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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.

Pore, Soham D.; Arora, Preeti

2014-01-01

2

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

PubMed

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; Dhakephalkar, Prashant K

2014-01-01

3

Draft Genome Sequences of Geobacillus sp. Strains CAMR5420 and CAMR12739.  

PubMed

Thermophilic Geobacillus spp. can efficiently hydrolyze hemicellulose polymers and are therefore of interest in biotechnological applications. Here we report the genome sequences of two hemicellulolytic strains, Geobacillus sp. CAMR12739 and CAMR5420. PMID:24903881

De Maayer, Pieter; Williamson, Carolyn E; Vennard, Christopher T; Danson, Michael J; Cowan, Don A

2014-01-01

4

Draft Genome Sequences of Geobacillus sp. Strains CAMR5420 and CAMR12739  

PubMed Central

Thermophilic Geobacillus spp. can efficiently hydrolyze hemicellulose polymers and are therefore of interest in biotechnological applications. Here we report the genome sequences of two hemicellulolytic strains, Geobacillus sp. CAMR12739 and CAMR5420.

De Maayer, Pieter; Williamson, Carolyn E.; Vennard, Christopher T.; Danson, Michael J.

2014-01-01

5

Complete Genome Sequence of Geobacillus sp. Strain GHH01, a Thermophilic Lipase-Secreting Bacterium  

PubMed Central

Geobacillus sp. strain GHH01 was isolated during a screening for producers of extracellular thermostable lipases. The completely sequenced and annotated 3.6-Mb genome encodes 3,478 proteins. The strain is genetically equipped to utilize a broad range of different substrates and might develop natural competence.

Wiegand, Sandra; Rabausch, Ulrich; Chow, Jennifer; Daniel, Rolf; Streit, Wolfgang R.

2013-01-01

6

Draft Genome Sequence of Lignocellulose-Degrading Thermophilic Bacterium Geobacillus sp. Strain WSUCF1  

PubMed Central

Geobacillus sp. strain WSUCF1 is a thermophilic spore-forming member of the phylum Firmicutes, isolated from a soil sample collected from the compost facility. We report the draft genome sequence of this isolate with an estimated genome size of 3.4 Mb. The genome sequence of this isolate revealed several genes encoding glycoside hydrolases, making it a potential candidate for plant biomass degradation.

Bhalla, Aditya; Kainth, Amoldeep Singh

2013-01-01

7

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

8

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.

2013-01-01

9

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.

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

10

A thermoalkaliphilic lipase of Geobacillus sp. T1  

Microsoft Academic Search

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\\u000a solubility and promoted the binding of GST moiety to the glutathione-Sepharose column. High-yield purification of T1 lipase\\u000a was achieved through two-step affinity chromatography with a final specific activity and yield of 958.2 U\\/mg and 51.5%,

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

2007-01-01

11

Draft Genome Sequence of Geobacillus thermopakistaniensis Strain MAS1.  

PubMed

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

Siddiqui, Masood Ahmed; Rashid, Naeem; Ayyampalayam, Saravanaraj; Whitman, William B

2014-01-01

12

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.

Rashid, Naeem; Ayyampalayam, Saravanaraj

2014-01-01

13

[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

14

Molecular cloning, over expression and characterization of thermoalkalophilic esterases isolated from Geobacillus sp  

Microsoft Academic Search

Due to potential use for variety of biotechnological applications, genes encoding thermoalkalophilic esterase from three different\\u000a Geobacillus strains isolated from thermal environmental samples in Balçova (Agamemnon) geothermal site were cloned and respective proteins\\u000a were expressed in Escherichia coli (E.coli) and characterized in detail. Three esterases (Est1, Est2, Est3) were cloned directly by PCR amplification using consensus\\u000a degenerate primers from genomic

Hasan Cihad Tekedar; Gül?ah ?anl?-Mohamed

2011-01-01

15

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.

2012-01-01

16

Isolation and characterization of arsenic resistant Geobacillus kaustophilus strain from geothermal soils.  

PubMed

A thermophilic, arsenate resistant bacterial strain was isolated from a geothermal field located in the area surrounding Monterotondo (Tuscany, Italy). Based on 16S rRNA gene analysis and recN comparisons the strain was identified as Geobacillus kaustophilus. Cells of the strain, designated A1, were rod-shaped, 2-3 ?m long and reacted negatively to Gram staining, despite its taxonomic classification as a Gram positive microorganism. Strain A1 is a thermophilic spore-forming bacterium, and grows optimally at pH 6.5 and 55 °C. An arsenate MIC of 80 mM was determined for strain A1, and the close relative G. kaustophilus DSM 7263(T) showed similar levels of arsenate resistance. These observations were consistent with the presence of arsenic detoxification genes in the genome of G. kaustophilus HTA426. Furthermore, strain A1 growth was not inhibited by 5 mM antimonite and 15 mM arsenite, the highest tested concentrations. This is the first description of arsenic resistance in a Geobacillus strain and supports the hypothesis that members of the genus may have a role in the biogeochemical cycling of arsenic. PMID:21656800

Cuebas, Mariola; Sannino, David; Bini, Elisabetta

2011-08-01

17

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

18

Novel thermostable endo-xylanase cloned and expressed from bacterium Geobacillus sp. WSUCF1.  

PubMed

A gene encoding a GH10 endo-xylanase from Geobacillus sp. WSUCF1 was cloned and expressed in Escherichia coli. Recombinant endo-xylanase (37kDa) exhibited high specific activity of 461.0U/mg of protein. Endo-xylanase was optimally active on birchwood xylan at 70°C and pH 6.5. The endo-xylanase was found to be highly thermostable at 50 and 60°C, retaining 82% and 50% of its original activity, respectively, after 60h. High xylan conversions (92%) were obtained with oat-spelt xylan hydrolysis. Higher glucan and xylan conversions were obtained on AFEX-treated corn stover with an enzyme cocktail containing WSUCF1 endo-xylanase (71% and 47%) as compared to enzyme cocktail containing commercial fungal endo-xylanase (64% and 41%). High specific activity, active at high pH's, wide substrate specificity, and higher hydrolytic activity on recalcitrant lignocellulose, make this endo-xylanase a suitable candidate for biofuel and bioprocess industries. PMID:24725385

Bhalla, Aditya; Bischoff, Kenneth M; Uppugundla, Nirmal; Balan, Venkatesh; Sani, Rajesh K

2014-08-01

19

Effectiveness of inoculation with isolated Geobacillus strains in the thermophilic stage of vegetable waste composting  

Microsoft Academic Search

An inoculum containing two amylolytic and three cellulolytic thermophilic bacteria, isolated from a preceding compost pile and identified as Geobacillus species by 16S rRNA gene sequencing, was applied to a mixture of market waste, rice straw and cow dung (5:1:0.2) so that the initial cell density was 2×108 colony forming unit (CFU) per gram dry weight at 55°C. The inoculation

Sutripta Sarkar; Rajdeep Banerjee; Sunanda Chanda; Pradeep Das; Sandipan Ganguly; Subrata Pal

2010-01-01

20

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

Microsoft Academic Search

Novel thermophilic and alkaliphilic bacteria for the processing of bast fibres were isolated using hemp pectin as substrate.\\u000a The strain PB94A, which showed the highest growth rate (µ?=?0.5\\/h) was identified as Geobacillus thermoglucosidasius (DSM 21625). The strain grew optimally at 60°C and pH 8.5. During growth on citrus pectin, the strain produced pectinolytic\\u000a lyases, which were excreted into the medium.

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

2009-01-01

21

Isolation and characterization of a thermotolerant ene reductase from Geobacillus sp. 30 and its heterologous expression in Rhodococcus opacus.  

PubMed

Rhodococcus opacus B-4 cells are adhesive to and even dispersible in water-immiscible hydrocarbons owing to their highly lipophilic nature. In this study, we focused on the high operational stability of thermophilic enzymes and applied them to a biocatalytic conversion in an organic reaction medium using R. opacus B-4 as a lipophilic capsule of enzymes to deliver them into the organic medium. A novel thermo- and organic-solvent-tolerant ene reductase, which can catalyze the enantioselective reduction of ketoisophorone to (6R)-levodione, was isolated from Geobacillus sp. 30, and the gene encoding the enzyme was heterologously expressed in R. opacus B-4. Another thermophilic enzyme which catalyzes NAD(+)-dependent dehydrogenation of cyclohexanol was identified from the gene-expression library of Thermus thermophilus and the gene was coexpressed in R. opacus B-4 for cofactor regeneration. While the recombinant cells were not viable in the mixture due to high reaction temperature, 634 mM of (6R)-levodione could be produced with an enantiopurity of 89.2 % ee by directly mixing the wet cells of the recombinant R. opacus with a mixture of ketoisophorone and cyclohexanol at 50 °C. The conversion rate observed with the heat-killed recombinant cells was considerably higher than that obtained with a cell-free enzyme solution, demonstrating that the accessibility between the substrates and enzymes could be improved by employing R. opacus cells as a lipophilic enzyme capsule. These results imply that a combination of thermophilic enzymes and lipophilic cells can be a promising approach for the biocatalytic production of water-insoluble chemicals. PMID:24927695

Tsuji, Naoto; Honda, Kohsuke; Wada, Mayumi; Okano, Kenji; Ohtake, Hisao

2014-07-01

22

Transformable facultative thermophile Geobacillus stearothermophilus NUB3621 as a host strain for metabolic engineering.  

PubMed

Metabolic engineers develop inexpensive enantioselective syntheses of high-value compounds, but their designs are sometimes confounded by the misfolding of heterologously expressed proteins. Geobacillus stearothermophilus NUB3621 is a readily transformable facultative thermophile. It could be used to express and properly fold proteins derived from its many mesophilic or thermophilic Bacillaceae relatives or to direct the evolution of thermophilic variants of mesophilic proteins. Moreover, its capacity for high-temperature growth should accelerate chemical transformation rates in accordance with the Arrhenius equation and reduce the risks of microbial contamination. Its tendency to sporulate in response to nutrient depletion lowers the costs of storage and transportation. Here, we present a draft genome sequence of G. stearothermophilus NUB3621 and describe inducible and constitutive expression plasmids that function in this organism. These tools will help us and others to exploit the natural advantages of this system for metabolic engineering applications. PMID:24788326

Blanchard, Kristen; Robic, Srebrenka; Matsumura, Ichiro

2014-08-01

23

Preconditioning with Cations Increases the Attachment of Anoxybacillus flavithermus and Geobacillus Species to Stainless Steel  

PubMed Central

Preconditioning of Anoxybacillus flavithermus E16 and Geobacillus sp. strain F75 with cations prior to attachment often significantly increased (P ? 0.05) the number of viable cells that attached to stainless steel (by up to 1.5 log CFU/cm2) compared with unconditioned bacteria. It is proposed that the transition of A. flavithermus and Geobacillus spp. from milk formulations to stainless steel product contact surfaces in milk powder manufacturing plants is mediated predominantly by bacterial physiological factors (e.g., surface-exposed adhesins) rather than the concentrations of cations in milk formulations surrounding bacteria.

