent or glucose concentration. On the untreated substrate, IK4 enzymes even outperformed a 5-fold load of commercial enzyme, suggesting that xylanase or accessory enzymes are a limiting factor on this type of recalcitrant substrate. On the other substrates, IK4 preparations showed intermediate behaviour if compared with the commercial enzyme at 10FPU/g substrate and at 5-fold load. IK4 also nearly halved the time to release 50% of the hydrolysable sugar equivalents (T(50%)), with respect to the other preparations at the same enzymatic load. DNS assay and oxygraphic method gave highly correlated results for the 3 saccharified substrates. The study suggests that accessory enzymes like xylanase play a key role in improving the performance of cellulase preparations on herbaceous lignocellulosic feedstocks like switchgrass. PMID:22500897

Cianchetta, Stefano; Galletti, Stefania; Burzi, Pier Luigi; Cerato, Claudio

2012-05-10

213

Responses to Stress and Nutrient Availability by the Marine Ultramicrobacterium Sphingomonas sp. Strain RB2256  

PubMed Central

Sphingomonas sp. strain RB2256 was isolated from Resurrection Bay in Alaska and possibly represents the dominant bacterial species in some oligotrophic marine environments. Strain RB2256 has a high-affinity nutrient uptake system when growing under nutrient-limiting conditions, and growing cells are very small (<0.08 (mu)m(sup3)). These characteristics indicate that RB2256 is highly evolved for withstanding nutrient limitations and grazing pressure by heterotrophic nanoflagellates. In this study, strain RB2256 was subjected to nutrient starvation and other stresses (high temperature, ethanol, and hydrogen peroxide). It was found that growing cells were remarkably resistant, being able to survive at a temperature of 56(deg)C, in 25 mM hydrogen peroxide, or in 20% ethanol. In addition, growing cells were generally as resistant as starved cells. The fact that vegetative cells of this strain are inherently resistant to such high levels of stress-inducing agents indicates that they possess stress resistance mechanisms which are different from those of other nondifferentiating bacteria. Only minor changes in cell volume (0.03 to 0.07 (mu)m(sup3)) and maximum specific growth rate (0.13 to 0.16 h(sup-1)) were obtained for cells growing in media with different organic carbon concentrations (0.8 to 800 mg of C per liter). Furthermore, when glucose-limited, chemostat-grown cultures or multiple-nutrient-starved batch cultures were suddenly subjected to excess glucose, maximum growth rates were reached immediately. This immediate response to nutrient upshift suggests that the protein-synthesizing machinery is constitutively regulated. In total, these results are strong evidence that strain RB2256 possesses novel physiological and molecular strategies that allow it to predominant in natural seawater. PMID:16535292

Eguchi, M.; Nishikawa, T.; MacDonald, K.; Cavicchioli, R.; Gottschal, J. C.; Kjelleberg, S.

1996-01-01

214

Biosynthesis of polyunsaturated fatty acids in the oleaginous marine diatom Fistulifera sp. strain JPCC DA0580.  

PubMed

Studies of polyunsaturated fatty acid (PUFA) biosynthesis in microalgae are of great importance for many reasons, including the production of biofuel and variable omega 3-long chain PUFAs. The elucidation of the PUFA biosynthesis pathway is necessary for bioengineering to increase or decrease PUFA content in certain microalgae. In this study, we identified the PUFA synthesis pathway in the oleaginous marine diatom, Fistulifera sp. strain JPCC DA0580, a promising candidate for biodiesel production. The data revealed not only the presence of the desaturases and elongases involved in eicosapentaenoic acid (EPA) synthesis, but also the unexpected localization of ?3-desaturase expression in the chloroplast. This suggests that this microalga might perform the final step of EPA synthesis in the chloroplast and not in the endoplasmic reticulum (ER) like other diatoms. The detailed fatty acid profile suggests that the EPA was synthesized only through the ?6-pathway in this strain, which was also different from other diatoms. Finally, the transcriptome analysis demonstrated an overall down-regulation of desaturases and elongases over incubation time. These genetic features might explain the decrease of PUFA percentage over incubation time in this strain. The important insights into metabolite synthesis acquired here will be useful for future metabolic engineering to control PUFA content in this diatom. PMID:24335525

Liang, Yue; Maeda, Yoshiaki; Sunaga, Yoshihiko; Muto, Masaki; Matsumoto, Mitsufumi; Yoshino, Tomoko; Tanaka, Tsuyoshi

2013-01-01

215

Responses to arsenate stress by Comamonas sp. strain CNB-1 at genetic and proteomic levels.  

PubMed

Comamonas sp. strain CNB-1, a chloronitrobenzene-degrading bacterium, was demonstrated to possess higher arsenate tolerance as compared with the mutant strain CNB-2. pCNB1, a plasmid harboured by CNB-1 but not CNB-2, contained the genetic cluster ars(RPBC)Com, which putatively encodes arsenate-resistance regulator, family II arsenate reductase, arsenite efflux pump and family I arsenate reductase, respectively, in Comamonas strain CNB-1. The arsC-negative Escherichia coli could gain arsenate resistance by transformation with arsPCom or arsCCom, indicating that these two genes might express functional forms of arsenate reductases. Intriguingly, when CNB-1 cells were exposed to arsenate, the transcription of arsPCom and arsCCom was measurable by RT-PCR, but only ArsPCom was detectable at protein level. To explore the proteins responding to arsenate stress, CNB-1 cells were cultured with and without arsenate and differential proteomics was carried out by two-dimensional PAGE (2-DE) and MALDI-TOF MS. A total of 31 differential 2-DE spots were defined upon image analysis and 23 proteins were identified to be responsive specifically to arsenate. Of these spots, 18 were unique proteins. These proteins were identified to be phosphate transporters, heat-shock proteins involved in protein refolding, and enzymes participating in carbon and energy metabolism. PMID:17975079

Zhang, Yun; Ma, Ying-Fei; Qi, Su-Wei; Meng, Bo; Chaudhry, Muhammad Tausif; Liu, Si-Qi; Liu, Shuang-Jiang

2007-11-01

216

Biosynthesis of Polyunsaturated Fatty Acids in the Oleaginous Marine Diatom Fistulifera sp. Strain JPCC DA0580  

PubMed Central

Studies of polyunsaturated fatty acid (PUFA) biosynthesis in microalgae are of great importance for many reasons, including the production of biofuel and variable omega 3-long chain PUFAs. The elucidation of the PUFA biosynthesis pathway is necessary for bioengineering to increase or decrease PUFA content in certain microalgae. In this study, we identified the PUFA synthesis pathway in the oleaginous marine diatom, Fistulifera sp. strain JPCC DA0580, a promising candidate for biodiesel production. The data revealed not only the presence of the desaturases and elongases involved in eicosapentaenoic acid (EPA) synthesis, but also the unexpected localization of ?3-desaturase expression in the chloroplast. This suggests that this microalga might perform the final step of EPA synthesis in the chloroplast and not in the endoplasmic reticulum (ER) like other diatoms. The detailed fatty acid profile suggests that the EPA was synthesized only through the ?6-pathway in this strain, which was also different from other diatoms. Finally, the transcriptome analysis demonstrated an overall down-regulation of desaturases and elongases over incubation time. These genetic features might explain the decrease of PUFA percentage over incubation time in this strain. The important insights into metabolite synthesis acquired here will be useful for future metabolic engineering to control PUFA content in this diatom. PMID:24335525

Liang, Yue; Maeda, Yoshiaki; Sunaga, Yoshihiko; Muto, Masaki; Matsumoto, Mitsufumi; Yoshino, Tomoko; Tanaka, Tsuyoshi

2013-01-01

217

Studies revealing bioremediation potential of the strain Burkholderia sp. GB-01 for abamectin contaminated soils.  

PubMed

Burkholderia sp. GB-01 strain was used to study different factors affecting its growth for inoculum production and then evaluated for abamectin degradation in soil for optimization under various conditions. The efficiency of abamectin degradation in soil by strain GB-01 was seen to be dependent on soil pH, temperature, initial abamectin concentration, and inoculum size along with inoculation frequency. Induction studies showed that abamectin depletion was faster when degrading cells were induced by pre-exposure to abamectin. Experiments performed with varying concentrations (2-160 mg Kg(-1)) of abamectin-spiked soils showed that strain GB-01 could effectively degrade abamectin over the range of 2-40 mg Kg(-1). The doses used were higher than the recommended dose for an agricultural application of abamectin, taking in account the over-use or spill situations. A cell density of approximately 10(8) viable cells g(-1) dry weight of soil was found to be suitable for bioremediation over a temperature range of 30-35°C and soil pH 7.5-8.5. This is the first report on bacterial degradation of abamectin in soil by a Burkholderia species, and our results indicated that this bacterium may be useful for efficient removal of abamectin from contaminated soils. PMID:22806778

Ali, Shinawar Waseem; Yu, Fang-bo; Li, Lian-tai; Li, Xiao-hui; Gu, Li-feng; Jiang, Jian-dong; Li, Shun-peng

2012-01-01

218

[Isolation, identification and characterization of a diethylstilbestrol-degrading bacterial strain Serratia sp].  

PubMed

Utilizing the diethylstilbestrol (DES)-degrading bacteria to biodegrade DES is a most reliable technique for cleanup of DES pollutants from the environment. However, little information is available heretofore on the isolation of DES-degrading bacteria and their DES removal performance in the environment. A novel bacterium capable of degrading DES was isolated from the activated sludge of a wastewater treatment plant. According to its morphology, physiochemical characteristics, and 16S rDNA sequence analysis, this strain was identified as Serratia sp.. The strain was an aerobic bacterium, and it could degrade 68.3% of DES (50 mg x L(-1)) after culturing for 7 days at 30 degrees C, 150 r x min(-1) in shaking flasks. The optimal conditions for DES biodegradation by the obtained strain were 30 degrees C, 40-60 mg x L(-1) DES, pH 7.0, 5% of inoculation volume, 0 g x L(-1) of added NaCl, and 10 mL of liquid medium volume in 100 mL flask. PMID:25338395

Xu, Ran-Fang; Sun, Min-Xia; Liu, Juan; Wang, Hong; Li, Xin; Zhu, Xue-Zhu; Ling, Wan-Ting

2014-08-01

219

Transcription of the extended hyp-operon in Nostoc sp. strain PCC 7120  

PubMed Central

Background The maturation of hydrogenases into active enzymes is a complex process and e.g. a correctly assembled active site requires the involvement of at least seven proteins, encoded by hypABCDEF and a hydrogenase specific protease, encoded either by hupW or hoxW. The N2-fixing cyanobacterium Nostoc sp. strain PCC 7120 may contain both an uptake and a bidirectional hydrogenase. The present study addresses the presence and expression of hyp-genes in Nostoc sp. strain PCC 7120. Results RT-PCRs demonstrated that the six hyp-genes together with one ORF may be transcribed as a single operon. Transcriptional start points (TSPs) were identified 280 bp upstream from hypF and 445 bp upstream of hypC, respectively, demonstrating the existence of several transcripts. In addition, five upstream ORFs located in between hupSL, encoding the small and large subunits of the uptake hydrogenase, and the hyp-operon, and two downstream ORFs from the hyp-genes were shown to be part of the same transcript unit. A third TSP was identified 45 bp upstream of asr0689, the first of five ORFs in this operon. The ORFs are annotated as encoding unknown proteins, with the exception of alr0692 which is identified as a NifU-like protein. Orthologues of the four ORFs asr0689-alr0692, with a highly conserved genomic arrangement positioned between hupSL, and the hyp genes are found in several other N2-fixing cyanobacteria, but are absent in non N2-fixing cyanobacteria with only the bidirectional hydrogenase. Short conserved sequences were found in six intergenic regions of the extended hyp-operon, appearing between 11 and 79 times in the genome. Conclusion This study demonstrated that five ORFs upstream of the hyp-gene cluster are co-transcribed with the hyp-genes, and identified three TSPs in the extended hyp-gene cluster in Nostoc sp. strain PCC 7120. This may indicate a function related to the assembly of a functional uptake hydrogenase, hypothetically in the assembly of the small subunit of the enzyme. PMID:18442387

Agervald, Asa; Stensjo, Karin; Holmqvist, Marie; Lindblad, Peter

2008-01-01

220

Copper tolerance in Frankia sp. strain EuI1c involves surface binding and copper transport.  

PubMed

Several Frankia strains have been shown to be copper-tolerant. The mechanism of their copper tolerance was investigated for Frankia sp. strain EuI1c. Copper binding was shown by binding studies. Unusual globular structures were observed on the surface of the bacterium. These globular structures were composed of aggregates containing many relatively smaller "leaf-like" structures. Scanning electron microscopy with energy-dispersive X-ray (SEM-EDAX) analysis of these structures indicated elevated copper and phosphate levels compared to the control cells. Fourier transform infrared spectroscopy (FTIR) analysis indicated an increase in extracellular phosphate on the cell surface of copper-stressed cells. Bioinformatics' analysis of the Frankia sp. strain EuI1c genome revealed five potential cop genes: copA, copZ, copC, copCD, and copD. Experiments with Frankia sp. strain EuI1c using qRT-PCR indicated an increase in messenger RNA (mRNA) levels of the five cop genes upon Cu(2+) stress. After 5 days of Cu(2+) stress, the copA, copZ, copC, copCD, and copD mRNA levels increased 25-, 8-, 18-, 18-, and 25-fold, respectively. The protein profile of Cu(2+)-stressed Frankia sp. strain EuI1c cells revealed the upregulation of a 36.7 kDa protein that was identified as FraEuI1c_1092 (sulfate-binding periplasmic transport protein). Homologues of this gene were only present in the genomes of the Cu(2+)-resistant Frankia strains (EuI1c, DC12, and CN3). These data indicate that copper tolerance by Frankia sp. strain EuI1c involved the binding of copper to the cell surface and transport proteins. PMID:24903815

Rehan, Medhat; Furnholm, Teal; Finethy, Ryan H; Chu, Feixia; El-Fadly, Gomaah; Tisa, Louis S

2014-09-01

221

Influence of Molecular Size and Ligninase Pretreatment on Degradation of Lignins by Xanthomonas sp. Strain 99  

PubMed Central

The purpose of this study was to examine the relationship between the molecular size of lignin in several preparations and extent of degradation (mineralization) by Xanthomonas sp. strain 99. The influence of ligninase pretreatment was also examined. Five synthetic lignins and one 14C-methylated spruce lignin were used. The extent of mineralization to 14CO2 was greatest for the samples containing the most low-molecular-weight material, and the low-molecular-weight portions were preferentially (or perhaps solely) degraded. Pretreatment of the five synthetic lignins with crude ligninase increased their molecular size and decreased their degradability by the xanthomonad. Pretreatment of the methylated spruce lignin with crude ligninase caused both polymerization and depolymerization but resulted in a net decrease in bacterial degradability. Our results suggest that the xanthomonad can degrade lignins only up to a molecular weight of 600 to 1,000. PMID:16347444

Kern, Hartmut W.; Kirk, T. Kent

1987-01-01

222

Degradation of 2-hydroxybiphenyl and 2,2 prime -dihydroxybiphenyl by Pseudomonas sp. strain HBP1  

SciTech Connect

Pseudomonas sp. strain HBP1 was found to grow on 2-hydroxy- and 2,2{prime}-dihydroxy-biphenyl as the sole carbon and energy sources. The first step in the degradation of these compounds was catalyzed by an NADH-dependent monooxygenase. The enzyme inserted a hydroxyl group adjacent to the already existing hydroxyl group to form 2,3-dihydroxybiphenyl when acting on 2-hydroxybiphenyl and to form 2,2{prime},3-trihydroxybiphenyl when acting on 2,2{prime}-dihydroxybiphenyl. To be substrates of the monooxygenase, compounds required a 2-hydroxyphenyl-R structure, with R being a hydrophobic group (e.g., methyl, ethyl, propyl, sec-butyl, phenyl, or 2-hydroxyphenyl). Several chlorinated hydroxybiphenyls served as pseudosubstrates by effecting consumption of NADH and oxygen without being hydroxylated. Further degradation of 2,3-dihydroxy- and 2,2{prime},3-trihydroxybiphenyl involved meta cleavage, with subsequent formation of benzoate and salicylate, respectively.

Kohler, H.P.E.; Kohler-Staub, D.; Focht, D.D. (Univ. of California, Riverside (USA))

1988-11-01

223

Saccharification of corn fiber using enzymes from Aureobasidium sp. strain NRRL Y-2311-1  

SciTech Connect

Crude enzyme preparations from Aureobasidium sp. strain NRRL Y-2311-1 were characterized and tested for the capacity to saccharify corn fiber. Cultures grown on xylan, corn fiber, and alkaline hydrogen peroxide (AHP)-pretreated corn fiber produced specific levels of endoxylanase, amylase, protease, cellulose, and other activities. Using equal units of endoxylanase activity, crude enzymes from AHP-pretreated corn fiber cultures were most effective in saccharification. Multiple enzyme activities were implicated in this process. Pretreatment of corn fiber with AHP nearly doubled the susceptibility of hemicellulose to enzymatic digestion. Up to 138 mg xylose, 125 mg arabinose, and 490 mg glucose were obtained per g pretreated corn fiber under conditions tested. 31 refs., 2 figs., 4 tabs.

Leathers, T.D.; Gupta, S.C. [Dept. of Agriculture, Peoria, IL (United States)

1996-06-01

224

Metabolism of Hydroxydibenzofurans, Methoxydibenzofurans, Acetoxydibenzofurans, and Nitrodibenzofurans by Sphingomonas sp. Strain HH69  

PubMed Central

The metabolism of 11 substituted dibenzofurans by the dibenzofuran-degrading Sphingomonas sp. strain HH69 was investigated. Strain HH69 utilizes 2-, 3-, and 4-acetoxydibenzofuran as well as 2-, 3-, and 4-hydroxydibenzofuran as sole sources of carbon and energy. The degradation of acetoxydibenzofurans is initiated by hydrolysis of the ester bonds, yielding the corresponding hydroxydibenzofurans and acetate. Strain HH69 grew on 2-methoxydibenzofuran only after it was adapted to the utilization of 5-methoxysalicylic acid, whereas 3- and 4-methoxydibenzofuran as well as 2- and 3-nitrodibenzofuran were only cooxidized. During the breakdown of all eight hydroxy-, methoxy-, and nitrodibenzofurans studied here, the corresponding substituted salicylic acids accumulated in the culture broth. In the cases of 2- and 3-hydroxydibenzofuran as well as 2- and 3-nitrodibenzofuran, salicylic acid was also formed. Those four dibenzofurans which did not serve as carbon sources for strain HH69 were converted to a nonutilizable salicylic acid derivative. From turnover experiments with the mutant HH69/II, which is deficient in meta-cleavage, 2,2(prm1),3,4(prm1)-tetrahydroxybiphenyl, 2,2(prm1),3-trihydroxy-5(prm1)-methoxybiphenyl, 2,2(prm1),3-trihydroxy-5(prm1)-nitrobiphenyl, and 2,2(prm1),3-trihydroxy-4(prm1)-nitrobiphenyl were isolated as the main products formed from 3-hydroxydibenzofuran, 2-methoxydibenzofuran, and 2- and 3-nitrodibenzofuran, respectively. These results indicate significant regioselectivity for the dioxygenolytic cleavage of the ether bond of these monosubstituted dibenzofurans, with a preference for the nonsubstituted aromatic nucleus. Substituted trihydroxybiphenyls are converted further by meta-cleavage followed by the removal of the side chain of the resulting product. A stepwise degradation of this side chain was found to be involved in the metabolism of 2-hydroxydibenzofuran. PMID:16535067

Harms, H.; Wilkes, H.; Wittich, R.; Fortnagel, P.

1995-01-01

225

Repression of the Antifungal Activity of Pseudomonas sp. Strain DF41 by the Stringent Response ?  

PubMed Central

The stringent response (SR) enables bacteria to adapt to nutrient limitation through production of the nucleotides guanosine tetraphosphate and guanosine pentaphosphate, collectively known as (p)ppGpp. Two enzymes are responsible for the intracellular pools of (p)ppGpp: RelA acts as a synthetase, while SpoT can function as either a synthetase or a hydrolase. We investigated how the SR affects the ability of the biological control agent Pseudomonas sp. strain DF41 to inhibit the fungal pathogen Sclerotinia sclerotiorum (Lib.) de Bary. Strain DF41 relA and relA spoT mutants were generated and found to exhibit increased antifungal activity. Strain DF41 produces a lipopeptide (LP) molecule that is essential for Sclerotinia biocontrol. LP production and protease activity were both elevated in the relA and relA spoT mutants. Addition of relA but not spoT in trans restored the mutant phenotype to that of the parent. Next, we investigated whether an association exists between the SR and known regulators of biocontrol, including the Gac system and RpoS. A gacS mutant of strain DF41 produced less (p)ppGpp and exhibited a 1.7-fold decrease in relA expression compared to the wild type, suggesting that relA forms part of the Gac regulon. We discovered that rpoS transcription was reduced significantly in the SR mutants. Furthermore, rpoS provided in trans restored protease activity to wild-type levels but did not attenuate antifungal activity. Finally, relA expression was decreased in the mutants, indicating that the SR is required for maximum expression of relA. PMID:21705548

Manuel, Jerrylynn; Berry, Chrystal; Selin, Carrie; Fernando, W. G. Dilantha; de Kievit, Teresa R.

2011-01-01

226

Metabolism of hydroxydibenzofurans, methoxydibenzofurans, acetoxydibenzofurans, and nitrodibenzofurans by Sphingomonas sp. strain HH69  

SciTech Connect

The metabolism of 11 substituted dibenzofurans by the dibenzofuran-degrading Sphingomonas sp. strain HH69 was investigated. Strain HH69 utilizes 2-, 3-, and 4-acetoxydibenzofuran as well as 2-, 3-, and 4-hydroxydibenzofuran as sole sources of carbon and energy. The degradation of acetoxydibenzofurans is initiated by hydrolysis of the ester bonds, yielding the corresponding hydroxydibenzofurans and acetate. Strain HH69 grew on 2-methoxydibenzofuran only after it was adapted to the utilization of 5-methoxysalicylic acid, whereas 3- and 4-methoxydibenzofuran as well as 2- and 3-nitrodibenzofuran were only cooxidized. During the breakdown of all eight hydroxy-, methoxy-, and nitrodibenzofurans studied here, the corresponding substituted salicylic acids accumulated in the culture broth. In the cases of 2- and 3-hydroxydibenzofuran as well as 2- and 3-nitrodibenzofuran, salicylic acid was also formed. Those four dibenzofurans which did not serve as carbon sources for strain HH69 were converted to a nonutilizable salicylic acid derivative. From turnover experiments with the mutant HH69/II, which is deficient in meta-cleavage, 2,2{prime}, 3,4{prime}-tetrahydroxybiphenyl, 2,2{prime},3-trihydroxy-5{prime}-methoxybiphenyl, 2,2{prime},3-trihydroxy-5{prime}-nitrobiphenyl, and 2,2{prime},3-trihydroxy-4{prime}-nitrobiphenyl were isolated as the main products formed from 3-hydroxydibenzofuran, 2-methoxydibenzofuran, and 2- and 3-nitrodibenzo-furan, respectively. These results indicate significant regioselectivity for the dioxygenolytic cleavage of the ether bond of these monosubstituted dibenzofurans, with a preference for the nonsubstituted aromatic nucleus. Substituted trihydroxybiphenyls are converted further by meta-cleavage followed by the removal of the side chain of the resulting product. A stepwise degradation of this side chain was found to be involved in the metabolism of 2-hydroxydibenzofuran. 34 refs., 5 figs., 2 tabs.

Harms, H. [Swiss Federal Institute for Environmental Science and Technology, Duebendorf (Switzerland)]|[Universitaet of Hamburg (Germany); Wittich, R.M.; Fortnagel, P. [Universitaet of Hamburg (Germany)

1995-07-01

227

Compositional and toxicological evaluation of the diazotrophic cyanobacterium, Cyanothece sp. strain ATCC 51142  

NASA Technical Reports Server (NTRS)

Compositional analyses of Cyanothece sp. strain ATCC 51142 showed high protein (50-60%) and low fat (0.4-1%) content, and the ability to synthesize vitamin B12. The amino acid profile indicated that Cyanothece sp. was a balanced protein source. Fatty acids of the 18:3n-3 type were also present. Mineral analyses indicated that the cellular biomass may be a good source of Fe, Zn and Na. Caloric content was 4.5 to 5.1 kcal g dry weight-1 and the carbon content was approximately 40% on a dry weight basis. Nitrogen content was 8 to 9% on a dry weight basis and total nucleic acids were 1.3% on a dry weight basis. Short-term feeding studies in rats followed by histopathology found no toxicity or dietary incompatibility problems. The level of uric acid and allantoin in urine and tissues was low, suggesting no excess of nucleic acids, as sometimes reported in the past for a cyanobacteria-containing diet. The current work discusses the potential implications of these results for human nutrition applications.

Schneegurt, M. A.; Arieli, B.; McKeehen, J. D.; Stephens, S. D.; Nielsen, S. S.; Saha, P. R.; Trumbo, P. R.; Sherman, L. A.; Mitchell, C. A. (Principal Investigator)

1995-01-01

228

Biodegradation of cefdinir by a novel yeast strain, Ustilago sp. SMN03 isolated from pharmaceutical wastewater.  

PubMed

Cefdinir, a semi-synthetic third generation cephalosporin antibiotic being considered as an emerging pollutant, demands removal from aquatic ecosystems. A yeast strain isolated from pharmaceutical wastewater which was identified as Ustilago sp. SMN03 by molecular techniques and was found to be capable of utilizing cefdinir as a sole carbon source. The isolate was found to degrade 81 % of cefdinir within 6 days under optimized conditions viz. pH 6.0, temperature 30 °C, a shaking speed of 120 rpm, an inoculum dosage of 4 % (w/v) and an initial cefdinir concentration of 200 mg L(-1). Kinetic studies revealed that cefdinir degradation followed the pseudo-first order model, a rate constant of 0.222 per day and a half-life period of 3.26 days. Using LC-MS analysis, six novel intermediates formed during the cefdinir degradation were identified and characterized. FT-IR analysis showed that the functional groups ranging from 1,766 to 1,519 cm(-1), characteristic for lactam ring were completely removed during the cefdinir degradation. The opening of the ?-lactam ring was one of the major steps in the cefdinir degradation process. Based on the results from the present study, a possible pathway of cefdinir degradation by Ustilago sp. SMN03 was proposed. To the best of our knowledge, this is the first report on microbial degradation of cefdinir by yeast. PMID:25086584

Selvi, A; Salam, Jaseetha Abdul; Das, Nilanjana

2014-11-01

229

Distinct Actions by Paenibacillus sp. Strain E18 ?-l-Arabinofuranosidases and Xylanase in Xylan Degradation  

PubMed Central

We cloned a Paenibacillus sp. strain E18 5.3-kb xylanolytic gene cluster that contains three open reading frames encoding two family 43 ?-l-arabinofuranosidases (Abf43A and Abf43B) and one family 10 xylanase (XynBE18). The deduced amino acid sequences of Abf43A and Abf43B were at most 68% and 63% identical to those of two putative family 43 proteins from Clostridium sp. strain DL-VIII (EHI98634.1 and EHI98635.1), respectively, but were only 11% identical to each other. Recombinant Abf43A and Abf43B had similar activities at 45°C and pH 6.0 but varied in thermostabilities and substrate specificities. Abf43B was active against only 4-nitrophenyl ?-l-arabinofuranoside, whereas Abf43A acted on 4-nitrophenyl ?-l-arabinofuranoside, wheat arabinoxylan, 4-nitrophenyl ?-d-xylopyranoside, and sugar beet arabinan. The sequential and combined effects on xylan degradation by XynBE18, Abf43A, and Abf43B were characterized. For beechwood, birchwood, and oat spelt xylans as the substrates, synergistic effects were found when XynBE18 and Abf43A or Abf43B were incubated together and when the substrates were first incubated with Abf43A or Abf43B and then with XynBE18. Further high-performance liquid chromatography (HPLC) analysis showed that the amounts of xylobiose and xylose increased sharply in the aforementioned reactions. For water-soluble wheat arabinoxylan as the substrate, Abf43A not only released arabinose but also had a synergistic effect with XynBE18. Synergy may arise as the result of removal of arabinose residues from xylans by ?-l-arabinofuranosidases, which eliminates steric hindrance caused by the arabinose side chains and which allows xylanases to then degrade the xylan backbone, producing short xylooligosaccharides. PMID:23335774

Shi, Pengjun; Chen, Xiaoyan; Meng, Kun; Huang, Huoqing; Bai, Yingguo; Luo, Huiying; Yang, Peilong

2013-01-01

230

DL-7-azatryptophan and citrulline metabolism in the cyanobacterium Anabaena sp. strain 1F.  

PubMed Central

An alternative route for the primary assimilation of ammonia proceeds via glutamine synthetase-carbamyl phosphate synthetase and its inherent glutaminase activity in Anabaena sp. strain 1F, a marine filamentous, heterocystous cyanobacterium. Evidence for the presence of this possible alternative route to glutamate was provided by the use of amino acid analogs as specific enzyme inhibitors, enzymological studies, and radioistopic labeling experiments. The amino acid pool patterns of continuous cultures of Anabaena sp. strain 1F were markedly influenced by the nitrogen source. A relatively high concentration of glutamate was maintained in the amino acid pools of all cultures irrespective of the nitrogen source, reflecting the central role of glutamate in nitrogen metabolism. The addition of 1.0 microM azaserine increased the intracellular pools of glutamate and glutamine. All attempts to detect any enzymatic activity for glutamate synthase by measuring the formation of L-[14C]glutamate from 2-keto-[1-14C]glutarate and glutamine failed. The addition of 10 microM DL-7-azatryptophan caused a transient accumulation of intracellular citrulline and alanine which was not affected by the presence of chloramphenicol. The in vitro activity of carbamyl phosphate synthetase and glutaminase increased severalfold in the presence of azatryptophan. Results from radioisotopic labeling experiments with [14C]bicarbonate and L-[1-14C]ornithine also indicated that citrulline was formed via carbamyl phosphate synthetase and ornithine transcarbamylase. In addition to its effects on nitrogen metabolism, azatryptophan also affected carbon metabolism by inhibiting photosynthetic carbon assimilation and photosynthetic oxygen evolution. Images PMID:2880834

Chen, C H; Van Baalen, C; Tabita, F R

1987-01-01

231

Multiple Light Inputs Control Phototaxis in Synechocystis sp. Strain PCC6803†  

PubMed Central

The phototactic behavior of individual cells of the cyanobacterium Synechocystis sp. strain PCC6803 was studied with a glass slide-based phototaxis assay. Data from fluence rate-response curves and action spectra suggested that there were at least two light input pathways regulating phototaxis. We observed that positive phototaxis in wild-type cells was a low fluence response, with peak spectral sensitivity at 645 and 704 nm. This red-light-induced phototaxis was inhibited or photoreversible by infrared light (760 nm). Previous work demonstrated that a taxD1 mutant (Cyanobase accession no. sll0041; also called pisJ1) lacked positive but maintained negative phototaxis. Therefore, the TaxD1 protein, which has domains that are similar to sequences found in both bacteriophytochrome and the methyl-accepting chemoreceptor protein, is likely to be the photoreceptor that mediates positive phototaxis. Wild-type cells exhibited negative phototaxis under high-intensity broad-spectrum light. This phenomenon is predominantly blue light responsive, with a maximum sensitivity at approximately 470 nm. A weakly negative phototactic response was also observed in the spectral region between 600 and 700 nm. A ?taxD1 mutant, which exhibits negative phototaxis even under low-fluence light, has a similar action maximum in the blue region of the spectrum, with minor peaks from green to infrared (500 to 740 nm). These results suggest that while positive phototaxis is controlled by the red light photoreceptor TaxD1, negative phototaxis in Synechocystis sp. strain PCC6803 is mediated by one or more (as yet) unidentified blue light photoreceptors. PMID:12591877

Ng, Wing-On; Grossman, Arthur R.; Bhaya, Devaki

2003-01-01

232

Synechococcus sp. Strain PCC 7002 Transcriptome: Acclimation to Temperature, Salinity, Oxidative Stress, and Mixotrophic Growth Conditions.  