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

2013-01-01

24

Complete nucleotide sequence of pGS18, a 62.8-kb plasmid from Geobacillus stearothermophilus strain 18  

Microsoft Academic Search

The complete nucleotide sequence (62.8 kb) of pGS18, the largest sequenced plasmid to date from the species Geobacillus stearothermophilus, was determined. Computational analysis of sequence data revealed 65 putative open reading frames (ORFs); 38 were carried\\u000a on one strand and 27 were carried on the other. These ORFs comprised 84.1% of the pGS18 sequence. Twenty-five ORFs (38.4%)\\u000a were assigned to putative

Milda Stuknyte; Simone Guglielmetti; Diego Mora; Nomeda Kuisiene; Carlo Parini; Donaldas Citavicius

2008-01-01

25

A novel endoglucanase from the thermophilic bacterium Geobacillus sp. 70PC53 with high activity and stability over a broad range of temperatures  

Microsoft Academic Search

A thermophilic Geobacillus bacterium secreting high activity of endo-glucanase (EC 3.2.1.4) was isolated from rice straw compost supplemented with pig\\u000a manure. A full-length gene of 1,104 bp, celA, encoding this glycosyl hydrolase family 5 endo-glucanase of 368 amino acids was isolated. No related gene from Geobacillus has been reported previously. The recombinant CelA expressed in Escherichia coli had an optimal activity

I-Son Ng; Chen-Wei Li; Yi-Fang Yeh; Po Ting Chen; Jiun-Ly Chir; Chin-Hua Ma; Su-May Yu; Tuan-hua David Ho; Chii-Gong Tong

2009-01-01

26

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.

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

2012-01-01

27

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

28

Steroid biotransformation by different strains of Micrococcus sp.  

PubMed

A strain of Micrococcus sp. was isolated for its capability of side chain degradation of cholesterol. This strain was characterized and identified as Micrococcus roseus. It was found to be the best strain for the production of androsta-1,4-diene-3,17-dione and androst-4-ene-3,17-dione compared with other Micrococcus strains. PMID:11501468

Dogra, N; Qazi, G N

2001-01-01

29

Alkylated benzothiophene desulfurization by Rhodococcus sp. strain T09.  

PubMed

A benzothiophene desulfurizing bacterium was isolated and identified as Rhodococcus sp. strain T09. Growth assays revealed that this strain assimilated, as the sole sulfur source, various organosulfur compounds that cannot be assimilated by the well-studied dibenzothiophene-desulfurizing Rhodococcus sp. IGTS8. The cellular growth rate of strain T09 for the alkylated benzothiophenes depended on the alkylated position and the length of the alkyl moiety. PMID:10803960

Matsui, T; Onaka, T; Tanaka, Y; Tezuka, T; Suzuki, M; Kurane, R

2000-03-01

30

Steroid biotransformation by different strains of Micrococcus sp  

Microsoft Academic Search

A strain ofMicrococcus sp. was isolated for its capability of side chain degradation of cholesterol. This strain was characterized and identified\\u000a asMicrococcus roseus. It was found to be the best strain for the production of androsta-1,4-diene-3, 17-dione and androst-4-ene-3, 17-dione compared\\u000a with otherMicrococcus strains.

N. Dogra; G. N. Qazi

2001-01-01

31

Complete Genome Sequence of Antarctic Bacterium Psychrobacter sp. Strain G.  

PubMed

Here, we report the complete genome sequence of Psychrobacter sp. strain G, isolated from King George Island, Antarctica, which can produce lipolytic enzymes at low temperatures. The genomics information of this strain will facilitate the study of the physiology, cold adaptation properties, and evolution of this genus. PMID:24051316

Che, Shuai; Song, Lai; Song, Weizhi; Yang, Meng; Liu, Guiming; Lin, Xuezheng

2013-01-01

32

Desulfurization of dibenzothiophene by Corynebacterium sp. strain SY1  

Microsoft Academic Search

Strain SY1, identified as a Corynebacterium sp., was isolated on the basis of the ability to utilize dibenzothiophene (DBT) as a sole source of sulfur. Strain SY1 could utilize a wide range of organic and inorganic sulfur compounds, such as DBT sulfone, dimethyl sulfide, dimethyl sulfoxide, dimethyl sulfone, CSâ, FeSâ, and even elemental sulfur. Strain SY1 metabolized DBT to dibenzothiophene-5-oxide,

Toshio Omori; L. Monna; Yuko Saiki; Tohru Kodama

1992-01-01

33

Sequence of ornithine decarboxylase from Lactobacillus sp. strain 30a.  

PubMed Central

A gene encoding biodegradative ornithine decarboxylase from Lactobacillus sp. strain 30a was isolated from a genomic DNA library and sequenced. Primer extension analysis revealed two transcription initiation sites. The deduced amino acid sequence is compared with the amino acid sequences of five previously reported bacterial decarboxylases, and conserved pyridoxal phosphate motif residues are identified.

Hackert, M L; Carroll, D W; Davidson, L; Kim, S O; Momany, C; Vaaler, G L; Zhang, L

1994-01-01

34

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.

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

2012-01-01

35

Biodegradation of 2-nitrotoluene by Micrococcus sp. strain SMN-1.  

PubMed

A bacterial consortium capable of degrading nitroaromatic compounds was isolated from pesticide-contaminated soil samples by selective enrichment on 2-nitrotoluene as a sole source of carbon and energy. The three different bacterial isolates obtained from bacterial consortium were identified as Bacillus sp. (A and C), Bacillus flexus (B) and Micrococcus sp. (D) on the basis of their morphological and biochemical characteristics and by phylogenetic analysis based on 16S rRNA gene sequences. The pathway for the degradation of 2-nitrotoluene by Micrococcus sp. strain SMN-1 was elucidated by the isolation and identification of metabolites, growth and enzymatic studies. The organism degraded 2-nitrotoluene through 3-methylcatechol by a meta-cleavage pathway, with release of nitrite. PMID:20582618

Mulla, Sikandar I; Hoskeri, Robertcyril S; Shouche, Yogesh S; Ninnekar, Harichandra Z

2011-02-01

36

Pseudomonas benzenivorans sp. nov. and Pseudomonas saponiphila sp. nov., represented by xenobiotics degrading type strains.  

PubMed

Two strains of gram-negative bacteria isolated because of their abilities to decompose xenobiotic compounds were subjected to a polyphasic taxonomic study. On the basis of 16S rRNA gene sequence analysis, the two strains were found to belong to the genus Pseudomonas. Benzene degrading strain DSM 8628(T) was moderately related to P. flavescens NCPP 3063(T) (98.3% similarity), P. monteilii CIP 104883(T), and P. plecoglossicida FPC 951(T) (98.1%). Strain DSM 9751(T) capable to grow with cetyltrimethylammonium chloride as the sole carbon source showed the highest similarity values with P. tremae CFBP 2341(T) and P. meliae MAFF 301463(T) (98.0%), both related to Pseudomonas syringae. The fatty acid pattern of strain DSM 8628(T) was distinct from patterns of other members of the genus Pseudomonas in combining a high ratio of 3OH-C(12:1) (5.1%), a low ratio of 2OH-C(12:0) (0.2%) and a relatively low ratio of C(18:1)omega7c (23.8%). On the basis of phylogenetic analysis, physiological properties and the composition of whole cell fatty acids, two novel species, Pseudomonas benzenivorans sp. nov. with the type strain DSM 8628(T) (=CIP 109857(T)) and Pseudomonas saponiphila sp. nov. with the type strain DSM 9751(T) (=CIP 109856(T)), are proposed. PMID:19771475

Lang, Elke; Burghartz, Melanie; Spring, Stefan; Swiderski, Jolanthe; Spröer, Cathrin

2010-02-01

37

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

38

Uptake of Zinc in Pseudomonas sp. Strain UDG26  

PubMed Central

Zinc resistance in Pseudomonas sp. strain UDG26 was inducible. Induction led to enhanced uptake of the metal. A zinc-sensitive variant (UDG86) took up significantly less metal ion than the resistant one did. The affinity of uninduced and sensitive cells to zinc was less than that of resistant, induced cells. Metal accumulation by induced cells was not inhibited by azide, while 2,4-dinitrophenol and N-N? -dicyclohexylcarbodiimide enhanced zinc uptake because of inhibition of efflux. Transcription and translation inhibitors drastically reduced zinc accumulation, bringing it to the level found in the sensitive strain. These results suggest the involvement of protein(s) in zinc resistance.

Mago, Rohit; Srivastava, Sheela

1994-01-01

39

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.

2014-01-01

40

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

41

Desulfurization of dibenzothiophene by Corynebacterium sp. strain SY1.  

PubMed Central

Strain SY1, identified as a Corynebacterium sp., was isolated on the basis of the ability to utilize dibenzothiophene (DBT) as a sole source of sulfur. Strain SY1 could utilize a wide range of organic and inorganic sulfur compounds, such as DBT sulfone, dimethyl sulfide, dimethyl sulfoxide, dimethyl sulfone, CS2, FeS2, and even elemental sulfur. Strain SY1 metabolized DBT to dibenzothiophene-5-oxide, DBT sulfone, and 2-hydroxybiphenyl, which was subsequently nitrated to produce at least two different hydroxynitrobiphenyls during cultivation. These metabolites were separated by silica gel column chromatography and identified by nuclear magnetic resonance, UV, and mass spectral techniques. Resting cells of SY1 desulfurized toluenesulfonic acid and released sulfite anion. On the basis of these results, a new DBT degradation pathway is proposed.

Omori, T; Monna, L; Saiki, Y; Kodama, T

1992-01-01

42

Complete genome sequence of Paenibacillus sp. strain JDR-2.  

PubMed

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

2012-03-19

43

Pseudomonas sp. Strain 273, an Aerobic ?,?-DichloroalkaneDegrading Bacterium  

PubMed Central

A gram-negative, aerobic bacterium was isolated from soil; this bacterium grew in 50% (vol/vol) suspensions of 1,10-dichlorodecane (1,10-DCD) as the sole source of carbon and energy. Phenotypic and small-subunit ribosomal RNA characterizations identified the organism, designated strain 273, as a member of the genus Pseudomonas. After induction with 1,10-DCD, Pseudomonas sp. strain 273 released stoichiometric amounts of chloride from C5 to C12 ?,?-dichloroalkanes in the presence of oxygen. No dehalogenation occurred under anaerobic conditions. The best substrates for dehalogenation and growth were C9 to C12 chloroalkanes. The isolate also grew with nonhalogenated aliphatic compounds, and decane-grown cells dechlorinated 1,10-DCD without a lag phase. In addition, cells grown on decane dechlorinated 1,10-DCD in the presence of chloramphenicol, indicating that the 1,10-DCD-dechlorinating enzyme system was also induced by decane. Other known alkane-degrading Pseudomonas species did not grow with 1,10-DCD as a carbon source. Dechlorination of 1,10-DCD was demonstrated in cell extracts of Pseudomonas sp. strain 273. Cell-free activity was strictly oxygen dependent, and NADH stimulated dechlorination, whereas EDTA had an inhibitory effect.

Wischnak, Catrin; Loffler, Frank E.; Li, Jieran; Urbance, John W.; Muller, Rudolf

1998-01-01

44

Gliding motility of Mycoplasma sp. nov. strain 163K.  