PubMed

Synechococcus sp. strain PCC 7002 is a unicellular, euryhaline cyanobacterium. It is a model organism for studies of cyanobacterial metabolism and has great potential for biotechnological applications. It exhibits an exceptional tolerance of high-light irradiation and shows very rapid growth. The habitats from which this and closely related strains were isolated are subject to changes in several environmental factors, including light, nutrient supply, temperature, and salinity. In this study global transcriptome profiling via RNAseq has been used to perform a comparative and integrated study of global changes in cells grown at different temperatures, at different salinities, and under mixotrophic conditions, when a metabolizable organic carbon source was present. Furthermore, the transcriptomes were investigated for cells that were subjected to a heat shock and that were exposed to oxidative stress. Lower growth temperatures caused relatively minor changes of the transcriptome; the most prominent changes affected fatty acid desaturases. A heat shock caused severe changes of the transcriptome pattern; transcripts for genes associated with major metabolic pathways declined and those for different chaperones increased dramatically. Oxidative stress, however, left the transcript pattern almost unaffected. When grown at high salinity, Synechococcus sp. PCC 7002 had increased expression of genes involved in compatible solute biosynthesis and showed increased mRNA levels for several genes involved in electron transport. Transcripts of two adjacent genes dramatically increased upon growth at high salinity; the respective proteins are putatively involved in coping with oxidative stress and in triggering ion channels. Only minor changes were observed when cells were grown at low salinity or when the growth medium was supplemented with glycerol. However, the transcriptome data suggest that cells must acclimate to excess reducing equivalents when a reduced C-source is present. PMID:23087677

Ludwig, Marcus; Bryant, Donald A

2012-01-01

233

Reclassification of Brevibacillus brevis strains NCIMB 13288 and DSM 6472 (=NRRL NRS-887) as Aneurinibacillus danicus sp. nov. and Brevibacillus limnophilus sp. nov.  

PubMed

Comparison of the hypervariable region (269-279 bases in length) at the 5' end of the 16S rDNA sequences of 29 bacterial strains that were identified previously as Brevibacillus brevis showed that 13 strains clustered with Aneurinibacillus species, eight strains clustered with Bacillus species and eight strains clustered with Brevibacillus species. Based on DNA-DNA hybridization results, 27 strains, not including [Brevibacillus brevis] NCIMB 13288 and [Brevibacillus brevis] DSM 6472, were reidentified as Aneurinibacillus migulanus, Aneurinibacillus thermoaerophilus, Bacillus methanolicus, Bacillus oleronius, Brevibacillus agri, Brevibacillus brevis and Brevibacillus parabrevis. [Brevibacillus brevis] NCIMB 13288, which was located in the Aneurinibacillus cluster, showed low DNA-DNA relatedness (<14 %) and low 16S rDNA sequence similarity (96.8-97.9 %) to other Aneurinibacillus species. [Brevibacillus brevis] DSM 6472, which was located in the Brevibacillus cluster, also showed low DNA-DNA relatedness (<12 %) and low 16S rDNA sequence similarity (95.4-98.8 %) to other Brevibacillus species. These genotypic and phylogenetic data, plus phenotypic and chemotaxonomic characteristics, suggest that [Brevibacillus brevis] NCIMB 13288 (=IAM 15048) and [Brevibacillus brevis] DSM 6472 (=NRRL NRS-887) represent novel species of the genera Aneurinibacillus and Brevibacillus, respectively, for which the names Aneurinibacillus danicus sp. nov. and Brevibacillus limnophilus sp. nov. are proposed. PMID:15023954

Goto, Keiichi; Fujita, Rieko; Kato, Yuko; Asahara, Mika; Yokota, Akira

2004-03-01

234

Taxonomic identification, phenanthrene uptake activity, and membrane lipid alterations of the PAH degrading Arthrobacter sp. strain Sphe3  

Microsoft Academic Search

This report describes phenanthrene uptake as well as the effect of phenanthrene on the membrane phospholipid and fatty acid\\u000a composition in a newly isolated bacterial strain, Sphe3, that we taxonomically identified as Arthrobacter sp. Strain Sphe3 is able to utilize phenanthrene as a carbon source at high rates and appears to internalize phenanthrene\\u000a with two mechanisms: a passive diffusion when

Aristeidis Kallimanis; Stathis Frillingos; Constantin Drainas; Anna Irini Koukkou

2007-01-01

235

Degradation of polycyclic aromatic hydrocarbons by a newly isolated dibenzofuran-utilizing Janibacter sp. strain YY-1  

Microsoft Academic Search

The dibenzofuran (DF)-utilizing bacterium strain YY-1 was newly isolated from soil. The isolate was identified as Janibacter sp. with respect to its 16S rDNA sequence and fatty acid profiles, as well as various physiological characteristics. In addition to DF, strain YY-1 could grow on fluorene and dibenzothiophene as sole sources of carbon and energy. It was also able to cometabolize

A. Yamazoe; O. Yagi; H. Oyaizu

2004-01-01

236

Catabolism of 2,7-dichloro- and 2,4,8-trichlorodibenzofuran by Sphingomonas sp strain RW1  

Microsoft Academic Search

  Due to their physicochemical and toxicological properties, polychlorinated dibenzofurans are regarded as a class of compounds\\u000a providing reason for serious environmental concern. While the nonhalogenated basic structure dibenzofuran is effectively mineralized\\u000a by appropriate bacterial strains, its polychlorinated derivatives are not. To elucidate the ability of the strain Sphingomonas sp RW1 to metabolize some of these chlorinated derivatives, we performed turnover

T Keim; W Francke; S Schmidt; P Fortnagel

1999-01-01

237

Sulfolobus tokodaii sp. nov. (f. Sulfolobus sp. strain 7), a new member of the genus Sulfolobus isolated from Beppu Hot Springs, Japan  

Microsoft Academic Search

The taxonomic position of a thermoacidophilic crenarchaeote Sulfolobus sp. strain 7, previously isolated from the Beppu Hot Springs in the geothermal area of Kyushu Island, Japan, was investigated by cloning and sequencing, by phylogenetic analysis of the 16S rRNA gene sequence, by DNA-DNA homology with similar species, and by biochemical characterization of the isolate. This isolate is an obligate aerobe

Toshiharu Suzuki; Toshio Iwasaki; Taketoshi Uzawa; Kurt Hara; Naoki Nemoto; Takahide Kon; Toshiaki Ueki; Akihiko Yamagishi; Tairo Oshima

2002-01-01

238

Draft Genome Sequence of Pseudozyma brasiliensis sp. nov. Strain GHG001, a High Producer of Endo-1,4-Xylanase Isolated from an Insect Pest of Sugarcane.  

PubMed

Here, we present the nuclear and mitochondrial genome sequences of Pseudozyma brasiliensis sp. nov. strain GHG001. P. brasiliensis sp. nov. is the closest relative of Pseudozyma vetiver. P. brasiliensis sp. nov. is capable of growing on xylose or xylan as a sole carbon source and has great biotechnological potential. PMID:24356824

Oliveira, Juliana Velasco de Castro; Dos Santos, Renato Augusto Corrêa; Borges, Thuanny A; Riaño-Pachón, Diego Mauricio; Goldman, Gustavo Henrique

2013-01-01

239

Using Transcriptomics To Improve Butanol Tolerance of Synechocystis sp. Strain PCC 6803  

PubMed Central

Cyanobacteria are emerging as promising hosts for production of advanced biofuels such as n-butanol and alkanes. However, cyanobacteria suffer from the same product inhibition problems as those that plague other microbial biofuel hosts. High concentrations of butanol severely reduce growth, and even small amounts can negatively affect metabolic processes. An understanding of how cyanobacteria are affected by their biofuel product can enable identification of engineering strategies for improving their tolerance. Here we used transcriptome sequencing (RNA-Seq) to assess the transcriptome response of Synechocystis sp. strain PCC 6803 to two concentrations of exogenous n-butanol. Approximately 80 transcripts were differentially expressed at 40 mg/liter butanol, and 280 transcripts were different at 1 g/liter butanol. Our results suggest a compromised cell membrane, impaired photosynthetic electron transport, and reduced biosynthesis. Accumulation of intracellular reactive oxygen species (ROS) scaled with butanol concentration. Using the physiology and transcriptomics data, we selected several genes for overexpression in an attempt to improve butanol tolerance. We found that overexpression of several proteins, notably, the small heat shock protein HspA, improved tolerance to butanol. Transcriptomics-guided engineering created more solvent-tolerant cyanobacteria strains that could be the foundation for a more productive biofuel host. PMID:24056459

Anfelt, Josefine; Hallstrom, Bjorn; Nielsen, Jens; Uhlen, Mathias

2013-01-01

240

Anilofos Tolerance and Its Mineralization by the Cyanobacterium Synechocystis sp. Strain PUPCCC 64  

PubMed Central

This study deals with anilofos tolerance and its mineralization by the common rice field cyanobacterium Synechocystis sp. strain PUPCCC 64. The organism tolerated anilofos up to 25 mg L?1. The herbicide caused inhibitory effects on photosynthetic pigments of the test organism in a dose-dependent manner. The organism exhibited 60, 89, 96, 85 and 79% decrease in chlorophyll a, carotenoids, phycocyanin, allophycocyanin and phycoerythrin, respectively, in 20 mg L?1 anilofos on day six. Activities of superoxide dismutase, catalase and peroxidase increased by 1.04 to 1.80 times over control cultures in presence of 20 mg L?1 anilofos. Glutathione content decreased by 26% while proline content was unaffected by 20 mg L?1 anilofos. The test organism showed intracellular uptake and metabolized the herbicide. Uptake of herbicide by test organism was fast during initial six hours followed by slow uptake until 120 hours. The organism exhibited maximum anilofos removal at 100 mg protein L?1, pH 8.0 and 30°C. Its growth in phosphate deficient basal medium in the presence of anilofos (2.5 mg L?1) indicated that herbicide was used by the strain PUPCCC 64 as a source of phosphate. PMID:23382844

Singh, D. P.; Khattar, J. I. S.; Kaur, Mandeep; Kaur, Gurdeep; Gupta, Meenu; Singh, Yadvinder

2013-01-01

241

Genome Sequence of Maribius sp. Strain MOLA 401, a Marine Roseobacter with a Quorum-Sensing Cell-Dependent Physiology  

PubMed Central

Maribius sp. strain MOLA401 is an alphaproteobacterium isolated from a coral reef lagoon located in New Caledonia, France. We report the genome sequence and its annotation which, interestingly, reveals the presence of genes involved in quorum sensing. This is the first report of a full genome within the genus Maribius. PMID:25278539

Doberva, Margot; Sanchez-Ferandin, Sophie; Ferandin, Yoan; Intertaglia, Laurent; Joux, Fabien; Lebaron, Philippe

2014-01-01

242

Draft Genome Sequence of Marine-Derived Streptomyces sp. Strain AA0539, Isolated from the Yellow Sea, China  

PubMed Central

Here, we report the draft genome sequence of Streptomyces sp. strain AA0539, isolated from marine sediment of the Yellow Sea, China. Its small genome (?5.8 Mb) contains large, unique genes and gene clusters for diverse secondary metabolites, suggesting great potential as a source for the discovery of novel natural products. PMID:23144381

Xiong, Zhi-Qiang

2012-01-01

243

Draft Genome Sequence of the Aromatic Hydrocarbon-Degrading Bacterium Sphingobium sp. Strain Ant17, Isolated from Antarctic Soil  

PubMed Central

Here, we present the draft genome sequence of Sphingobium sp. strain Ant17, an aromatic hydrocarbon-degrading bacterium that was isolated from Antarctic oil-contaminated soil. An analysis of this genome can lead to insights into the mechanisms of xenobiotic degradation processes at low temperatures and potentially aid in bioremediation applications. PMID:24723703

Guerrero, Leandro D.; Makhalanyane, Thulani P.; Aislabie, Jackie M.

2014-01-01

244

Draft Genome Sequence of Chryseobacterium sp. Strain P1-3, a Keratinolytic Bacterium Isolated from Poultry Waste  

PubMed Central

Chryseobacterium sp. strain P1-3, harboring keratin degrading activity, has recently been isolated from poultry waste. Here, we report the 4.6-Mbp draft genome sequence of the keratinolytic bacterium with a G+C content of 37.0% and 4,087 protein-coding genes. PMID:25428979

Park, Gun-Seok; Hong, Sung-Jun; Lee, Chang-Hyun; Khan, Abdur Rahim; Ullah, Ihsan; Jung, Byung Kwon; Choi, JungBae; Kwak, Yunyoung; Back, Chang-Gi; Jung, Hee-Young

2014-01-01

245

Draft Genome Sequence of Bacillus sp. Strain BSC154, Isolated from Biological Soil Crust of Moab, Utah.  

PubMed

Bacillus sp. BSC154 was isolated from a biological soil crust near Moab, Utah. The strain appears to be capable of chemotaxis and biofilm production. The BSC154 genome contains iron siderophore production, nitrate reduction, mixed acid-butanediol fermentation, and assimilatory and dissimilatory sulfate metabolism pathways. PMID:25395651

Bailey, Alexis C; Kellom, Matthew; Poret-Peterson, Amisha T; Noonan, Kathryn; Hartnett, Hilairy E; Raymond, Jason

2014-01-01

246

Involvement of nitric oxide synthase in sucrose-enhanced hydrogen peroxide tolerance of Rhodococcus sp. strain APG1,  

E-print Network

Involvement of nitric oxide synthase in sucrose-enhanced hydrogen peroxide tolerance of Rhodococcus Lancaster, Jr. Abstract Hydrogen peroxide (H2O2) tolerance of Rhodococcus sp. strain APG1, previously; Hydrogen peroxide tolerance; Plant­microorganism interaction; Endophytic colonization Bacteria colonize

Cohen, Michael F.

247

Draft Genome Sequence of Cellulosimicrobium sp. Strain MM, Isolated from Arsenic-Rich Microbial Mats of a Himalayan Hot Spring  

PubMed Central

Microbial mats situated at the Manikaran hot springs (>95°C) are characterized by their high arsenic content (140 ppb), qualifying as a stressed niche. Here, we report the annotated draft genome (3.85 Mb) of Cellulosimicrobium sp. strain MM, isolated from these microbial mats, consisting of 3,718 coding sequences, with an average % G+C of 74.4%. PMID:25301656

Sharma, Anukriti; Hira, Princy; Shakarad, Mallikarjun

2014-01-01

248

Draft Genome Sequence of Frankia sp. Strain BMG5.12, a Nitrogen-Fixing Actinobacterium Isolated from Tunisian Soils.  

PubMed

Members of the actinomycete genus Frankia form a nitrogen-fixing symbiosis with 8 different families of actinorhizal plants. We report a draft genome sequence for Frankia sp. strain BMG5.12, a nitrogen-fixing actinobacterium isolated from Tunisian soils with the ability to infect Elaeagnus angustifolia and Myrica gale. PMID:23846272

Nouioui, Imen; Beauchemin, Nicholas; Cantor, Michael N; Chen, Amy; Detter, J Chris; Furnholm, Teal; Ghodhbane-Gtari, Faten; Goodwin, Lynne; Gtari, Maher; Han, Cliff; Han, James; Huntemann, Marcel; Hua, Susan Xinyu; Ivanova, Natalia; Kyrpides, Nikos; Markowitz, Victor; Mavrommatis, Kostas; Mikhailova, Natalia; Nordberg, Henrik P; Ovchinnikova, Galina; Pagani, Ioanna; Pati, Amrita; Sen, Arnab; Sur, Saubashya; Szeto, Ernest; Thakur, Subarna; Wall, Luis; Wei, Chia-Lin; Woyke, Tanja; Tisa, Louis S

2013-01-01

249

Draft Genome Sequence of Frankia sp. Strain BCU110501, a Nitrogen-Fixing Actinobacterium Isolated from Nodules of Discaria trinevis  

PubMed Central

Frankia forms a nitrogen-fixing symbiosis with actinorhizal plants. We report a draft genome sequence for Frankia sp. strain BCU110501, a nitrogen-fixing actinobacterium isolated from nodules of Discaria trinevis grown in the Patagonia region of Argentina. PMID:23846281

Wall, Luis G.; Beauchemin, Nicholas; Cantor, Michael N.; Chaia, Eugenia; Chen, Amy; Detter, J. Chris; Furnholm, Teal; Ghodhbane-Gtari, Faten; Goodwin, Lynne; Gtari, Maher; Han, Cliff; Han, James; Huntemann, Marcel; Hua, Susan Xinyu; Ivanova, Natalia; Kyrpides, Nikos; Markowitz, Victor; Mavrommatis, Kostas; Mikhailova, Natalia; Nordberg, Henrik P.; Nouioui, Imen; Ovchinnikova, Galina; Pagani, Ioanna; Pati, Amrita; Sen, Arnab; Sur, Saubashya; Szeto, Ernest; Thakur, Subarna; Wei, Chia-Lin; Woyke, Tanja

2013-01-01

250

Draft Genome Sequence of Frankia sp. Strain BMG5.12, a Nitrogen-Fixing Actinobacterium Isolated from Tunisian Soils  

PubMed Central

Members of the actinomycete genus Frankia form a nitrogen-fixing symbiosis with 8 different families of actinorhizal plants. We report a draft genome sequence for Frankia sp. strain BMG5.12, a nitrogen-fixing actinobacterium isolated from Tunisian soils with the ability to infect Elaeagnus angustifolia and Myrica gale. PMID:23846272

Nouioui, Imen; Beauchemin, Nicholas; Cantor, Michael N.; Chen, Amy; Detter, J. Chris; Furnholm, Teal; Ghodhbane-Gtari, Faten; Goodwin, Lynne; Gtari, Maher; Han, Cliff; Han, James; Huntemann, Marcel; Hua, Susan Xinyu; Ivanova, Natalia; Kyrpides, Nikos; Markowitz, Victor; Mavrommatis, Kostas; Mikhailova, Natalia; Nordberg, Henrik P.; Ovchinnikova, Galina; Pagani, Ioanna; Pati, Amrita; Sen, Arnab; Sur, Saubashya; Szeto, Ernest; Thakur, Subarna; Wall, Luis; Wei, Chia-Lin; Woyke, Tanja

2013-01-01

251

Draft Genome Sequence of Frankia sp. Strain BCU110501, a Nitrogen-Fixing Actinobacterium Isolated from Nodules of Discaria trinevis.  

PubMed

Frankia forms a nitrogen-fixing symbiosis with actinorhizal plants. We report a draft genome sequence for Frankia sp. strain BCU110501, a nitrogen-fixing actinobacterium isolated from nodules of Discaria trinevis grown in the Patagonia region of Argentina. PMID:23846281

Wall, Luis G; Beauchemin, Nicholas; Cantor, Michael N; Chaia, Eugenia; Chen, Amy; Detter, J Chris; Furnholm, Teal; Ghodhbane-Gtari, Faten; Goodwin, Lynne; Gtari, Maher; Han, Cliff; Han, James; Huntemann, Marcel; Hua, Susan Xinyu; Ivanova, Natalia; Kyrpides, Nikos; Markowitz, Victor; Mavrommatis, Kostas; Mikhailova, Natalia; Nordberg, Henrik P; Nouioui, Imen; Ovchinnikova, Galina; Pagani, Ioanna; Pati, Amrita; Sen, Arnab; Sur, Saubashya; Szeto, Ernest; Thakur, Subarna; Wei, Chia-Lin; Woyke, Tanja; Tisa, Louis S

2013-01-01

252

Complete Genome Sequence of Rahnella sp Strain Y9602, a Gammaproteobacterium Isolate from Metal- and Radionuclide-Contaminated Soil  

SciTech Connect

Rahnella sp. strain Y9602 is a gammaproteobacterium isolated from contaminated subsurface soils that is capable of promoting uranium phosphate mineralization as a result of constitutive phosphatase activity. Here we report the first complete genome sequence of an isolate belonging to the genus Rahnella.

Martinez, Robert J [University of Alabama, Tuscaloosa; Bruce, David [Los Alamos National Laboratory (LANL); Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Han, James [U.S. Department of Energy, Joint Genome Institute; Han, Cliff [Los Alamos National Laboratory (LANL); Held, Brittany [Los Alamos National Laboratory (LANL); Mikhailova, Natalia [U.S. Department of Energy, Joint Genome Institute; Nolan, Matt [U.S. Department of Energy, Joint Genome Institute; Pennacchio, Len [U.S. Department of Energy, Joint Genome Institute; Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Tapia, Roxanne [Los Alamos National Laboratory (LANL); Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute; Sobeckya, Patricia A. [University of Alabama, Tuscaloosa

2012-01-01

253

Physicochemical Parameters for Growth of the Sea Ice Bacteria Glaciecola punicea ACAM 611T and Gelidibacter sp. Strain IC158  

PubMed Central

The water activity and pH ranges for growth of Glaciecola punicea (a psychrophile) were extended when this organism was grown at suboptimal rather than optimal temperatures. No such extension was observed for Gelidibacter sp. strain IC158 (a psychrotolerant bacterium) at analogous temperatures. Salinity and pH may be primary physicochemical parameters controlling bacterial community development in sea ice. PMID:10427082

Nichols, D. S.; Greenhill, A. R.; Shadbolt, C. T.; Ross, T.; McMeekin, T. A.

1999-01-01

254

Complete Genome Sequence of the Streptococcus sp. Strain VT 162, Isolated from the Saliva of Pediatric Oncohematology Patients  

PubMed Central

Streptococcus sp. strain VT 162 was isolated from the saliva of pediatric oncohematology patients. Its full genome is 2,045,418 bp. The availability of this genome will provide insights into the composition of microbial flora among pediatric oncohematology patients and the host interaction and pathogenicity of this species. PMID:25013137

Tetz, George V.; Tetz, Victor V.

2014-01-01

255

Draft Genome Sequence of Cellulosimicrobium sp. Strain MM, Isolated from Arsenic-Rich Microbial Mats of a Himalayan Hot Spring.  

PubMed

Microbial mats situated at the Manikaran hot springs (>95°C) are characterized by their high arsenic content (140 ppb), qualifying as a stressed niche. Here, we report the annotated draft genome (3.85 Mb) of Cellulosimicrobium sp. strain MM, isolated from these microbial mats, consisting of 3,718 coding sequences, with an average % G+C of 74.4%. PMID:25301656

Sharma, Anukriti; Hira, Princy; Shakarad, Mallikarjun; Lal, Rup

2014-01-01

256

Complete Genome Sequence of the Denitrifying and N2O-Reducing Bacterium Azoarcus sp. Strain KH32C  

PubMed Central

We report the finished and annotated genome sequence of a denitrifying and N2O-reducing betaproteobacterium, Azoarcus sp. strain KH32C. The genome is composed of one chromosome and one megaplasmid and contains genes for plant-microbe interactions and the gene clusters for aromatic-compound degradations. PMID:22328754

Tago, Kanako; Oshima, Kenshiro; Hattori, Masahira; Ishii, Satoshi; Otsuka, Shigeto; Senoo, Keishi

2012-01-01

257

Complete genome sequence of the denitrifying and N2O-reducing bacterium Azoarcus sp. strain KH32C.  

PubMed

We report the finished and annotated genome sequence of a denitrifying and N(2)O-reducing betaproteobacterium, Azoarcus sp. strain KH32C. The genome is composed of one chromosome and one megaplasmid and contains genes for plant-microbe interactions and the gene clusters for aromatic-compound degradations. PMID:22328754

Nishizawa, Tomoyasu; Tago, Kanako; Oshima, Kenshiro; Hattori, Masahira; Ishii, Satoshi; Otsuka, Shigeto; Senoo, Keishi

2012-03-01

258

The use of fecundity, lobe biometry and the RAPD-PCR technique in order to compare strains of Tetranychus sp  

Microsoft Academic Search

In Belgium, recently two new red carmine forms of Tetranychus sp. have appeared on tomato crops in glasshouses and in maize crops. These forms maintain their red colour even during summer and on other host plants such as French bean. Our aim was to establish their status and to compare them with strains of Tetranychus urticae and Tetranychus cinnabarinus. A

Thierry Hance; Pierre Neuberg; Christine Noèl-Lastelle

1998-01-01

259

Degradation of Chlorobenzenes at Nanomolar Concentrations by Burkholderia sp. Strain PS14 in Liquid Cultures and in Soil  

PubMed Central

The utilization of 1,2,4,5-tetrachloro-, 1,2,4-trichloro-, the three isomeric dichlorobenzenes and fructose as the sole carbon and energy sources at nanomolar concentrations was studied in batch experiments with Burkholderia sp. strain PS14. In liquid culture, all chlorobenzenes were metabolized within 1 h from their initial concentration of 500 nM to below their detection limits of 0.5 nM for 1,2,4,5-tetrachloro- and 1,2,4-trichlorobenzene and 7.5 nM for the three dichlorobenzene isomers, with 63% mineralization of the tetra- and trichloroisomers. Fructose at the same initial concentration was, in contrast, metabolized over a 4-h incubation period down to a residual concentration of approximately 125 nM with 38% mineralization during this time. In soil microcosms, Burkholderia sp. strain PS14 metabolized tetrachlorobenzene present at 64.8 ppb and trichlorobenzene present at 54.4 ppb over a 72-h incubation period to below the detection limits of 0.108 and 0.09 ppb, respectively, with approximately 80% mineralization. A high sorptive capacity of Burkholderia sp. strain PS14 for 1,2,4,5-tetrachlorobenzene was found at very low cell density. The results demonstrate that Burkholderia sp. strain PS14 exhibits a very high affinity for chlorobenzenes at nanomolar concentrations. PMID:10347041

Rapp, Peter; Timmis, Kenneth N.

1999-01-01

260

Draft Genome Sequence and Description of Janthinobacterium sp. Strain CG3, a Psychrotolerant Antarctic Supraglacial Stream Bacterium  

PubMed Central

Here we present the draft genome sequence of Janthinobacterium sp. strain CG3, a psychrotolerant non-violacein-producing bacterium that was isolated from the Cotton Glacier supraglacial stream. The genome sequence of this organism will provide insight as to the mechanisms necessary for bacteria to survive in UV-stressed icy environments. PMID:24265494

Smith, Heidi; Akiyama, Tatsuya; Franklin, Michael; Woyke, Tanja; Teshima, Hazuki; Davenport, Karen; Daligault, Hajnalka; Erkkila, Tracy; Goodwin, Lynne; Gu, Wei; Xu, Yan; Chain, Patrick

2013-01-01

261

Genome Sequence of Maribius sp. Strain MOLA 401, a Marine Roseobacter with a Quorum-Sensing Cell-Dependent Physiology.  

PubMed

Maribius sp. strain MOLA401 is an alphaproteobacterium isolated from a coral reef lagoon located in New Caledonia, France. We report the genome sequence and its annotation which, interestingly, reveals the presence of genes involved in quorum sensing. This is the first report of a full genome within the genus Maribius. PMID:25278539

Doberva, Margot; Sanchez-Ferandin, Sophie; Ferandin, Yoan; Intertaglia, Laurent; Joux, Fabien; Lebaron, Philippe; Lami, Raphaël

2014-01-01

262

Draft genome sequence and comparative analysis of the superb aromatic-hydrocarbon degrader Rhodococcus sp. strain DK17.  

PubMed

Rhodococcus sp. strain DK17 is capable of utilizing various derivatives of benzene and bicyclics containing both aromatic and alicyclic moieties as sole carbon and energy sources. Here, we present the 9,107,362-bp draft genome sequence of DK17 and its genomic analysis in comparison with other members of the genus Rhodococcus. PMID:22843580

Yoo, Miyoun; Kim, Dockyu; Choi, Ki Young; Chae, Jong-Chan; Zylstra, Gerben J; Kim, Eungbin

2012-08-01

263

Genome Sequences of Two Temperate Phages, ?CB2047-A and ?CB2047-C, Infecting Sulfitobacter sp. Strain 2047  

PubMed Central

We announce the complete genome sequences of two temperate Podoviridae, Sulfitobacter phages ?CB2047-A and ?CB2047-C, which infect Sulfitobacter sp. strain 2047, a member of the Roseobacter clade. This is the first report of temperate podophage infecting members of the Sulfitobacter genus of the Roseobacter clade. PMID:24903862

Ankrah, Nana Y. D.; Budinoff, Charles R.; Wilson, William H.; Wilhelm, Steven W.

2014-01-01

264

Draft Genome Sequence of Bacillus sp. Strain BSC154, Isolated from Biological Soil Crust of Moab, Utah  

PubMed Central

Bacillus sp. BSC154 was isolated from a biological soil crust near Moab, Utah. The strain appears to be capable of chemotaxis and biofilm production. The BSC154 genome contains iron siderophore production, nitrate reduction, mixed acid-butanediol fermentation, and assimilatory and dissimilatory sulfate metabolism pathways. PMID:25395651

Bailey, Alexis C.; Kellom, Matthew; Poret-Peterson, Amisha T.; Noonan, Kathryn; Hartnett, Hilairy E.

2014-01-01

265

Draft Genome Sequence of Massilia sp. Strain BSC265, Isolated from Biological Soil Crust of Moab, Utah  

PubMed Central

Massilia sp. BSC265 was isolated from a biological soil crust near Moab, Utah. The strain appears to be capable of chemotaxis and exopolysaccharide synthesis for biofilm adhesion. The BSC265 genome contains a complete dissimilatory nitrate reduction pathway as well as a TCA cycle, making it a facultative anaerobe. PMID:25395652

Bailey, Alexis C.; Kellom, Matthew; Poret-Peterson, Amisha T.; Noonan, Kathryn; Hartnett, Hilairy E.

2014-01-01

266

Draft Genome Sequence of Microvirga sp. Strain BSC39, Isolated from Biological Soil Crust of Moab, Utah  

PubMed Central

Microvirga sp. BSC39 was isolated from a biological soil crust near Moab, Utah. The strain appears to be capable of chemotaxis and exopolysaccharide synthesis for biofilm adhesion. The BSC39 genome contains iron siderophore uptake and hydrolysis enzymes; however, it lacks siderophore synthesis pathways, suggesting the uptake of siderophores produced by neighboring microbes. PMID:25395650

Bailey, Alexis C.; Kellom, Matthew; Poret-Peterson, Amisha T.; Noonan, Kathryn; Hartnett, Hilairy E.

2014-01-01

267

Multiple mechanisms of uranium immobilization by Cellulomonas sp. strain ES6.  

PubMed

Removal of hexavalent uranium (U(VI)) from aqueous solution was studied using a Gram-positive facultative anaerobe, Cellulomonas sp. strain ES6, under anaerobic, non-growth conditions in bicarbonate and PIPES buffers. Inorganic phosphate was released by cells during the experiments providing ligands for formation of insoluble U(VI) phosphates. Phosphate release was most probably the result of anaerobic hydrolysis of intracellular polyphosphates accumulated by ES6 during aerobic growth. Microbial reduction of U(VI) to U(IV) was also observed. However, the relative magnitudes of U(VI) removal by abiotic (phosphate-based) precipitation and microbial reduction depended on the buffer chemistry. In bicarbonate buffer, X-ray absorption fine structure (XAFS) spectroscopy showed that U in the solid phase was present primarily as a non-uraninite U(IV) phase, whereas in PIPES buffer, U precipitates consisted primarily of U(VI)-phosphate. In both bicarbonate and PIPES buffer, net release of cellular phosphate was measured to be lower than that observed in U-free controls suggesting simultaneous precipitation of U and PO?³?. In PIPES, U(VI) phosphates formed a significant portion of U precipitates and mass balance estimates of U and P along with XAFS data corroborate this hypothesis. High-resolution transmission electron microscopy (HR-TEM) and energy dispersive X-ray spectroscopy (EDS) of samples from PIPES treatments indeed showed both extracellular and intracellular accumulation of U solids with nanometer sized lath structures that contained U and P. In bicarbonate, however, more phosphate was removed than required to stoichiometrically balance the U(VI)/U(IV) fraction determined by XAFS, suggesting that U(IV) precipitated together with phosphate in this system. When anthraquinone-2,6-disulfonate (AQDS), a known electron shuttle, was added to the experimental reactors, the dominant removal mechanism in both buffers was reduction to a non-uraninite U(IV) phase. Uranium immobilization by abiotic precipitation or microbial reduction has been extensively reported; however, the present work suggests that strain ES6 can remove U(VI) from solution simultaneously through precipitation with phosphate ligands and microbial reduction, depending on the environmental conditions. Cellulomonadaceae are environmentally relevant subsurface bacteria and here, for the first time, the presence of multiple U immobilization mechanisms within one organism is reported using Cellulomonas sp. strain ES6. PMID:20872821

Sivaswamy, Vaideeswaran; Boyanov, Maxim I; Peyton, Brent M; Viamajala, Sridhar; Gerlach, Robin; Apel, William A; Sani, Rajesh K; Dohnalkova, Alice; Kemner, Kenneth M; Borch, Thomas

2011-02-01

268

"Dehalococcoides" sp. Strain CBDB1 Extensively Dechlorinates the Commercial Polychlorinated Biphenyl Mixture Aroclor 1260? †  

PubMed Central

“Dehalococcoides” sp. strain CBDB1 in pure culture dechlorinates a wide range of PCB congeners with three to eight chlorine substituents. Congener-specific high-resolution gas chromatography revealed that CBDB1 extensively dechlorinated both Aroclor 1248 and Aroclor 1260 after four months of incubation. For example, 16 congeners comprising 67.3% of the total PCBs in Aroclor 1260 were decreased by 64%. We confirmed the dechlorination of 43 different PCB congeners. The most prominent dechlorination products were 2,3?,5-chlorinated biphenyl (25-3-CB) and 24-3-CB from Aroclor 1248 and 235-25-CB, 25-25-CB, 24-25-CB, and 235-236-CB from Aroclor 1260. Strain CBDB1 removed flanked para chlorines from 3,4-, 2,4,5-, and 3,4,5-chlorophenyl rings, primarily para chlorines from 2,3,4,5-chlorophenyl rings, primarily meta chlorines from 2,3,4- and 2,3,4,6-chlorophenyl rings, and either meta or para chlorines from 2,3,4,5,6-chlorophenyl rings. The site of attack on the 2,3,4-chorophenyl ring was heavily influenced by the chlorine configuration on the opposite ring. This dechlorination pattern matches PCB Process H dechlorination, which was previously observed in situ both in the Acushnet Estuary (New Bedford, MA) and in parts of the Hudson River (New York). Accordingly, we propose that Dehalococcoides bacteria similar to CBDB1 are potential agents of Process H PCB dechlorination in the environment. This is the first time that a complex naturally occurring PCB dechlorination pattern has been reproduced in the laboratory using a single bacterial strain. PMID:19429555

Adrian, Lorenz; Dudkova, Vlasta; Demnerova, Katarina; Bedard, Donna L.

2009-01-01

269

"Dehalococcoides" sp. strain CBDB1 extensively dechlorinates the commercial polychlorinated biphenyl mixture aroclor 1260.  

PubMed

"Dehalococcoides" sp. strain CBDB1 in pure culture dechlorinates a wide range of PCB congeners with three to eight chlorine substituents. Congener-specific high-resolution gas chromatography revealed that CBDB1 extensively dechlorinated both Aroclor 1248 and Aroclor 1260 after four months of incubation. For example, 16 congeners comprising 67.3% of the total PCBs in Aroclor 1260 were decreased by 64%. We confirmed the dechlorination of 43 different PCB congeners. The most prominent dechlorination products were 2,3',5-chlorinated biphenyl (25-3-CB) and 24-3-CB from Aroclor 1248 and 235-25-CB, 25-25-CB, 24-25-CB, and 235-236-CB from Aroclor 1260. Strain CBDB1 removed flanked para chlorines from 3,4-, 2,4,5-, and 3,4,5-chlorophenyl rings, primarily para chlorines from 2,3,4,5-chlorophenyl rings, primarily meta chlorines from 2,3,4- and 2,3,4,6-chlorophenyl rings, and either meta or para chlorines from 2,3,4,5,6-chlorophenyl rings. The site of attack on the 2,3,4-chorophenyl ring was heavily influenced by the chlorine configuration on the opposite ring. This dechlorination pattern matches PCB Process H dechlorination, which was previously observed in situ both in the Acushnet Estuary (New Bedford, MA) and in parts of the Hudson River (New York). Accordingly, we propose that Dehalococcoides bacteria similar to CBDB1 are potential agents of Process H PCB dechlorination in the environment. This is the first time that a complex naturally occurring PCB dechlorination pattern has been reproduced in the laboratory using a single bacterial strain. PMID:19429555

Adrian, Lorenz; Dudková, Vlasta; Demnerová, Katarina; Bedard, Donna L

2009-07-01

270

Defluorination of organofluorine sulfur compounds by Pseudomonas sp. strain D2  

SciTech Connect

Little is known of the potential for biodegradation of fluorinated sulfonates. Because of the apparent stability of fluorinated organics, their bioactivity, and their potential for accumulation in the environment, it is important to understand their environmental fate and the mechanisms by which they might be degraded. To evaluate this potential, the following model compounds were selected: difluoromethane sulfonate (DFMS), trifluoromethane sulfonate (TFMS), 2,2,2-trifluoroethane sulfonate (TES), perfluorooctane sulfonate (PFOS), and 1H,1H,2H,2H-perfluorooctane sulfonate (H-PFOS). A laboratory isolate designated Pseudomonas sp. strain D2 completely defluorinated DFMS under aerobic sulfur-limiting conditions in a defined mineral medium. Strain D2 utilized DFMS as the sole source of sulfur, but not as a source of carbon or energy. DFMS utilization was inhibited by other forms of sulfur, and noncompetitive inhibition kinetics were observed, with K{sub i}-values of 3--4 {micro}M for sulfate, sulfite, methane sulfonate, and cystine. Strain D2 was subsequently used to evaluate degradation of other fluorinated sulfonates. Growth and defluorination were only observed for those compounds containing hydrogen (TES and H-PFOS). TFMS and PFOS were not degraded. TES was completely defluorinated, and H-PFOS was partially defluorinated. No volatile transformation products were detected for TES or DFMS, but six volatile products were detected for H-PFOS. All of the volatile products contained oxygen and fluorine, but not sulfur. This is the first report of defluorination of fluorinated sulfonates, a linkage between sulfur assimilation and defluorination, and generation of volatile fluorinated biotransformation products.

Key, B.D.; Criddle, C.S. [Michigan State Univ., East Lansing, MI (United States)] [Michigan State Univ., East Lansing, MI (United States); Howell, R.D. [3M Environmental Technology and Safety Services, St. Paul, MN (United States)] [3M Environmental Technology and Safety Services, St. Paul, MN (United States)

1998-08-01

271

Genomic characterization of thermophilic Geobacillus species isolated from the deepest sea mud of the Mariana Trench.  

PubMed

The thermophilic strains HTA426 and HTA462 isolated from the Mariana Trench were identified as Geobacillus kaustophilus and G. stearothermophilus, respectively, based on physiologic and phylogenetic analyses using 16S rDNA sequences and DNA-DNA relatedness. The genome size of HTA426 and HTA462 was estimated at 3.23-3.49 Mb and 3.7-4.49 Mb, respectively. The nucleotide sequences of three independent lambda-phage inserts of G. stearothermophilus HTA462 have been determined. The organization of protein coding sequences (CDSs) in the two lambda-phage inserts was found to differ from that in the contigs corresponding to each lambda insert assembled by the shotgun clones of the G. kaustophilus HTA426 genome, although the CDS organization in another lambda insert is identical to that in the HTA426 genome. PMID:15168170

Takami, Hideto; Nishi, Shinro; Lu, Jei; Shimamura, Shigeru; Takaki, Yoshihiro

2004-10-01

272

Novel alkaline- and heat-stable serine proteases from alkalophilic Bacillus sp. strain GX6638.  

PubMed Central

An alkalophilic Bacillus sp., strain GX6638 (ATCC 53278), was isolated from soil and shown to produce a minimum of three alkaline proteases. The proteases were purified by ion-exchange chromatography and were distinguishable by their isoelectric point, molecular weight, and electrophoretic mobility. Two of the proteases, AS and HS, which exhibited the greatest alkaline and thermal stability, were characterized further. Protease HS had an apparent molecular weight of 36,000 and an isoelectric point of approximately 4.2, whereas protease AS had a molecular weight of 27,500 and an isoelectric point of 5.2. Both enzymes had optimal proteolytic activities over a broad pH range (pH 8 to 12) and exhibited temperature optima of 65 degrees C. Proteases HS and AS were further distinguished by their proteolytic activities, esterolytic activities, sensitivity to inhibitors, and their alkaline and thermal stability properties. Protease AS was extremely alkali stable, retaining 88% of initial activity at pH 12 over a 24-h incubation period at 25 degrees C; protease HS exhibited similar alkaline stability properties to pH 11. In addition, protease HS had exceptional thermal stability properties. At pH 9.5 (0.1 M CAPS buffer, 5 mM EDTA), the enzyme had a half-life of more than 200 min at 50 degrees C and 25 min at 60 degrees C. At pH above 9.5, protease HS readily lost enzymatic activity even in the presence of exogenously supplied Ca2+. In contrast, protease AS was more stable at pH above 9.5, and Ca2+ addition extended the half-life of the enzyme 10-fold at 60 degrees C. In contrast, protease AS was more stable at pH above 9.5, and Ca2+ addition extended the half-life of the enzyme 10-fold at 60 degrees C. The data presented here clearly indicate that these two alkaline proteases from Bacillus sp. strain GX6638 represent novel proteases that differ fundamentally from the proteases previously described for members of the genus Bacillus. Images PMID:3108241

Durham, D R; Stewart, D B; Stellwag, E J

1987-01-01

273

Staurosporine from the endophytic Streptomyces sp. strain CNS-42 acts as a potential biocontrol agent and growth elicitor in cucumber.  

PubMed

Chinese medicinal plants and their surrounding rhizospheric soil serve as promising sources of actinobacteria. A total of 180 actinobacteria strains were isolated from the rhizosphere soil, leaves, stems, and roots of nine selected plants and have been identified as potential biocontrol agents against Fusarium oxysporum f. sp. cucumerinum. An endophytic strain CNS-42 isolated from Alisma orientale showed the largest zone of inhibition demonstrating a potent effect against F. oxysporum f. sp. cucumerinum and a broad antimicrobial activity against bacteria, yeasts, and other pathogenic fungi. The in vivo biocontrol assays showed that the disease severity index was significantly reduced (P < 0.05), and plant shoot fresh weight and height increased greatly (P < 0.05) in plantlets treated with strain CNS-42 compared to the negative control. This isolate was identified as Streptomyces sp. based on cultural, physiological, morphological characteristics, and 16S rRNA gene analysis. Further bioassay-guided isolation and purification revealed that staurosporine was responsible for its antifungal and plant growth promoting activities and the latter property of staurosporine is reported for the first time. The in vivo assay was further performed and indicated that staurosporine showed good growth promoting effect on the plant shoot biomass of cucumber. This is the first critical evidence identifying CNS-42 as a biocontrol agent for the soil borne pathogen, F. oxysporum f. sp. cucumerinum. PMID:25035061

Li, Xiaolin; Huang, Pei; Wang, Qian; Xiao, Lie; Liu, Miaomiao; Bolla, Krishna; Zhang, Bo; Zheng, Linyong; Gan, Bingcheng; Liu, Xueting; Zhang, Lixin; Zhang, Xiaoping

2014-09-01

274

A Novel (S)-6-Hydroxynicotine Oxidase Gene from Shinella sp. Strain HZN7.  

PubMed

Nicotine is an important environmental toxicant in tobacco waste. Shinella sp. strain HZN7 can metabolize nicotine into nontoxic compounds via variations of the pyridine and pyrrolidine pathways. However, the catabolic mechanism of this variant pathway at the gene or enzyme level is still unknown. In this study, two 6-hydroxynicotine degradation-deficient mutants, N7-M9 and N7-W3, were generated by transposon mutagenesis. The corresponding mutant genes, designated nctB and tnp2, were cloned and analyzed. The nctB gene encodes a novel flavin adenine dinucleotide-containing (S)-6-hydroxynicotine oxidase that converts (S)-6-hydroxynicotine into 6-hydroxy-N-methylmyosmine and then spontaneously hydrolyzes into 6-hydroxypseudooxynicotine. The deletion and complementation of the nctB gene showed that this enzyme is essential for nicotine or (S)-6-hydroxynicotine degradation. Purified NctB could also convert (S)-nicotine into N-methylmyosmine, which spontaneously hydrolyzed into pseudooxynicotine. The kinetic constants of NctB toward (S)-6-hydroxynicotine (Km = 0.019 mM, kcat = 7.3 s(-1)) and nicotine (Km = 2.03 mM, kcat = 0.396 s(-1)) indicated that (S)-6-hydroxynicotine is the preferred substrate in vivo. NctB showed no activities toward the R enantiomer of nicotine or 6-hydroxynicotine. Strain HZN7 could degrade (R)-nicotine into (R)-6-hydroxynicotine without any further degradation. The tnp2 gene from mutant N7-W3 encodes a putative transposase, and its deletion did not abolish the nicotine degradation activity. This study advances the understanding of the microbial diversity of nicotine biodegradation. PMID:25002425

Qiu, Jiguo; Wei, Yin; Ma, Yun; Wen, Rongti; Wen, Yuezhong; Liu, Weiping

2014-09-15

275

Cloning of a Novel Arylamidase Gene from Paracoccus sp. Strain FLN-7 That Hydrolyzes Amide Pesticides  

PubMed Central

The bacterial isolate Paracoccus sp. strain FLN-7 hydrolyzes amide pesticides such as diflubenzuron, propanil, chlorpropham, and dimethoate through amide bond cleavage. A gene, ampA, encoding a novel arylamidase that catalyzes the amide bond cleavage in the amide pesticides was cloned from the strain. ampA contains a 1,395-bp open reading frame that encodes a 465-amino-acid protein. AmpA was expressed in Escherichia coli BL21 and homogenously purified using Ni-nitrilotriacetic acid affinity chromatography. AmpA is a homodimer with an isoelectric point of 5.4. AmpA displays maximum enzymatic activity at 40°C and a pH of between 7.5 and 8.0, and it is very stable at pHs ranging from 5.5 to 10.0 and at temperatures up to 50°C. AmpA efficiently hydrolyzes a variety of secondary amine compounds such as propanil, 4-acetaminophenol, propham, chlorpropham, dimethoate, and omethoate. The most suitable substrate is propanil, with Km and kcat values of 29.5 ?M and 49.2 s?1, respectively. The benzoylurea insecticides (diflubenzuron and hexaflumuron) are also hydrolyzed but at low efficiencies. No cofactor is needed for the hydrolysis activity. AmpA shares low identities with reported arylamidases (less than 23%), forms a distinct lineage from closely related arylamidases in the phylogenetic tree, and has different biochemical characteristics and catalytic kinetics with related arylamidases. The results in the present study suggest that AmpA is a good candidate for the study of the mechanism for amide pesticide hydrolysis, genetic engineering of amide herbicide-resistant crops, and bioremediation of amide pesticide-contaminated environments. PMID:22544249

Zhang, Jun; Yin, Jin-Gang; Hang, Bao-Jian; Cai, Shu; Li, Shun-Peng

2012-01-01

276

Characterization of a New Providencia sp. Strain X1 Producing Multiple Xylanases on Wheat Bran  

PubMed Central

Providencia sp. strain X1 showing the highest xylanase activity among six bacterial isolates was isolated from saw-dust decomposing site. Strain X1 produced cellulase-free extracellular xylanase, which was higher in wheat bran medium than in xylan medium, when cultivated at pH 8.0 and 35°C. Zymogram analysis of crude preparation of enzymes obtained while growing on wheat bran and birchwood xylan revealed the presence of seven and two distinct xylanases with estimated molecular weight of 33; 35; 40; 48; 60; 75; and 95?kDa and 33 and 44?kDa, respectively. The crude xylanases were produced on wheat bran medium and showed optimum activity at pH 9.0 and 60°C. The thermotolerance studies showed activity retention of 100% and 85% at 40°C and 60°C after 30 min preincubation at pH 9.0. It was tolerant to lignin, ferulic acid, syringic acid, and guaiacol and retained 90% activity after ethanol treatment. The enzyme preparation was also tolerant to methanol and acetone and showed good activity retention in the presence of metal ions such as Fe2+, Mg2+, Zn2+, and Ca2+. The crude enzyme preparation was classified as endoxylanase based on the product pattern of xylan hydrolysis. Pretreatment of kraft pulp with crude xylanases for 3?h at 60°C led to a decrease in kappa number by 28.5%. The properties of present xylanases make them potentially useful for industrial applications. PMID:24348154

Kumar, Sharad; Singh, Sudheer Kumar; Kumar, Mahadeo

2013-01-01

277

Genome sequence of Rhizobium sp. strain CCGE510, a symbiont isolated from nodules of the endangered wild bean Phaseolus albescens.  

PubMed

We present the genome sequence of Rhizobium sp. strain CCGE510, a nitrogen fixing bacterium taxonomically affiliated with the R. leguminosarum-R. etli group, isolated from wild Phaseolus albescens nodules grown in native pine forests in western Mexico. P. albescens is an endangered bean species phylogenetically related to P. vulgaris. In spite of the close host relatedness, Rhizobium sp. CCGE510 does not establish an efficient symbiosis with P. vulgaris. This is the first genome of a Rhizobium symbiont from a Phaseolus species other than P. vulgaris, and it will provide valuable new insights about symbiont-host specificity. PMID:23105056

Servín-Garcidueñas, Luis E; Rogel, Marco A; Ormeño-Orrillo, Ernesto; Delgado-Salinas, Alfonso; Martínez-Romero, Julio; Sánchez, Federico; Martínez-Romero, Esperanza

2012-11-01

278

Tributyl phosphate biodegradation to butanol and phosphate and utilization by a novel bacterial isolate, Sphingobium sp. strain RSMS.  

PubMed

A Sphingobium sp. strain isolated from radioactive solid waste management site (RSMS) completely degraded 7.98 g/L of tributyl phosphate (TBP) from TBP containing suspensions in 3 days. It also completely degraded 20 mM dibutyl phosphate (DBP) within 2 days. The strain tolerated high levels of TBP and showed excellent stability with respect to TBP degradation over several repeated subcultures. On solid minimal media or Luria Bertani media supplemented with TBP, the RSMS strain showed a clear zone of TBP degradation around the colony. Gas chromatography and spectrophotometry analyses identified DBP as the intermediate and butanol and phosphate as the products of TBP biodegradation. The RSMS strain utilized both TBP and DBP as the sole source of carbon and phosphorous for its growth. The butanol released was completely utilized by the strain as a carbon source thereby leaving no toxic residue in the medium. Degradation of TBP or DBP was found to be suppressed by high concentration of glucose which also inhibited TBP or DBP dependent growth. The results highlight the potential of Sphingobium sp. strain RSMS for bioremediation of TBP and for further molecular investigation. PMID:23963271

Rangu, Shyam Sunder; Muralidharan, Bindu; Tripathi, S C; Apte, Shree Kumar

2014-03-01

279

Genomic and Transcriptomic Analyses of the Facultative Methanotroph Methylocystis sp. Strain SB2 Grown on Methane or Ethanol  

PubMed Central

A minority of methanotrophs are able to utilize multicarbon compounds as growth substrates in addition to methane. The pathways utilized by these microorganisms for assimilation of multicarbon compounds, however, have not been explicitly examined. Here, we report the draft genome of the facultative methanotroph Methylocystis sp. strain SB2 and perform a detailed transcriptomic analysis of cultures grown with either methane or ethanol. Evidence for use of the canonical methane oxidation pathway and the serine cycle for carbon assimilation from methane was obtained, as well as for operation of the complete tricarboxylic acid (TCA) cycle and the ethylmalonyl-coenzyme A (EMC) pathway. Experiments with Methylocystis sp. strain SB2 grown on methane revealed that genes responsible for the first step of methane oxidation, the conversion of methane to methanol, were expressed at a significantly higher level than those for downstream oxidative transformations, suggesting that this step may be rate limiting for growth of this strain with methane. Further, transcriptomic analyses of Methylocystis sp. strain SB2 grown with ethanol compared to methane revealed that on ethanol (i) expression of the pathway of methane oxidation and the serine cycle was significantly reduced, (ii) expression of the TCA cycle dramatically increased, and (iii) expression of the EMC pathway was similar. Based on these data, it appears that Methylocystis sp. strain SB2 converts ethanol to acetyl-coenzyme A, which is then funneled into the TCA cycle for energy generation or incorporated into biomass via the EMC pathway. This suggests that some methanotrophs have greater metabolic flexibility than previously thought and that operation of multiple pathways in these microorganisms is highly controlled and integrated. PMID:24610846

Vorobev, Alexey; Jagadevan, Sheeja; Jain, Sunit; Anantharaman, Karthik; Dick, Gregory J.; Vuilleumier, Stéphane

2014-01-01

280

Genomic and transcriptomic analyses of the facultative methanotroph Methylocystis sp. strain SB2 grown on methane or ethanol.  

PubMed

A minority of methanotrophs are able to utilize multicarbon compounds as growth substrates in addition to methane. The pathways utilized by these microorganisms for assimilation of multicarbon compounds, however, have not been explicitly examined. Here, we report the draft genome of the facultative methanotroph Methylocystis sp. strain SB2 and perform a detailed transcriptomic analysis of cultures grown with either methane or ethanol. Evidence for use of the canonical methane oxidation pathway and the serine cycle for carbon assimilation from methane was obtained, as well as for operation of the complete tricarboxylic acid (TCA) cycle and the ethylmalonyl-coenzyme A (EMC) pathway. Experiments with Methylocystis sp. strain SB2 grown on methane revealed that genes responsible for the first step of methane oxidation, the conversion of methane to methanol, were expressed at a significantly higher level than those for downstream oxidative transformations, suggesting that this step may be rate limiting for growth of this strain with methane. Further, transcriptomic analyses of Methylocystis sp. strain SB2 grown with ethanol compared to methane revealed that on ethanol (i) expression of the pathway of methane oxidation and the serine cycle was significantly reduced, (ii) expression of the TCA cycle dramatically increased, and (iii) expression of the EMC pathway was similar. Based on these data, it appears that Methylocystis sp. strain SB2 converts ethanol to acetyl-coenzyme A, which is then funneled into the TCA cycle for energy generation or incorporated into biomass via the EMC pathway. This suggests that some methanotrophs have greater metabolic flexibility than previously thought and that operation of multiple pathways in these microorganisms is highly controlled and integrated. PMID:24610846

Vorobev, Alexey; Jagadevan, Sheeja; Jain, Sunit; Anantharaman, Karthik; Dick, Gregory J; Vuilleumier, Stéphane; Semrau, Jeremy D

2014-05-01

281

Response surface optimization for efficient dye removal by isolated strain Pseudomonas sp.  

NASA Astrophysics Data System (ADS)

Response surface methodology (RSM) involving the central composite design (CCD) was employed to optimize three important process variables for the decolourization of synthetic dye solutions containing Remazol Turquoise Blue (RTB) and Reactive Black 5 (RB5) with isolated bacterial strain Pseudomonas sp. The interaction between three variables i.e. Initial concentration of dye, carbon source and nitrogen source were studied and modeled. According to the Analysis of variance (ANOVA) results the predicted results were found to be in good agreement with experimental results ( R 2: 0.9726; Adj R 2: 0.9480 for RTB and R 2: 0.9789; Adj R 2: 0.9750 for RB5) which indicated excellent evaluation of experimental data from the second order polynomial regression model. Mathematical models were developed by the proposed system, for each process variable showed the effect of each factor and their interactions on biodecolourization process. The optimum concentrations of Dye, Carbon source, and Nitrogen source were found to be 20 mgL-1, 1.5 g/L and 1.5 g/L, respectively for RTB and RB5 to obtain maximum dye removing capacity. Predicted values were validated with experimental results, which indicated appropriateness of the employed model and the success of RSM.

Senthilkumar, Shanmugam; Perumalsamy, Muthiah; Prabhuy, Harinarayan Janardhana; AhmedBasha, Chiya; Anantharaman, Narayan

2012-09-01

282

Identification of alkane hydroxylase genes in Rhodococcus sp. strain TMP2 that degrades a branched alkane  

E-print Network

Abstract Rhodococcus sp. TMP2 is an alkanedegrading strain that can grow with a branched alkane as a sole carbon source. TMP2 degrades considerable amounts of pristane at 20°C but not at 30°C. In order to gain insights into microbial alkane degradation, we characterized one of the key enzymes for alkane degradation. TMP2 contains at least five genes for membrane-bound, non-heme iron, alkane hydroxylase, known as AlkB (alkB1–5). Phylogenetical analysis using bacterial alkB genes indicates that TMP2 is a close relative of the alkane-degrading bacteria, such as Rhodococcus erythropolis NRRL B-16531 and Q15. RT-PCR analysis showed that expressions of the genes for AlkB1 and AlkB2 were apparently induced by the addition of pristane at a low temperature. The results suggest that TMP2 recruits certain alkane hydroxylase systems to utilize a branched alkane under low temperature conditions.

Masaaki Morikawa; D. Takei; K. Washio; M. Morikawa

283

Kinetics of Molybdenum Reduction to Molybdenum Blue by Bacillus sp. Strain A.rzi  

PubMed Central

Molybdenum is very toxic to agricultural animals. Mo-reducing bacterium can be used to immobilize soluble molybdenum to insoluble forms, reducing its toxicity in the process. In this work the isolation of a novel molybdate-reducing Gram positive bacterium tentatively identified as Bacillus sp. strain A.rzi from a metal-contaminated soil is reported. The cellular reduction of molybdate to molybdenum blue occurred optimally at 4?mM phosphate, using 1% (w/v) glucose, 50?mM molybdate, between 28 and 30°C and at pH 7.3. The spectrum of the Mo-blue product showed a maximum peak at 865?nm and a shoulder at 700?nm. Inhibitors of bacterial electron transport system (ETS) such as rotenone, sodium azide, antimycin A, and potassium cyanide could not inhibit the molybdenum-reducing activity. At 0.1?mM, mercury, copper, cadmium, arsenic, lead, chromium, cobalt, and zinc showed strong inhibition on molybdate reduction by crude enzyme. The best model that fitted the experimental data well was Luong followed by Haldane and Monod. The calculated value for Luong's constants pmax, Ks, Sm, and n was 5.88??mole Mo-blue hr?1, 70.36?mM, 108.22?mM, and 0.74, respectively. The characteristics of this bacterium make it an ideal tool for bioremediation of molybdenum pollution. PMID:24369531

Othman, A. R.; Bakar, N. A.; Halmi, M. I. E.; Johari, W. L. W.; Ahmad, S. A.; Jirangon, H.; Syed, M. A.; Shukor, M. Y.

2013-01-01

284

A thermostable humic acid peroxidase from Streptomyces sp. strain AH4: purification and biochemical characterization.  

PubMed

An extracellular thermostable humic acid peroxidase (HaP3) was isolated from a Streptomyces sp. strain AH4. MALDI-TOF MS analysis showed that the purified enzyme was a monomer with a molecular mass of 60,215.18Da. The 26N-terminal residues of HaP3 displayed high homology with Streptomyces peroxidases. Optimal peroxidase activity was obtained at pH 5 and 80°C. HaP3 was stable at pH and temperature ranges of 4-8 and 60-90°C for 72 and 4h, respectively. HaP3 catalyzed the oxidation of 2,4-dichlorophenol, commercial humic acid, guiacol, and 2,6-dichlorophenol (50mM); L-3,4-dihydroxyphenylalanine (40 mM); 4-chlorophenol, 2,4,5-trichlorophenol, and 2,4,6-trichlorophenol (30 mM) in the presence of hydrogen peroxide. Sodium azide and potassium cyanide inhibited HaP3, which indicated the presence of heme components. These properties make HaP3 a potential strong candidate for future application in the elimination of natural humic acids in drinking water. PMID:22342039

Fodil, Djamila; Jaouadi, Bassem; Badis, Abdelmalek; Nadia, Zaraî Jaouadi; Ferradji, Fatma Zohra; Bejar, Samir; Boutoumi, Houcine

2012-05-01

285

Purification and Properties of a Xylan-Binding Endoxylanase from Alkaliphilic Bacillus sp. Strain K-1  

PubMed Central

An alkaliphilic bacterium, Bacillus sp. strain K-1, produces extracellular xylanolytic enzymes such as xylanases, ?-xylosidase, arabinofuranosidase, and acetyl esterase when grown in xylan medium. One of the extracellular xylanases that is stable in an alkaline state was purified to homogeneity by affinity adsorption-desorption on insoluble xylan. The enzyme bound to insoluble xylan but not to crystalline cellulose. The molecular mass of the purified xylan-binding xylanase was estimated to be approximately 23 kDa. The enzyme was stable at alkaline pHs up to 12. The optimum temperature and optimum pH of the enzyme activity were 60°C and 5.5, respectively. Metal ions such as Fe2+, Ca2+, and Mg2+ greatly increased the xylanase activity, whereas Mn2+ strongly inhibited it. We also demonstrated that the enzyme could hydrolyze the raw lignocellulosic substances effectively. The enzymatic products of xylan hydrolysis were a series of short-chain xylooligosaccharides, indicating that the enzyme was an endoxylanase. PMID:9925602

Ratanakhanokchai, Khanok; Kyu, Khin Lay; Tanticharoen, Morakot

1999-01-01

286

Inhibitor studies of dissimilative Fe(III) reduction by Pseudomonas sp. strain 200 (Pseudomonas ferrireductans)  

SciTech Connect

Aerobic respiration and dissimilative iron reduction were studied in pure, batch cultures of Pseudomonas sp. strain 200 (Pseudomonas ferrireductans). Specific respiratory inhibitors were used to identify elements of electron transport chains involved in the reduction of molecular oxygen and Fe(III). When cells were grown at a high oxygen concentration, dissimilative iron reduction occurred via an abbreviated electron transport chain. The induction of alternative respiratory pathways resulted from growth at low oxygen tension (<0.01 atm (1 atm = 101.29 kPa)). Induced cells were capable of O/sub 2/ utilization at moderately increased rates; dissimilative iron reduction was accelerated by a factor of 6 to 8. In cells grown at low oxygen tension, dissimilative iron reduction appeared to be uncoupled from oxidative phosphorylation. Models of induced and uninduced electron transport chains, including a mathematical treatment of chemical inhibition within the uninduced, aerobic electron transport system, are presented. In uninduced cells respiring anaerobically, electron transport was limited by ferrireductase activity. This limitation may disappear among induced cells.

Arnold, R.G.; DiChristina, T.J.; Hoffman, M.R.

1986-08-01

287

D-erythrose supports nitrogenase activity in isolated Anabaena sp. strain 7120 heterocysts.  

PubMed Central

Among organic compounds tested for their ability to support nitrogenase activity in isolated heterocysts of Anabaena sp. strain 7120 under argon, D-erythrose (5 mM) was unique in supporting acetylene reduction at 10 times the control rates. Higher concentrations of D-erythrose exhibited substrate inhibition. At 50 kPa of H2, all concentrations of D-erythrose inhibited H2-supported acetylene reduction. The effects of D-erythrose on nitrogenase activity were explored. Erythrose enhanced 15N2 incorporation by heterocysts, but NADP+ did not enhance erythrose-supported acetylene reduction. H2 protected nitrogenase from O2 inactivation, but erythrose did not; erythrose did not counter protection by H2. Tests with inhibitors of electron transport showed that erythrose-supported acetylene reduction requires electron flow through ferredoxin, a b-type cytochrome, and a 2,5-dibromo-3-methyl-6-isopropyl-p-benzoquinone-sensitive transfer agent whose electron flow is not mediated through the plastoquinone and Rieske iron protein. PMID:6229527

Privalle, L S; Burris, R H

1984-01-01

288

Primary structure of microbial transglutaminase from Streptoverticillium sp. strain s-8112.  

PubMed

The complete amino acid sequence of transglutaminase (EC 2.3.2.13) (TGase), which is produced by a microorganism, Streptoverticillium sp. strain s-8112, and catalyzes the acyl transfer reaction between gamma-carboxyamide groups of glutamine residues in proteins and various primary amines, has been established by a combination of fast atom bombardment mass spectrometry and standard Edman degradation of peptide fragments produced by treatment of the TGase with various proteolytic enzymes and purified by a reversed-phase high performance liquid chromatography. The TGase consists of 331 amino acid residues with a chemical molecular weight of 37,863, in agreement with the observed molecular weight (37,869.2 +/- 8.8) determined from its electrospray ionization mass spectrum. The sequence of the enzyme is very different from those of mammalian TGases represented by guinea pig liver enzyme. The enzyme contains a sole Cys residue, which is essential for its catalytic activity. Hydropathy analysis indicated that the secondary structure of the region around the active site Cys residue is similar to those of mammalian TGases. These results suggest that this microbial protein evolved by a different pathway from that of mammalian TGases and acquired acyl transfer activity during the evolutional process. PMID:8099353

Kanaji, T; Ozaki, H; Takao, T; Kawajiri, H; Ide, H; Motoki, M; Shimonishi, Y

1993-06-01

289

A further insight into the mechanism of Ag + biosorption by Lactobacillus sp. strain A09  

NASA Astrophysics Data System (ADS)

The mechanism of Ag + biosorption by resting cell of Lactobacillus sp. strain A09 has been further investigated at the molecular level using spectroscopic techniques. The values of estimated equilibrium constants, rate constants, half-life periods and apparent enthalpies of the binding reaction were calculated via the determination of Ag + adsorbed by the biomass using atomic absorption spectrophotometry (AAS). The reductive ratio of the Ag + to Ag 0 by the A09 biomass was examined by X-ray photoelectron spectroscopy (XPS). Analysis for sulfur and nitrogen atomic contents in dry powder of the biomass with EA-1110 elemental analysis (EA) showed that amino acid residues retaining the reductive property of Ag + to Ag 0 are very small quantity, whereas glucose content in the hydrolysates of the biomass analyzed by ultraviolet-visible spectrophotometry (UV-vis) indicated that the amount of reducing sugars in the biomass is much larger than 2.71%. The fourier transform infrared (FTIR) spectrophotometry on blank and silver-loaded biomass demonstrated that the chemical functional group such as the free aldehyde group of the hemiacetalic hydroxyl group from reducing sugars, i.e. the hydrolysates of the polysaccharides from the cell wall plays a leading role in serving as the electron donor for reducing the Ag + to Ag 0. This result was further supported by characterizations on the interaction of the Ag + with glucose using X-ray powder diffractometry (XRD) and FTIR spectroscopy.