PubMed Central

The gliding movements of Mycoplasma sp. nov. strain 163K cells were characterized by photomicrographic and microcinematographic studies. The capability of gliding proved to be a very stable property of strain 163K. Cells were continuously moving, without interruption by resting periods, on glass as well as on plastic surfaces covered with liquid medium. Gliding cells always moved in the direction of their headlike structure; their course did not indicate any preference for a certain direction. Under appropriate growth conditions, cells showed linear and circular movements. Under inadequate conditions, cells glided in narrow circles or entered into zigzag trembling and tumbling movements. Organisms glided as single cells, in pairs, and in multicellular configurations. Movement patterns and gliding velocity were significantly affected by the cultivation and preparation time, the medium viscosity, and the storage and observation temperature. The number of passages on artificial media and the composition of the media used did not have a striking influence on gliding motility, but movements were effectively inhibited by homologous antiserum. The data obtained suggest that at least some of the structures associated with gliding are heat sensitive and located on the cell surface, that the gliding mechanism requires an intact energy metabolism, and, finally, that gliding motility is an extremely stable genetic property of Mycoplasma sp. nov. strain 163K. Images

Rosengarten, R; Kirchhoff, H

1987-01-01

45

Biodegradation of bisphenol A and related compounds by Sphingomonas sp. strain BP-7 isolated from seawater.  

PubMed

A bacterium capable of assimilating 2,2-bis(4-hydroxyphenyl)propane (bisphenol A), strain BP-7, was isolated from offshore seawater samples on a medium containing bisphenol A as sole source of carbon and energy, and identified as Sphingomonas sp. strain BP-7. Other strains, Pseudomonas sp. strain BP-14, Pseudomonas sp. strain BP-15, and strain no. 24A, were also isolated from bisphenol A-enrichment culture of the seawater. These strains did not degrade bisphenol A, but accelerated the degradation of bisphenol A by Sphingomonas sp. strain BP-7. A mixed culture of Sphingomonas sp. strain BP-7 and Pseudomonas sp. strain BP-14 showed complete degradation of 100 ppm bisphenol A within 7 d in SSB-YE medium, while Sphingomonas sp. strain BP-7 alone took about 40 d for complete consumption of bisphenol A accompanied by accumulation of 4-hydroxyacetophenone. On a nutritional supplementary medium, Sphingomonas sp. strain BP-7 completely degraded bisphenol A and 4-hydroxyacetophenone within 20 h. The strain degraded a variety of bisphenols, such as 1,1-bis(4-hydroxyphenyl)ethane, 2,2-bis(4-hydroxy-3-methylphenyl)propane, 2,2-bis(4-hydroxyphenyl)butane, and 1,1-bis(4-hydroxyphenyl)cyclohexane, and hydroxy aromatic compounds such as 4-hydroxyacetophenone, 4-hydroxybenzoic acid, catechol, protocatechuic acid, and hydroquinone. The strain did not degrade bis(4-hydroxyphenyl)methane, bis(4-hydroxyphenyl)sulfone, or bis(4-hydroxyphenyl)sulfide. PMID:17213659

Sakai, Kiyofumi; Yamanaka, Hayato; Moriyoshi, Kunihiko; Ohmoto, Takashi; Ohe, Tatsuhiko

2007-01-01

46

Salpingitis in geese associated with Mycoplasma sp. strain 1220.  

PubMed

An outbreak of disease in a White Rhine laying goose flock was characterized by increased water uptake, increased mortality, production of eggs with abnormal shells, a 25% drop in egg production and 40% embryo mortality. Affected dead or sacrificed birds had sero-fibrinogranulocytic peritonitis and salpingitis, infiltration of the lamina propria in the uterus and heterophil granulocytes in the isthmus and magnum of the oviduct. Mycoplasmas, mainly identified as Mycoplasma sp. strain 1220, were isolated from the airsac, liver, ovary, magnum and peritoneum of some affected geese. Strain 1220 was originally isolated from a Hungarian gander with phallus inflammation and, according to detailed biochemical and serological examinations, it is expected to represent a new avian species within the genus Mycoplasma. PMID:19468942

Dobos-Kovács, Mihály; Varga, Zsuzsanna; Czifra, György; Stipkovits, László

2009-06-01

47

Complete Genome Sequence of Pseudomonas sp. Strain TKP, Isolated from a ?-Hexachlorocyclohexane-Degrading Mixed Culture.  

PubMed

Pseudomonas sp. strain TKP does not degrade ?-hexachlorocyclohexane (?-HCH), but it persistently coexists with the ?-HCH-degrading Sphingobium sp. strain TKS in a mixed culture enriched by ?-HCH. Here, we report the complete genome sequence of strain TKP, which consists of one circular chromosome with a size of 7 Mb. PMID:24482516

Ohtsubo, Yoshiyuki; Kishida, Kouhei; Sato, Takuya; Tabata, Michiro; Kawasumi, Toru; Ogura, Yoshitoshi; Hayashi, Tetsuya; Tsuda, Masataka; Nagata, Yuji

2014-01-01

48

Biodegradation of ether pollutants by Pseudonocardia sp. strain ENV478.  

PubMed

A bacterium designated Pseudonocardia sp. strain ENV478 was isolated by enrichment culturing on tetrahydrofuran (THF) and was screened to determine its ability to degrade a range of ether pollutants. After growth on THF, strain ENV478 degraded THF (63 mg/h/g total suspended solids [TSS]), 1,4-dioxane (21 mg/h/g TSS), 1,3-dioxolane (19 mg/h/g TSS), bis-2-chloroethylether (BCEE) (12 mg/h/g TSS), and methyl tert-butyl ether (MTBE) (9.1 mg/h/g TSS). Although the highest rates of 1,4-dioxane degradation occurred after growth on THF, strain ENV478 also degraded 1,4-dioxane after growth on sucrose, lactate, yeast extract, 2-propanol, and propane, indicating that there was some level of constitutive degradative activity. The BCEE degradation rates were about threefold higher after growth on propane (32 mg/h/g TSS) than after growth on THF, and MTBE degradation resulted in accumulation of tert-butyl alcohol. Degradation of 1,4-dioxane resulted in accumulation of 2-hydroxyethoxyacetic acid (2HEAA). Despite its inability to grow on 1,4-dioxane, strain ENV478 degraded this compound for > 80 days in aquifer microcosms. Our results suggest that the inability of strain ENV478 and possibly other THF-degrading bacteria to grow on 1,4-dioxane is related to their inability to efficiently metabolize the 1,4-dioxane degradation product 2HEAA but that strain ENV478 may nonetheless be useful as a biocatalyst for remediating 1,4-dioxane-contaminated aquifers. PMID:16885268

Vainberg, Simon; McClay, Kevin; Masuda, Hisako; Root, Duane; Condee, Charles; Zylstra, Gerben J; Steffan, Robert J

2006-08-01

49

Isolation and characterisation of Nocardioides sp. SP12, an atrazine-degrading bacterial strain possessing the gene trzN from bulk- and maize rhizosphere soil  

Microsoft Academic Search

We report the characterisation of Nocardioides sp. SP12, an atrazine-degrading bacteria isolated from atrazine-treated bulk- and maize rhizosphere soil. Based on 16S rDNA alignment, strain SP12 showed close phylogenic relationships with Nocardioides sp. C157 and Nocardioides simplex. Internal transcribed spacer (ITS) sequences of strain SP12 were longer than those of other Nocardioides sp. and present Ala- and Ile-tRNA unlike Actinomycetales.

S Piutti; E Semon; D Landry; A Hartmann; S Dousset; E Lichtfouse; E Topp; G Soulas; F Martin-Laurent

2003-01-01

50

Leucobacter chromiiresistens sp. nov., a chromate-resistant strain.  

PubMed

A Gram-positive, irregular rod-shaped, non-motile, yellow-pigmented bacterium, strain JG 31(T), was isolated in the course of identifying chromium-resistant soil bacteria. 16S rRNA gene sequence analysis of the isolated bacterium indicated its phylogenetic position within the genus Leucobacter. Binary 16S rRNA gene sequence alignments of the isolated bacterium with the 11 species of the genus recognized at the time of writing revealed sequence similarities of more than 97?% with Leucobacter alluvii (GenBank accession no: AM072820; 99.4?%), Leucobacter iarius (AM040493; 98.2?%), Leucobacter aridicollis (AJ781047; 97.8?%), Leucobacter komagatae (AB007419; 97.4?%), Leucobacter chironomi (EU346911; 97.1?%) and Leucobacter luti (AM072819; 97.1?%). In contrast, DNA-DNA hybridization experiments showed similarity values below 28?% for DNA samples from the most closely related type strains of L. alluvii, L. aridicollis and L. iarius. Protein analysis by matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and automated RiboPrinting using the restriction enzyme PvuII differentiated strain JG 31(T) from all type strains of the genus Leucobacter. The dominant fatty acids of the novel isolate were anteiso-C(15?:?0), anteiso-C(17?:?0) and iso-C(16?:?0), while the quinone system consisted of menaquinones MK-11, MK-10, MK-9 and MK-8. In a B-type cross-linked peptidoglycan, the cell-wall amino acids were alanine, glycine, threonine, glutamic acid and 2,4-diaminobutyric acid. Strain JG 31(T) was able to grow in a medium containing up to 300 mM K(2)CrO(4) and showed cellular aggregation in response to chromate stress. From biochemical and genomic analyses, the new strain is considered to represent a novel species of the genus Leucobacter, for which the name Leucobacter chromiiresistens sp. nov. is proposed. The type strain is strain JG 31(T) (?=?DSM 22788(T) ?=?CCOS 200(T)). PMID:20511468

Sturm, Gunnar; Jacobs, Johanna; Spröer, Cathrin; Schumann, Peter; Gescher, Johannes

2011-04-01

51

Degradation of alkylphenol ethoxylates by Pseudomonas sp. strain TR01.  

PubMed Central

An alkylphenol ethoxylate-degrading bacterium was isolated from activated sludge of a municipal sewage treatment plant by enrichment culture. This organism was found to belong to the genus Pseudomonas; since no corresponding species was identified, we designated it as Pseudomonas sp. strain TR01. This strain had an optimal temperature and pH of 30 degrees C and 7, respectively, for both growth and the degradation of Triton N-101 (a nonylphenol ethoxylate in which the average number of ethylene oxide [EO] units is 9.5). The strain was unable to mineralize Triton N-101 but was able to degrade its EO chain exclusively. The resulting dominant intermediate was identified by normal-phase high-performance liquid chromatography (HPLC) and gas chromatography-mass spectrometry as a nonylphenol ethoxylate with 2 mol of EO units. A carboxylated metabolite, [(nonylphenoxy)ethoxy]acetic acid, was detected by gas chromatography-mass spectrometry. This bacterium also metabolized alcohol ethoxylates with various numbers of EO units but not polyethylene glycols whatever their degree of polymerization. By oxygen consumption assay, the alkyl group or arene corresponding to the hydrophobic part of alcohol ethoxylates or alkylphenol ethoxylates was shown to contribute to the induction of the metabolic system of the EO chain of Triton N-101, instead of the EO chain itself, which corresponds to its hydrophilic part. Thus, the isolated pseudomonad bacterium has unique substrate assimilability: it metabolizes the EO chain only when the chain linked to bulky hydrophobic groups.

Maki, H; Masuda, N; Fujiwara, Y; Ike, M; Fujita, M

1994-01-01

52

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

PubMed

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

Lima, Alex Ranieri Jerônimo; Siqueira, Andrei Santos; Dos Santos, Bruno Garcia Simões; da Silva, Fábio Daniel Florêncio; Lima, Clayton Pereira; Cardoso, Jedson Ferreira; Vianez Júnior, João Lídio da Silva Gonçalves; Dall'Agnol, Leonardo Teixeira; McCulloch, John Anthony; Nunes, Márcio Roberto Teixeira; Gonçalves, Evonnildo Costa

2014-01-01

53

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

PubMed Central

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.