Lin, Zhongyu; Zhou, Chaohui; Wu, Jianming; Zhou, Jianzhang; Wang, Lin

2005-04-01

290

Oxidation of aminonitrotoluenes by 2,4-DNT dioxygenase of Burkholderia sp. strain DNT.  

PubMed

Aminonitrotoluenes form rapidly from the reduction of dinitrotoluenes (DNTs) which are priority pollutants and animal carcinogens. For example, 4-amino-2-nitrotoluene (4A2NT) and 2A4NT accumulate from the reduction of 2,4-DNT during its aerobic biodegradation. Here, we show that 2,4-DNT dioxygenase (DDO) from Burkholderia sp. strain DNT oxidizes the aminonitrotoluenes 2A3NT, 2A6NT, 4A3NT, and 5A2NT to 2-amino-3-nitrobenzylalcohol, 2-amino-4-nitro-m-cresol and 3-amino-5-nitro-p-cresol, 4-amino-3-nitrobenzylalcohol and aminonitrocresol, and 2-amino-5-nitro-o-cresol, respectively. 2A5NT and 3A4NT are oxidized to aminonitrocresols and/or aminonitrobenzylalcohols, and 4A2NT is oxidized to aminonitrocresol. Only 2A4NT, a reduced compound derived from 2,4-DNT, was not oxidized by DDO or its three variants. The alpha subunit mutation I204Y resulted in two to fourfold faster oxidization of the aminonitrotoluenes. Though these enzymes are dioxygenases, they acted like monooxygenases by adding a single hydroxyl group, which did not result in the release of nitrite. PMID:16315327

Leungsakul, Thammajun; Keenan, Brendan G; Mori, Masa-aki; Morton, Martha D; Stuart, James D; Smets, Barth F; Wood, Thomas K

2006-02-01

291

Purification and characterization of haloalcohol dehalogenase from Arthrobacter sp. strain AD2.  

PubMed Central

An enzyme capable of dehalogenating vicinal haloalcohols to their corresponding epoxides was purified from the 3-chloro-1,2-propanediol-utilizing bacterium Arthrobacter sp. strain AD2. The inducible haloalcohol dehalogenase converted 1,3-dichloro-2-propanol, 3-chloro-1,2-propanediol, 1-chloro-2-propanol, and their brominated analogs, 2-bromoethanol, as well as chloroacetone and 1,3-dichloroacetone. The enzyme possessed no activity for epichlorohydrin (3-chloro-1,2-epoxypropane) or 2,3-dichloro-1-propanol. The dehalogenase had a broad pH optimum at about 8.5 and a temperature optimum of 50 degrees C. The enzyme followed Michaelis-Menten kinetics, and the Km values for 1,3-dichloro-2-propanol and 3-chloro-1,2-propanediol were 8.5 and 48 mM, respectively. Chloroacetic acid was a competitive inhibitor, with a Ki of 0.50 mM. A subunit molecular mass of 29 kDa was determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. With gel filtration, a molecular mass of 69 kDa was found, indicating that the native protein is a dimer. The amino acid composition and N-terminal amino acid sequence are given. Images PMID:1846134

van den Wijngaard, A J; Reuvekamp, P T; Janssen, D B

1991-01-01

292

Isolation of a Paenibacillus sp. Strain and Structural Elucidation of Its Broad-Spectrum Lipopeptide Antibiotic  

PubMed Central

This research was initiated to search for novel antimicrobial compounds produced by food or environmental microorganisms. A new bacterial strain, designated OSY-SE, which produces a unique and potent antimicrobial agent was isolated from soil. The isolate was identified as a Paenibacillus sp. through cultural, biochemical, and genetic analyses. An antimicrobial compound was extracted from Paenibacillus OSY-SE with acetonitrile and purified using liquid chromatography. After analyses by mass spectrometry (MS) and nuclear magnetic resonance (NMR), the antimicrobial compound was determined to be a cyclic lipopeptide consisting of a C15 fatty acyl (FA) chain and 13 amino acids. The deduced sequence is FA-Orn-Val-Thr-Orn-Ser-Val-Lys-Ser-Ile-Pro-Val-Lys-Ile. The carboxyl-terminal Ile is connected to Thr by ester linkage. The new compound, designated paenibacterin, showed antagonistic activities against most Gram-positive and Gram-negative bacteria tested, including Listeria monocytogenes, methicillin-resistant Staphylococcus aureus, Escherichia coli O157:H7, and Salmonella enterica serovar Typhimurium. Paenibacterin is resistant to trypsin, lipase, ?-glucosidase, and lysozyme. Its antimicrobial activity was lost after digestion by pronase and polymyxin acylase. Paenibacterin is readily soluble in water and fairly stable to exposure to heat and a wide range of pH values. The new isolate and its antimicrobial agent are being investigated for usefulness in food and medical applications. PMID:22367082

Guo, Yaoqi; Huang, En; Yuan, Chunhua; Zhang, Liwen

2012-01-01

293

Cloning of a gene from Pseudomonas sp. strain PG2982 conferring increased glyphosate resistance.  

PubMed Central

A plasmid carrying a 2.4-kilobase-pair fragment of DNA from Pseudomonas sp. strain PG2982 has been isolated which was able to increase the glyphosate resistance of Escherichia coli cells. The increase in resistance was dependent on the presence of a plasmid-encoded protein with a molecular weight of approximately 33,000, the product of a translational fusion between a gene on the vector, pACYC184, and the insert DNA. An overlapping region of the PG2982 chromosome carrying the entire gene (designated igrA) was cloned, and a plasmid (pPG18) carrying the gene was also able to increase glyphosate resistance in E. coli. A protein with a molecular weight of approximately 40,000 was encoded by the PG2982 DNA contained in pPG18. This plasmid was not able to complement a mutation in the gene for 5-enolpyruvylshikimate-3-phosphate synthase (aroA) in E. coli, and modification of glyphosate by E. coli cells containing the plasmid could not be demonstrated. The nucleotide sequence of the PG2982 DNA contained an open reading frame able to encode a protein with a calculated molecular weight of 39,396. Images PMID:2268152

Fitzgibbon, J E; Braymer, H D

1990-01-01

294

Aerobic Biodegradation of 2,4-Dinitroanisole by Nocardioides sp. Strain JS1661.  

PubMed

2,4-Dinitroanisole (DNAN) is an insensitive munition ingredient used in explosive formulations as a replacement for 2,4,6-trinitrotoluene (TNT). Little is known about the environmental behavior of DNAN. There are reports of microbial transformation to dead-end products, but no bacteria with complete biodegradation capability have been reported. Nocardioides sp. strain JS1661 was isolated from activated sludge based on its ability to grow on DNAN as the sole source of carbon and energy. Enzyme assays indicated that the first reaction involves hydrolytic release of methanol to form 2,4-dinitrophenol (2,4-DNP). Growth yield and enzyme assays indicated that 2,4-DNP underwent subsequent degradation by a previously established pathway involving formation of a hydride-Meisenheimer complex and release of nitrite. Identification of the genes encoding the key enzymes suggested recent evolution of the pathway by recruitment of a novel hydrolase to extend the well-characterized 2,4-DNP pathway. PMID:25281383

Fida, Tekle Tafese; Palamuru, Shannu; Pandey, Gunjan; Spain, Jim C

2014-12-15

295

The biology of Frankia sp. strains in the post-genome era.  

PubMed

Progress in understanding symbiotic determinants involved in the N(2)-fixing actinorhizal plant symbioses has been slow but steady. Problems persist with studying the bacterial contributions to the symbiosis using traditional microbiological techniques. However, recent years have seen the emergence of several genomes from Frankia sp. strains and the development of techniques for manipulating plant gene expression. Approaches to understanding the bacterial side of the symbiosis have employed a range of techniques that reveal the proteomes and transcriptomes from both cultured and symbiotic frankiae. The picture beginning to emerge provides some perspective on the heterogeneity of frankial populations in both conditions. In general, frankial populations in root nodules seem to maintain a rather robust metabolism that includes nitrogen fixation and substantial biosynthesis and energy-generating pathways, along with a modified ammonium assimilation program. To date, particular bacterial genes have not been implicated in root nodule formation but some hypotheses are emerging with regard to how the plant and microorganism manage to coexist. In particular, frankiae seem to present a nonpathogenic presence to the plant that may have the effect of minimizing some plant defense responses. Future studies using high-throughput approaches will likely clarify the range of bacterial responses to symbiosis that will need to be understood in light of the more rapidly advancing work on the plant host. PMID:21848398

Benson, David R; Brooks, James M; Huang, Ying; Bickhart, Derek M; Mastronunzio, Juliana E

2011-11-01

296

Discovery and characterization of a 5-hydroxymethylfurfural oxidase from Methylovorus sp. strain MP688.  

PubMed

In the search for useful and renewable chemical building blocks, 5-hydroxymethylfurfural (HMF) has emerged as a very promising candidate, as it can be prepared from sugars. HMF can be oxidized to 2,5-furandicarboxylic acid (FDCA), which is used as a substitute for petroleum-based terephthalate in polymer production. On the basis of a recently identified bacterial degradation pathway for HMF, candidate genes responsible for selective HMF oxidation have been identified. Heterologous expression of a protein from Methylovorus sp. strain MP688 in Escherichia coli and subsequent enzyme characterization showed that the respective gene indeed encodes an efficient HMF oxidase (HMFO). HMFO is a flavin adenine dinucleotide-containing oxidase and belongs to the glucose-methanol-choline-type flavoprotein oxidase family. Intriguingly, the activity of HMFO is not restricted to HMF, as it is active with a wide range of aromatic primary alcohols and aldehydes. The enzyme was shown to be relatively thermostable and active over a broad pH range. This makes HMFO a promising oxidative biocatalyst that can be used for the production of FDCA from HMF, a reaction involving both alcohol and aldehyde oxidations. PMID:24271187

Dijkman, Willem P; Fraaije, Marco W

2014-02-01

297

A novel regulatory role of the Rnf complex of Azoarcus sp. strain BH72.  

PubMed

The superfamily of P(II) proteins contains the most widely distributed signalling proteins in nature. Remarkable is the variety of targets whose activity is affected by protein-protein interactions. Here we identified as novel partner for interaction with GlnK an Rnf complex, known to couple the energy of ion transport to reduce ferredoxins. The endophytic diazotrophic betaproteobacterium Azoarcus sp. strain BH72 harbours two rnf-like clusters in the genome, of which only the rnf1 cluster was induced under conditions of N(2) fixation under control of the transcriptional activator NifA. Rapid inactivation ('DraT-independent switch off') of nitrogenase activity upon ammonium upshift was dependent on the Rnf1 complex. Membrane sequestration of GlnK in steady-state N-surplus conditions occurred in its unmodified form, signalling N-surplus, and was dependent on presence of the Rnf1 complex, suggesting physical interaction. In vitro binding studies by Far-Western analysis indicated interactions of RnfC1 with specifically GlnK but not with GlnB. As ammonium upshift led to decreased activity of the Rnf1 complex in membranes, it might be inactivated by GlnK binding, leading to an interruption of electron flow to nitrogenase and thus a rapid, DraT-independent nitrogenase switch off. Our data imply a hitherto unknown interaction partner for a P(II)-like protein and an additional process under its control. PMID:22188282

Sarkar, Abhijit; Köhler, Jörg; Hurek, Thomas; Reinhold-Hurek, Barbara

2012-01-01

298

Microbial System for Polysaccharide Depolymerization: Enzymatic Route for Xanthan Depolymerization by Bacillus sp. Strain GL1  

PubMed Central

An enzymatic route for the depolymerization of a heteropolysaccharide (xanthan) in Bacillus sp. strain GL1, which was closely related to Brevibacillus thermoruber, was determined by analyzing the structures of xanthan depolymerization products. The bacterium produces extracellular xanthan lyase catalyzing the cleavage of the glycosidic bond between pyruvylated mannosyl and glucuronyl residues in xanthan side chains (W. Hashimoto et al., Appl. Environ. Microbiol. 64:3765–3768, 1998). The modified xanthan after the lyase reaction was then depolymerized by extracellular ?-d-glucanase to a tetrasaccharide, without the terminal mannosyl residue of the side chain in a pentasaccharide, a repeating unit of xanthan. The tetrasaccharide was taken into cells and converted to a trisaccharide (unsaturated glucuronyl-acetylated mannosyl-glucose) by ?-d-glucosidase. The trisaccharide was then converted to the unsaturated glucuronic acid and a disaccharide (mannosyl-glucose) by unsaturated glucuronyl hydrolase. Finally, the disaccharide was hydrolyzed to mannose and glucose by ?-d-mannosidase. This is the first complete report on xanthan depolymerization by bacteria. Novel ?-d-glucanase, one of the five enzymes involved in the depolymerization route, was purified from the culture fluid. This enzyme was a homodimer with a subunit molecular mass of 173 kDa and was most active at pH 6.0 and 45°C. The enzyme specifically acted on xanthan after treatment with xanthan lyase and released the tetrasaccharide. PMID:10347037

Nankai, Hirokazu; Hashimoto, Wataru; Miki, Hikaru; Kawai, Shigeyuki; Murata, Kousaku

1999-01-01

299

Isolation of Paenibacillus sp. and Variovorax sp. strains from decaying woods and characterization of their potential for cellulose deconstruction.  

PubMed

Prospection of cellulose-degrading bacteria in natural environments allows the identification of novel cellulases and hemicellulases that could be useful in second-generation bioethanol production. In this work, cellulolytic bacteria were isolated from decaying native forest soils by enrichment on cellulose as sole carbon source. There was a predominance of Gram positive isolates that belonged to the phyla Proteobacteria and Firmicutes. Many primary isolates with cellulolytic activity were not pure cultures. From these consortia, isolation of pure constituents was attempted in order to test the hypothesis whether microbial consortia are needed for full degradation of complex substrates. Two isolates, CB1-2-A-5 and VG-4-A-2, were obtained as the pure constituents of CB1-2 and VG-4 consortia, respectively. Based on 16S RNA sequence, they could be classified as Variovorax paradoxus and Paenibacillus alvei. Noteworthy, only VG-4 consortium showed measurable xylan degrading capacity and signs of filter paper degradation. However, no xylan or filter paper degrading capacities were observed for the pure cultures isolated from it, suggesting that other members of this consortium were necessary for these hydrolyzing activities. Our results indicated that Paenibacillus sp. and Variovorax sp. as well as VG-4 consortium, might be a useful source of hydrolytic enzymes. Moreover, although Variovorax sp. had been previously identified in metagenomic studies of cellulolytic communities, this is the first report on the isolation and characterization of this microorganism as a cellulolytic genus. PMID:23301200

Ghio, Silvina; Lorenzo, Gonzalo Sabarís Di; Lia, Verónica; Talia, Paola; Cataldi, Angel; Grasso, Daniel; Campos, Eleonora

2012-01-01

300

Isolation and characterization of 3,5,6-trichloro-2-pyridinol-degrading Ralstonia sp. strain T6.  

PubMed

A 3,5,6-trichloro-2-pyridinol (TCP)-degrading strain, T6, was isolated by continuous enrichment culture and identified as Ralstonia sp. based on morphological, physiological and biochemical tests as well as 16S rDNA sequence analysis. The bacterium metabolized 100 mg/L TCP within 12 h and 700 mg/L TCP in 80 h. A green metabolite, putatively identified as 3,6-dihydroxypyridine-2,5-dione, was detected. This is the first report of TCP-degrading isolate from the genus of Ralstonia. Strain T6 could potentially be employed in bioremediation of TCP. PMID:20457514

Li, Jingquan; Liu, Juan; Shen, Wenjing; Zhao, Xiaoli; Hou, Ying; Cao, Hui; Cui, Zhongli

2010-10-01

301

Influence of Carbon Sources and Electron Shuttles on Ferric Iron Reduction by Cellulomonas sp. Strain ES6  

SciTech Connect

Microbially reduced iron minerals can reductively transform a variety of contaminants including heavy metals, radionuclides, chlorinated aliphatics, and nitroaromatics. A number of Cellulomonas spp. strains, including strain ES6, isolated from aquifer samples obtained at the U.S. Department of Energy's Hanford site in Washington, have been shown to be capable of reducing Cr(VI), TNT, natural organic matter, and soluble ferric iron [Fe(III)]. This research investigated the ability of Cellulomonas sp. strain ES6 to reduce solid phase and dissolved Fe(III) utilizing different carbon sources and various electron shuttling compounds. Results suggest that Fe(III) reduction by and growth of strain ES6 was dependent upon the type of electron donor, the form of iron present, and the presence of synthetic or natural organic matter, such as anthraquinone-2,6-disulfonate (AQDS) or humic substances. This research suggests that Cellulomonas sp. strain ES6 could play a significant role in metal reduction in the Hanford subsurface and that the choice of carbon source and organic matter addition can allow for independent control of growth and iron reduction activity.

Dr Robin Gerlach; Erin K. Field; Sridhar Viamajala; Brent M. Peyton; William A. Apel; Al B. Cunningham

2011-09-01

302

Influence of carbon sources and electron shuttles on ferric iron reduction by Cellulomonas sp. strain ES6.  

PubMed

Microbially reduced iron minerals can reductively transform a variety of contaminants including heavy metals, radionuclides, chlorinated aliphatics, and nitroaromatics. A number of Cellulomonas spp. strains, including strain ES6, isolated from aquifer samples obtained at the U.S. Department of Energy's Hanford site in Washington, have been shown to be capable of reducing Cr(VI), TNT, natural organic matter, and soluble ferric iron [Fe(III)]. This research investigated the ability of Cellulomonas sp. strain ES6 to reduce solid phase and dissolved Fe(III) utilizing different carbon sources and various electron shuttling compounds. Results suggest that Fe(III) reduction by and growth of strain ES6 was dependent upon the type of electron donor, the form of iron present, and the presence of synthetic or natural organic matter, such as anthraquinone-2,6-disulfonate (AQDS) or humic substances. This research suggests that Cellulomonas sp. strain ES6 could play a significant role in metal reduction in the Hanford subsurface and that the choice of carbon source and organic matter addition can allow for independent control of growth and iron reduction activity. PMID:21318474

Gerlach, Robin; Field, Erin K; Viamajala, Sridhar; Peyton, Brent M; Apel, William A; Cunningham, Al B

2011-09-01

303

DNA Microarray Analysis of Redox-Responsive Genes in the Genome of the Cyanobacterium Synechocystis sp. Strain PCC 6803  

Microsoft Academic Search

Whole-genome DNA microarrays were used to evaluate the effect of the redox state of the photosynthetic electron transport chain on gene expression in Synechocystis sp. strain PCC 6803. Two specific inhibitors of electron transport, 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU) and 2,5-dibromo-3-methyl-6-isopropyl- p-benzoquinone (DBMIB), were added to the cultures, and changes in accumulation of transcripts were examined. About 140 genes were highlighted as reproducibly

Yukako Hihara; Kintake Sonoike; Minoru Kanehisa; Masahiko Ikeuchi

2003-01-01

304

Cloning and characterization of a gene cluster involved in tetrahydrofuran degradation in Pseudonocardia sp. strain K1  

Microsoft Academic Search

A gene cluster involved in the utilization of tetrahydrofuran by Pseudonocardia sp. strain K1 was cloned and sequenced. Analysis of a 9.2-kb DNA fragment revealed eight ORFs. The genes designated as thmADBC encode the components of a putative monooxygenase exhibiting a high similarity to different binuclear-iron-containing multicomponent monooxygenases. thmA encodes the derived 545-amino-acid oxygenase f-subunit, thmD the 360-amino-acid reductase component,

Barbara Thiemer; Jan R. Andreesen; Thomas Schräder

2003-01-01

305

Effects of insecticides on plant-growth-promoting activities of phosphate solubilizing rhizobacterium Klebsiella sp. strain PS19  

Microsoft Academic Search

In this study, four technical grade insecticides, fipronil, pyriproxyfen, imidacloprid and thiamethoxam were applied at the recommended and the higher doses to investigate their effects on plant growth-promoting activities of phosphate-solubilizing Klebsiella sp. strain PS19, isolated from mustard rhizosphere. All tested insecticides displayed a concentration-dependent inhibition in plant growth promoting traits, like, inorganic phosphate solubilization, biosynthesis of phytohormones and siderophores,

Munees Ahemad; Mohammad Saghir Khan

2011-01-01

306

X-ray Crystal Structure of Benzoate 1,2Dioxygenase Reductase from Acinetobacter sp. Strain ADP1  

Microsoft Academic Search

One of the major processes for aerobic biodegradation of aromatic compounds is initiated by Rieske dioxygenases. Benzoate dioxygenase contains a reductase component, BenC, that is responsible for the two-electron transfer from NADH via FAD and an iron–sulfur cluster to the terminal oxygenase component. Here, we present the structure of BenC from Acinetobacter sp. strain ADP1 at 1.5Å resolution. BenC contains

Andreas Karlsson; Zanna M. Beharry; D. Matthew Eby; Eric D. Coulter; Ellen L. Neidle; Donald M. Kurtz Jr; Hans Eklund; S. Ramaswamy

2002-01-01

307

Purification, molecular characterization and reactivity with aromatic compounds of a laccase from basidiomycete Trametes sp. strain AH28-2  

Microsoft Academic Search

A recently isolated basidiomycete, Trametes sp. strain AH28-2, can be induced to produce a high level of laccases when grown on a cellobiose-asparagine liquid medium. After induction by kraft lignin, two major isozymes were detected in the fermentation supernatant of the fungus. The principal component laccase A, which accounts for about 85% of the total activity, can be purified to

Y. Z. Xiao; X. M. Tu; J. Wang; M. Zhang; Q. Cheng; W. Y. Zeng; Y. Y. Shi

2003-01-01

308

Genome Sequence of Pseudomonas sp. Strain P482, a Tomato Rhizosphere Isolate with Broad-Spectrum Antimicrobial Activity  

PubMed Central

The tomato rhizosphere isolate Pseudomonas sp. strain P482 is a member of a diverse group of fluorescent pseudomonads. P482 produces a yet unidentified broad-spectrum antimicrobial compound(s), active inter alia (i.a.) against Dickeya spp. Here, we present a nearly complete genome of P482 obtained by a hybrid assembly of Illumina and PacBio sequencing data. PMID:24970823

Krzyzanowska, Dorota M.; Ossowicki, Adam

2014-01-01

309

Reclassification of rhizosphere bacteria including strains causing corky root of lettuce and proposal of Rhizorhapis suberifaciens gen. nov., comb. nov., Sphingobium mellinum sp. nov., Sphingobium xanthum sp. nov. and Rhizorhabdus argentea gen. nov., sp. nov.  

PubMed

The genus Rhizorhapis gen. nov. (to replace the illegitimate genus name Rhizomonas) is proposed for strains of Gram-negative bacteria causing corky root of lettuce, a widespread and important lettuce disease worldwide. Only one species of the genus Rhizomonas was described, Rhizomonas suberifaciens, which was subsequently reclassified as Sphingomonas suberifaciens based on 16S rRNA gene sequences and the presence of sphingoglycolipid in the cell envelope. However, the genus Sphingomonas is so diverse that further reclassification was deemed necessary. Twenty new Rhizorhapis gen. nov.- and Sphingomonas-like isolates were obtained from lettuce or sow thistle roots, or from soil using lettuce seedlings as bait. These and previously reported isolates were characterized in a polyphasic study including 16S rRNA gene sequencing, DNA-DNA hybridization, DNA G+C content, whole-cell fatty acid composition, morphology, substrate oxidation, temperature and pH sensitivity, and pathogenicity to lettuce. The isolates causing lettuce corky root belonged to the genera Rhizorhapis gen. nov., Sphingobium, Sphingopyxis and Rhizorhabdus gen. nov. More specifically, we propose to reclassify Rhizomonas suberifaciens as Rhizorhapis suberifaciens gen. nov., comb. nov. (type strain, CA1(T)?=?LMG 17323(T)?=?ATCC 49355(T)), and also propose the novel species Sphingobium xanthum sp. nov., Sphingobium mellinum sp. nov. and Rhizorhabdus argentea gen. nov., sp. nov. with the type strains NL9(T) (?=?LMG 12560(T)?=?ATCC 51296(T)), WI4(T) (?=?LMG 11032(T)?=?ATCC 51292(T)) and SP1(T) (?=?LMG 12581(T)?=?ATCC 51289(T)), respectively. Several strains isolated from lettuce roots belonged to the genus Sphingomonas, but none of them were pathogenic. PMID:24436067

Francis, Isolde M; Jochimsen, Kenneth N; De Vos, Paul; van Bruggen, Ariena H C

2014-04-01

310

Exo-Oligosaccharides of Rhizobium sp. Strain NGR234 Are Required for Symbiosis with Various Legumes  

PubMed Central

Rhizobia are nitrogen-fixing bacteria that establish endosymbiotic associations with legumes. Nodule formation depends on various bacterial carbohydrates, including lipopolysaccharides, K-antigens, and exopolysaccharides (EPS). An acidic EPS from Rhizobium sp. strain NGR234 consists of glucosyl (Glc), galactosyl (Gal), glucuronosyl (GlcA), and 4,6-pyruvylated galactosyl (PvGal) residues with ?-1,3, ?-1,4, ?-1,6, ?-1,3, and ?-1,4 glycoside linkages. Here we examined the role of NGR234 genes in the synthesis of EPS. Deletions within the exoF, exoL, exoP, exoQ, and exoY genes suppressed accumulation of EPS in bacterial supernatants, a finding that was confirmed by chemical analyses. The data suggest that the repeating subunits of EPS are assembled by an ExoQ/ExoP/ExoF-dependent mechanism, which is related to the Wzy polymerization system of group 1 capsular polysaccharides in Escherichia coli. Mutation of exoK (NGR?exoK), which encodes a putative glycanase, resulted in the absence of low-molecular-weight forms of EPS. Analysis of the extracellular carbohydrates revealed that NGR?exoK is unable to accumulate exo-oligosaccharides (EOSs), which are O-acetylated nonasaccharide subunits of EPS having the formula Gal(Glc)5(GlcA)2PvGal. When used as inoculants, both the exo-deficient mutants and NGR?exoK were unable to form nitrogen-fixing nodules on some hosts (e.g., Albizia lebbeck and Leucaena leucocephala), but they were able to form nitrogen-fixing nodules on other hosts (e.g., Vigna unguiculata). EOSs of the parent strain were biologically active at very low levels (yield in culture supernatants, ?50 ?g per liter). Thus, NGR234 produces symbiotically active EOSs by enzymatic degradation of EPS, using the extracellular endo-?-1,4-glycanase encoded by exoK (glycoside hydrolase family 16). We propose that the derived EOSs (and not EPS) are bacterial components that play a crucial role in nodule formation in various legumes. PMID:16923883

Staehelin, Christian; Forsberg, Lennart S.; D'Haeze, Wim; Gao, Mu-Yun; Carlson, Russell W.; Xie, Zhi-Ping; Pellock, Brett J.; Jones, Kathryn M.; Walker, Graham C.; Streit, Wolfgang R.; Broughton, William J.

2006-01-01

311

Exo-oligosaccharides of Rhizobium sp. strain NGR234 are required for symbiosis with various legumes.  

PubMed

Rhizobia are nitrogen-fixing bacteria that establish endosymbiotic associations with legumes. Nodule formation depends on various bacterial carbohydrates, including lipopolysaccharides, K-antigens, and exopolysaccharides (EPS). An acidic EPS from Rhizobium sp. strain NGR234 consists of glucosyl (Glc), galactosyl (Gal), glucuronosyl (GlcA), and 4,6-pyruvylated galactosyl (PvGal) residues with beta-1,3, beta-1,4, beta-1,6, alpha-1,3, and alpha-1,4 glycoside linkages. Here we examined the role of NGR234 genes in the synthesis of EPS. Deletions within the exoF, exoL, exoP, exoQ, and exoY genes suppressed accumulation of EPS in bacterial supernatants, a finding that was confirmed by chemical analyses. The data suggest that the repeating subunits of EPS are assembled by an ExoQ/ExoP/ExoF-dependent mechanism, which is related to the Wzy polymerization system of group 1 capsular polysaccharides in Escherichia coli. Mutation of exoK (NGROmegaexoK), which encodes a putative glycanase, resulted in the absence of low-molecular-weight forms of EPS. Analysis of the extracellular carbohydrates revealed that NGROmegaexoK is unable to accumulate exo-oligosaccharides (EOSs), which are O-acetylated nonasaccharide subunits of EPS having the formula Gal(Glc)5(GlcA)2PvGal. When used as inoculants, both the exo-deficient mutants and NGROmegaexoK were unable to form nitrogen-fixing nodules on some hosts (e.g., Albizia lebbeck and Leucaena leucocephala), but they were able to form nitrogen-fixing nodules on other hosts (e.g., Vigna unguiculata). EOSs of the parent strain were biologically active at very low levels (yield in culture supernatants, approximately 50 microg per liter). Thus, NGR234 produces symbiotically active EOSs by enzymatic degradation of EPS, using the extracellular endo-beta-1,4-glycanase encoded by exoK (glycoside hydrolase family 16). We propose that the derived EOSs (and not EPS) are bacterial components that play a crucial role in nodule formation in various legumes. PMID:16923883

Staehelin, Christian; Forsberg, Lennart S; D'Haeze, Wim; Gao, Mu-Yun; Carlson, Russell W; Xie, Zhi-Ping; Pellock, Brett J; Jones, Kathryn M; Walker, Graham C; Streit, Wolfgang R; Broughton, William J

2006-09-01

312

NH4+ transport system of a psychrophilic marine bacterium, Vibrio sp. strain ABE-1.  

PubMed

NH4(+) transport system of a psychrophilic marine bacterium Vibrio sp. strain ABE-1 (Vibrio ABE-1) was examined by measuring the uptake of [14C]methylammonium ion (14CH3NH3+) into the intact cells. 14CH3NH3+ uptake was detected in cells grown in medium containing glutamate as the sole nitrogen source, but not in those grown in medium containing NH4Cl instead of glutamate. Vibrio ABE-1 did not utilize CH3NH3+ as a carbon or nitrogen source. NH4Cl and nonradiolabeled CH3NH3+ completely inhibited 14CH3NH3+ uptake. These results indicate that 14CH3NH3+ uptake in this bacterium is mediated via an NH4+ transport system and not by a specific carrier for CH3NH3+. The respiratory substrate succinate was required to drive 14CH3NH3+ uptake and the uptake was completely inhibited by KCN, indicating that the uptake was energy dependent. The electrochemical potentials of H+ and/or Na+ across membranes were suggested to be the driving forces for the transport system because the ionophores carbonylcyanide m-chlorophenylhydrazone and monensin strongly inhibited uptake activities at pH 6.5 and 8.5, respectively. Furthermore, KCl activated 14CH3NH3+ uptake. The 14CH3NH3+ uptake activity of Vibrio ABE-1 was markedly high at temperatures between 0 degrees and 15 degrees C, and the apparent Km value for CH3NH3+ of the uptake did not change significantly over the temperature range from 0 degrees to 25 degrees C. Thus, the NH4+ transport system of this bacterium was highly active at low temperatures. PMID:10356994

Chou, M; Matsunaga, T; Takada, Y; Fukunaga, N

1999-05-01

313

Characterization of the response to zinc deficiency in the cyanobacterium Anabaena sp. strain PCC 7120.  

PubMed

Zur regulators control zinc homeostasis by repressing target genes under zinc-sufficient conditions in a wide variety of bacteria. This paper describes how part of a survey of duplicated genes led to the identification of the open reading frame all2473 as the gene encoding the Zur regulator of the cyanobacterium Anabaena sp. strain PCC 7120. All2473 binds to DNA in a zinc-dependent manner, and its DNA-binding sequence was characterized, which allowed us to determine the relative contribution of particular nucleotides to Zur binding. A zur mutant was found to be impaired in the regulation of zinc homeostasis, showing sensitivity to elevated concentrations of zinc but not other metals. In an effort to characterize the Zur regulon in Anabaena, 23 genes containing upstream putative Zur-binding sequences were identified and found to be regulated by Zur. These genes are organized in six single transcriptional units and six operons, some of them containing multiple Zur-regulated promoters. The identities of genes of the Zur regulon indicate that Anabaena adapts to conditions of zinc deficiency by replacing zinc metalloproteins with paralogues that fulfill the same function but presumably with a lower zinc demand, and with inducing putative metallochaperones and membrane transport systems likely being involved in the scavenging of extracellular zinc, including plasma membrane ABC transport systems and outer membrane TonB-dependent receptors. Among the Zur-regulated genes, the ones showing the highest induction level encode proteins of the outer membrane, suggesting a primary role for components of this cell compartment in the capture of zinc cations from the extracellular medium. PMID:22389488

Napolitano, Mauro; Rubio, Miguel Ángel; Santamaría-Gómez, Javier; Olmedo-Verd, Elvira; Robinson, Nigel J; Luque, Ignacio

2012-05-01

314

Characterization of the Response to Zinc Deficiency in the Cyanobacterium Anabaena sp. Strain PCC 7120  

PubMed Central

Zur regulators control zinc homeostasis by repressing target genes under zinc-sufficient conditions in a wide variety of bacteria. This paper describes how part of a survey of duplicated genes led to the identification of the open reading frame all2473 as the gene encoding the Zur regulator of the cyanobacterium Anabaena sp. strain PCC 7120. All2473 binds to DNA in a zinc-dependent manner, and its DNA-binding sequence was characterized, which allowed us to determine the relative contribution of particular nucleotides to Zur binding. A zur mutant was found to be impaired in the regulation of zinc homeostasis, showing sensitivity to elevated concentrations of zinc but not other metals. In an effort to characterize the Zur regulon in Anabaena, 23 genes containing upstream putative Zur-binding sequences were identified and found to be regulated by Zur. These genes are organized in six single transcriptional units and six operons, some of them containing multiple Zur-regulated promoters. The identities of genes of the Zur regulon indicate that Anabaena adapts to conditions of zinc deficiency by replacing zinc metalloproteins with paralogues that fulfill the same function but presumably with a lower zinc demand, and with inducing putative metallochaperones and membrane transport systems likely being involved in the scavenging of extracellular zinc, including plasma membrane ABC transport systems and outer membrane TonB-dependent receptors. Among the Zur-regulated genes, the ones showing the highest induction level encode proteins of the outer membrane, suggesting a primary role for components of this cell compartment in the capture of zinc cations from the extracellular medium. PMID:22389488

Napolitano, Mauro; Rubio, Miguel Ángel; Santamaría-Gómez, Javier; Olmedo-Verd, Elvira; Robinson, Nigel J.

2012-01-01

315

X-Ray crystallographic and mutational studies of fluoroacetate dehalogenase from Burkholderia sp. strain FA1.  

PubMed

Fluoroacetate dehalogenase catalyzes the hydrolytic defluorination of fluoroacetate to produce glycolate. The enzyme is unique in that it catalyzes the cleavage of a carbon-fluorine bond of an aliphatic compound: the bond energy of the carbon-fluorine bond is among the highest found in natural products. The enzyme also acts on chloroacetate, although much less efficiently. We here determined the X-ray crystal structure of the enzyme from Burkholderia sp. strain FA1 as the first experimentally determined three-dimensional structure of fluoroacetate dehalogenase. The enzyme belongs to the alpha/beta hydrolase superfamily and exists as a homodimer. Each subunit consists of core and cap domains. The catalytic triad, Asp104-His271-Asp128, of which Asp104 serves as the catalytic nucleophile, was found in the core domain at the domain interface. The active site was composed of Phe34, Asp104, Arg105, Arg108, Asp128, His271, and Phe272 of the core domain and Tyr147, His149, Trp150, and Tyr212 of the cap domain. An electron density peak corresponding to a chloride ion was found in the vicinity of the N(epsilon1) atom of Trp150 and the N(epsilon2) atom of His149, suggesting that these are the halide ion acceptors. Site-directed replacement of each of the active-site residues, except for Trp150, by Ala caused the total loss of the activity toward fluoroacetate and chloroacetate, whereas the replacement of Trp150 caused the loss of the activity only toward fluoroacetate. An interaction between Trp150 and the fluorine atom is probably an absolute requirement for the reduction of the activation energy for the cleavage of the carbon-fluorine bond. PMID:19218394

Jitsumori, Keiji; Omi, Rie; Kurihara, Tatsuo; Kurata, Atsushi; Mihara, Hisaaki; Miyahara, Ikuko; Hirotsu, Ken; Esaki, Nobuyoshi

2009-04-01

316

Molecular Characterization of a Novel Peroxidase from the Cyanobacterium Anabaena sp. Strain PCC 7120 ?  

PubMed Central

The open reading frame alr1585 of Anabaena sp. strain PCC 7120 encodes a heme-dependent peroxidase (Anabaena peroxidase [AnaPX]) belonging to the novel DyP-type peroxidase family (EC 1.11.1.X). We cloned and heterologously expressed the active form of the enzyme in Escherichia coli. The purified enzyme was a 53-kDa tetrameric protein with a pI of 3.68, a low pH optima (pH 4.0), and an optimum reaction temperature of 35°C. Biochemical characterization revealed an iron protoporphyrin-containing heme peroxidase with a broad specificity for aromatic substrates such as guaiacol, 4-aminoantipyrine and pyrogallol. The enzyme efficiently catalyzed the decolorization of anthraquinone dyes like Reactive Blue 5, Reactive Blue 4, Reactive Blue 114, Reactive Blue 119, and Acid Blue 45 with decolorization rates of 262, 167, 491, 401, and 256 ?M·min?1, respectively. The apparent Km and kcat/Km values for Reactive Blue 5 were 3.6 ?M and 1.2 × 107 M?1 s?1, respectively, while the apparent Km and kcat/Km values for H2O2 were 5.8 ?M and 6.6 × 106 M?1 s?1, respectively. In contrast, the decolorization activity of AnaPX toward azo dyes was relatively low but was significantly enhanced 2- to ?50-fold in the presence of the natural redox mediator syringaldehyde. The specificity and catalytic efficiency for hydrogen donors and synthetic dyes show the potential application of AnaPX as a useful alternative of horseradish peroxidase or fungal DyPs. To our knowledge, this study represents the only extensive report in which a bacterial DyP has been tested in the biotransformation of synthetic dyes. PMID:19801472

Ogola, Henry Joseph Oduor; Kamiike, Takaaki; Hashimoto, Naoya; Ashida, Hiroyuki; Ishikawa, Takahiro; Shibata, Hitoshi; Sawa, Yoshihiro

2009-01-01

317

Heterologous Expression and Characterization of the Manganese-Oxidizing Protein from Erythrobacter sp. Strain SD21.  

PubMed

The manganese (Mn)-oxidizing protein (MopA) from Erythrobacter sp. strain SD21 is part of a unique enzymatic family that is capable of oxidizing soluble Mn(II). This enzyme contains two domains, an animal heme peroxidase domain, which contains the catalytic site, followed by a C-terminal calcium binding domain. Different from the bacterial Mn-oxidizing multicopper oxidase enzymes, little is known about MopA. To gain a better understanding of MopA and its role in Mn(II) oxidation, the 238-kDa full-length protein and a 105-kDa truncated protein containing only the animal heme peroxidase domain were cloned and heterologously expressed in Escherichia coli. Despite having sequence similarity to a peroxidase, hydrogen peroxide did not stimulate activity, nor was activity significantly decreased in the presence of catalase. Both pyrroloquinoline quinone (PQQ) and hemin increased Mn-oxidizing activity, and calcium was required. The Km for Mn(II) of the full-length protein in cell extract was similar to that of the natively expressed protein, but the Km value for the truncated protein in cell extract was approximately 6-fold higher than that of the full-length protein, suggesting that the calcium binding domain may aid in binding Mn(II). Characterization of the heterologously expressed MopA has provided additional insight into the mechanism of bacterial Mn(II) oxidation, which will aid in understanding the role of MopA and Mn oxidation in bioremediation and biogeochemical cycling. PMID:25172859

Nakama, Katherine; Medina, Michael; Lien, Ahn; Ruggieri, Jordan; Collins, Krystle; Johnson, Hope A

2014-11-01

318

Synechococcus sp. strain PCC 7002 nifJ mutant lacking pyruvate:ferredoxin oxidoreductase.  

PubMed

The nifJ gene codes for pyruvate:ferredoxin oxidoreductase (PFOR), which reduces ferredoxin during fermentative catabolism of pyruvate to acetyl-coenzyme A (acetyl-CoA). A nifJ knockout mutant was constructed that lacks one of two pathways for the oxidation of pyruvate in the cyanobacterium Synechococcus sp. strain PCC 7002. Remarkably, the photoautotrophic growth rate of this mutant increased by 20% relative to the wild-type (WT) rate under conditions of light-dark cycling. This result is attributed to an increase in the quantum yield of photosystem II (PSII) charge separation as measured by photosynthetic electron turnover efficiency determined using fast-repetition-rate fluorometry (F(v)/F(m)). During autofermentation, the excretion of acetate and lactate products by nifJ mutant cells decreased 2-fold and 1.2-fold, respectively. Although nifJ cells displayed higher in vitro hydrogenase activity than WT cells, H(2) production in vivo was 1.3-fold lower than the WT level. Inhibition of acetate-CoA ligase and pyruvate dehydrogenase complex by glycerol eliminated acetate production, with a resulting loss of reductant and a 3-fold decrease in H(2) production by nifJ cells compared to WT cells. Continuous electrochemical detection of dissolved H(2) revealed two temporally resolved phases of H(2) production during autofermentation, a minor first phase and a major second phase. The first phase was attributed to reduction of ferredoxin, because its level decreased 2-fold in nifJ cells. The second phase was attributed to glycolytic NADH production and decreased 20% in nifJ cells. Measurement of the intracellular NADH/NAD(+) ratio revealed that the reductant generated by PFOR contributing to the first phase of H(2) production was not in equilibrium with bulk NADH/NAD(+) and that the second phase corresponded to the equilibrium NADH-mediated process. PMID:21317262

McNeely, Kelsey; Xu, Yu; Ananyev, Gennady; Bennette, Nicholas; Bryant, Donald A; Dismukes, G Charles

2011-04-01

319

Expanding the Direct HetR Regulon in Anabaena sp. Strain PCC 7120  

PubMed Central

In response to a lack of environmental combined nitrogen, the filamentous cyanobacterium Anabaena sp. strain PCC 7120 differentiates nitrogen-fixing heterocyst cells in a periodic pattern. HetR is a transcription factor that coordinates the regulation of this developmental program. An inverted repeat-containing sequence in the hepA promoter required for proheterocyst-specific transcription was identified based on sequence similarity to a previously characterized binding site for HetR in the promoter of hetP. The binding affinity of HetR for the hepA site is roughly an order of magnitude lower than that for the hetP binding site. A BLAST search of the Anabaena genome identified 166 hepA-like sites that occur as single or tandem sites (two binding sites separated by 13 bp). The vast majority of these sites are present in predicted intergenic regions. HetR bound five representative single binding sites in vitro, and binding was abrogated by transversions in the binding sites that conserved the inverted repeat nature of the sites. Binding to four representative tandem sites was not observed. Transcriptional fusions of the green fluorescent protein gene gfp with putative promoter regions associated with the representative binding sites indicated that HetR could function as either an activator or repressor and that activation was cell-type specific. Taken together, we have expanded the direct HetR regulon and propose a model in which three categories of HetR binding sites, based on binding affinity and nucleotide sequence, contribute to three of the four phases of differentiation. PMID:24375104

Videau, Patrick; Ni, Shuisong; Rivers, Orion S.; Ushijima, Blake; Feldmann, Erik A.; Cozy, Loralyn M.; Kennedy, Michael A.

2014-01-01

320

Cold-adapted and rhizosphere-competent strain of Rahnella sp. with broad-spectrum plant growth-promotion potential.  

PubMed

A phosphate-solubilizing bacterial strain isolated from Hippophae rhamnoides rhizosphere was identified as Rahnella sp. based on its phenotypic features and 16S rRNA gene sequence. The bacterial strain showed the growth characteristics of a cold-adapted psychrotroph, with the multiple plant growth-promoting traits of inorganic and organic phosphate solubilization, 1-aminocyclopropane-1- carboxylate-deaminase activity, ammonia generation, and siderophore production. The strain also produced indole- 3-acetic acid, indole-3-acetaldehyde, indole-3-acetamide, indole-3-acetonitrile, indole-3-lactic acid, and indole-3- pyruvic acid in tryptophan-supplemented nutrient broth. Gluconic, citric and isocitric acids were the major organic acids detected during tricalcium phosphate solubilization. A rifampicin-resistant mutant of the strain exhibited high rhizosphere competence without disturbance to the resident microbial populations in pea rhizosphere. Seed bacterization with a charcoal-based inoculum significantly increased growth in barley, chickpea, pea, and maize under the controlled environment. Microplot testing of the inoculum at two different locations in pea also showed significant increase in growth and yield. The attributes of coldtolerance, high rhizosphere competence, and broad-spectrum plant growth-promoting activity exhibited the potential of Rahnella sp. BIHB 783 for increasing agriculture productivity. PMID:21193830

Vyas, Pratibha; Joshi, Robin; Sharma, K C; Rahi, Praveen; Gulati, Ashu; Gulati, Arvind

2010-12-01

321

Genome sequence of the acid-tolerant Burkholderia sp. strain WSM2230 from Karijini National Park, Australia  

PubMed Central

Burkholderia sp. strain WSM2230 is an aerobic, motile, Gram-negative, non-spore-forming acid-tolerant rod isolated from acidic soil collected in 2001 from Karijini National Park, Western Australia, using Kennedia coccinea (Coral Vine) as a host. WSM2230 was initially effective in nitrogen-fixation with K. coccinea, but subsequently lost symbiotic competence. Here we describe the features of Burkholderia sp. strain WSM2230, together with genome sequence information and its annotation. The 6,309,801 bp high-quality-draft genome is arranged into 33 scaffolds of 33 contigs containing 5,590 protein-coding genes and 63 RNA-only encoding genes. The genome sequence of WSM2230 failed to identify nodulation genes and provides an explanation for the observed failure of the laboratory grown strain to nodulate. The genome of this strain is one of 100 sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project.

Walker, Robert; Watkin, Elizabeth; Tian, Rui; Brau, Lambert; O'Hara, Graham; Goodwin, Lynne; Han, James; Lobos, Elizabeth; Huntemann, Marcel; Pati, Amrita; Woyke, Tanja; Mavromatis, Konstantinos; Markowitz, Victor; Ivanova, Natalia; Kyrpides, Nikos; Reeve, Wayne

2013-01-01

322

Genome Sequence of Thermotoga sp Strain RQ2, a Hyperthermophilic Bacterium Isolated from a Geothermally Heated Region of the Seafloor near Ribeira Quente, the Azores  

SciTech Connect

Thermotoga sp. strain RQ2 is probably a strain of Thermotoga maritima. Its complete genome sequence allows for an examination of the extent and consequences of gene flow within Thermotoga species and strains. Thermotoga sp. RQ2 differs from T. maritima in its genes involved in myo-inositol metabolism. Its genome also encodes an apparent fructose phosphotransferase system (PTS) sugar transporter. This operon is also found in Thermotoga naphthophila strain RKU-10 but no other Thermotogales. These are the first reported PTS transporters in the Thermotogales.

Swithers, Kristen S [University of Connecticut, Storrs; DiPippo, Jonathan L [University of Connecticut, Storrs; Bruce, David [Los Alamos National Laboratory (LANL); Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Tapia, Roxanne [Los Alamos National Laboratory (LANL); Han, Cliff [Los Alamos National Laboratory (LANL); Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute; Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Pennacchio, Len [U.S. Department of Energy, Joint Genome Institute; Nolan, Matt [U.S. Department of Energy, Joint Genome Institute; Mikhailova, Natalia [U.S. Department of Energy, Joint Genome Institute; Lykidis, A [U.S. Department of Energy, Joint Genome Institute; Land, Miriam L [ORNL; Stetter, Karl O [Universitat Regensburg, Regensburg, Germany; Nelson, Karen E [J. Craig Venter Institute; Gogarten, Peter [University of Connecticut, Storrs; Noll, Kenneth M [University of Connecticut, Storrs

2011-01-01

323

Detection of a Rickettsia Closely Related to Rickettsia aeschlimannii, "Rickettsia heilongjiangensis," Rickettsia sp. Strain RpA4, and Ehrlichia muris in Ticks Collected in Russia and Kazakhstan  

PubMed Central

Using PCR, we screened 411 ticks from four genera collected in Russia and Kazakhstan for the presence of rickettsiae and ehrlichiae. In Russia, we detected “Rickettsia heilongjiangensis,” Rickettsia sp. strain RpA4, and Ehrlichia muris. In Kazakhstan, we detected Rickettsia sp. strain RpA4 and a rickettsia closely related to Rickettsia aeschlimannii. These agents should be considered in a differential diagnosis of tick-borne infections in these areas. PMID:15131195

Shpynov, Stanislav; Fournier, Pierre-Edouard; Rudakov, Nikolay; Tankibaev, Marat; Tarasevich, Irina; Raoult, Didier

2004-01-01

324

Genome Sequence of Vibrio sp. Strain EJY3, an Agarolytic Marine Bacterium Metabolizing 3,6-Anhydro-l-Galactose as a Sole Carbon Source  

PubMed Central

The metabolic fate of 3,6-anhydro-l-galactose (l-AHG) is unknown in the global marine carbon cycle. Vibrio sp. strain EJY3 is an agarolytic marine bacterium that can utilize l-AHG as a sole carbon source. To elucidate the metabolic pathways of l-AHG, we have sequenced the complete genome of Vibrio sp. strain EJY3. PMID:22535948

Roh, Hanseong; Yun, Eun Ju; Lee, Saeyoung; Ko, Hyeok-Jin; Kim, Sujin; Kim, Byung-Yong; Song, Heesang; Lim, Kwang-il

2012-01-01

325

Degradation of 2,4-dinitroanisole (DNAN) by metabolic cooperative activity of Pseudomonas sp. strain FK357and Rhodococcus imtechensis strain RKJ300.  

PubMed

2,4-Dinitroanisole (DNAN) is an insensitive explosive ingredient used by many defense agencies as a replacement for 2,4,6-trinitrotoluene. Although the biotransformation of DNAN under anaerobic condition has been reported, aerobic microbial degradation pathway has not been elucidated. An n-methyl-4-nitroaniline degrading bacterium Pseudomonas sp. strain FK357 transformed DNAN into 2,4-dinitrophenol (2,4-DNP) as an end product. Interestingly, when strain FK357 was co-cultured with a 2,4-DNP degrading Rhodococcus imtechensis strain RKJ300, complete and high rate of DNAN degradation was observed with no accumulation of intermediates. Enzyme assay using cell extracts of strain FK357 demonstrated that O-demethylation reaction is the first step of DNAN degradation with formation of 2,4-DNP and formaldehyde as intermediates. Subsequently, 2,4-DNP was degraded by strain RKJ300 via the formation of hydride-Meisenheimer complex. The present study clearly demonstrates that complete degradation of DNAN occurs as a result of the metabolic cooperative activity of two members within a bacterial consortium. PMID:24075532

Khan, Fazlurrahman; Pal, Deepika; Ghosh, Anuradha; Cameotra, Swaranjit Singh

2013-11-01

326

Genome Analysis Coupled with Physiological Studies Reveals a Diverse Nitrogen Metabolism in Methylocystis sp. Strain SC2  

PubMed Central

Background Methylocystis sp. strain SC2 can adapt to a wide range of methane concentrations. This is due to the presence of two isozymes of particulate methane monooxygenase exhibiting different methane oxidation kinetics. To gain insight into the underlying genetic information, its genome was sequenced and found to comprise a 3.77 Mb chromosome and two large plasmids. Principal Findings We report important features of the strain SC2 genome. Its sequence is compared with those of seven other methanotroph genomes, comprising members of the Alphaproteobacteria, Gammaproteobacteria, and Verrucomicrobia. While the pan-genome of all eight methanotroph genomes totals 19,358 CDS, only 154 CDS are shared. The number of core genes increased with phylogenetic relatedness: 328 CDS for proteobacterial methanotrophs and 1,853 CDS for the three alphaproteobacterial Methylocystaceae members, Methylocystis sp. strain SC2 and strain Rockwell, and Methylosinus trichosporium OB3b. The comparative study was coupled with physiological experiments to verify that strain SC2 has diverse nitrogen metabolism capabilities. In correspondence to a full complement of 34 genes involved in N2 fixation, strain SC2 was found to grow with atmospheric N2 as the sole nitrogen source, preferably at low oxygen concentrations. Denitrification-mediated accumulation of 0.7 nmol 30N2/hr/mg dry weight of cells under anoxic conditions was detected by tracer analysis. N2 production is related to the activities of plasmid-borne nitric oxide and nitrous oxide reductases. Conclusions/Perspectives Presence of a complete denitrification pathway in strain SC2, including the plasmid-encoded nosRZDFYX operon, is unique among known methanotrophs. However, the exact ecophysiological role of this pathway still needs to be elucidated. Detoxification of toxic nitrogen compounds and energy conservation under oxygen-limiting conditions are among the possible roles. Relevant features that may stimulate further research are, for example, absence of CRISPR/Cas systems in strain SC2, high number of iron acquisition systems in strain OB3b, and large number of transposases in strain Rockwell. PMID:24130670

Blom, Jochen; Liesack, Werner

2013-01-01

327

Light-activated heterotrophic growth of the cyanobacterium Synechocystis sp. strain PCC 6803: a blue-light-requiring process.  

PubMed Central

A glucose-tolerant strain of Synechocystis sp. strain 6803 will not grow on glucose under complete darkness unless given a daily pulse of white light, typically 5 min of 40 mumol m-2 s-1 (light-pulsed conditions). The light pulse is insufficient for photoautotrophy, as glucose is required and growth yield is dependent on glucose concentration. Growth rate is independent of fluence, but growth yield is dependent on fluence, saturating at 40 to 75 mumol m-2 s-1. A Synechocystis strain 6803 psbA mutant strain grows under light-pulsed conditions at rates similar to those for the glucose-tolerant strain, indicating that photosystem II is not required for growth. The relative spectral sensitivity of the growth of light-pulsed cultures (growth only in blue light, 400 to 500 nm, maximum at 450 nm) precludes energetic contribution from cyclic electron transport around photosystem I. Pulses of long-wavelength light (i.e., 550 and 650 nm) did not support the growth of Synechocystis strain 6803 and, when supplied before or after a blue-light pulse, did not inhibit blue-light-stimulated growth of Synechocystis strain 6803. We conclude that the required blue-light pulse does not support growth via photosynthetic electron transport but appears instead to function as an environmental signal regulating heterotrophic metabolism, cell division, or other photomorphogenic processes. We have termed the growth of Synechocystis strain 6803 pulsed with light and kept otherwise in complete darkness light-activated heterotrophic growth. This observation of a blue-light requirement for the growth of Synechocystis strain 6803 represents a novel blue light effect on the growth of a cyanobacterium. PMID:1902208

Anderson, S L; McIntosh, L

1991-01-01

328

Organization of nif gene cluster in Frankia sp. EuIK1 strain, a symbiont of Elaeagnus umbellata.  

PubMed

The nucleotide sequence of a 20.5-kb genomic region harboring nif genes was determined and analyzed. The fragment was obtained from Frankia sp. EuIK1 strain, an indigenous symbiont of Elaeagnus umbellata. A total of 20 ORFs including 12 nif genes were identified and subjected to comparative analysis with the genome sequences of 3 Frankia strains representing diverse host plant specificities. The nucleotide and deduced amino acid sequences showed highest levels of identity with orthologous genes from an Elaeagnus-infecting strain. The gene organization patterns around the nif gene clusters were well conserved among all 4 Frankia strains. However, characteristic features appeared in the location of the nifV gene for each Frankia strain, depending on the type of host plant. Sequence analysis was performed to determine the transcription units and suggested that there could be an independent operon starting from the nifW gene in the EuIK strain. Considering the organization patterns and their total extensions on the genome, we propose that the nif gene clusters remained stable despite genetic variations occurring in the Frankia genomes. PMID:21769644

Oh, Chang Jae; Kim, Ho Bang; Kim, Jitae; Kim, Won Jin; Lee, Hyoungseok; An, Chung Sun

2012-01-01

329

Characterization of Transcriptional Regulatory Genes for Biphenyl Degradation in Rhodococcus sp. Strain RHA1  

PubMed Central

Transcription of the bphA1A2A3A4C1B genes, which are responsible for the conversion of biphenyl and polychlorinated biphenyl to the meta-cleavage products in Rhodococcus sp. strain RHA1, was examined. The bphA1 promoter (PbphA1) was identified and was shown to promote transcription induction by biphenyl and ethylbenzene. An 8.8-kb HindIII fragment that promotes transcription induction of PbphA1 in Rhodococcus erythropolis IAM1399 was isolated from the region downstream of bphB by using a reporter plasmid containing PbphA1. Analysis of the nucleotide sequence of this fragment revealed a set of putative two-component regulatory system genes, which were designated bphS and bphT. Deletion analysis of the 8.8-kb HindIII fragment indicated that bphT is responsible for the basal activation of PbphA1 and that both bphS and bphT are required for the elevated basal activation of and transcriptional induction by biphenyl of PbphA1. These results support the notion that bphS and bphT encode a sensor kinase and a response regulator, respectively, of a two-component regulatory system. The bphS and bphT genes promote transcriptional induction by a variety of aromatic compounds, including biphenyl, benzene, alkylbenzenes, and chlorinated benzenes. A promoter activity assay and reverse transcription (RT)-PCR analysis revealed a weak constitutive promoter in the adjacent region upstream of bphS. RT-PCR analysis indicated that there is induced transcription of bphA1 through bphT, in which PbphA1 is thought to take part. An insertionally inactivated bphS mutant, SDR1, did not grow on biphenyl. Growth was restored by introduction of an intact bphS gene into SDR1. These results indicate that at least bphS is indispensably responsible for the growth of RHA1 on biphenyl. PMID:15028699

Takeda, Hisashi; Yamada, Akihiro; Miyauchi, Keisuke; Masai, Eiji; Fukuda, Masao

2004-01-01

330

Two-stage cultivation of two Chlorella sp. strains by simultaneous treatment of brewery wastewater and maximizing lipid productivity.  

PubMed

A cultivation system in the two-stage photoautotrophic-photoheterotrophic/mixotrophic mode was adapted to maximize lipid productivity of two freshwater strains of Chlorella sp. grown in brewery wastewater (BWW). The endogenous Chlorella sp. isolated from BWW had a higher growth rate than wild-type Chlorella vulgaris (UTEX-265) while C. vulgaris (UTEX-265) had a higher maximal biomass and lipid contents than that of endogenous Chlorella sp., resulting in more than 90% of the inorganic nutrients in both total nitrogen (TN) and phosphorus (TP) was removed during the first stage in the two-stage photoautotrophic-photoheterotrophic mode in each Chlorella sp. The maximal biomass and lipid contents of C. vulgaris (UTEX-265) for single stage photoautotrophic cultivation were 1.5 g/L and 18%, respectively. Importantly, during two-stage photoautotrophic-photoheterotrophic cultivation for C. vulgaris (UTEX-265), the biomass was increased to 3.5 g/L, and the lipid productivity was increased from 31.1 to 108.0mg/L day. PMID:23411453

Farooq, Wasif; Lee, Young-Chul; Ryu, Byung-Gon; Kim, Byung-Hyuk; Kim, Hee-Sik; Choi, Yoon-E; Yang, Ji-Won

2013-03-01

331

Characterization of a novel angular dioxygenase from fluorene-degrading Sphingomonas sp. strain LB126  

Microsoft Academic Search

In this study, the genes involved in the initial attack on fluorene by Sphingomonas sp. LB126 were investigated. The ? and ? subunits of a dioxygenase complex (FlnA1A2), showing 63% and 51% sequence identity respectively, with the subunits of an angular dioxygenase from Gram-positive Terrabacter sp. DBF63, were identified. When overexpressed in E. coli, FlnA1A2 was responsible for the angular

Luc Schuler; Sinead M. Ni Chadhain; Yves Jouanneau; Christine Meyer; Gerben J. Zylstra; Pascal Hols; Spiros N. Agathos

2009-01-01

332

Degradation of environmental endocrine disruptor di-2-ethylhexyl phthalate by a newly discovered bacterium, Microbacterium sp. strain CQ0110Y.  

PubMed

In this study di-2-ethylhexyl phthalate (DEHP)-degradation strain CQ0110Y was isolated from activated sludge. According to the biophysical/biochemical characteristics and analysis of 16S rDNA, the strain was identified as Microbacterium sp. The results of this study showed the optimal pH value and optimal temperature which influenced the degradation rate in wastewater: pH 6.5-7.5, 25-35 degrees C. Kinetics of degradation reaction had been performed at different initial concentrations and different time. Analyzed with SPSS10.0 software, the DEHP degradation can be described as the same exponential model when the initial DEHP concentration was lower than 1,350 mg/l. The kinetics equation was ln C = -0.4087t + A, with the degradation half life of DEHP in wastewater (1.59 days). To the best of our knowledge, this is the first reported case of DEHP degradation by Microbacterium sp. strain. PMID:17089119

Chen, Ji-An; Li, Xiang; Li, Jun; Cao, Jia; Qiu, Zhiqun; Zhao, Qing; Xu, Chuan; Shu, Weiqun

2007-03-01

333

Transcriptomic analysis of responses to exudates reveal genes required for rhizosphere competence of the endophyte Azoarcus sp. strain BH72.  

PubMed

Endophytic colonization is a very complex process which is not yet completely understood. Molecules exuded by the plants may act as signals which influence the ability of the microbe to colonize the host or survive in the rhizosphere. Here we used the whole genome microarray approach to investigate the response of the diazotrophic model endophyte, Azoarcus sp. strain BH72, to exudates of O. sativa cv. Nipponbare in order to identify differentially regulated genes. On exposure to exudates, an overall expression of 4.4% of the 3992 protein coding genes of Azoarcus sp. strain BH72 was altered, out of which 2.4% was upregulated and 2.0% was downregulated. Genes with modulated expression included a few whose involvement in plant-microbe interaction had already been established, whereas a large fraction comprised of genes encoding proteins with putative or unknown functions. Mutational analysis of several differentially regulated genes like those encoding a minor pilin PilX, signal transduction proteins containing GGDEF domains and a serine-threonine kinase as a putative component of the type IV secretion system (T6SS), revealed their role in host colonization. Our data suggest that strain BH72 may be primed for the endophytic lifestyle by exudates, as the expression of bacterial genes relevant for endophytic colonization of roots is induced by root exudates. PMID:22616609

Shidore, Teja; Dinse, Theresa; Öhrlein, Johannes; Becker, Anke; Reinhold-Hurek, Barbara

2012-10-01

334

Metabolism of the Aliphatic Nitramine 4-Nitro-2,4-Diazabutanal by Methylobacterium sp. Strain JS178  

PubMed Central

The aliphatic nitramine 4-nitro-2,4-diazabutanal (NDAB; C2H5N3O3) is a ring cleavage metabolite that accumulates during the aerobic degradation of the energetic compound hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) by various Rhodococcus spp. NDAB is also produced during the alkaline hydrolysis of either RDX or octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) and during the photolysis of RDX. Traces of NDAB were observed in a soil sampled from an ammunition-manufacturing facility contaminated with both HMX and RDX, suggesting natural attenuation. In this study, we report the isolation of a soil bacterium that is able to degrade NDAB under aerobic conditions. The isolate is a pink-pigmented facultative methylotroph affiliated with the genus Methylobacterium. The strain, named Methylobacterium sp. strain JS178, degrades NDAB as a sole nitrogen source, with concomitant growth and formation of 1 molar equivalent of nitrous oxide (N2O). Comparison of the growth yield of strain JS178 grown on NDAB, nitrite (NO2?), or ammonium (NH4+) as a nitrogen source revealed that 1 N equivalent is assimilated from each mole of NDAB, which completes the nitrogen mass balance. In radiotracer experiments, strain JS178 mineralized 1 C of the [14C]NDAB produced in situ from [14C]RDX by Rhodococcus sp. strain DN22. Studies on the regulation of NDAB degradation indicated that allantoin, an intermediate in the purine catabolic pathway and a central molecule in the storage and transport of nitrogen in plants, up-regulated the enzyme(s) involved in the degradation of the nitramine. The results reveal the potential for the sequential participation of rhodococci and methylobacteria to effect the complete degradation of RDX. PMID:16085803

Fournier, Diane; Trott, Sandra; Hawari, Jalal; Spain, Jim

2005-01-01

335

Molecular Characterization of Protease Activity in Serratia sp. Strain SCBI and Its Importance in Cytotoxicity and Virulence.  