Aliyu, Habibu; De Maayer, Pieter; Rees, Jasper; Tuffin, Marla

2014-01-01

54

Complete genome sequence of Arthrobacter sp. strain FB24  

PubMed Central

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, Cindy H.; Barabote, Ravi; Thompson, Sue; Bruce, David; Detter, Chris; Brettin, Thomas; Han, Cliff; Beasley, Federico; Chen, Weimin; Konopka, Allan; Xie, Gary

2013-01-01

55

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

56

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).

Chakraborty, Anirban

2013-01-01

57

N-terminal amino acid sequence of mutant strain Brevibacterium sp. adipamidase.  

PubMed

The adipamidase of a mutant strain Brevibacterium sp. R312 involved in the degradation of adiponitrile to adipic acid was purified. Its N-terminal amino acid sequence was shown to be identical to Brevibacterium sp. R312 enantio selective amidase and Rhodococcus sp. N-774 amidase. PMID:8274001

Azza, S; Moreau, J L; Chebrou, H; Arnaud, A; Galzy, P

1993-01-01

58

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.

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

2013-01-01

59

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

60

Genome sequence of the plant growth-promoting rhizobacterium Bacillus sp. strain 916.  

PubMed

Bacillus sp. strain 916, isolated from the soil, showed strong activity against Rhizoctonia solani. Here, we present the high-quality draft genome sequence of Bacillus sp. strain 916. Its 3.9-Mb genome reveals a number of genes whose products are possibly involved in promotion of plant growth or antibiosis. PMID:22965091

Wang, Xiaoyu; Luo, Chuping; Chen, Zhiyi

2012-10-01

61

Peculiarities of Ethanol Metabolism in an Acinetobacter sp. Mutant Strain Defective in Exopolysaccharide Synthesis  

Microsoft Academic Search

Activities of the key enzymes of ethanol metabolism were assayed in ethanol-grown cells of an Acinetobacter sp. mutant strain unable to synthesize exopolysaccharides (EPS). The original EPS-producing strain could not be used for enzyme analysis because its cells could not to be separated from the extremely viscous EPS with a high molecular weight. In Acinetobacter sp., ethanol oxidation to acetaldehyde

T. P. Pirog; I. G. Sokolov; Yu. V. Kuz'minskaya; Yu. R. Malashenko

2002-01-01

62

Draft Genome Sequences of Vibrio sp. Strains Isolated from Tetrodotoxin-Bearing Scavenging Gastropod  

PubMed Central

Vibrio sp. strains JCM 18905 and JCM 19053 were isolated from a tetrodotoxin (TTX)-bearing scavenging gastropod, and Vibrio sp. strain JCM 18904 was isolated from a sea cucumber. All these are closely related to Vibrio alginolyticus. Their comparative genome information is useful for studies of TTX production in bacteria.

Kawauchi, Ayumi; Nakahara, Tomomi; Zhang, Xiaochi; Taniyama, Shigeto; Takatani, Tomohiro; Arakawa, Osamu; Oshima, Kenshiro; Suda, Wataru; Kitamura, Keiko; Iida, Toshiya; Iino, Takao; Inoue, Tetsushi; Hongoh, Yuichi; Hattori, Masahira

2014-01-01

63

Draft Genome Sequence of the Alga-Aggregating Bacterium Bacillus sp. Strain RP1137.  

PubMed

Bacillus sp. strain RP1137 is a bacterium that is able to rapidly and efficiently aggregate biofuel-producing microalgae. By 16S rRNA gene sequencing, it was found to be related to the industrially important Bacillus megaterium. Here, we report the draft genome sequence of Bacillus sp. strain RP1137. PMID:24385572

Powell, Ryan J; Bachvaroff, Tsvetan R; Hill, Russell T

2014-01-01

64

Draft Genome Sequences of Vibrio sp. Strains Isolated from Tetrodotoxin-Bearing Scavenging Gastropod.  

PubMed

Vibrio sp. strains JCM 18905 and JCM 19053 were isolated from a tetrodotoxin (TTX)-bearing scavenging gastropod, and Vibrio sp. strain JCM 18904 was isolated from a sea cucumber. All these are closely related to Vibrio alginolyticus. Their comparative genome information is useful for studies of TTX production in bacteria. PMID:24948773

Kudo, Toshiaki; Kawauchi, Ayumi; Nakahara, Tomomi; Zhang, Xiaochi; Taniyama, Shigeto; Takatani, Tomohiro; Arakawa, Osamu; Oshima, Kenshiro; Suda, Wataru; Kitamura, Keiko; Iida, Toshiya; Iino, Takao; Inoue, Tetsushi; Hongoh, Yuichi; Hattori, Masahira; Ohkuma, Moriya

2014-01-01

65

Draft Genome Sequence of Ralstonia sp. Strain GA3-3, Isolated from Australian Suburban Soil  

PubMed Central

Ralstonia sp. strain GA3-3 is a hexachlorocyclohexane (HCH)-degrading bacterial strain isolated from suburban soil in Canberra, Australia. The genome of strain GA3-3 was sequenced to investigate its ability to degrade ?-HCH. Here, we report the annotated genome sequence of this strain.

Pearce, Stephen L.; Pushiri, Hafizah; Oakeshott, John G.; Russell, Robyn J.

2013-01-01

66

Heterologous expression, secretion and characterization of the Geobacillus thermoleovorans US105 type I pullulanase  

Microsoft Academic Search

Pullulanase type I of Geobacillus thermoleovorans US105 strain (PUL US105) was produced and secreted efficiently in the E. coli periplasmic or extracellular fraction using two different signal peptides. Hence, the open reading frame was connected downstream\\u000a of the lipase A signal peptide of Bacillus subtilis strain leading to an efficient secretion of an active form enzyme on the periplasmic fraction.

Dorra Zouari Ayadi; Mamdouh Ben Ali; Sonia Jemli; Sameh Ben Mabrouk; Monia Mezghani; Ezzedine Ben Messaoud; Samir Bejar

2008-01-01

67

40 CFR 180.1120 - Streptomyces sp. strain K61; exemption from the requirement of a tolerance.  

Code of Federal Regulations, 2013 CFR

...2013-07-01 2013-07-01 false Streptomyces sp. strain K61; exemption from the...Exemptions From Tolerances § 180.1120 Streptomyces sp. strain K61; exemption from...tolerance. The biological pesticide Streptomyces sp. strain K61 is...

2013-07-01

68

Genome sequence of Gluconacetobacter sp. strain SXCC-1, isolated from Chinese vinegar fermentation starter.  

PubMed

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

2011-07-01

69

Geobacillus thermodenitrificans subsp. calidus, subsp. nov., a thermophilic and ?-glucosidase producing bacterium isolated from Kizilcahamam, Turkey.  

PubMed

An ?-glucosidase producing, thermophilic, facultatively anaerobic, and endospore-forming, motile, rod-shaped bacterial strain F84b(T) was isolated from a high temperature well-pipeline sediment sample in Kizilcahamam, Turkey. The growth occurred at temperatures, pH and salinities ranging from 45 to 69ºC (optimum 60ºC), 7.0 to 8.5 (optimum 8.0) and 0 to 5% (w/v) (optimum 3.5%), respectively. Strain F84b(T) was able to grow on a wide range of carbon sources. Starch and tyrosine utilization, amylase, catalase and oxidase activities, nitrate reduction, and gas production from nitrate were all positive. The G+C content of the genomic DNA was 49.6 mol%. The menaquinone content was MK-7. The dominant cellular fatty acids were iso-C17:0, iso-C15:0, and C16:0. In phylogenetic analysis of 16S rRNA gene sequence, strain F84b(T) showed high sequence similarity to Geobacillus thermodenitrificans (99.8%) and to Geobacillus subterraneus (99.3%) with DNA hybridization values of 74.3% and 29.1%, respectively. In addition, the Rep-PCR and the intergenic 16S-23S rRNA gene fingerprinting profiles differentiated strain F84b(T) from the Geobacillus species studied. The results obtained from the physiological and biochemical characters, the menaquinone contents, the borderline DNA-DNA hybridization homology, and the genomic fingerprinting patterns had allowed phenotypic, chemotaxonomic and genotypic differentiation of strain F84b(T) from G. thermodenitrificans. Therefore, strain F84b(T) is assigned to be a new subspecies of G. thermodenitrificans, for which the name Geobacillus thermodenitrificans subsp. calidus, subsp. nov. is proposed (The type strain F84b(T) = DSM 22629(T) = NCIMB 14582(T)). PMID:21606609

Cihan, Arzu Coleri; Ozcan, Birgul; Tekin, Nilgun; Cokmus, Cumhur

2011-01-01

70

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

Lapidus, I R; Berg, H C

1982-01-01

71

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

72

Influence of heavy metals on the activity of antioxidant enzymes in the metal resistant strains of Ochrobactrum and Bacillus sp.  

PubMed

Three bacterial strains, a cadmium resistant Ochrobactrum sp. designated as CdSP9 and two strains of Bacillus sp. named PbSP6 and AsSP9 resistant to lead and arsenate, respectively were characterized here with respect to their oxidative enzyme activities. The bacterial strains were grown in basal medium supplemented with 50 microg ml(-1) of respective elements to determine the changes in the level of oxidative enzymes. The superoxide dismutase activity increased in all three isolates, but the catalase activity and malondialdehyde concentration were relatively more in CdSP9 than PbSP6 and AsSP9. The glutathione peroxidase, however, remained almost uninduced in CdSP9 but was enhanced in PbSP6 and AsSP9. A possible role of these enzymes in metal tolerance is evident from these results. PMID:24555333

Pandey, Sanjeev; Barai, Prabir Kumar; Maiti, Tushar K

2013-11-01

73

Genome Sequence of Citrobacter sp. Strain A1, a Dye-Degrading Bacterium  

PubMed Central

Citrobacter sp. strain A1, isolated from a sewage oxidation pond, is a facultative aerobe and mesophilic dye-degrading bacterium. This organism degrades azo dyes efficiently via azo reduction and desulfonation, followed by the successive biotransformation of dye intermediates under an aerobic environment. Here we report the draft genome sequence of Citrobacter sp. A1.

Chan, Giek Far; Gan, Han Ming

2012-01-01

74

Physiological responses of the halophilic archaeon Halobacterium sp. strain NRC1 to desiccation and gamma irradiation  

Microsoft Academic Search

We report that the halophilic archaeon Halobacterium sp. strain NRC-1 is highly resistant to desiccation, high vacuum and 60Co gamma irradiation. Halobacterium sp. was able to repair extensive double strand DNA breaks (DSBs) in its genomic DNA, produced both by desiccation and by gamma irradiation, within hours of damage induction. We propose that resistance to high vacuum and 60Co gamma

Molly Kottemann; Adrienne Kish; Chika Iloanusi; Sarah Bjork; Jocelyne DiRuggiero

2005-01-01

75

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.

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

2010-01-01

76

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

Microsoft Academic Search

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

JACOBUS C. HAGE; SYBE HARTMANS

1999-01-01

77

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

78

Draft Genome Sequence of Deinococcus sp. Strain RL Isolated from Sediments of a Hot Water Spring.  