PubMed

A newly recognized Serratia species, termed South African Caenorhabditis briggsae isolate (SCBI), is both a mutualist of the nematode Caenorhabditis briggsae KT0001 and a pathogen of lepidopteran insects. Serratia sp. strain SCBI displays high proteolytic activity, and because secreted proteases are known virulence factors for many pathogens, the purpose of this study was to identify genes essential for extracellular protease activity in Serratia sp. strain SCBI and to determine what role proteases play in insect pathogenesis and cytotoxicity. A bank of 2,100 transposon mutants was generated, and six SCBI mutants with defective proteolytic activity were identified. These mutants were also defective in cytotoxicity. The mutants were found defective in genes encoding the following proteins: alkaline metalloprotease secretion protein AprE, a BglB family transcriptional antiterminator, an inosine/xanthosine triphosphatase, GidA, a methyl-accepting chemotaxis protein, and a PIN domain protein. Gene expression analysis on these six mutants showed significant downregulation in mRNA levels of several different types of predicted protease genes. In addition, transcriptome sequencing (RNA-seq) analysis provided insight into how inactivation of AprE, GidA, and a PIN domain protein influences motility and virulence, as well as protease activity. Using quantitative reverse transcription-PCR (qRT-PCR) to further characterize expression of predicted protease genes in wild-type Serratia sp. SCBI, the highest mRNA levels for the alkaline metalloprotease genes (termed prtA1 to prtA4) occurred following the death of an insect host, while two serine protease and two metalloprotease genes had their highest mRNA levels during active infection. Overall, these results indicate that proteolytic activity is essential for cytotoxicity in Serratia sp. SCBI and that its regulation appears to be highly complex. PMID:25182493

Petersen, Lauren M; Tisa, Louis S

2014-11-15

336

Isobutanol production at elevated temperatures in thermophilic Geobacillus thermoglucosidasius.  

PubMed

The potential advantages of biological production of chemicals or fuels from biomass at high temperatures include reduced enzyme loading for cellulose degradation, decreased chance of contamination, and lower product separation cost. In general, high temperature production of compounds that are not native to the thermophilic hosts is limited by enzyme stability and the lack of suitable expression systems. Further complications can arise when the pathway includes a volatile intermediate. Here we report the engineering of Geobacillus thermoglucosidasius to produce isobutanol at 50°C. We prospected various enzymes in the isobutanol synthesis pathway and characterized their thermostabilities. We also constructed an expression system based on the lactate dehydrogenase promoter from Geobacillus thermodenitrificans. With the best enzyme combination and the expression system, 3.3g/l of isobutanol was produced from glucose and 0.6g/l of isobutanol from cellobiose in G. thermoglucosidasius within 48h at 50°C. This is the first demonstration of isobutanol production in recombinant bacteria at an elevated temperature. PMID:24721011

Lin, Paul P; Rabe, Kersten S; Takasumi, Jennifer L; Kadisch, Marvin; Arnold, Frances H; Liao, James C

2014-07-01

337

Evidence that some Frankia sp. strains are able to cross boundaries between Alnus and Elaeagnus host specificity groups.  

PubMed

Phenotypic and genotypic methods were used to prove the existence of Frankia strains isolated from an Elaeagnus sp. that are able to cross the inoculation barriers and infect Alnus spp. also. Repeated cycles of inoculation, nodulation, and reisolation were performed under axenic conditions. Frankia wild-type strain UFI 13270257 and three of its coisolates did exhibit complete infectivity and effectiveness on Elaeagnus spp. and Hippophaë rhamnoides and variable infectivity on Alnus spp. Microscopical observation of host plant roots showed that these strains are able to infect Alnus spp. by penetrating deformed root hairs. Reisolates obtained from nodules induced on monoxenic Alnus glutinosa, Alnus incana, and Elaeagnus angustifolia resembled the parent strains in host infectivity range, in planta and in vitro morphophysiology, isoenzymes, and nif and rrn restriction fragment length polymorphisms, thus fulfilling Koch's postulates on both host plant genera. Alnus and Elaeagnus group-specific polymerase chain reaction DNA amplifications, DNA-DNA hybridizations, and partial gene sequences coding for 16S rRNA provided evidence for the genetic uniformity of wild-type strains and their inclusion into one and the same genomic species, clearly belonging to the Elaeagnus group of Frankia species. PMID:1352442

Bosco, M; Fernandez, M P; Simonet, P; Materassi, R; Normand, P

1992-05-01

338

Lipomyces chichibuensis sp. nov., isolated in Japan, and reidentification of the type strains of Lipomyces kononenkoae and Lipomyces spencermartinsiae.  

PubMed

We isolated two strains of a novel Lipomyces species from soil collected in Chichibu forest, Saitama prefecture, Japan. Based on their morphological and biochemical characteristics, along with multilocus sequence typing using the D1/D2 domain of the large-subunit (LSU) rRNA gene, the internal transcribed spacer (ITS) region and the translation elongation factor 1 alpha gene (EF-1?), the two strains were shown to represent a novel species of the genus Lipomyces, described as Lipomyces chichibuensis sp. nov. (type strain CB08-2(T)?=?NBRC 109582(T)?=?CBS 12929(T); Mycobank no. MB808164). In addition, we reidentified the type strains of Lipomyces kononenkoae and Lipomyces spencermartinsiae maintained in culture collections based on phenotypic characters and/or DNA-DNA hybridization to ensure correct future identification of species of the genus Lipomyces. The correct type strains of L. kononenkoae and L. spencermartinsiae are NBRC 107661(T) (?=?CBS 2514(T)) and NBRC 10376(T) (?=?CBS 5608(T)), respectively. PMID:24812367

Yamazaki, Atsushi; Kawasaki, Hiroko

2014-08-01

339

Identification and Characterization of an Archaeal Kojibiose Catabolic Pathway in the Hyperthermophilic Pyrococcus sp. Strain ST04  

PubMed Central

A unique gene cluster responsible for kojibiose utilization was identified in the genome of Pyrococcus sp. strain ST04. The proteins it encodes hydrolyze kojibiose, a disaccharide product of glucose caramelization, and form glucose-6-phosphate (G6P) in two steps. Heterologous expression of the kojibiose-related enzymes in Escherichia coli revealed that two genes, Py04_1502 and Py04_1503, encode kojibiose phosphorylase (designated PsKP, for Pyrococcus sp. strain ST04 kojibiose phosphorylase) and ?-phosphoglucomutase (PsPGM), respectively. Enzymatic assays show that PsKP hydrolyzes kojibiose to glucose and ?-glucose-1-phosphate (?-G1P). The Km values for kojibiose and phosphate were determined to be 2.53 ± 0.21 mM and 1.34 ± 0.04 mM, respectively. PsPGM then converts ?-G1P into G6P in the presence of 6 mM MgCl2. Conversion activity from ?-G1P to G6P was 46.81 ± 3.66 U/mg, and reverse conversion activity from G6P to ?-G1P was 3.51 ± 0.13 U/mg. The proteins are highly thermostable, with optimal temperatures of 90°C for PsKP and 95°C for PsPGM. These results indicate that Pyrococcus sp. strain ST04 converts kojibiose into G6P, a substrate of the glycolytic pathway. This is the first report of a disaccharide utilization pathway via phosphorolysis in hyperthermophilic archaea. PMID:24391053

Jung, Jong-Hyun; Seo, Dong-Ho; Holden, James F.

2014-01-01

340

Anatoxin-a Synthetase Gene Cluster of the Cyanobacterium Anabaena sp. Strain 37 and Molecular Methods To Detect Potential Producers?†  

PubMed Central

Cyanobacterial mass occurrences are common in fresh and brackish waters. They pose a threat to water users due to toxins frequently produced by the cyanobacterial species present. Anatoxin-a and homoanatoxin-a are neurotoxins synthesized by various cyanobacteria, e.g., Anabaena, Oscillatoria, and Aphanizomenon. The biosynthesis of these toxins and the genes involved in anatoxin production were recently described for Oscillatoria sp. strain PCC 6506 (A. Méjean et al., J. Am. Chem. Soc. 131:7512-7513, 2009). In this study, we identified the anatoxin synthetase gene cluster (anaA to anaG and orf1; 29 kb) in Anabaena sp. strain 37. The gene (81.6% to 89.2%) and amino acid (78.8% to 86.9%) sequences were highly similar to those of Oscillatoria sp. PCC 6506, while the organization of the genes differed. Molecular detection methods for potential anatoxin-a and homoanatoxin-a producers of the genera Anabaena, Aphanizomenon, and Oscillatoria were developed by designing primers to recognize the anaC gene. Anabaena and Oscillatoria anaC genes were specifically identified in several cyanobacterial strains by PCR. Restriction fragment length polymorphism (RFLP) analysis of the anaC amplicons enabled simultaneous identification of three producer genera: Anabaena, Oscillatoria, and Aphanizomenon. The molecular methods developed in this study revealed the presence of both Anabaena and Oscillatoria as potential anatoxin producers in Finnish fresh waters and the Baltic Sea; they could be applied for surveys of these neurotoxin producers in other aquatic environments. PMID:21873484

Rantala-Ylinen, Anne; Kana, Suvi; Wang, Hao; Rouhiainen, Leo; Wahlsten, Matti; Rizzi, Ermanno; Berg, Katri; Gugger, Muriel; Sivonen, Kaarina

2011-01-01

341

The bio operon on the acquired symbiosis island of Mesorhizobium sp. strain R7A includes a novel gene involved in pimeloyl-CoA synthesis  

Microsoft Academic Search

The symbiosis island of Mesorhizobium sp. strain R7A is a 500 kb chromosomal genetic element that upon transfer converts nonsymbiotic mesorhizobia to symbionts able to nodulate and fix nitrogen with Lotus corniculatus. Four genomic species of nonsymbiotic mesorhizobia have been isolated. All were auxotrophic for thiamin and biotin and three were auxotrophic for nicotinate, whereas derivatives of the strains containing

John T. Sullivan; Steven D. Brown; R. Rogers Yocum; Clive W. Ronson

342

High-Quality Draft Genome Sequence of Pseudomonas sp. BRG100, a Strain with Bioherbicidal Properties against Setaria viridis (Green Foxtail) and Other Pests of Agricultural Significance.  

PubMed

Pseudomonas sp. BRG100 inhibits the growth of certain agricultural pests and is a potentially useful biopesticide for weeds and plant diseases. We have sequenced the 6.25-Mbp genome of this strain and assembled it into 4 scaffolds. Genome sequence comparisons revealed that this strain may represent a novel species of Pseudomonas. PMID:25278538

Dumonceaux, Tim J; Town, Jennifer; Links, Matthew G; Boyetchko, Sue

2014-01-01

343

High-Quality Draft Genome Sequence of Pseudomonas sp. BRG100, a Strain with Bioherbicidal Properties against Setaria viridis (Green Foxtail) and Other Pests of Agricultural Significance  

PubMed Central

Pseudomonas sp. BRG100 inhibits the growth of certain agricultural pests and is a potentially useful biopesticide for weeds and plant diseases. We have sequenced the 6.25-Mbp genome of this strain and assembled it into 4 scaffolds. Genome sequence comparisons revealed that this strain may represent a novel species of Pseudomonas. PMID:25278538

Town, Jennifer; Links, Matthew G.; Boyetchko, Sue

2014-01-01

344

Draft Whole-Genome Sequence of Serratia marcescens Strain MCB, Associated with Oscheius sp. MCB (Nematoda: Rhabditidae) Isolated from South Africa.  

PubMed

Here we report on the draft genome sequence of Serratia marcescens strain MCB associated with Oscheius sp. MCB (Nematoda: Rhabditidae) isolated from South African soil. S. marcescens strain MCB has 5,304,212-bp genome size with 4,877 genes and a G+C content of 59.1%. PMID:25237022

Serepa, Mahloro H; Gray, Vincent M

2014-01-01

345

Draft Genome Sequence of Pseudoalteromonas sp. Strain NW 4327 (MTCC 11073, DSM 25418), a Pathogen of the Great Barrier Reef Sponge Rhopaloeides odorabile  

PubMed Central

To date, only one marine sponge pathogen (Pseudoalteromonas sp. strain NW 4327) has fulfilled Koch’s postulates. We report the 4.48-Mbp draft genome sequence of this strain, which is pathogenic to the Great Barrier Reef sponge Rhopaloeides odorabile. The sequence provides valuable information on sponge-pathogen interactions, including the mode of transmission and associated virulence factors. PMID:24482504

Choudhury, Jayanta D.; Pramanik, Arnab; Webster, Nicole S.; Llewellyn, Lyndon E.; Gachhui, Ratan

2014-01-01

346

Draft Genome Sequence of Pseudoalteromonas sp. Strain NW 4327 (MTCC 11073, DSM 25418), a Pathogen of the Great Barrier Reef Sponge Rhopaloeides odorabile.  

PubMed

To date, only one marine sponge pathogen (Pseudoalteromonas sp. strain NW 4327) has fulfilled Koch's postulates. We report the 4.48-Mbp draft genome sequence of this strain, which is pathogenic to the Great Barrier Reef sponge Rhopaloeides odorabile. The sequence provides valuable information on sponge-pathogen interactions, including the mode of transmission and associated virulence factors. PMID:24482504

Choudhury, Jayanta D; Pramanik, Arnab; Webster, Nicole S; Llewellyn, Lyndon E; Gachhui, Ratan; Mukherjee, Joydeep

2014-01-01

347

Draft Whole-Genome Sequence of Serratia marcescens Strain MCB, Associated with Oscheius sp. MCB (Nematoda: Rhabditidae) Isolated from South Africa  

PubMed Central

Here we report on the draft genome sequence of Serratia marcescens strain MCB associated with Oscheius sp. MCB (Nematoda: Rhabditidae) isolated from South African soil. S. marcescens strain MCB has 5,304,212-bp genome size with 4,877 genes and a G+C content of 59.1%. PMID:25237022

Gray, Vincent M.

2014-01-01

348

Draft Genome Sequence of Flavobacterium sp. Strain F52, Isolated from the Rhizosphere of Bell Pepper (Capsicum annuum L. cv. Maccabi)  

PubMed Central

Here we report the draft genome sequence of Flavobacterium sp. strain F52, isolated from the rhizosphere of bell pepper (Capsicum annuum L. cv. Maccabi). Flavobacterium spp. are ubiquitous in the rhizospheres of agricultural crops; however, little is known about their physiology. To our knowledge, this is the first published genome of a root-associated Flavobacterium strain. PMID:22965088

Kolton, Max; Green, Stefan J.; Harel, Yael Meller; Sela, Noa; Elad, Yigal

2012-01-01

349

Molecular characterization of idiA and adjacent genes in the cyanobacteria Synechococcus sp. strains PCC 6301 and PCC 7942.  

PubMed

IdiA (iron-deficiency-induced protein A) is a protein expressed at highly elevated levels in Synechococcus sp. strains PCC 6301 and PCC 7942 under Fe- or Mn-limiting growth conditions. Besides being similar to two bacterial Fe-binding proteins, SfuA and FbpA, IdiA shows similarity to two ORFs (slr0513 and sir1295) of Synechocystis sp. PCC 6803. Northern blot analysis detected one transcript of about 1300 nt in RNA extracted from Synechococcus sp. PCC 6301 and PCC 7942 grown under Fe deficiency. The intensity of this transcript was considerably reduced in Fe-sufficient culture. It could be further shown that the regulation of IdiA expression is at the transcriptional level and that transcription and translation of IdiA are closely linked. Primer extension analysis indicated a single transcriptional start site 193 nt upstream of the first presumed translational start codon. Moreover, molecular characterization of the entire 5.8 kb chromosomal HindIII DNA fragment carrying the idiA gene from Synechococcus sp. PCC 6301 led to the identification of six long ORFs in addition to idiA. The two genes adjacent to idiA, and dpsA located 2018 nt downstream of idiA, were insertionally inactivated in Synechococcus sp. PCC 7942 and the corresponding mutants were partially characterized. These experiments provide evidence that the gene products of idiB, located immediately downstream of idiA, and of dpsA are involved in the activation of IdiA expression, since the absence of each of these two gene products prevents the greatly elevated expression of IdiA under nutrient deficiency. PMID:10411274

Michel, K P; Krüger, F; Pühler, A; Pistorius, E K

1999-06-01

350

GH51 Arabinofuranosidase and Its Role in the Methylglucuronoarabinoxylan Utilization System in Paenibacillus sp. Strain JDR-2.  

PubMed

Methylglucuronoarabinoxylan (MeGAXn) from agricultural residues and energy crops is a significant yet underutilized biomass resource for production of biofuels and chemicals. Mild thermochemical pretreatment of bagasse yields MeGAXn requiring saccharifying enzymes for conversion to fermentable sugars. A xylanolytic bacterium, Paenibacillus sp. strain JDR-2, produces an extracellular cell-associated GH10 endoxylanse (XynA1) which efficiently depolymerizes methylglucuronoxylan (MeGXn) from hardwoods coupled with assimilation of oligosaccharides for further processing by intracellular GH67 ?-glucuronidase, GH10 endoxylanase, and GH43 ?-xylosidase. This process has been ascribed to genes that comprise a xylan utilization regulon that encodes XynA1 and includes a gene cluster encoding transcriptional regulators, ABC transporters, and intracellular enzymes that convert assimilated oligosaccharides to fermentable sugars. Here we show that Paenibacillus sp. JDR-2 utilized MeGAXn without accumulation of oligosaccharides in the medium. The Paenibacillus sp. JDR-2 growth rate on MeGAXn was 3.1-fold greater than that on oligosaccharides generated from MeGAXn by XynA1. Candidate genes encoding GH51 arabinofuranosidases with potential roles were identified. Following growth on MeGAXn, quantitative reverse transcription-PCR identified a cluster of genes encoding a GH51 arabinofuranosidase (AbfB) and transcriptional regulators which were coordinately expressed along with the genes comprising the xylan utilization regulon. The action of XynA1 on MeGAXn generated arabinoxylobiose, arabinoxylotriose, xylobiose, xylotriose, and methylglucuronoxylotriose. Recombinant AbfB processed arabinoxylooligosaccharides to xylooligosaccharides and arabinose. MeGAXn processing by Paenibacillus sp. JDR-2 may be achieved by extracellular depolymerization by XynA1 coupled to assimilation of oligosaccharides and further processing by intracellular enzymes, including AbfB. Paenibacillus sp. JDR-2 provides a GH10/GH67 system complemented with genes encoding intracellular GH51 arabinofuranosidases for efficient utilization of MeGAXn. PMID:25063665

Sawhney, Neha; Preston, James F

2014-10-01

351

Investigation of the Amycolatopsis sp. Strain ATCC 39116 Vanillin Dehydrogenase and Its Impact on the Biotechnical Production of Vanillin  

PubMed Central

The actinomycete Amycolatopsis sp. strain ATCC 39116 is capable of synthesizing large amounts of vanillin from ferulic acid, which is a natural cell wall component of higher plants. The desired intermediate vanillin is subject to undesired catabolism caused by the metabolic activity of a hitherto unknown vanillin dehydrogenase (VDHATCC 39116). In order to prevent the oxidation of vanillin to vanillic acid and thereby to obtain higher yields and concentrations of vanillin, the responsible vanillin dehydrogenase in Amycolatopsis sp. ATCC 39116 was investigated for the first time by using data from our genome sequence analysis and further bioinformatic approaches. The vdh gene was heterologously expressed in Escherichia coli, and the encoded vanillin dehydrogenase was characterized in detail. VDHATCC 39116 was purified to apparent electrophoretic homogeneity and exhibited NAD+-dependent activity toward vanillin, coniferylaldehyde, cinnamaldehyde, and benzaldehyde. The enzyme showed its highest level of activity toward vanillin at pH 8.0 and at a temperature of 44°C. In a next step, a precise vdh deletion mutant of Amycolatopsis sp. ATCC 39116 was generated. The mutant lost its ability to grow on vanillin and did not show vanillin dehydrogenase activity. A 2.3-times-higher vanillin concentration and a substantially reduced amount of vanillic acid occurred with the Amycolatopsis sp. ATCC 39116 ?vdh::Kmr mutant when ferulic acid was provided for biotransformation in a cultivation experiment on a 2-liter-bioreactor scale. Based on these results and taking further metabolic engineering into account, the Amycolatopsis sp. ATCC 39116 ?vdh::Kmr mutant represents an optimized and industrially applicable platform for the biotechnological production of natural vanillin. PMID:23064333

Fleige, Christian; Hansen, Gunda; Kroll, Jens

2013-01-01

352

4-Chlorobenzoate Uptake in Comamonas sp. Strain DJ12 Is Mediated by a Tripartite ATP-Independent Periplasmic Transporter  

Microsoft Academic Search

The fcb gene cluster involved in the hydrolytic dehalogenation of 4-chlorobenzoate is organized in the order fcbB-fcbA-fcbT1-fcbT2-fcbT3-fcbC in Comamonas sp. strain DJ-12. The genes are operonic and inducible with 4-chloro-, 4-iodo-, and 4-bromobenzoate. The fcbT1, fcbT2, and fcbT3 genes encode a transporter in the secondary TRAP (tripartite ATP-independent periplasmic) family. An fcbT1T2T3 knockout mutant shows a much slower growth rate

Jong-Chan Chae; Gerben J. Zylstra

2006-01-01

353

Genome sequence of the anaerobic bacterium Bacillus sp. strain ZYK, a selenite and nitrate reducer from paddy soil.  

PubMed

Bacillus sp. strain ZYK, a member of the phylum Firmicutes, is of interest for its ability to reduce nitrate and selenite and for its resistance to arsenic under anaerobic conditions. Here we describe some key features of this organism, together with the complete genome sequence and annotation. The 3,575,797 bp long chromosome with its 3,454 protein-coding and 70 RNA genes, and the information gained from its sequence will be relevant to the elucidation of microbially-mediated transformations of nitrogen, selenium and arsenic in paddy soil. PMID:25197451

Bao, Peng; Su, Jian-Qiang; Hu, Zheng-Yi; Häggblom, Max M; Zhu, Yong-Guan

2014-06-15

354

Extending the alkene substrate range of vinyl chloride utilizing Nocardioides sp. strain JS614 with ethene oxide  

Microsoft Academic Search

Nocardioides sp. strain JS614 grows on the C2 alkenes ethene (Eth), vinyl chloride, and vinyl fluoride as sole carbon sources. The presence of 400–800 ?M ethene oxide\\u000a (EtO) extended the growth substrate range to propene (C3) and butene (C4). Propene-dependent growth of JS614 was CO2 dependent and was prevented by the carboxylase\\/reductase inhibitor 2-bromoethanesulfonic acid, sodium salt (BES), while growth\\u000a on

Anne E. Taylor; Daniel J. Arp; Peter J. Bottomley; Lewis Semprini

2010-01-01

355

Role of heavy metal resistant Ochrobactrum sp. and Bacillus spp. strains in bioremediation of a rice cultivar and their PGPR like activities.  

PubMed

The present study demonstrates the metal toxicity ameliorating and growth promoting abilities of three different bacterial isolates when applied to rice as host plant. The three bacterial strains included a cadmium resistant Ochrobactrum sp., a lead resistant Bacillus sp. and an arsenic resistant Bacillus sp. designated as CdSP9, PbSP6, and AsSP9, respectively. When these isolates were used as inocula applied to metal-treated rice plants of variety Satabdi, the germination percentage, relative root elongation (RRE), amylase and protease activities were increased. The toxic effect of metal was reduced in presence of these bacteria. The overall biomass and root/shoot ratio were also enhanced by bacterial inoculation. Hydroponic studies showed that the superoxide dismutase (SOD) activity and malondialdehyde (MDA) level, which had been increased in the presence of metal stress in rice roots, were lowered by the bacterial inoculation. In addition, all three strains were 1-aminocyclopropane-1-carboxylate (ACC) deaminase and catalase positive, whereas siderophore producing ability was lacking in PbSP6. However, both PbSP6 and AsSP9 were protease positive and could hydrolyse starch. The data indicate that these bacteria have promise for bioremediation as well as for plant growth promotion. PMID:23456706

Pandey, Sanjeev; Ghosh, Pallab Kumar; Ghosh, Sisir; De, Tarun Kumar; Maiti, Tushar Kanti

2013-02-01

356

Arsenic transforming abilities of groundwater bacteria and the combined use of Aliihoeflea sp. strain 2WW and goethite in metalloid removal.  

PubMed

Several technologies have been developed for lowering arsenic in drinking waters below the World Health Organization limit of 10 ?g/L. When in the presence of the reduced form of inorganic arsenic, i.e. arsenite, one options is pre-oxidation of arsenite to arsenate and adsorption on iron-based materials. Microbial oxidation of arsenite is considered a sustainable alternative to the chemical oxidants. In this contest, the present study investigates arsenic redox transformation abilities of bacterial strains in reductive groundwater from Lombardia (Italy), where arsenite was the main arsenic species. Twenty isolates were able to reduce 75 mg/L arsenate to arsenite, and they were affiliated to the genera Pseudomonas, Achromobacter and Rhodococcus and genes of the ars operon were detected. Three arsenite oxidizing strains were isolated: they belonged to Rhodococcus sp., Achromobacter sp. and Aliihoeflea sp., and aioA genes for arsenite oxidase were detected in Aliihoeflea sp. strain 2WW and in Achromobacter sp. strain 1L. Uninduced resting cells of strain 2WW were used in combination with goethite for arsenic removal in a model system, in order to test the feasibility of an arsenic removal process. In the presence of 200 ?g/L arsenite, the combined 2WW-goethite system removed 95% of arsenic, thus lowering it to 8 ?g/L. These results indicate that arsenite oxidation by strain 2WW combined to goethite adsorption is a promising approach for arsenic removal from contaminated groundwater. PMID:24411461

Corsini, Anna; Zaccheo, Patrizia; Muyzer, Gerard; Andreoni, Vincenza; Cavalca, Lucia

2014-03-30

357

Physiological sources of reductant for nitrogen fixation activity in Nostoc sp. strain UCD 7801 in symbiotic association with Anthoceros punctatus.  

PubMed Central

Pure cultures of the symbiotic cyanobacterium-bryophyte association with Anthoceros punctatus were reconstituted by using Nostoc sp. strain UCD 7801 or its 3-(3,4-dichlorophenol)-1,1-dimethylurea (DCMU)-resistant mutant strain, UCD 218. The cultures were grown under high light intensity with CO2 as the sole carbon source and then incubated in the dark to deplete endogenous reductant pools before measurements of nitrogenase activities (acetylene reduction). High rates of light-dependent acetylene reduction were obtained both before starvation in the dark and after recovery from starvation, regardless of which of the two Nostoc strains was reconstituted in the association. Rates of acetylene reduction by symbiotic tissue with the wild-type Nostoc strain decreased 99 and 96% after 28 h of incubation in the dark and after reexposure to light in the presence of 5 microM DCMU, respectively. Supplementation of the medium with glucose restored nitrogenase activity in the dark to a rate that was 64% of the illuminated rate. In the light and in the presence of 5 microM DCMU, acetylene reduction could be restored to 91% of the uninhibited rate by the exogenous presence of various carbohydrates. The rate of acetylene reduction in the presence of DCMU was 34% of the uninhibited rate of tissue in association with the DCMU-resistant strain UCD 218. This result implies that photosynthates produced immediately by the cyanobacterium can supply at least one-third of the reductant required for nitrogenase activity on a short-term basis in the symbiotic association. However, high steady-state rates of nitrogenase activity by symbiotic Nostoc strains appear to depend on endogenous carbohydrate reserves, which are presumably supplied as photosynthate from both A. punctatus tissue and the Nostoc strain. PMID:1938924

Steinberg, N A; Meeks, J C

1991-01-01

358

Molecular characterization of the alpha subunit of multicomponent phenol hydroxylase from 4-chlorophenol-degrading Pseudomonas sp. strain PT3.  

PubMed

Multicomponent phenol hydroxylases (mPHs) are diiron enzymes that use molecular oxygen to hydroxylate a variety of phenolic compounds. The DNA sequence of the alpha subunit (large subunit) of mPH from 4-chlorophenol (4-CP)-degrading bacterial strain PT3 was determined. Strain PT3 was isolated from oil-contaminated soil samples adjacent to automobile workshops and oil stations after enrichment and establishment of a chlorophenol-degrading consortium. Strain PT3 was identified as a member of Pseudomonas sp. based on sequence analysis of the 16S rRNA gene fragment. The 4-CP catabolic pathway by strain PT3 was tentatively proposed to proceed via a meta-cleavage pathway after hydroxylation to the corresponding chlorocatechol. This hypothesis was supported by polymerase chain reaction (PCR) detection of the LmPH encoding sequence and UV/VIS spectrophotometric analysis of the culture filtrate showing accumulation of 5-chloro-2-hydroxymuconic semialdehyde (5-CHMS) with ?max 380. The detection of catabolic genes involved in 4-CP degradation by PCR showed the presence of both mPH and catechol 2,3-dioxygenase (C23DO). Nucleotide sequence analysis of the alpha subunit of mPH from strain PT3 revealed specific phylogenetic grouping to known mPH. The metal coordination encoding regions from strain PT3 were found to be conserved with those from the homologous dinuclear oxo-iron bacterial monooxygenases. Two DE(D)XRH motifs was detected in LmPH of strain PT3 within an approximate 100 amino acid interval, a typical arrangement characteristic of most known PHs. PMID:24390833

El-Sayed, Wael S; Ibrahim, Mohamed K; Ouf, Salama A

2014-01-01

359

Isolation, identification and characterization of a new lipolytic Pseudomonas sp., strain AHD?1, from Tunisian soil  

Microsoft Academic Search

A novel, lipid?degrading bacterium (strain AHD?1) was isolated from soil regularly contaminated with washing?machine wastewater in Sfax, Tunisia. When this strain was grown in a medium containing 2% triacylglycerol, the hydrolysis products were found to be diacylglycerols, monoacylglycerols and free fatty acids. This strain was an aerobic, mesophilic, Gram?negative, motile, non?sporulating bacterium, capable of growing optimally at pH 7 and

Imen Fendri; Ali Chaari; Abdelhafidh Dhouib; Brahim Jlassi; Abdelkarim Abousalham; Frédéric Carrière; Sami Sayadi; Slim Abdelkafi

2010-01-01

360

Identification of a Novel Dihydrodaidzein Racemase Essential for Biosynthesis of Equol from Daidzein in Lactococcus sp. Strain 20-92  

PubMed Central

Equol is metabolized from daidzein, a soy isoflavone, by the gut microflora. In this study, we identified a novel dihydrodaidzein racemase (l-DDRC) that is involved in equol biosynthesis in a lactic acid bacterium, Lactococcus sp. strain 20-92, and confirmed that histidine-tagged recombinant l-DDRC (l-DDRC-His) was able to convert both the (R)- and (S)-enantiomers of dihydrodaidzein to the racemate. Moreover, we showed that recombinant l-DDRC-His was essential for in vitro equol production from daidzein by a recombinant enzyme mixture and that efficient in vitro equol production from daidzein was possible using at least four enzymes, including l-DDRC. We also proposed a model of the metabolic pathway from daidzein to equol in Lactococcus strain 20-92. PMID:22582059

Takahashi, Masayuki; Miyazawa, Norihiro; Abiru, Yasuhiro; Uchiyama, Shigeto; Hishigaki, Haretsugu

2012-01-01

361

FORMALDEHYDE GAS INACTIVATION OF BACILLUS ANTHRACIS, BACILLUS SUBTILIS AND GEOBACILLUS STEAROTHERMOPHILUS SPORES ON INDOOR SURFACE MATERIALS.  

EPA Science Inventory

Research evaluated the decontamination of Bacillus anthracis, Bacillus subtilis, and Geobacillus stearothermophilus spores on indoor surface material using formaldehyde gas. Spores were dried on seven types of indoor surfaces and exposed to 1100 ppm formaldehyde gas for 10 hr. Fo...