PubMed

Deinococcus sp. strain RL, a moderately thermophilic bacterium, was isolated from sediments of a hot water spring in Manikaran, India. Here, we report the draft genome (2.79 Mbp) of this strain, which contains 62 contigs and 2,614 coding DNA sequences, with an average G+C content of 69.4%. PMID:25035332

Mahato, Nitish Kumar; Tripathi, Charu; Verma, Helianthous; Singh, Neha; Lal, Rup

2014-01-01

79

Draft Genome Sequence of Shewanella sp. Strain HN-41, Which Produces Arsenic-Sulfide Nanotubes  

PubMed Central

The dissimilatory metal reducing bacterium Shewanella sp. strain HN-41 was first reported to produce novel photoactive As-S nanotubes via reduction of As(V) and S2O32? under anaerobic conditions. Here we report the draft genome sequence and annotation of strain HN-41.

Kim, Dong-Hun; Jiang, Shenghua; Lee, Ji-Hoon; Cho, Yong-Joon; Chun, Jongsik; Choi, Sang-Haeng; Park, Hong-Seog; Hur, Hor-Gil

2011-01-01

80

Draft Genome Sequence of the 2-Chloro-4-Nitrophenol-Degrading Bacterium Arthrobacter sp. Strain SJCon  

PubMed Central

We report the 4.39-Mb draft genome sequence of the 2-chloro-4-nitrophenol-degrading bacterium Arthrobacter sp. strain SJCon, isolated from a pesticide-contaminated site. The draft genome sequence of strain SJCon will be helpful in studying the genetic pathways involved in the degradation of several aromatic compounds.

Vikram, Surendra; Kumar, Shailesh; Vaidya, Bhumika; Pinnaka, Anil Kumar

2013-01-01

81

Draft Genome Sequence for Caulobacter sp. Strain OR37, a Bacterium Tolerant to Heavy Metals.  

PubMed

Caulobacter sp. strain OR37 belongs to the class Alphaproteobacteria and was isolated from subsurface sediments in Oak Ridge, TN. Strain OR37 is noteworthy due to its tolerance to high concentrations of heavy metals, such as uranium, nickel, cobalt, and cadmium, and we present its draft genome sequence here. PMID:23792749

Utturkar, Sagar M; Bollmann, Annette; Brzoska, Ryann M; Klingeman, Dawn M; Epstein, Slava E; Palumbo, Anthony V; Brown, Steven D

2013-01-01

82

Draft Genome Sequence of Deinococcus sp. Strain RL Isolated from Sediments of a Hot Water Spring  

PubMed Central

Deinococcus sp. strain RL, a moderately thermophilic bacterium, was isolated from sediments of a hot water spring in Manikaran, India. Here, we report the draft genome (2.79 Mbp) of this strain, which contains 62 contigs and 2,614 coding DNA sequences, with an average G+C content of 69.4%.

Mahato, Nitish Kumar; Tripathi, Charu; Verma, Helianthous; Singh, Neha

2014-01-01

83

Reduction of Photoautotrophic Productivity in the Cyanobacterium Synechocystis sp. Strain PCC 6803 by Phycobilisome Antenna Truncation  

PubMed Central

Truncation of the algal light-harvesting antenna is expected to enhance photosynthetic productivity. The wild type and three mutant strains of Synechocystis sp. strain 6803 with a progressively smaller phycobilisome antenna were examined under different light and CO2 conditions. Surprisingly, such antenna truncation resulted in decreased whole-culture productivity for this cyanobacterium.

Page, Lawrence E.; Liberton, Michelle

2012-01-01

84

Complete Genome Sequence of the Chloromethane-Degrading Hyphomicrobium sp. Strain MC1  

PubMed Central

Hyphomicrobium sp. strain MC1 is an aerobic methylotroph originally isolated from industrial sewage. This prosthecate bacterium was the first strain reported to grow with chloromethane as the sole carbon and energy source. Its genome, consisting of a single 4.76-Mb chromosome, is the first for a chloromethane-degrading bacterium to be formally reported.

Vuilleumier, Stephane; Nadalig, Thierry; Farhan Ul Haque, Muhammad; Magdelenat, Ghislaine; Lajus, Aurelie; Roselli, Sandro; Muller, Emilie E. L.; Gruffaz, Christelle; Barbe, Valerie; Medigue, Claudine; Bringel, Francoise

2011-01-01

85

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

PubMed

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; Fromme, Petra

2014-01-01

86

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

87

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.

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

2013-01-01

88

Genome Sequence of the Pyrene- and Fluoranthene-Degrading Bacterium Cycloclasticus sp. Strain PY97M  

PubMed Central

Cycloclasticus sp. strain PY97M was isolated from a phenanthrene-degrading consortium, enriched from Yellow Sea sediment of China. Here, we present the draft genome sequence of strain PY97M, which contains 2,359,509 bp with a G+C content of 41.92% and contains 2, 264 protein-coding genes and 40 tRNAs.

Cui, Zhisong; Xu, Guangsu; Li, Qian; Gao, Wei

2013-01-01

89

Draft Genome Sequence of the 2-Chloro-4-Nitrophenol-Degrading Bacterium Arthrobacter sp. Strain SJCon.  

PubMed

We report the 4.39-Mb draft genome sequence of the 2-chloro-4-nitrophenol-degrading bacterium Arthrobacter sp. strain SJCon, isolated from a pesticide-contaminated site. The draft genome sequence of strain SJCon will be helpful in studying the genetic pathways involved in the degradation of several aromatic compounds. PMID:23516196

Vikram, Surendra; Kumar, Shailesh; Vaidya, Bhumika; Pinnaka, Anil Kumar; Raghava, Gajendra Pal Singh

2013-01-01

90

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

PubMed

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; Erijman, Leonardo

2014-01-01

91

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.

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

2014-01-01

92

Degradation of 4-fluorophenol by Arthrobacter sp. strain IF1  

Microsoft Academic Search

A Gram-positive bacterial strain capable of aerobic biodegradation of 4-fluorophenol (4-FP) as the sole source of carbon and\\u000a energy was isolated by selective enrichment from soil samples collected near an industrial site. The organism, designated\\u000a strain IF1, was identified as a member of the genus Arthrobacter on the basis of 16S ribosomal RNA gene sequence analysis. Arthrobacter strain IF1 was

Maria Isabel M. Ferreira; Julian R. Marchesi; Dick B. Janssen

2008-01-01

93

Isolation and characterization of polycyclic aromatic hydrocarbons-degrading Sphingomonas sp. strain ZL5  

Microsoft Academic Search

A bacterial strain ZL5, capable of growing on phenanthrene as a sole carbon and energy source but not naphthalene, was isolated by selective enrichment from crude-oil-contaminated soil of Liaohe Oil Field in China. The isolate was identified as a Sphingomonas sp. strain on the basis of 16S ribosomal DNA analysis. Strain ZL5 grown on phenanthrene exhibited catechol 2,3-dioxygenase (C23O) activity

Yongsheng Liu; Jie Zhang; Zhongze Zhang

2004-01-01

94

Metabolism of 2-hydroxyphenylglyoxylate by Moraxella sp. strain VS1  

Microsoft Academic Search

A bacterium, designated as Moraxella sp., was enriched with 2-hydroxyphenylglyoxylate (2HPGA) as sole source of carbon and energy. Identified metabolites and enzyme activities determined with whole cells and extracts indicated that 2HPGA was degraded by an inducible sequence of enzymes via salicylaldehyde, salicylate, and gentisate; only minute amounts of salicylate were converted to catechol. Further evidence was obtained that permeases

Verona Schmidt; Rolf-Michael Wittich; Peter Fortnagel

1991-01-01

95

Lactococcus lactis SpOx Spontaneous Mutants: a Family of Oxidative-Stress-Resistant Dairy Strains§  

PubMed Central

Numerous industrial bacteria generate hydrogen peroxide (H2O2), which may inhibit the growth of other bacteria in mixed ecosystems. We isolated spontaneous oxidative-stress-resistant (SpOx) Lactococcus lactis mutants by using a natural selection method with milk-adapted strains on dairy culture medium containing H2O2. Three SpOx mutants displayed greater H2O2 resistance. One of them, SpOx3, demonstrated better behavior in different oxidative-stress situations: (i) higher long-term survival upon aeration in LM17 and milk and (ii) the ability to grow with H2O2-producing Lactobacillus delbrueckii subsp. delbrueckii strains. Furthermore, the transit kinetics of the SpOx3 mutant in the digestive tract of a human flora-associated mouse model was not affected.

Rochat, Tatiana; Gratadoux, Jean-Jacques; Corthier, Gerard; Coqueran, Berard; Nader-Macias, Maria-Elena; Gruss, Alexandra; Langella, Philippe

2005-01-01

96

Efficient biotransformation of herbicide diuron by bacterial strain Micrococcus sp. PS1  

Microsoft Academic Search

A Gram-positive, Micrococcus sp. strain PS-1 capable of utilizing phenylurea herbicide diuron as a sole carbon source at a high concentration (up to 250 ppm)\\u000a was isolated from diuron storage site by selective enrichment study. The taxonomic characterization with 16S rRNA gene sequencing\\u000a (1,477 bp) identified PS-1 as a member of Micrococcus sp. It was studied for the degradation of diuron and

Priyanka Sharma; Adity Chopra; Swaranjit Singh Cameotra; C. Raman Suri

2010-01-01

97

Genome Sequence of Marine Bacterium Idiomarina sp. Strain 28-8, Isolated from Korean Ark Shells  

PubMed Central

Idiomarina sp. strain 28-8 is an aerobic, Gram-negative, flagellar bacterium isolated from the bodies of ark shells (Scapharca broughtonii) collected from underwater sediments in Gangjin Bay, South Korea. Here, we present the draft genome sequence of Idiomarina sp. 28-8 (2,971,606 bp, with a G+C content of 46.9%), containing 2,795 putative coding sequences.

Kim, Woo-Jin; Kim, Young-Ok; Kim, Dong-Gyun; Nam, Bo-Hye; Kong, Hee Jeong; Jung, Hyungtaek; Lee, Sang-Jun; Kim, Dong-Wook

2013-01-01

98

Use of immobilized cells of the strain Corynebacterium sp. for 4-nitrophenol degradation  

Microsoft Academic Search

4-Nitrophenol degrading bacterial strainCorynebacterium sp. 8\\/3 was isolated from chemically polluted soil. The product of cometabolic transformation of 4-nitrophenol was identified\\u000a as 4-nitrocatechol., Effect of immobilization (encapsulation in calcium alginate) ofCorynebacterium sp. cells on the process of 4-nitrophenol transformation was investigated. 4-Nitrophenol was converted by encapsulated cells\\u000a and encapsulation had a protective effect, on 4-nitrophenol degrading bacteria in repeated cycles

L. Kotou?ková; J. Vav?ík; M. N?mec; J. Plocek; Z. Zdráhal

1997-01-01

99

Physical genome map of the unicellular cyanobacterium Synechococcus sp. strain PCC 7002.  

PubMed Central

A physical restriction map of the genome of the cyanobacterium Synechococcus sp. strain PCC 7002 was assembled from AscI, NotI, SalI, and SfiI digests of intact genomic DNA separated on a contour-clamped homogeneous electric field pulsed-field gel electrophoresis system. An average genome size of 2.7 x 10(6) bp was calculated from 21 NotI, 37 SalI, or 27 SfiI fragments obtained by the digestions. The genomic map was assembled by using three different strategies: linking clone analysis, pulsed-field fragment hybridization, and individual clone hybridization to singly and doubly restriction-digested large DNA fragments. The relative positions of 21 genes or operons were determined, and these data suggest that the gene order is not highly conserved between Synechococcus sp. strain PCC 7002 and Anabaena sp. strain PCC 7120. Images

Chen, X; Widger, W R

1993-01-01

100

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.

Dodge, Anthony G.; Wackett, Lawrence P.

2005-01-01

101

Polyhydroxyalkanoate (PHA) production using waste vegetable oil by Pseudomonas sp. strain DR2.  

PubMed

To produce polyhydroxyalkanoate (PHA) from inexpensive substrates by bacteria, vegetable-oil-degrading bacteria were isolated from a rice field using enrichment cultivation. The isolated Pseudomonas sp. strain DR2 showed clear orange or red spots of accumulated PHA granules when grown on phosphate and nitrogen limited medium containing vegetable oil as the sole carbon source and stained with Nile blue A. Up to 37.34% (w/w) of intracellular PHA was produced from corn oil, which consisted of three major 3-hydroxyalkanoates; octanoic (C8:0, 37.75% of the total 3-hydroxyalkanoate content of PHA), decanoic (C10:0, 36.74%), and dodecanoic (C12:0, 11.36%). Pseudomonas sp. strain DR2 accumulated up to 23.52% (w/w) of PHAMCL from waste vegetable oil. The proportion of 3- hydroxyalkanoate of the waste vegetable-oil-derived PHA [hexanoic (5.86%), octanoic (45.67%), decanoic (34.88%), tetradecanoic (8.35%), and hexadecanoic (5.24%)] showed a composition ratio different from that of the corn-oil-derived PHA. Strain DR2 used three major fatty acids in the same ratio, and linoleic acid was the major source of PHA production. Interestingly, the production of PHA in Pseudomonas sp. strain DR2 could not occur in either acetate- or butyrate-amended media. Pseudomonas sp. strain DR2 accumulated a greater amount of PHA than other well-studied strains (Chromobacterium violaceum and Ralstonia eutropha H16) when grown on vegetable oil. The data showed that Pseudomonas sp. strain DR2 was capable of producing PHA from waste vegetable oil. PMID:18756101

Song, Jin Hwan; Jeon, Che Ok; Choi, Mun Hwan; Yoon, Sung Chul; Park, Woojun

2008-08-01

102

Genome sequence of the lupin-nodulating Bradyrhizobium sp. strain WSM1417.  

PubMed

Bradyrhizobium sp. strain WSM1417 is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from an effective nitrogen (N2) fixing root nodule of Lupinus sp. collected in Papudo, Chile, in 1995. However, this microsymbiont is a poorly effective N2 fixer with the legume host Lupinus angustifolius L.; a lupin species of considerable economic importance in both Chile and Australia. The symbiosis formed with L. angustifolius produces less than half of the dry matter achieved by the symbioses with commercial inoculant strains such as Bradyrhizobium sp. strain WSM471. Therefore, WSM1417 is an important candidate strain with which to investigate the genetics of effective N2 fixation in the lupin-bradyrhizobia symbioses. Here we describe the features of Bradyrhizobium sp. strain WSM1417, together with genome sequence information and annotation. The 8,048,963 bp high-quality-draft genome is arranged in a single scaffold of 2 contigs, contains 7,695 protein-coding genes and 77 RNA-only encoding genes, and is one of 20 rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 Community Sequencing Program. PMID:24976884

Reeve, Wayne; Terpolilli, Jason; Melino, Vanessa; Ardley, Julie; Tian, Rui; De Meyer, Sofie; Tiwari, Ravi; Yates, Ronald; O'Hara, Graham; Howieson, John; Ninawi, Mohamed; Teshima, Hazuki; Bruce, David; Detter, Chris; Tapia, Roxanne; Han, Cliff; Wei, Chia-Lin; Huntemann, Marcel; Han, James; Chen, I-Min; Mavrommatis, Konstantinos; Markowitz, Victor; Ivanova, Natalia; Ovchinnikova, Galina; Pagani, Ioanna; Pati, Amrita; Goodwin, Lynne; Peters, Lin; Woyke, Tanja; Kyrpides, Nikos

2013-12-20

103

Genome sequence of the lupin-nodulating Bradyrhizobium sp. strain WSM1417  

PubMed Central

Bradyrhizobium sp. strain WSM1417 is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from an effective nitrogen (N2) fixing root nodule of Lupinus sp. collected in Papudo, Chile, in 1995. However, this microsymbiont is a poorly effective N2 fixer with the legume host Lupinus angustifolius L.; a lupin species of considerable economic importance in both Chile and Australia. The symbiosis formed with L. angustifolius produces less than half of the dry matter achieved by the symbioses with commercial inoculant strains such as Bradyrhizobium sp. strain WSM471. Therefore, WSM1417 is an important candidate strain with which to investigate the genetics of effective N2 fixation in the lupin-bradyrhizobia symbioses. Here we describe the features of Bradyrhizobium sp. strain WSM1417, together with genome sequence information and annotation. The 8,048,963 bp high-quality-draft genome is arranged in a single scaffold of 2 contigs, contains 7,695 protein-coding genes and 77 RNA-only encoding genes, and is one of 20 rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 Community Sequencing Program.

Reeve, Wayne; Terpolilli, Jason; Melino, Vanessa; Ardley, Julie; Tian, Rui; De Meyer, Sofie; Tiwari, Ravi; Yates, Ronald; O'Hara, Graham; Howieson, John; Ninawi, Mohamed; Teshima, Hazuki; Bruce, David; Detter, Chris; Tapia, Roxanne; Han, Cliff; Wei, Chia-Lin; Huntemann, Marcel; Han, James; Chen, I-Min; Mavrommatis, Konstantinos; Markowitz, Victor; Ivanova, Natalia; Ovchinnikova, Galina; Pagani, Ioanna; Pati, Amrita; Goodwin, Lynne; Peters, Lin; Woyke, Tanja; Kyrpides, Nikos

2013-01-01

104

Draft Genome Sequence of Sphingobium sp. Strain BHC-A, Revealing Genes for the Degradation of Hexachlorocyclohexane  

PubMed Central

Here, we report the draft genome sequence of Sphingobium sp. strain BHC-A, a lin gene-based hexachlorocyclohexane (HCH)-degrading strain, isolated from soil that suffered long-term HCH contamination in an insecticide factory.

Xue, Chao; Cao, Li; Zhang, Rong; He, Jian; Li, Shunpeng

2014-01-01

105

Draft Genome Sequence of Sphingobium sp. Strain BHC-A, Revealing Genes for the Degradation of Hexachlorocyclohexane.  

PubMed

Here, we report the draft genome sequence of Sphingobium sp. strain BHC-A, a lin gene-based hexachlorocyclohexane (HCH)-degrading strain, isolated from soil that suffered long-term HCH contamination in an insecticide factory. PMID:24699958

Xue, Chao; Cao, Li; Zhang, Rong; He, Jian; Li, Shunpeng; Hong, Qing

2014-01-01

106

Identification and nitrogen regulation of the cyanase gene from the cyanobacteria Synechocystis sp. strain PCC 6803 and Synechococcus sp. strain PCC 7942.  

PubMed Central

An open reading frame (slr0899) on the genome of Synechocystis sp. strain PCC 6803 encodes a polypeptide of 149 amino acid residues, the sequence of which is 40% identical to that of cyanase from Escherichia coli. Introduction into a cyanase-deficient E. coli strain of a plasmid-borne slr0899 resulted in expression of low but significant activity of cyanase. Targeted interruption of a homolog of slr0899 from Synechococcus sp. strain PCC 7942, encoding a protein 77% identical to that encoded by slr0899, resulted in loss of cellular cyanase activity. These results indicated that slr0899 and its homolog in the strain PCC 7942 represent the cyanobacterial cyanase gene (designated cynS). While cynS of strain PCC 6803 is tightly clustered with the four putative molybdenum cofactor biosynthesis genes located downstream, cynS of strain PCC 7942 was found to be tightly clustered with the two genes located upstream, which encode proteins similar to the subunits of the cyanobacterial nitrate-nitrite transporter. In both strains, cynS was transcribed as a part of a large transcription unit and the transcription was negatively regulated by ammonium. Cyanase activity was low in ammonium-grown cells and was induced 7- to 13-fold by inhibition of ammonium fixation or by transfer of the cells to ammonium-free media. These findings indicated that cyanase is an ammonium-repressible enzyme in cyanobacteria, the expression of which is regulated at the level of transcription. Similar to other ammonium-repressible genes in cyanobacteria, expression of cynS required NtcA, a global nitrogen regulator of cyanobacteria.

Harano, Y; Suzuki, I; Maeda, S; Kaneko, T; Tabata, S; Omata, T

1997-01-01

107

Dissimilatory Iodate Reduction by Marine Pseudomonas sp. Strain SCT  

Microsoft Academic Search

Bacterial iodate (IO3 ) reduction is poorly understood largely due to the limited number of available isolates as well as the paucity of information about key enzymes involved in the reaction. In this study, an iodate- reducing bacterium, designated strain SCT, was newly isolated from marine sediment slurry. SCT is phylo- genetically closely related to the denitrifying bacterium Pseudomonas stutzeri

Seigo Amachi; Nahito Kawaguchi; Yasuyuki Muramatsu; Satoshi Tsuchiya; Yuko Watanabe; Hirofumi Shinoyama; Takaaki Fujii

2007-01-01

108

Phenotypic and physiological changes in Acinetobacter sp. strain DR1 with exogenous plasmid.  

PubMed

The genus Acinetobacter has been recognized to take up exogenous DNA from the environment. In this study, we conducted natural transformation with a novel diesel-degrading Acinetobacter sp. strain, designated strain DR1, using the broad host range plasmid pRK415. Many factors, including temperature, quantities of DNA, and aeration have proven critically important for efficient natural transformation. Interestingly, the Acinetobacter sp. strain DR1 (pRK415) differed both phenotypically and physiologically from the wild-type strain in several regards, including motility, biofilm formation ability, and responses to oxidative stress: the transformed cells were rendered more sensitive to hydrogen peroxide and cumene hydroperoxide, and their motilities and biofilm formation activity were also attenuated. Our data demonstrated that caution should be exercised when conducting genetic manipulation with plasmids, due to the possibility that phenotypic and physiological changes in the host might occur along with the uptake of plasmids. PMID:20607540

Park, Jungsoon; Park, Woojun

2011-01-01

109

Bile acids are new products of a marine bacterium, Myroides sp. strain SM1.  

PubMed

Strain SM1 was isolated as a biosurfactant-producing microorganism from seawater and presumptively identified as Myroides sp., based on morphology, biochemical characteristics and 16S rDNA sequence. The strain produced surface-active compounds in marine broth, which were purified, using emulsification activity for n-hexadecane as an indicator. The purified compounds were identified by thin-layer chromatography, (1)H- and (13)C-NMR spectra and fast atom bombardment mass spectrometry as cholic acid, deoxycholic acid and their glycine conjugates. Type strains of the genus Myroides, M. odoratus JCM7458 and M. odoramitimus JCM7460, also produced these compounds. Myroides sp. strain SM1 possessed a biosynthetic route to cholic acid from cholesterol. Thus, bile acids were found as new products of prokaryotic cells, genus Myroides. PMID:15549287

Maneerat, Suppasil; Nitoda, Teruhiko; Kanzaki, Hiroshi; Kawai, Fusako

2005-06-01

110

Degradation of acyl-homoserine lactone molecules by Acinetobacter sp. strain C1010.  