362

Screening and genetic characterization of thermo-tolerant Synechocystis sp. PCC6803 strains created by adaptive evolution  

PubMed Central

Background Temperature tolerance is an important aspect for commercial scale outdoor cultivation of microalgae and cyanobacteria. While various genes are known to be related to Synechocystis sp. PCC6803's heat shock response, there is very limited published data concerning the specific genes involved in long term thermal tolerance. We have previously used random mutagenesis and adaptive evolution to generate a mixture of strains of Synechocystis sp. PCC6803 with significantly increased thermal tolerance. The genetic modifications leading to the phenotypes of the newly generated strains are the focus of this work. Results We used a custom screening platform, based on 96-deepwell microplate culturing in an in house designed cultivation chamber integrated in a liquid handling robot for screening and selection; in addition we also used a more conventional system. The increased thermal tolerances of the isolated monoclonal strains were validated in larger bioreactors and their whole genomes sequenced. Comparison of the sequence information to the parental wild type identified various mutations responsible for the enhanced phenotypes. Among the affected genes identified are clpC, pnp, pyk2, sigF, nlpD, pyrR, pilJ and cya1. Conclusions The applied methods (random mutagenesis, in vivo selection, screening, validation, whole genome sequencing) were successfully applied to identify various mutations, some of which are very unlikely to have been identified by other approaches. Several of the identified mutations are found in various strains and (due to their distribution) are likely to have occurred independently. This, coupled with the relatively low number of affected genes underscores the significance of these specific mutations to convey thermal tolerance in Synechocystis. PMID:25029912

2014-01-01

363

The uptake hydrogenase in the unicellular diazotrophic cyanobacterium Cyanothece sp. strain PCC 7822 protects nitrogenase from oxygen toxicity.  

PubMed

Cyanothece sp. strain PCC 7822 is a unicellular, diazotrophic cyanobacterium that can produce large quantities of H2 when grown diazotrophically. This strain is also capable of genetic manipulations and can represent a good model for improving H2 production from cyanobacteria. To this end, a knockout mutation was made in the hupL gene (?hupL), and we determined how this would affect the amount of H2 produced. The ?hupL mutant demonstrated virtually no nitrogenase activity or H2 production when grown under N2-fixing conditions. To ensure that this mutation only affected the hupL gene, a complementation strain was constructed readily with wild-type properties; this indicated that the original insertion was only in hupL. The mutant had no uptake hydrogenase activity but had increased bidirectional hydrogenase (Hox) activity. Western blotting and immunocytochemistry under the electron microscope indicated that the mutant had neither HupL nor NifHDK, although the nif genes were transcribed. Interestingly, biochemical analysis demonstrated that both HupL and NifH could be membrane associated. The results indicated that the nif genes were transcribed but that NifHDK was either not translated or was translated but rapidly degraded. We hypothesized that the Nif proteins were made but were unusually susceptible to O2 damage. Thus, we grew the mutant cells under anaerobic conditions and found that they grew well under N2-fixing conditions. We conclude that in unicellular diazotrophs, like Cyanothece sp. strain PCC 7822, the HupLS complex helps remove oxygen from the nitrogenase, and that this is a more important function than merely oxidizing the H2 produced by the nitrogenase. PMID:24317398

Zhang, Xiaohui; Sherman, Debra M; Sherman, Louis A

2014-02-01

364

Taxonomic studies of deep-sea barophilic Shewanella strains and description of Shewanella violacea sp. nov.  

PubMed

Several barophilic Shewanella species have been isolated from deep-sea sediments at depths of 2,485-6,499 m. From the results of taxonomic studies, all of these isolates have been identified as strains of Shewanella benthica except for strain DSS12. Strain DSS12 is a member of a novel, moderately barophilic Shewanella species isolated from the Ryukyu Trench at a depth of 5,110 m. On Marine Agar 2216 plates, this organism produced a violet pigment, whereas the colonies of other isolates (S. benthica) were rose-colored. Phylogenetic analysis based on 16 S ribosomal RNA gene sequences showed that strain DSS12 represents a separate lineage within the genus Shewanella that is closely related to S. benthica and particularly to the members of the Shewanella barophiles branch. The temperature range for growth and some of the biochemical characteristics indicate that strain DSS12 differs from other Shewanella species. Furthermore, strain DSS12 displayed a low level of DNA similarity to the Shewanella type strains. Based on these differences, it is proposed that strain DSS12 represents a new deep-sea Shewanella species. The name Shewanella violacea (JCM 10179) is proposed. PMID:9818352

Nogi, Y; Kato, C; Horikoshi, K

1998-10-01

365

Orally Administered Thermostable N-Acyl Homoserine Lactonase from Bacillus sp. Strain AI96 Attenuates Aeromonas hydrophila Infection in Zebrafish  

PubMed Central

N-Acylated homoserine lactone (AHL) lactonases are capable of degrading signal molecules involved in bacterial quorum sensing and therefore represent a new approach to control bacterial infection. Here a gene responsible for the AHL lactonase activity of Bacillus sp. strain AI96, 753 bp in length, was cloned and then expressed in Escherichia coli. The deduced amino acid sequence of Bacillus sp. AI96 AiiA (AiiAAI96) is most similar to those of other Bacillus sp. AHL lactonases (?80% sequence identity) and was consequently categorized as a member of the metallo-?-lactamase superfamily. AiiAAI96 maintains ?100% of its activity at 10°C to 40°C at pH 8.0, and it is very stable at 70°C at pH 8.0 for at least 1 h; no other Bacillus AHL lactonase has been found to be stable under these conditions. AiiAAI96 resists digestion by proteases and carp intestinal juice, and it has broad-spectrum substrate specificity. The supplementation of AiiAAI96 into fish feed by oral administration significantly attenuated Aeromonas hydrophila infection in zebrafish. This is the first report of the oral administration of an AHL lactonase for the efficient control of A. hydrophila. PMID:22247159

Cao, Yanan; He, Suxu; Zhang, Meichao; Mao, Wei; Zhang, Huitu

2012-01-01

366

Efficient production of laccases by Trametes sp. AH28-2 in cocultivation with a Trichoderma strain.  

PubMed

A biocontrol fungus isolated from rotting wood was identified as a Trichoderma strain (named as Trichoderma sp. ZH1) by internal transcribed spacer (ITS) sequences of rRNA genes. The laccase yield of Trametes sp. AH28-2 in cocultivation with Trichoderma sp. ZH1 reached 6,210 U l(-1), approximately identical to those induced by toxic aromatic inducers. Cocultures maintained 60-70 % of their highest laccase activity obtained at 5 days after inoculation of the biocontrol fungus, at least for 20 days. Furthermore, a novel laccase isozyme (LacC) was obtained through the fungal interactions. The molecular weight of LacC is about 64 kDa, and its isoelectric point is 6.6. The temperature and pH optimum for LacC to oxidize guaiacol are 55 degrees C and 5.0, respectively. LacC is stable both at 60 degrees C and pH 4.0-8.0. Furthermore, the K (m) values of LacC for various substrates were also determined. Our work demonstrates a safe strategy for the production of industrial laccases, instead of the traditional method of chemical induction. PMID:16622678

Zhang, H; Hong, Y Z; Xiao, Y Z; Yuan, J; Tu, X M; Zhang, X Q

2006-11-01

367

Site-Directed Mutagenesis of the Anabaena sp. Strain PCC 7120 Nitrogenase Active Site To Increase Photobiological Hydrogen Production? †  

PubMed Central

Cyanobacteria use sunlight and water to produce hydrogen gas (H2), which is potentially useful as a clean and renewable biofuel. Photobiological H2 arises primarily as an inevitable by-product of N2 fixation by nitrogenase, an oxygen-labile enzyme typically containing an iron-molybdenum cofactor (FeMo-co) active site. In Anabaena sp. strain 7120, the enzyme is localized to the microaerobic environment of heterocysts, a highly differentiated subset of the filamentous cells. In an effort to increase H2 production by this strain, six nitrogenase amino acid residues predicted to reside within 5 Å of the FeMo-co were mutated in an attempt to direct electron flow selectively toward proton reduction in the presence of N2. Most of the 49 variants examined were deficient in N2-fixing growth and exhibited decreases in their in vivo rates of acetylene reduction. Of greater interest, several variants examined under an N2 atmosphere significantly increased their in vivo rates of H2 production, approximating rates equivalent to those under an Ar atmosphere, and accumulated high levels of H2 compared to the reference strains. These results demonstrate the feasibility of engineering cyanobacterial strains for enhanced photobiological production of H2 in an aerobic, nitrogen-containing environment. PMID:20709836

Masukawa, Hajime; Inoue, Kazuhito; Sakurai, Hidehiro; Wolk, C. Peter; Hausinger, Robert P.

2010-01-01

368

Metal Reduction and Iron Biomineralization by a Psychrotolerant Fe(III)-Reducing Bacterium, Shewanella sp. Strain PV-4  

PubMed Central

A marine psychrotolerant, dissimilatory Fe(III)-reducing bacterium, Shewanella sp. strain PV-4, from the microbial mat at a hydrothermal vent of Loihi Seamount in the Pacific Ocean has been further characterized, with emphases on metal reduction and iron biomineralization. The strain is able to reduce metals such as Fe(III), Co(III), Cr(VI), Mn(IV), and U(VI) as electron acceptors while using lactate, formate, pyruvate, or hydrogen as an electron donor. Growth during iron reduction occurred over the pH range of 7.0 to 8.9, a sodium chloride range of 0.05 to 5%, and a temperature range of 0 to 37°C, with an optimum growth temperature of 18°C. Unlike mesophilic dissimilatory Fe(III)-reducing bacteria, which produce mostly superparamagnetic magnetite (<35 nm), this psychrotolerant bacterium produces well-formed single-domain magnetite (>35 nm) at temperatures from 18 to 37°C. The genome size of this strain is about 4.5 Mb. Strain PV-4 is sensitive to a variety of commonly used antibiotics except ampicillin and can acquire exogenous DNA (plasmid pCM157) through conjugation. PMID:16672462

Roh, Yul; Gao, Haichun; Vali, Hojatollah; Kennedy, David W.; Yang, Zamin K.; Gao, Weimin; Dohnalkova, Alice C.; Stapleton, Raymond D.; Moon, Ji-Won; Phelps, Tommy J.; Fredrickson, James K.; Zhou, Jizhong

2006-01-01

369

Biodegradation of malachite green by Pseudomonas sp. strain DY1 under aerobic condition: characteristics, degradation products, enzyme analysis and phytotoxicity.  

PubMed

Malachite green (MG), a widely-used and recalcitrant dye, has been confirmed to be carcinogenic and mutagenic against many organisms. The main objective of this study is to investigate the capability of Pseudomonas sp. strain DY1 to decolorize MG, and to explore the possible mechanism. The results showed that this strain demonstrated high decolorizing capability (90.3-97.2%) at high concentrations of MG (100-1,000 mg/l) under shaking condition within 24 h. In static conditions, lower but still effective decolorization (78.9-84.3%) was achieved. The optimal pH and temperature for the decolorization was pH 6.6 and 28-30°C, respectively. Mg(2+) and Mn(2+) (1 mM) were observed to significantly enhance the decolorization. The intermediates of the MG degradation under aerobic condition identified by UV-visible, GC-MS and LC-MS analysis included malachite green carbinol, (dimethyl amino-phenyl)-phenyl-methanone, N,N-dimethylaniline, (methyl amino-phenyl)-phenyl-methanone, (amino phenyl)-phenyl methanone and di-benzyl methane. The enzyme analysis indicated that Mn-peroxidase, NADH-DCIP and MG reductase were involved in the biodegradation of MG. Moreover, phytotoxicity of MG and detoxification for MG by the strain were observed. Therefore, this strain could be potentially used for bioremediation of MG. PMID:21253837

Du, Lin-Na; Wang, Sheng; Li, Gang; Wang, Bing; Jia, Xiao-Ming; Zhao, Yu-Hua; Chen, Yun-Long

2011-03-01

370

Oscillating behavior of carbohydrate granule formation and dinitrogen fixation in the cyanobacterium Cyanothece sp. strain ATCC 51142  

NASA Technical Reports Server (NTRS)

It has been shown that some aerobic, unicellular, diazotrophic cyanobacteria temporally separate photosynthetic O2 evolution and oxygen-sensitive N2 fixation. Cyanothece sp. ATCC strain 51142 is an aerobic, unicellular, diazotrophic cyanobacterium that fixes N2 during discrete periods of its cell cycle. When the bacteria are maintained under diurnal light-dark cycles, N2 fixation occurs in the dark. Similar cycling is observed in continuous light, implicating a circadian rhythm. Under N2-fixing conditions, large inclusion granules form between the thylakoid membranes. Maximum granulation, as observed by electron microscopy, occurs before the onset of N2 fixation, and the granules decrease in number during the period of N2 fixation. The granules can be purified from cell homogenates by differential centrifugation. Biochemical analyses of the granules indicate that these structures are primarily carbohydrate, with some protein. Further analyses of the carbohydrate have shown that it is a glucose polymer with some characteristics of glycogen. It is proposed that N2 fixation is driven by energy and reducing power stored in these inclusion granules. Cyanothece sp. strain ATCC 51142 represents an excellent experimental organism for the study of the protective mechanisms of nitrogenase, metabolic events in cyanobacteria under normal and stress conditions, the partitioning of resources between growth and storage, and biological rhythms.

Schneegurt, M. A.; Sherman, D. M.; Nayar, S.; Sherman, L. A.; Mitchell, C. A. (Principal Investigator)

1994-01-01

371

Genome sequence of the acid-tolerant Burkholderia sp. strain WSM2232 from Karijini National Park, Australia  

PubMed Central

Burkholderia sp. strain WSM2232 is an aerobic, motile, Gram-negative, non-spore-forming acid-tolerant rod that was trapped in 2001 from acidic soil collected from Karijini National Park (Australia) using Gastrolobium capitatum as a host. WSM2232 was effective in nitrogen fixation with G. capitatum but subsequently lost symbiotic competence during long-term storage. Here we describe the features of Burkholderia sp. strain WSM2232, together with genome sequence information and its annotation. The 7,208,311 bp standard-draft genome is arranged into 72 scaffolds of 72 contigs containing 6,322 protein-coding genes and 61 RNA-only encoding genes. The loss of symbiotic capability can now be attributed to the loss of nodulation and nitrogen fixation genes from the genome. This rhizobial genome is one of 100 sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project. PMID:25197442

Walker, Robert; Watkin, Elizabeth; Tian, Rui; Brau, Lambert; O'Hara, Graham; Goodwin, Lynne; Han, James; Reddy, Tatiparthi; Huntemann, Marcel; Pati, Amrita; Woyke, Tanja; Mavromatis, Konstantinos; Markowitz, Victor; Ivanova, Natalia; Kyrpides, Nikos; Reeve, Wayne

2013-01-01

372

Expression of Shewanella oneidensis MR-1 [FeFe]-Hydrogenase Genes in Anabaena sp. Strain PCC 7120  

PubMed Central

H2 generated from renewable resources holds promise as an environmentally innocuous fuel that releases only energy and water when consumed. In biotechnology, photoautotrophic oxygenic diazotrophs could produce H2 from water and sunlight using the cells' endogenous nitrogenases. However, nitrogenases have low turnover numbers and require large amounts of ATP. [FeFe]-hydrogenases found in other organisms can have 1,000-fold higher turnover numbers and no specific requirement for ATP but are very O2 sensitive. Certain filamentous cyanobacteria protect nitrogenase from O2 by sequestering the enzyme within internally micro-oxic, differentiated cells called heterocysts. We heterologously expressed the [FeFe]-hydrogenase operon from Shewanella oneidensis MR-1 in Anabaena sp. strain PCC 7120 using the heterocyst-specific promoter PhetN. Active [FeFe]-hydrogenase was detected in and could be purified from aerobically grown Anabaena sp. strain PCC 7120, but only when the organism was grown under nitrate-depleted conditions that elicited heterocyst formation. These results suggest that the heterocysts protected the [FeFe]-hydrogenase against inactivation by O2. PMID:23023750

Gartner, Katrin; Lechno-Yossef, Sigal; Cornish, Adam J.; Wolk, C. Peter

2012-01-01

373

Heterocyst development and diazotrophic metabolism in terminal respiratory oxidase mutants of the cyanobacterium Anabaena sp. strain PCC 7120.  

PubMed

Heterocyst development was analyzed in mutants of the heterocyst-forming cyanobacterium Anabaena sp. strain PCC 7120 bearing inactivated cox2 and/or cox3 genes, encoding heterocyst-specific terminal respiratory oxidases. At the morphological level, the cox2 cox3 double mutant (strain CSAV141) was impaired in membrane reorganization involving the so-called honeycomb system that in the wild-type strain is largely or exclusively devoted to respiration, accumulated glycogen granules at conspicuously higher levels than the wild type (in both vegetative cells and heterocysts), and showed a delay in carboxysome degradation upon combined nitrogen deprivation. Consistently, chemical analysis confirmed higher accumulation of glycogen in strain CSAV141 than in the wild type. No impairment was observed in the formation of the glycolipid or polysaccharide layers of the heterocyst envelope, consistent with the chemical detection of heterocyst-specific glycolipids, or in the expression of the heterocyst-specific genes nifHDK and fdxH. However, nitrogenase activity under oxic conditions was impaired in strain CSAV135 (cox3) and undetectable in strain CSAV141 (cox2 cox3). These results show that these dedicated oxidases are required for normal development and performance of the heterocysts and indicate a central role of Cox2 and, especially, of Cox3 in the respiratory activity of the heterocysts, decisively contributing to protection of the N(2) fixation machinery against oxygen. However, in contrast to the case for other diazotrophic bacteria, expression of nif genes in Anabaena seems not to be affected by oxygen. PMID:17416650

Valladares, Ana; Maldener, Iris; Muro-Pastor, Alicia M; Flores, Enrique; Herrero, Antonia

2007-06-01

374

Identification and Characterization of a Novel Class of Extracellular Poly(3-Hydroxybutyrate) Depolymerase from Bacillus sp. Strain NRRL B-14911?  

PubMed Central

The catalytic, linker, and denatured poly(3-hydroxybutyrate) (dPHB)-binding domains of bacterial extracellular PHB depolymerases (PhaZs) are classified into several different types. We now report a novel class of extracellular PHB depolymerase from Bacillus sp. strain NRRL B-14911. Its catalytic domain belongs to type 1, whereas its putative linker region neither possesses the sequence features of the three known types of linker domains nor exhibits significant amino acid sequence similarity to them. Instead, this putative linker region can be divided into two distinct linker domains of novel types: LD1 and LD2. LD1 shows significant amino acid sequence similarity to certain regions of a large group of PHB depolymerase-unrelated proteins. LD2 and its homologs are present in a small group of PhaZs. The remaining C-terminal portion of this PhaZ can be further divided into two distinct domains: SBD1 and SBD2. Each domain showed strong binding to dPHB, and there is no significant sequence similarity between them. Each domain neither possesses the sequence features of the two known types of dPHB-binding domains nor shows significant amino acid sequence similarity to them. These unique features indicate the presence of two novel and distinct types of dPHB-binding domains. Homologs of these novel domains also are present in the extracellular PhaZ of Bacillus megaterium and the putative extracellular PhaZs of Bacillus pseudofirmus and Bacillus sp. strain SG-1. The Bacillus sp. NRRL B-14911 PhaZ appears to be a representative of a novel class of extracellular PHB depolymerases. PMID:21948827

Ma, Wan-Ting; Lin, Ju-Hui; Chen, Hui-Ju; Chen, Syuan-Yi; Shaw, Gwo-Chyuan

2011-01-01

375

Cloning and recombinant expression of a cellulase from the cellulolytic strain Streptomyces sp. G12 isolated from compost  

PubMed Central

Background The use of lignocellulosic materials for second generation ethanol production would give several advantages such as minimizing the conflict between land use for food and fuel production, providing less expensive raw materials than conventional agricultural feedstock, allowing lower greenhouse gas emissions than those of first generation ethanol. However, cellulosic biofuels are not produced at a competitive level yet, mainly because of the high production costs of the cellulolytic enzymes. Therefore, this study was aimed at discovering new cellulolytic microorganisms and enzymes. Results Different bacteria isolated from raw composting materials obtained from vegetable processing industry wastes were screened for their cellulolytic activity on solid medium containing carboxymethylcellulose. Four strains belonging to the actinomycetes group were selected on the basis of their phenotypic traits and cellulolytic activity on solid medium containing carboxymethylcellulose. The strain showing the highest cellulolytic activity was identified by 16S rRNA sequencing as belonging to Streptomyces genus and it was designated as Streptomyces sp. strain G12. Investigating the enzymes responsible for cellulase activity produced by Streptomyces G12 by proteomic analyses, two endoglucanases were identified. Gene coding for one of these enzymes, named CelStrep, was cloned and sequenced. Molecular analysis showed that the celstrep gene has an open reading frame encoding a protein of 379 amino acid residues, including a signal peptide of 37 amino acid residues. Comparison of deduced aminoacidic sequence to the other cellulases indicated that the enzyme CelStrep can be classified as a family 12 glycoside hydrolase. Heterologous recombinant expression of CelStrep was carried out in Escherichia coli, and the active recombinant enzyme was purified from culture supernatant and characterized. It catalyzes the hydrolysis of carboxymethylcellulose following a Michaelis–Menten kinetics with a KM of 9.13?mg/ml and a vmax of 3469??M?min-1. The enzyme exhibits a half life of around 24?h and 96?h at 60°C and 50°C, respectively and shows a retention of around 80% of activity after 96?h at 40°C. Conclusions In this manuscript, we describe the isolation of a new cellulolytic strain, Streptomyces sp. G12, from industrial waste based compost, the identification of the enzymes putatively responsible for its cellulolytic activity, the cloning and the recombinant expression of the gene coding for the Streptomyces sp. G12 cellulase CelStrep, that was characterized showing to exhibit a relevant thermoresistance increasing its potential for cellulose conversion. PMID:23267666

2012-01-01

376

Bacteroides sp. Strain D8, the First Cholesterol-Reducing Bacterium Isolated from Human Feces  

Microsoft Academic Search

terol-to-coprostanol conversion. Resting-cell assays showed that strain D8 could reduce 1.5 mol of choles- terol\\/mg bacterial protein\\/h. Strain D8 was a gram-negative, non-spore-forming, rod-shaped organism iden- tified as a member of the genus Bacteroides closely related to Bacteroides vulgatus, based on its morphological and biochemical characteristics. The 16S rRNA gene sequence of strain D8 was most similar (>99.5%) to those

Philippe Gerard; Pascale Lepercq; Marion Leclerc; Francoise Gavini; Pierre Raibaud; Catherine Juste

2007-01-01

377

Thermophilic protease-producing Geobacillus from Buranga hot springs in Western Uganda.  

PubMed

Two proteolytic thermophilic aerobic bacterial strains, PA-9 and PA-5, were isolated from Buranga hot springs in western Uganda. The cells were rods, approximately 10-12 microm in length and 3 microm in width. Isolate PA-9 grew at between 38 degrees C and 68 degrees C (optimum, 62 degrees C), and PA-5 grew at between 37 degrees C and 72 degrees C (optimum, 60 degrees C). Both isolates grew optimally at pH 7.5-8.5. Their 16S rRNA gene sequences indicated that they belong to the newly described genus Geobacillus. Zymogram analysis of the crude enzyme extracts revealed the presence of two extracellular proteases for isolate PA-5, and at least eight for isolate PA-9. The optimum temperature and pH for casein-degrading activity were 70 degrees C, pH 6.5 for isolate PA-9, but caseinolytic activity could also be observed at 2 degrees C. In the case of isolate PA-5, optimal activity was observed over a temperature and pH range of 50-70 degrees C and pH 5-10, respectively. PMID:12070695

Hawumba, Joseph F; Theron, Jacques; Brözel, Volker S

2002-08-01

378

Isolation and characterization of alkalotolerant Pseudomonas sp. strain ISTDF1 for degradation of dibenzofuran  

Microsoft Academic Search

An alkalotolerant Pseudomonas strain was enriched and isolated from effluent of the pulp and paper industry. This strain was able to degrade dibenzofuran\\u000a and utilize it as a sole source of energy and carbon. The GC–MS based detection of various intermediary metabolites of biodegradation\\u000a suggested the involvement of angular as well as lateral pathway of dibenzofuran biodegradation. The GC–MS based

Prashant Kumar Jaiswal; Shweta Kohli; Madhuban Gopal; Indu Shekhar Thakur

2011-01-01

379

Isolation and characterization of an isoproturon mineralizing Sphingomonas sp. strain SH from a French agricultural soil  

Microsoft Academic Search

The phenylurea herbicide isoproturon, 3-(4-isopropylphenyl)-1,1-dimethylurea (IPU), was found to be rapidly mineralized in\\u000a an agricultural soil in France that had been periodically exposed to IPU. Enrichment cultures from samples of this soil isolated\\u000a a bacterial strain able to mineralize IPU. 16S rRNA sequence analysis showed that this strain belonged to the phylogeny of\\u000a the genus Sphingomonas (96% similarity with Sphingomonas

Sabir Hussain; Marion Devers-Lamrani; Najoi El Azhari; Fabrice Martin-Laurent

2011-01-01

380

Biodegradation of bisphenol A by cells and cell lysate from Sphingomonas sp. strain AO1  

Microsoft Academic Search

The capacity and pathway of bisphenol A [BPA; 2,2-bis(4-hydroxyphenyl)propane] degradation in Sphingomonassp. strain AO1, which was isolated from the soil of a vegetable-growing field in Japan, were investigated. The bacterial strain was able to grow in a basal mineral salt medium containing BPA as the sole carbon source (BSMB medium), and was able to degrade 115 µ g?ml-1 BPA in

Miho Sasaki; Jun-ichi Maki; Ko-ichi Oshiman; Yoshinobu Matsumura; Tetsuaki Tsuchido

2005-01-01

381

Transformation of chenodeoxycholic acid by thermophilic Geobacillus stearothermophilus.  

PubMed

We performed a series of experiments with Geobacillus stearothermophilus, a thermophile isolated from oil-contaminated soil in the Kuwaiti desert. The organism has a good potential for the transformation of a broad spectrum of organic molecules such as steroids, amino acids, and aromatic hydrocarbons. In the present study, we tested its potential for the transformation of a bile component, chenodeoxycholic acid (CDCA). Five transformed products, namely, cholic acid, methylcholate, methylchenodeoxycholate, 3?-hydroxy-7-oxo-5?-cholanic acid, and 7?-hydroxy-3-oxo-5?-cholanic acid, were the major transformation products catalyzed by G. stearothermophilus. Under aerobic conditions, no evidence of side chain degradation, ring cleavage, or dehydrogenation was found among the metabolites of CDCA. CDCA transformation by a thermophile is reported for the first time. PMID:21838799

Afzal, Mohammad; Oommen, Sosamma; Al-Awadi, Samira

2011-01-01

382

Characterization of a thermophilic bacteriophage of Geobacillus kaustophilus.  

PubMed

GBK2 is a bacteriophage, isolated from a backyard compost pile, that infects the thermophile Geobacillus kaustophilus. GBK2 has a circularly permuted genome of 39,078 bp with a G+C content of 43 %. Annotation of the genome reveals 62 putative open reading frames (ORFs), 25 of which (40.3 %) show homology to known proteins and 37 of which (59.7 %) are proteins with unknown functions. Twelve of the identified ORFs had the greatest homology to genes from the phage SPP1, a phage that infects the mesophile Bacillus subtilis. The overall genomic arrangement of GBK2 is similar to that of SPP1, with the majority of GBK2 SPP1-like genes coding for proteins involved in DNA replication and metabolism. PMID:24796554

Marks, Timothy J; Hamilton, Paul T

2014-10-01

383

Cloning and characterization of a modular GH5 ?-1,4-mannanase with high specific activity from the fibrolytic bacterium Cellulosimicrobium sp. strain HY-13  

Microsoft Academic Search

The gene (1272-bp) encoding a ?-1,4-mannanase from a gut bacterium of Eisenia fetida, Cellulosimicrobium sp. strain HY-13 was cloned and expressed in Escherichia coli. The recombinant ?-1,4-mannanase (rManH) was approximately 44.0kDa and has a catalytic GH5 domain that is 65% identical to that of the Micromonospora sp. ?-1,4-mannosidase. The enzyme exhibited the highest catalytic activity toward mannans at 50°C and

Do Young Kim; Su-Jin Ham; Hyun Ju Lee; Han-Young Cho; Ji-Hoon Kim; Yi-Joon Kim; Dong-Ha Shin; Young Ha Rhee; Kwang-Hee Son; Ho-Yong Park

2011-01-01

384

Purification and Characterization of Phosphonoglycans from Glycomyces sp. Strain NRRL B-16210 and Stackebrandtia nassauensis NRRL B-16338  

PubMed Central

Two related actinomycetes, Glycomyces sp. strain NRRL B-16210 and Stackebrandtia nassauensis NRRL B-16338, were identified as potential phosphonic acid producers by screening for the gene encoding phosphoenolpyruvate (PEP) mutase, which is required for the biosynthesis of most phosphonates. Using a variety of analytical techniques, both strains were subsequently shown to produce phosphonate-containing exopolysaccharides (EPS), also known as phosphonoglycans. The phosphonoglycans were purified by sequential organic solvent extractions, methanol precipitation, and ultrafiltration. The EPS from the Glycomyces strain has a mass of 40 to 50 kDa and is composed of galactose, xylose, and five distinct partially O-methylated galactose residues. Per-deutero-methylation analysis indicated that galactosyl residues in the polysaccharide backbone are 3,4-linked Gal, 2,4-linked 3-MeGal, 2,3-linked Gal, 3,6-linked 2-MeGal, and 4,6-linked 2,3-diMeGal. The EPS from the Stackebrandtia strain is comprised of glucose, galactose, xylose, and four partially O-methylated galactose residues. Isotopic labeling indicated that the O-methyl groups in the Stackebrandtia phosphonoglycan arise from S-adenosylmethionine. The phosphonate moiety in both phosphonoglycans was shown to be 2-hydroxyethylphosphonate (2-HEP) by 31P nuclear magnetic resonance (NMR) and mass spectrometry following strong acid hydrolysis of the purified molecules. Partial acid hydrolysis of the purified EPS from Glycomyces yielded 2-HEP in ester linkage to the O-5 or O-6 position of a hexose and a 2-HEP mono(2,3-dihydroxypropyl)ester. Partial acid hydrolysis of Stackebrandtia EPS also revealed the presence of 2-HEP mono(2,3-dihydroxypropyl)ester. Examination of the genome sequences of the two strains revealed similar pepM-containing gene clusters that are likely to be required for phosphonoglycan synthesis. PMID:24584498

Yu, Xiaomin; Price, Neil P. J.; Evans, Bradley S.

2014-01-01

385

Physiological and genetic description of dissimilatory perchlorate reduction by the novel marine bacterium Arcobacter sp. strain CAB.  

PubMed

A novel dissimilatory perchlorate-reducing bacterium (DPRB), Arcobacter sp. strain CAB, was isolated from a marina in Berkeley, CA. Phylogenetically, this halophile was most closely related to Arcobacter defluvii strain SW30-2 and Arcobacter ellisii. With acetate as the electron donor, strain CAB completely reduced perchlorate (ClO4(-)) or chlorate (ClO3(-)) [collectively designated (per)chlorate] to innocuous chloride (Cl(-)), likely using the perchlorate reductase (Pcr) and chlorite dismutase (Cld) enzymes. When grown with perchlorate, optimum growth was observed at 25 to 30°C, pH 7, and 3% NaCl. Transmission electron microscopy (TEM) and scanning electron microscopy (SEM) preparations were dominated by free-swimming straight rods with 1 to 2 polar flagella per cell. Strain CAB utilized a variety of organic acids, fructose, and hydrogen as electron donors coupled to (per)chlorate reduction. Further, under anoxic growth conditions strain CAB utilized the biogenic oxygen produced as a result of chlorite dismutation to oxidize catechol via the meta-cleavage pathway of aerobic catechol degradation and the catechol 2,3-dioxygenase enzyme. In addition to (per)chlorate, oxygen and nitrate were alternatively used as electron acceptors. The 3.48-Mb draft genome encoded a distinct perchlorate reduction island (PRI) containing several transposases. The genome lacks the pcrC gene, which was previously thought to be essential for (per)chlorate reduction, and appears to use an unrelated Arcobacter c-type cytochrome to perform the same function. IMPORTANCE The study of dissimilatory perchlorate-reducing bacteria (DPRB) has largely focused on freshwater, mesophilic, neutral-pH environments. This study identifies a novel marine DPRB in the genus Arcobacter that represents the first description of a DPRB associated with the Campylobacteraceae. Strain CAB is currently the only epsilonproteobacterial DPRB in pure culture. The genome of strain CAB lacks the pcrC gene found in all other DPRB tested, demonstrating a new variation on the (per)chlorate reduction pathway. The ability of strain CAB to oxidize catechol via the oxygenase-dependent meta-cleavage pathway in the absence of external oxygen by using the biogenic oxygen produced from the dismutation of chlorite provides a valuable model for understanding the anaerobic degradation of a broad diversity of xenobiotics which are recalcitrant to anaerobic metabolism but labile to oxygenase-dependent mechanisms. PMID:23695836

Carlström, Charlotte I; Wang, Ouwei; Melnyk, Ryan A; Bauer, Stefan; Lee, Joyce; Engelbrektson, Anna; Coates, John D

2013-01-01

386

The heat shock protein ClpB mediates the development of thermotolerance in the cyanobacterium Synechococcus sp. strain PCC 7942.  