PubMed

A bacterium C1010, isolated from the rhizospheres of cucumbers in fields in Korea, degraded the microbial quorum-sensing molecules, hexanoyl homoserine lactone (HHSL), and octadecanoyl homoserine lactone (OHSL). Morphological characteristics and 16S rRNA sequence analysis identified C1010 as Acinetobacter sp. strain C1010. This strain was able to degrade the acyl-homoserine lactones (AHLs) produced by the biocontrol bacterium, Pseudomonas chlororaphis O6, and a phytopathogenic bacterium, Burkholderia glumae. Co-cultivation studies showed that the inactivation of AHLs by C1010 inhibited production of phenazines by P. chlororaphis O6. In virulence tests, the C1010 strain attenuated soft rot symptom caused by Erwinia carotovora ssp. carotovora. We suggest Acinetobacter sp. strain C1010 could be a useful bacterium to manipulate biological functions that are regulated by AHLs in various Gram-negative bacteria. PMID:15644910

Kang, Beom Ryong; Lee, Jung Hoon; Ko, Sug Ju; Lee, Yong Hwan; Cha, Jae Soon; Cho, Baik Ho; Kim, Young Cheol

2004-11-01

111

Bile acids are new products of a marine bacterium, Myroides sp. strain SM1  

Microsoft Academic Search

Strain SM1 was isolated as a biosurfactant-producing microorganism from seawater and presumptively identified as Myroides sp., based on morphology, biochemical characteristics and 16S rDNA sequence. The strain produced surface-active compounds in marine broth, which were purified, using emulsification activity for n-hexadecane as an indicator. The purified compounds were identified by thin-layer chromatography, 1H- and 13C-NMR spectra and fast atom bombardment

Suppasil Maneerat; Teruhiko Nitoda; Hiroshi Kanzaki; Fusako Kawai

2005-01-01

112

Decolourisation of Remazol Brilliant Blue R via a novel Bjerkandera sp. strain  

Microsoft Academic Search

A novel strain of Bjerkandera sp. (B33\\/3), with particularly high decolourisation activities upon Poly R-478 and Remazol Brilliant Blue R (RBBR) dyes, was isolated. The role of the ligninolytic extracellular enzymes produced by this strain on decolourisation of RBBR was studied in some depth. The basis of decolourisation is an enzyme-mediated process, in which the main enzyme responsible is a

Patr??cia R Moreira; E Almeida-Vara; G Sena-Martins; I Polónia; F Xavier Malcata; J Cardoso Duarte

2001-01-01

113

Degradation of azo dyes containing aminonaphthol by Sphingomonas sp strain 1CX  

Microsoft Academic Search

Sphingomonas   sp strain 1CX was isolated from a wastewater treatment plant and is capable of aerobically degrading a suite of azo dyes,\\u000a using them as a sole source of carbon and nitrogen. All azo dyes known to be decolorized by strain 1CX (Orange II, Acid Orange\\u000a 8, Acid Orange 10, Acid Red 4, and Acid Red 88) have in their

M F Coughlin; B K Kinkle; P L Bishop

1999-01-01

114

Comparison of two multimetal resistant bacterial strains: Enterobacter sp. YSU and Stenotrophomonas maltophilia ORO2.  

PubMed

The Y-12 plant in Oak Ridge, TN, which manufactured nuclear weapons during World War II and the Cold War, contaminated East Fork Poplar Creek with heavy metals. The multimetal resistant bacterial strain, Stenotrophomonas maltophilia Oak Ridge strain O2 (S. maltophilia O2), was isolated from East Fork Poplar Creek. Sequence analysis of 16s rDNA suggested that our working strain of S. maltophilia O2 was a strain of Enterobacter. Phylogenetic tree analysis and biochemical tests confirmed that it belonged to an Enterobacter species. This new strain was named Enterobacter sp. YSU. Using a modified R3A growth medium, R3A-Tris, the Hg(II), Cd(II), Zn(II), Cu(II), Au(III), Cr(VI), Ag(I), As(III), and Se(IV) MICs for a confirmed strain of S. maltophilia O2 were 0.24, 0.33, 5, 5, 0.25, 7, 0.03, 14, and 40 mM, respectively, compared to 0.07, 0.24, 0.8, 3, 0.05, 0.4, 0.08, 14, and 40 mM, respectively, for Enterobacter sp. YSU. Although S. maltophilia O2 was generally more metal resistant than Enterobacter sp. YSU, in comparison to Escherichia coli strain HB101, Enterobacter sp. YSU was resistant to Hg(II), Cd(II), Zn(II), Au(III), Ag(I), As(III), and Se(IV). By studying metal resistances in these two strains, it may be possible to understand what makes one microorganism more metal resistant than another microorganism. This work also provided benchmark MICs that can be used to evaluate the metal resistance properties of other bacterial isolates from East Fork Poplar Creek and other metal contaminated sites. PMID:19688378

Holmes, Andrew; Vinayak, Anubhav; Benton, Cherise; Esbenshade, Aaron; Heinselman, Carlisle; Frankland, Daniel; Kulkarni, Samatha; Kurtanich, Adrienne; Caguiat, Jonathan

2009-11-01

115

Genome Sequence of the Methanotrophic Alphaproteobacterium Methylocystis sp. Strain Rockwell (ATCC 49242) ?  

PubMed Central

Methylocystis sp. strain Rockwell (ATCC 49242) is an aerobic methane-oxidizing alphaproteobacterium isolated from an aquifer in southern California. Unlike most methanotrophs in the Methylocystaceae family, this strain has a single pmo operon encoding particulate methane monooxygenase but no evidence of the genes encoding soluble methane monooxygenase. This is the first reported genome sequence of a member of the Methylocystis species of the Methylocystaceae family in the order Rhizobiales.

Stein, Lisa Y.; Bringel, Francoise; DiSpirito, Alan A.; Han, Sukkyun; Jetten, Mike S. M.; Kalyuzhnaya, Marina G.; Kits, K. Dimitri; Klotz, Martin G.; Op den Camp, Huub J. M.; Semrau, Jeremy D.; Vuilleumier, Stephane; Bruce, David C.; Cheng, Jan-Fang; Davenport, Karen W.; Goodwin, Lynne; Han, Shunsheng; Hauser, Loren; Lajus, Aurelie; Land, Miriam L.; Lapidus, Alla; Lucas, Susan; Medigue, Claudine; Pitluck, Sam; Woyke, Tanja

2011-01-01

116

Two Distinct Monooxygenases for Alkane Oxidation in Nocardioides sp. Strain CF8  

Microsoft Academic Search

Alkane monooxygenases in Nocardioides sp. strain CF8 were examined at the physiological and genetic levels. Strain CF8 can utilize alkanes ranging in chain length from C2 to C16. Butane degradation by butane-grown cells was strongly inhibited by allylthiourea, a copper-selective chelator, while hexane-, octane-, and decane-grown cells showed detectable butane degradation activity in the presence of allylthiourea. Growth on butane

NATSUKO HAMAMURA; CHRIS M. YEAGER; DANIEL J. ARP

2001-01-01

117

Molecular Characterization and Substrate Specificity of Nitrobenzene Dioxygenase from Comamonas sp. Strain JS765  

Microsoft Academic Search

Comamonas sp. strain JS765 can grow with nitrobenzene as the sole source of carbon, nitrogen, and energy. We report here the sequence of the genes encoding nitrobenzene dioxygenase (NBDO), which catalyzes the first step in the degradation of nitrobenzene by strain JS765. The components of NBDO were designated ReductaseNBZ, FerredoxinNBZ, OxygenaseNBZ, and OxygenaseNBZ, with the gene designations nbzAa, nbzAb, nbzAc,

Daniel J. Lessner; Glenn R. Johnson; Rebecca E. Parales; Jim C. Spain; David T. Gibson

2002-01-01

118

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.

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

2011-01-01

119

Biodegradation of cypermethrin by Micrococcus sp. strain CPN 1.  

PubMed

A bacterium capable of utilizing pyrethroid pesticide cypermethrin as sole source of carbon was isolated from soil and identified as a Micrococcus sp. The organism also utilized fenvalerate, deltamethrin, perimethrin, 3-phenoxybenzoate, phenol, protocatechuate and catechol as growth substrates. The organism degraded cypermethrin by hydrolysis of ester linkage to yield 3-phenoxybenzoate, leading to loss of its insecticidal activity. 3-Phenoxybenzoate was further metabolized by diphenyl ether cleavage to yield protocatechuate and phenol as evidenced by isolation and identification of metabolites and enzyme activities in the cell-free extracts. Protocatechuate and phenol were oxidized by ortho-cleavage pathway. Thus, the organism was versatile in detoxification and complete mineralization of pyrethroid cypermethrin. PMID:17431802

Tallur, Preeti N; Megadi, Veena B; Ninnekar, Harichandra Z

2008-02-01

120

Degradation of 4-fluorophenol by Arthrobacter sp. strain IF1  

PubMed Central

A Gram-positive bacterial strain capable of aerobic biodegradation of 4-fluorophenol (4-FP) as the sole source of carbon and energy was isolated by selective enrichment from soil samples collected near an industrial site. The organism, designated strain IF1, was identified as a member of the genus Arthrobacter on the basis of 16S ribosomal RNA gene sequence analysis. Arthrobacter strain IF1 was able to mineralize 4-FP up to concentrations of 5 mM in batch culture. Stoichiometric release of fluoride ions was observed, suggesting that there is no formation of halogenated dead-end products during 4-FP metabolism. The degradative pathway of 4-FP was investigated using enzyme assays and identification of intermediates by gas chromatography (GC), GC–mass spectrometry (MS), high-performance liquid chromatography, and liquid chromatography–MS. Cell-free extracts of 4-FP-grown cells contained no activity for catechol 1,2-dioxygenase or catechol 2,3-dioxygenase, which indicates that the pathway does not proceed through a catechol intermediate. Cells grown on 4-FP oxidized 4-FP, hydroquinone, and hydroxyquinol but not 4-fluorocatechol. During 4-FP metabolism, hydroquinone accumulated as a product. Hydroquinone could be converted to hydroxyquinol, which was further transformed into maleylacetic acid and ?-ketoadipic acid. These results indicate that the biodegradation of 4-FP starts with a 4-FP monooxygenase reaction that yields benzoquinone, which is reduced to hydroquinone and further metabolized via the ?-ketoadipic acid pathway.

Ferreira, Maria Isabel M.; Marchesi, Julian R.

2008-01-01

121

Isolation of Rhodococcus sp. Strain ECU0066, a New Sulfide Monooxygenase-Producing Strain for Asymmetric Sulfoxidation? †  

PubMed Central

A new and efficient sulfide monooxygenase-producing strain, ECU0066, was isolated and identified as a Rhodococcus sp. that could transform phenylmethyl sulfide (PMS) to (S)-sulfoxide with 99% enantiomeric excess via two steps of enantioselective oxidations. Its enzyme activity could be effectively induced by adding PMS or phenylmethyl sulfoxide (PMSO) directly to a rich medium at the early log phase (6 h) of fermentation, resulting in over 10-times-higher production of the enzyme. This bacterial strain also displayed fairly good activity and enantioselectivity toward seven other sulfides, indicating a good potential for practical application in asymmetric synthesis of chiral sulfoxides.