PubMed

The heat shock protein CIpB (HSP100) is a member of the diverse group of Clp polypeptides that function as molecular chaperones and/or regulators of energy-dependent proteolysis. A single-copy gene coding for a ClpB homolog was cloned and sequenced from the unicellular cyanobacterium Synechococcus sp. strain PCC 7942. The predicted polypeptide sequence was most similar to sequences of cytosolic ClpB from bacteria and higher plants (i.e., 70 to 75%). Inactivation of clpB in Synechococcus sp. strain PCC 7942 resulted in no significant differences from the wild-type phenotype under optimal growth conditions. In the wild type, two forms of ClpB were induced during temperature shifts from 37 to 47.5 or 50 degrees C, one of 92 kDa, which matched the predicted size, and another smaller protein of 78 kDa. Both proteins were absent in the delta clpB strain. The level of induction of the two ClpB forms in the wild type increased with increasingly higher temperatures, while the level of the constitutive ClpC protein remained unchanged. In the delta clpB strain, however, the ClpC content almost doubled during the heating period, presumably to compensate for the loss of ClpB activity. Photosynthetic measurements at 47.5 and 50 degrees C showed that the null mutant was no more susceptible to thermal inactivation than the wild type. Using photosynthesis as a metabolic indicator, an assay was developed for Synechococcus spp. to determine the importance of ClpB for acquired thermotolerance. Complete inactivation of photosynthetic oxygen evolution occurred in both the wild type and the delta clpB strain when they were shifted from 37 directly to 55 degrees C for 10 min. By preexposing the cells at 50 degrees C for 1.5 h, however, a significant level of photosynthesis was retained in the wild type but not in the mutant after the treatment at 55 degrees C for 10 min. Cell survival determinations confirmed that the loss of ClpB synthesis caused a fivefold reduction in the ability of Synechococcus cells to develop thermotolerance. These results clearly show that induction of ClpB at high temperatures is vital for sustained thermotolerance in Synechococcus spp., the first such example for either a photosynthetic or a prokaryotic organism. PMID:8759846

Eriksson, M J; Clarke, A K

1996-08-01

387

Isolation, characterization and antioxidative activity of C-phycocyanin from Limnothrix sp. strain 37-2-1  

PubMed Central

C-phycocyanin (C-PC) is a blue colored accessory photosynthetic pigment found in cyanobacteria. Some of the medicinal properties of Spirulina have been attributed to this pigment, which includes anticancer, antioxidant, and anti-inflammatory activity. We have screened cyanobacteria isolated from freshwater habitats in Florida for their high content of C-PC. Of 125 strains tested, one filamentous strain identified as Limnothrix sp. was selected for further research. This strain produced 18% C-PC of total dry biomass. Here we describe a simple method for obtaining C-PC of high purity without the use of ion exchange chromatography. The procedure is based on pigment precipitation from the cell lysate with an appropriate concentration of ammonium sulfate, then purification with activated carbon and chitosan, followed by a sample concentration using tangential flow filtration. We have shown that when the lower concentration of ammonium sulfate was used, C-PC with higher purity index was recovered. Characterization of C-PC from Limnothrix showed that it had an absorbance maximum at 620 nm and fluorescence at 639 nm. The molecular mass of intact C-PC was estimated to be ~50 kDa with ? and ? subunits forming dimmers. When C-PC content per unit biomass was compared to that of marketed Spirulina powder, we found that Limnothrix was superior. C-phycocyanin from Limnothrix had an antioxidative activity on DPPH free radicals similar to that found in a natural antioxidant – rutin. PMID:22353597

Gantar, Miroslav; Simovic, Dragan; Djilas, Sonja; Gonzalez, Walter W.; Miksovska, Jaroslava

2012-01-01

388

Denitrification by a soil bacterium with phthalate and other aromatic compounds as substrates. [Pseudomonas sp. strain P136  

SciTech Connect

A soil bacterium, Pseudomonas sp. strain P136, was isolated by selective enrichment for anaerobic utilization of o-phthalate through nitrate respiration. o-Phthalate, m-phthalate, p-phthalate, benzoate, cyclohex-1-ene-carboxylate, and cyclohex-3-ene-carboxylate were utilized by this strain under both aerobic and anaerobic conditions. m-Hydroxybenzoate and p-hydroxybenzoate were utilized only under anaerobic conditions. Cells grown anaerobically on one of these aromatic compounds also utilized all other aromatic compounds as substrates for denitrification without a lag period. On the other hand, cells grown on succinate utilized aromatic compounds after a lag period. Anaerobic growth on these substrates was dependent on the presence of nitrate and accompanied by the production of molecular nitrogen. The reduction of nitrite to nitrous oxide and the reduction of nitrous oxide to molecular nitrogen were also supported by anaerobic utilization of these aromatic compounds in this strain. Aerobically grown cells showed a lag period in denitrification with all substrates tested. Cells grown anaerobically on aromatic compounds also consumed oxygen. No lag period was observed for oxygen consumption during the transition period from anaerobic to aerobic conditions. Cells grown aerobically on one of these aromatic compounds were also adapted to utilize other aromatic compounds as substrates for respiration. However, cells grown on succinate showed a lag period during respiration with aromatic compounds.

Nozawa, T.; Maruyama, Y.

1988-06-01

389

Bioelectricity generation by a Gram-positive Corynebacterium sp. strain MFC03 under alkaline condition in microbial fuel cells.  

PubMed

This work studied an alkalophilic Gram-positive bacterium, Corynebacterium sp. strain MFC03, for its ability to produce electricity in the absence of an exogenous mediator under alkaline pH in microbial fuel cells (MFCs). The experimental results demonstrated that the strain MFC03 was capable of utilizing organic acids, sugars and alcohols as electron donors to generate electricity under above desired conditions. At an optimal pH of 9.0, the glucose-fed MFC achieved a maximum power density of 7.3 mW/m(2) and a Coulombic efficiency (CE) of 5.9%. In the presence of 0.1mM anthroquinone-2,6-disulfonate (AQDS), the maximum power density was enhanced to 41.8 mW/m(2) and CE was increased to 18.4%. The cyclic voltammetry measurements revealed that the electron transfer mechanism in the strain MFC03-based MFC was mainly via the excreted redox compounds in the medium solution. PMID:19879132

Liu, Min; Yuan, Yong; Zhang, Li-xia; Zhuang, Li; Zhou, Shun-gui; Ni, Jin-ren

2010-03-01

390

Molecular Determinants of the Regioselectivity of Toluene/o-Xylene Monooxygenase from Pseudomonas sp. Strain OX1? †  

PubMed Central

Bacterial multicomponent monooxygenases (BMMs) are a heterogeneous family of di-iron monooxygenases which share the very interesting ability to hydroxylate aliphatic and/or aromatic hydrocarbons. Each BMM possesses defined substrate specificity and regioselectivity which match the metabolic requirements of the strain from which it has been isolated. Pseudomonas sp. strain OX1, a strain able to metabolize o-, m-, and p-cresols, produces the BMM toluene/o-xylene monooxygenase (ToMO), which converts toluene to a mixture of o-, m-, and p-cresol isomers. In order to investigate the molecular determinants of ToMO regioselectivity, we prepared and characterized 15 single-mutant and 3 double-mutant forms of the ToMO active site pocket. Using the Monte Carlo approach, we prepared models of ToMO-substrate and ToMO-reaction intermediate complexes which allowed us to provide a molecular explanation for the regioselectivities of wild-type and mutant ToMO enzymes. Furthermore, using binding energy values calculated by energy analyses of the complexes and a simple mathematical model of the hydroxylation reaction, we were able to predict quantitatively the regioselectivities of the majority of the variant proteins with good accuracy. The results show not only that the fine-tuning of ToMO regioselectivity can be achieved through a careful alteration of the shape of the active site but also that the effects of the mutations on regioselectivity can be quantitatively predicted a priori. PMID:19074607

Notomista, Eugenio; Cafaro, Valeria; Bozza, Giuseppe; Di Donato, Alberto

2009-01-01

391

Genomic and Physiological Characterization of the Chromate-Reducing, Aquifer-Derived Firmicute Pelosinus sp. Strain HCF1  

NASA Astrophysics Data System (ADS)

Pelosinus species are fermentative firmicutes that were recently reported to be prominent members of microbial communities at contaminated subsurface sites in multiple locations. Here we report metabolic characteristics and their putative genetic basis in Pelosinus sp. strain HCF1, an isolate that predominated anaerobic, Cr(VI)-reducing columns constructed with Hanford 100H aquifer sediment (constituting 80% of the total bacterial population in the columns). Strain HCF1 ferments lactate to propionate and acetate (a complete fermentation pathway was identified in the genome) and its genome encodes both [NiFe]- and [FeFe]-hydrogenases for H2 cycling. This bacterium has unexpected capabilities and gene content associated with reduction of nitrogen oxides. In this strain, either H2 or lactate can act as a sole electron donor for nitrate, Cr(VI), and Fe(III) reduction. Transcriptional studies demonstrated differential expression of nitrate reductases and hydrogenases. Overall, the unexpected metabolic capabilities and gene content reported here broaden our perspective on what biogeochemical and ecological roles this species might play as a prominent member of microbial communities in subsurface environments.

Beller, H. R.; Han, R.; Karaoz, U.; Lim, H.; Brodie, E. L.

2012-12-01

392

Isolation and characterization of alkalotolerant Pseudomonas sp. strain ISTDF1 for degradation of dibenzofuran.  

PubMed

An alkalotolerant Pseudomonas strain was enriched and isolated from effluent of the pulp and paper industry. This strain was able to degrade dibenzofuran and utilize it as a sole source of energy and carbon. The GC-MS based detection of various intermediary metabolites of biodegradation suggested the involvement of angular as well as lateral pathway of dibenzofuran biodegradation. The GC-MS based detection of various intermediary metabolites of biodegradation suggested the involvement of angular as well as lateral pathway of dibenzofuran biodegradation. This diverse dioxygenation property of the strain allowed it to utilize various recalcitrant chlorinated xenobiotics and PAHs compounds. This strain showed optimum utilization (~85%) of dibenzofuran (200 mg l?¹) within 36 h at pH 10 at 40 °C. The growth of the strain was supported by a wide range of environmental conditions such as temperature, pH, and concentration of dibenzofuran, suggesting that it can be used for in situ bioremediation of dioxin-like compound. PMID:20686914

Jaiswal, Prashant Kumar; Kohli, Shweta; Gopal, Madhuban; Thakur, Indu Shekhar

2011-04-01

393

Efficient fermentation of Pinus sp. acid hydrolysates by an ethanologenic strain of Escherichia coli.  

PubMed Central

Process conditions for the acid hydrolysis of pine hemicellulose and cellulose have been described which provide a biocompatible sugar solution. By using an improved strain of recombinant Escherichia coli, strain KO11, hydrolysates supplemented with yeast extract and tryptone nutrients were converted to ethanol with an efficiency of 85% to over 100% on the basis of monomer sugar content (approximately 72 g/liter) and with the production of 35 g of ethanol per liter in 48 h. In the process described, approximately 347 liters of ethanol could be produced per dry metric ton of lignocellulose. PMID:1599258

Barbosa, M F; Beck, M J; Fein, J E; Potts, D; Ingram, L O

1992-01-01

394

Physiological and taxonomic description of the novel autotrophic, metal oxidizing bacterium, Pseudogulbenkiania sp. strain 2002  

Microsoft Academic Search

A lithoautotrophic, Fe(II) oxidizing, nitrate-reducing bacterium, strain 2002 (ATCC BAA-1479; =DSM 18807), was isolated as\\u000a part of a study on nitrate-dependent Fe(II) oxidation in freshwater lake sediments. Here we provide an in-depth phenotypic\\u000a and phylogenetic description of the isolate. Strain 2002 is a gram-negative, non-spore forming, motile, rod-shaped bacterium\\u000a which tested positive for oxidase, catalase, and urease. Analysis of the

Karrie A. Weber; David B. Hedrick; Aaron D. Peacock; J. Cameron Thrash; David C. White; Laurie A. Achenbach; John D. Coates

2009-01-01

395

Physicochemical effects on sulfite transformation in a lipid-rich Chlorella sp. strain  

NASA Astrophysics Data System (ADS)

SO2 is very rapidly hydrated to sulfurous acid in water solution at pH value above 6.0, whereby sulfite is yielded from the disassociation of protons. We aimed to improve the sulfite transformation efficiency and provide a basis for the direct utilization of SO2 from flue gas by a microalgal suspension. Chlorella sp. XQ-20044 was cultured in a medium with 20 mmol/L sodium sulfite under different physicochemical conditions. Under light conditions, sulfite concentration in the algal suspension reduced linearly over time, and was completely converted into sulfate within 8 h. The highest sulfite transformation rate (3.25 mmol/(L·h)) was obtained under the following conditions: 35°C, light intensity of 300 ?mol/(m2·s), NaHCO3 concentration of 6 g/L, initial cell density (OD540) of 0.8 and pH of 9-10. There was a positive correlation between sulfite transformation rate and the growth of Chlorella, with the conditions favorable to algal growth giving better sulfite transformation. Although oxygen in the air plays a role in the transformation of SO2- 3 to SO2- 4, the transformation is mainly dependent on the metabolic activity of algal cells. Chlorella sp. XQ-20044 is capable of tolerating high sulfite concentration, and can utilize sulfite as the sole sulfur source for maintaining healthy growth. We found that sulfite ?20 mmol/L had no obvious effect on the total lipid content and fatty acid profiles of the algae. Thus, the results suggest it is feasible to use flue gas for the mass production of feedstock for biodiesel using Chlorella sp. XQ-20044, without preliminary removal of SO2, assuming there is adequate control of the pH.

Liang, Fang; Wen, Xiaobin; Luo, Liming; Geng, Yahong; Li, Yeguang

2014-11-01

396

The chlorobenzoate dioxygenase genes of Burkholderia sp. strain NK8 involved in the catabolism of chlorobenzoates  

Microsoft Academic Search

Burkholderia sp. NK8 grows abundantly on 3-chlorobenzoate (3CB), 4-chlorobenzoate (4CB) and benzoate. The genes encoding the oxidation of (chloro)benzoates (cbeABCD) and catechol (catA, catBC), the LysR-type regulatory gene cbeR and the gene cbeE with unknown function, all of which form a single cluster in NK8, were cloned and analysed. The protein sequence of chlorobenzoate 1,2-dioxygenase (CbeABC) is 50-65% identical to

Perigio B. Francisco Jr; Naoto Ogawa; Katsuhisa Suzuki; Kiyotaka Miyashita

397

Degradation of Microcystin-LR and RR by a Stenotrophomonas sp. Strain EMS Isolated from Lake Taihu, China  

PubMed Central

A bacterial strain EMS with the capability of degrading microcystins (MCs) was isolated from Lake Taihu, China. The bacterium was tentatively identified as a Stenotrophomonas sp. The bacterium could completely consume MC-LR and MC-RR within 24 hours at a concentration of 0.7 ?g/mL and 1.7 ?g/mL, respectively. The degradation of MC-LR and MC-RR by EMS occurred preferentially in an alkaline environment. In addition, mlrA gene involved in the degradation of MC-LR and MC-RR was detected in EMS. Due to the limited literature this gene has rare homologues. Sequencing analysis of the translated protein from mlrA suggested that MlrA might be a transmembrane protein, which suggests a possible new protease family having unique function. PMID:20479990

Chen, Jian; Hu, Liang Bin; Zhou, Wei; Yan, Shao Hua; Yang, Jing Dong; Xue, Yan Feng; Shi, Zhi Qi

2010-01-01

398

Functional analysis of the phosphoprotein PII (glnB gene product) in the cyanobacterium Synechococcus sp. strain PCC 7942.  

PubMed Central

The PII protein (glnB gene product) in the cyanobacterium Synechococcus sp. strain PCC 7942 signals the cellular N status by being phosphorylated or dephosphorylated at a seryl residue. Here we show that the PII-modifying system responds to the activity of ammonium assimilation via the glutamine synthase-glutamate synthase pathway and to the state of CO2 fixation. To identify possible functions of PII in this microorganism, a PII-deficient mutant was created and its general phenotype was characterized. The analysis shows that the PII protein interferes with the regulation of enzymes required for nitrogen assimilation, although ammonium repression is still detectable in the PII-deficient mutant. We suggest that the phosphorylation and dephosphorylation of PII are part of a complex signal transduction network involved in global nitrogen control in cyanobacteria. In this regulatory process, PII might be involved in mediating the tight coordination between carbon and nitrogen assimilation. PMID:7721695

Forchhammer, K; Tandeau de Marsac, N

1995-01-01

399

Toxic effects of dissolved heavy metals on Desulfovibrio vulgaris and Desulfovibrio sp. strains.  

PubMed

Biological treatment of metal-containing wastewaters with sulphate-reducing bacteria (SRB) is an attractive technique for the bioremediation of this kind of medium. In order to design a suitable engineering process to address this environmental problem, it is crucial to understand the inhibitory effect of dissolved heavy metals on these bacteria. Batch studies were carried out to evaluate the toxic effects of several heavy metal ions [Cr(III), Cu(II), Mn(II), Ni(II) and Zn(II)] on two cultures of SRB (Desulfovibrio vulgaris and Desulfovibrio sp.). The experimental data indicate that SRB show different responses to each metal. At the highest metal concentration tolerated for each metal, the precipitation levels for D. vulgaris were as follows: 24.7%-15 ppm Cr(III), 45%-4 ppm Cu(II), 60%-10 ppm Mn(II), 96%-8.5 ppm Ni(II) and 9%-20 ppm Zn(II). The corresponding values for Desulfovibrio sp. were: 25.5%-15 ppm Cr(III), 71%-4 ppm Cu(II), 66.2%-10 ppm Mn(II), 96.1%-8.5 ppm Ni(II) and 93%-20 ppm Zn(II). Results obtained in batch studies will be taken into account for the subsequent design of a sulphate-reducing bioreactor to reduce levels of heavy metals present in different types of contaminated media. PMID:16386832

Cabrera, G; Pérez, R; Gómez, J M; Abalos, A; Cantero, D

2006-07-31

400

Three Types of Taxis Used in the Response of Acidovorax sp. Strain JS42 to 2-Nitrotoluene  

PubMed Central

Acidovorax sp. strain JS42 is able to utilize 2-nitrotoluene (2NT) as its sole carbon, nitrogen, and energy source. We report here that strain JS42 is chemotactic to 2NT and that the response is increased when cells are grown on compounds such as 2NT that are known to induce the first step of 2NT degradation. Assays with JS42 mutants unable to oxidize 2NT showed that the first step of 2NT metabolism was required for the induced response, but not for a portion of the constitutive response, indicating that 2NT itself is an attractant. The 2NT metabolite nitrite was shown to be a strong attractant for strain JS42, and sufficient nitrite was produced during the taxis assay to account for a large part of the induced response. A mutant with an inactivated ntdY gene, which is located adjacent to the 2NT degradation genes and codes for a putative methyl-accepting chemotaxis protein, showed a defect in taxis toward 2NT that may involve a reduced response to nitrite. Responses of a mutant defective for the energy-taxis receptor, Aer, indicated that a functional aer gene is required for a substantial part of the wild-type induced response to 2NT. In summary, strain JS42 utilizes three types of taxis to sense and respond to 2NT: constitutive 2NT-specific chemotaxis to directly sense 2NT, metabolism-dependent nitrite-specific chemotaxis that may be mediated by NtdY, and energy taxis mediated by Aer. PMID:22286989

Rabinovitch-Deere, Christine A.

2012-01-01

401

Three types of taxis used in the response of Acidovorax sp. strain JS42 to 2-nitrotoluene.  

PubMed

Acidovorax sp. strain JS42 is able to utilize 2-nitrotoluene (2NT) as its sole carbon, nitrogen, and energy source. We report here that strain JS42 is chemotactic to 2NT and that the response is increased when cells are grown on compounds such as 2NT that are known to induce the first step of 2NT degradation. Assays with JS42 mutants unable to oxidize 2NT showed that the first step of 2NT metabolism was required for the induced response, but not for a portion of the constitutive response, indicating that 2NT itself is an attractant. The 2NT metabolite nitrite was shown to be a strong attractant for strain JS42, and sufficient nitrite was produced during the taxis assay to account for a large part of the induced response. A mutant with an inactivated ntdY gene, which is located adjacent to the 2NT degradation genes and codes for a putative methyl-accepting chemotaxis protein, showed a defect in taxis toward 2NT that may involve a reduced response to nitrite. Responses of a mutant defective for the energy-taxis receptor, Aer, indicated that a functional aer gene is required for a substantial part of the wild-type induced response to 2NT. In summary, strain JS42 utilizes three types of taxis to sense and respond to 2NT: constitutive 2NT-specific chemotaxis to directly sense 2NT, metabolism-dependent nitrite-specific chemotaxis that may be mediated by NtdY, and energy taxis mediated by Aer. PMID:22286989

Rabinovitch-Deere, Christine A; Parales, Rebecca E

2012-04-01

402

A Novel Hydrolase Identified by Genomic-Proteomic Analysis of Phenylurea Herbicide Mineralization by Variovorax sp. Strain SRS16?†  

PubMed Central

The soil bacterial isolate Variovorax sp. strain SRS16 mineralizes the phenylurea herbicide linuron. The proposed pathway initiates with hydrolysis of linuron to 3,4-dichloroaniline (DCA) and N,O-dimethylhydroxylamine, followed by conversion of DCA to Krebs cycle intermediates. Differential proteomic analysis showed a linuron-dependent upregulation of several enzymes that fit into this pathway, including an amidase (LibA), a multicomponent chloroaniline dioxygenase, and enzymes associated with a modified chlorocatechol ortho-cleavage pathway. Purified LibA is a monomeric linuron hydrolase of ?55 kDa with a Km and a Vmax for linuron of 5.8 ?M and 0.16 nmol min?1, respectively. This novel member of the amidase signature family is unrelated to phenylurea-hydrolyzing enzymes from Gram-positive bacteria and lacks activity toward other tested phenylurea herbicides. Orthologues of libA are present in all other tested linuron-degrading Variovorax strains with the exception of Variovorax strains WDL1 and PBS-H4, suggesting divergent evolution of the linuron catabolic pathway in different Variovorax strains. The organization of the linuron degradation genes identified in the draft SRS16 genome sequence indicates that gene patchwork assembly is at the origin of the pathway. Transcription analysis suggests that a catabolic intermediate, rather than linuron itself, acts as effector in activation of the pathway. Our study provides the first report on the genetic organization of a bacterial pathway for complete mineralization of a phenylurea herbicide and the first report on a linuron hydrolase in Gram-negative bacteria. PMID:22003008

Bers, Karolien; Leroy, Baptiste; Breugelmans, Philip; Albers, Pieter; Lavigne, Rob; S?rensen, Sebastian R.; Aamand, Jens; De Mot, Rene; Wattiez, Ruddy; Springael, Dirk

2011-01-01

403

An Evolutionary Hot Spot: the pNGR234b Replicon of Rhizobium sp. Strain NGR234  

PubMed Central

Rhizobium sp. strain NGR234 has an exceptionally broad host range and is able to nodulate more than 112 genera of legumes. Since the overall organization of the NGR234 genome is strikingly similar to that of the narrow-host-range symbiont Rhizobium meliloti strain 1021 (also known as Sinorhizobium meliloti), the obvious question is why are the spectra of hosts so different? Study of the early symbiotic genes of both bacteria (carried by the SymA plasmids) did not provide obvious answers. Yet, both rhizobia also possess second megaplasmids that bear, among many other genes, those that are involved in the synthesis of extracellular polysaccharides (EPSs). EPSs are involved in fine-tuning symbiotic interactions and thus may help answer the broad- versus narrow-host-range question. Accordingly, we sequenced two fragments (total, 594 kb) that encode 575 open reading frames (ORFs). Comparisons revealed 19 conserved gene clusters with high similarity to R. meliloti, suggesting that a minimum of 28% (158 ORFs) of the genetic information may have been acquired from a common ancestor. The largest conserved cluster carried the exo and exs genes and contained 31 ORFs. In addition, nine highly conserved regions with high similarity to Agrobacterium tumefaciens C58, Bradyrhizobium japonicum USDA110, and Mesorhizobium loti strain MAFF303099, as well as two conserved clusters that are highly homologous to similar regions in the plant pathogen Erwinia carotovora, were identified. Altogether, these findings suggest that ?40% of the pNGR234b genes are not strain specific and were probably acquired from a wide variety of other microbes. The presence of 26 ORFs coding for transposases and site-specific integrases supports this contention. Surprisingly, several genes involved in the degradation of aromatic carbon sources and genes coding for a type IV pilus were also found. PMID:14702322

Streit, W. R.; Schmitz, R. A.; Perret, X.; Staehelin, C.; Deakin, W. J.; Raasch, C.; Liesegang, H.; Broughton, W. J.

2004-01-01

404

Biodegradation of methyl red by Bacillus sp. strain UN2: decolorization capacity, metabolites characterization, and enzyme analysis.  

PubMed

Azo dyes are recalcitrant and refractory pollutants that constitute a significant menace to the environment. The present study is focused on exploring the capability of Bacillus sp. strain UN2 for application in methyl red (MR) degradation. Effects of physicochemical parameters (pH of medium, temperature, initial concentration of dye, and composition of the medium) were studied in detail. The suitable pH and temperature range for MR degradation by strain UN2 were respectively 7.0-9.0 and 30-40 °C, and the optimal pH value and temperature were respectively 8.0 and 35 °C. Mg(2+) and Mn(2+) (1 mM) were found to significantly accelerate the MR removal rate, while the enhancement by either Fe(3+) or Fe(2+) was slight. Under the optimal degradation conditions, strain UN2 exhibited greater than 98 % degradation of the toxic azo dye MR (100 ppm) within 30 min. Analysis of samples from decolorized culture flasks confirmed biodegradation of MR into two prime metabolites: N,N'dimethyl-p-phenyle-nediamine and 2-aminobenzoic acid. A study of the enzymes responsible for the biodegradation of MR, in the control and cells obtained during (10 min) and after (30 min) degradation, showed a significant increase in the activities of azoreductase, laccase, and NADH-DCIP reductase. Furthermore, a phytotoxicity analysis demonstrated that the germination inhibition was almost eliminated for both the plants Triticum aestivum and Sorghum bicolor by MR metabolites at 100 mg/L concentration, yet the germination inhibition of parent dye was significant. Consequently, the high efficiency of MR degradation enables this strain to be a potential candidate for bioremediation of wastewater containing MR. PMID:24474566

Zhao, Ming; Sun, Peng-Fei; Du, Lin-Na; Wang, Guan; Jia, Xiao-Ming; Zhao, Yu-Hua

2014-05-01

405

Photophosphorylation and oxidative phosphorylation in intact cells and chromatophores of an aerobic photosynthetic bacterium, Erythrobacter sp. strain OCh114.  

PubMed Central

Light-induced ATP synthesis was studied in intact cells and chromatophores of Erythrobacter sp. strain OCh114. ATP synthesis was measured by both the pH method and the luciferin-luciferase luminescence method. The rate of ATP synthesis was moderate (a typical value of 0.65 mol of ATP per mol of bacteriochlorophyll per min), and synthesis was inhibited by antimycin A. ATP was synthesized under illumination only under aerobic conditions and not under anaerobic conditions. This characteristic was similar to that of other light-induced energy transduction processes in this bacterial species, such as oxidation of reaction center, oxidation of cytochrome c551, and translocation of H+, which were not observed under anaerobic conditions. This phenomenon was reconciled with the fact that the Erythrobacter sp. could not grow anaerobically even in the light. The characteristics of oxidative phosphorylation and ATP hydrolysis were also investigated. The respiratory ratio of chromatophores was 2.3. Typical rates of oxidative phosphorylation by NADH and by succinate were 2.9 mol of ATP per mol of bacteriochlorophyll per min (P/O = 0.22) and 1.1 mol of ATP per mol of bacteriochlorophyll per min (P/O = 0.19), respectively. A typical rate of ATP hydrolysis was 0.25 mol of ATP per mol of bacteriochlorophyll per min in chromatophores. ATPase and adenylate kinase are also involved in the metabolism of adenine nucleotides in this bacterium. PMID:3782035

Okamura, K; Mitsumori, F; Ito, O; Takamiya, K; Nishimura, M

1986-01-01

406

Purification and biochemical characterization of a highly thermostable xylanase from Actinomadura sp. strain Cpt20 isolated from poultry compost.  

PubMed

An extracellular thermostable xylanase from a newly isolated thermophilic Actinomadura sp. strain Cpt20 was purified and characterized. Based on matrix-assisted laser desorption-ionization time-of-flight mass spectrometry analysis, the purified enzyme is a monomer with a molecular mass of 20,110.13 Da. The 19 residue N-terminal sequence of the enzyme showed 84% homology with those of actinomycete endoxylanases. The optimum pH and temperature values for xylanase activity were pH 10 and 80 °C, respectively. This xylanase was stable within a pH range of 5-10 and up to a temperature of 90 °C. It showed high thermostability at 60 °C for 5 days and half-life times at 90 °C and 100 °C were 2 and 1 h, respectively. The xylanase was specific for xylans, showing higher specific activity on soluble oat-spelt xylan followed by beechwood xylan. This enzyme obeyed the Michaelis-Menten kinetics, with the K (m) and k (cat) values being 1.55 mg soluble oat-spelt xylan/ml and 388 min(-1), respectively. While the xylanase from Actinomadura sp. Cpt20 was activated by Mn(2+), Ca(2+), and Cu(2+), it was, strongly inhibited by Hg(2+), Zn(2+), and Ba(2+). These properties make this enzyme a potential candidate for future use in biotechnological applications particularly in the pulp and paper industry. PMID:22161140

Taibi, Zina; Saoudi, Boudjemaa; Boudelaa, Mokhtar; Trigui, Héla; Belghith, Hafedh; Gargouri, Ali; Ladjama, Ali

2012-02-01

407

Arsenite oxidation by Alcaligenes sp. strain RS-19 isolated from arsenic-contaminated mines in the Republic of Korea.  

PubMed

Arsenite [As(III)]-oxidizing bacteria play important roles in reducing arsenic [As] toxicity and mobility in As-contaminated areas. As-resistant bacteria were isolated from the soils of two abandoned mines in the Republic of Korea. The isolated bacteria showed relatively high resistances to As(III) up to 26 mM. The PCR-based 16S rRNA analysis revealed that the isolated As-resistant bacteria were close relatives to Serratia marcescensa, Pseudomonas putida, Pantoea agglomerans, and Alcaligenes sp. Among the five As-resistant bacterial isolates, Alcaligenes sp. strain RS-19 showed the highest As(III)-oxidizing activity in batch tests, completely oxidizing 1 mM of As(III) to As(V) within 40 h during heterotrophic growth. This study suggests that the indigenous bacteria have evolved to retain the ability to resist toxic As in the As-contaminated environments and moreover to convert the species to a less toxic form [e.g., from As(III) to As(V)] and also contribute the biogeochemical cycling of As by being involved in speciation of As. PMID:18642094

Yoon, In-Ho; Chang, Jin-Soo; Lee, Ji-Hoon; Kim, Kyoung-Woong

2009-02-01

408

Identification and Characterization of the Rhizobium sp. Strain GIN611 Glycoside Oxidoreductase Resulting in the Deglycosylation of Ginsenosides  

PubMed Central

Using enrichment culture, Rhizobium sp. strain GIN611 was isolated as having activity for deglycosylation of a ginsenoside, compound K (CK). The purified heterodimeric protein complex from Rhizobium sp. GIN611 consisted of tw