Li, Ai-Tao; Zhang, Jian-Dong; Xu, Jian-He; Lu, Wen-Ya; Lin, Guo-Qiang

2009-01-01

122

Characterization of the Arsenate Respiratory Reductase from Shewanella sp. Strain ANA3  

Microsoft Academic Search

Microbial arsenate respiration contributes to the mobilization of arsenic from the solid to the soluble phase in various locales worldwide. To begin to predict the extent to which As(V) respiration impacts arsenic geochemical cycling, we characterized the expression and activity of the Shewanella sp. strain ANA-3 arsenate respiratory reductase (ARR), the key enzyme involved in this metabolism. ARR is expressed

Davin Malasarn; Jennifer R. Keeffe; Dianne K. Newman

2008-01-01

123

Respiration of 2,4,6-Trinitrotoluene by Pseudomonas sp. Strain JLR11  

PubMed Central

Under anoxic conditions Pseudomonas sp. strain JLR11 can use 2,4,6-trinitrotoluene (TNT) as the sole N source, releasing nitrite from the aromatic ring and subsequently reducing it to ammonium and incorporating it into C skeletons. This study shows that TNT can also be used as a terminal electron acceptor in respiratory chains under anoxic conditions by Pseudomonas sp. strain JLR11. TNT-dependent proton translocation coupled to the reduction of TNT to aminonitrotoluenes has been observed in TNT-grown cells. This extrusion did not occur in nitrate-grown cells or in anaerobic TNT-grown cells treated with cyanide, a respiratory chain inhibitor. We have shown that in a membrane fraction prepared from Pseudomonas sp. strain JLR11 grown on TNT under anaerobic conditions, the synthesis of ATP was coupled to the oxidation of molecular hydrogen and to the reduction of TNT. This phosphorylation was uncoupled by gramicidin. Respiration by Pseudomonas sp. strain JLR11 is potentially useful for the biotreatment of TNT in polluted waters and soils, particularly in phytorhizoremediation, in which bacterial cells are transported to the deepest root zones, which are poor in oxygen.

Esteve-Nunez, Abraham; Lucchesi, Gloria; Philipp, Bodo; Schink, Bernhard; Ramos, Juan L.

2000-01-01

124

Genome sequence of the plant growth-promoting rhizobacterium Bacillus sp. strain JS.  

PubMed

Volatile and nonvolatile compounds emitted from the plant growth-promoting rhizobacterium Bacillus sp. strain JS enhance the growth of tobacco and lettuce. Here, we report the high-quality genome sequence of this bacterium. Its 4.1-Mb genome reveals a number of genes whose products are possibly involved in promotion of plant growth or antibiosis. PMID:22740679

Song, Ju Yeon; Kim, Hyun A; Kim, Ji-Seoung; Kim, Seon-Young; Jeong, Haeyoung; Kang, Sung Gyun; Kim, Byung Kwon; Kwon, Soon-Kyeong; Lee, Choong Hoon; Yu, Dong Su; Kim, Beom Seok; Kim, Sun-Hyung; Kwon, Suk Yoon; Kim, Jihyun F

2012-07-01

125

Complete Genome Sequence of Winogradskyella sp. Strain PG-2, a Proteorhodopsin-Containing Marine Flavobacterium.  

PubMed

Winogradskyella sp. strain PG-2 is a marine flavobacterium isolated from surface seawater. This organism contains proteorhodopsin, which can convert light energy into available forms of biochemical energy. Here, we present its complete genome sequence and annotation, which provide further insights into the life strategy of proteorhodopsin-mediated phototrophy in the ocean. PMID:24874677

Kumagai, Yohei; Yoshizawa, Susumu; Oshima, Kenshiro; Hattori, Masahira; Iwasaki, Wataru; Kogure, Kazuhiro

2014-01-01

126

Draft Genome Sequence of Sodium-Independent Alkaliphilic Microbacterium sp. Strain TS-1.  

PubMed

Alkaliphilic Microbacterium sp. strain TS-1, newly isolated from the jumping spider, showed Na(+)-independent growth and motility. Here, we report the draft genome sequence of this bacterium, which may provide beneficial information for Na(+)-independent alkaline adaptation mechanisms. PMID:24356828

Fujinami, Shun; Takeda, Kiyoko; Onodera, Takefumi; Satoh, Katsuya; Sano, Motohiko; Narumi, Issay; Ito, Masahiro

2013-01-01

127

Draft Genome Sequence of Sodium-Independent Alkaliphilic Microbacterium sp. Strain TS-1  

PubMed Central

Alkaliphilic Microbacterium sp. strain TS-1, newly isolated from the jumping spider, showed Na+-independent growth and motility. Here, we report the draft genome sequence of this bacterium, which may provide beneficial information for Na+-independent alkaline adaptation mechanisms.

Fujinami, Shun; Takeda, Kiyoko; Onodera, Takefumi; Satoh, Katsuya; Sano, Motohiko; Narumi, Issay

2013-01-01

128

Virulence Mechanisms of Photorhabdus sp. Strain K122 toward Wax Moth Larvae  

Microsoft Academic Search

Virulence of Photorhabdus sp. strain K122 was assessed by injecting whole cells, spent culture medium, and lysate fractions into the hemocoel of larvae of wax moth, Galleria mellonella. Virulence correlated with the growth rate of the cultures and all larvae died after the cultures entered the stationary phase. Maximal production of protease and lipase exoenzymes occurred at the stationary phase

David J Clarke; Barbara C. A Dowds

1995-01-01

129

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

130

Draft Genome Sequence of Sphingobium sp. Strain HDIPO4, an Avid Degrader of Hexachlorocyclohexane  

PubMed Central

Sphingobium sp. strain HDIPO4 was isolated from a hexachlorocyclohexane (HCH) dumpsite and degraded HCH isomers rapidly. The draft genome sequence of HDIPO4 (~4.7 Mbp) contains 143 contigs and 4,646 coding sequences with a G+C content of 65%.

Mukherjee, Udita; Kumar, Roshan; Mahato, Nitish Kumar; Khurana, J. P.

2013-01-01

131

De Novo Sequencing and Assembly of the Whole Genome of Novosphingobium sp. Strain PP1Y?  

PubMed Central

Novosphingobium sp. strain PP1Y is a marine bacterium specifically adapted to use fuels as an energy source. We sequenced and assembled its entire genome using the Roche 454 genome sequencer system, which led to the identification of two plasmids and one megaplasmid, besides a 3.9-Mb circular chromosome.

D'Argenio, V.; Petrillo, M.; Cantiello, P.; Naso, B.; Cozzuto, L.; Notomista, E.; Paolella, G.; Di Donato, A.; Salvatore, F.

2011-01-01

132

Metabolism of butyl benzyl phthalate by Gordonia sp. strain MTCC 4818  

Microsoft Academic Search

The microbial degradative characteristics of butyl benzyl phthalate (BBP) were investigated by the Gordonia sp. strain MTCC 4818 isolated from creosote-contaminated soil. The test organism can utilize a number of phthalate esters as sole sources of carbon and energy, where BBP was totally degraded within 4 days under shake culture conditions. High performance liquid chromatography profile of the metabolites isolated

Subhankar Chatterjee; Tapan K Dutta

2003-01-01

133

Deep Desulfurization of Extensively Hydrodesulfurized Middle Distillate Oil by Rhodococcus sp. Strain ECRD-1  

PubMed Central

Dibenzothiophene (DBT), and in particular substituted DBTs, are resistant to hydrodesulfurization (HDS) and can persist in fuels even after aggressive HDS treatment. Treatment by Rhodococcus sp. strain ECRD-1 of a middle distillate oil whose sulfur content was virtually all substituted DBTs produced extensive desulfurization and a sulfur level of 56 ppm.

Grossman, M. J.; Lee, M. K.; Prince, R. C.; Minak-Bernero, V.; George, G. N.; Pickering, I. J.

2001-01-01

134

Complete Genome Sequence of Winogradskyella sp. Strain PG-2, a Proteorhodopsin-Containing Marine Flavobacterium  

PubMed Central

Winogradskyella sp. strain PG-2 is a marine flavobacterium isolated from surface seawater. This organism contains proteorhodopsin, which can convert light energy into available forms of biochemical energy. Here, we present its complete genome sequence and annotation, which provide further insights into the life strategy of proteorhodopsin-mediated phototrophy in the ocean.

Kumagai, Yohei; Oshima, Kenshiro; Hattori, Masahira; Iwasaki, Wataru; Kogure, Kazuhiro

2014-01-01

135

Genome Sequence of the Plant Growth-Promoting Rhizobacterium Bacillus sp. Strain JS  

PubMed Central

Volatile and nonvolatile compounds emitted from the plant growth-promoting rhizobacterium Bacillus sp. strain JS enhance the growth of tobacco and lettuce. Here, we report the high-quality genome sequence of this bacterium. Its 4.1-Mb genome reveals a number of genes whose products are possibly involved in promotion of plant growth or antibiosis.

Song, Ju Yeon; Kim, Hyun A; Kim, Ji-Seoung; Kim, Seon-Young; Jeong, Haeyoung; Kang, Sung Gyun; Kim, Byung Kwon; Kwon, Soon-Kyeong; Lee, Choong Hoon; Yu, Dong Su; Kim, Beom Seok; Kim, Sun-Hyung

2012-01-01

136

OXIDATION OF BIPHENYL BY A MULTICOMPONENT ENZYME SYSTEM FROM PSEUDOMONAS SP. STRAIN LB400  

EPA Science Inventory

Pseudomonas sp. strain LB400 grows on biphenyl as the sole carbon and energy source. This organism also cooxidizes several chlorinated biphenyl congeners. Biphenyl dioxygenase activity in cell extract required addition of NAD(P)H as an electron donor for the conversion of bipheny...

137

Soybean growth-promotion by Pseudomonas sp. strain VS1 under salt stress.  

PubMed

In the present study, we employ Pseudomonas sp. strain VS1 showed in vitro plant growth-promotion characteristics and promoted soybean seed emergence under salt stress. Strain produced indole 3-acetic acid in the presence of salt stresses that exhibited high numbers of lateral root as compared to control. Bacterial strain exhibited growth in DF salt medium amended with 1-aminocyclopropane-1-carboxylate through ACC deaminase activity. Bacterial-treated soybean seeds were subjected to salt stress and significantly enhanced emergence at 7 days after seeding. Strain untreated soybean plants had a 33% seed germination when 200 mM NaCl was applied at 0 DAS and the root length was significantly decreased compared to the strain treated plants (LSD0.05 = 0.21). Most importantly, the application of 200 mM NaCl at 0 DAS resulted in only a 9% of lateral root in untreated plants as compared to strain treated plants. PMID:24171253

Kasotia, Amrita; Jain, Shekhar; Vaishnav, Anukool; Kumari, Sarita; Gaur, Rajarshi Kumar; Choudhary, Devendra Kumar

2012-07-15

138

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.

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

2014-01-01

139

Draft Genome Sequence of Pseudomonas sp. Strain M47T1, Carried by Bursaphelenchus xylophilus Isolated from Pinus pinaster  

PubMed Central

The draft genome sequence of Pseudomonas sp. strain M47T1, carried by the Bursaphelenchus xylophilus pinewood nematode, the causative agent of pine wilt disease, is presented. In Pseudomonas sp. strain M47T1, genes that make this a plant growth-promoting bacterium, as well as genes potentially involved in nematotoxicity, were identified.

Proenca, Diogo Neves; Espirito Santo, Christophe; Grass, Gregor

2012-01-01

140

Draft Genome Sequence of Serratia sp. Strain M24T3, Isolated from Pinewood Disease Nematode Bursaphelenchus xylophilus  

PubMed Central

Here we report the draft genome sequence of Serratia sp. strain M24T3, which is associated with pinewood nematode Bursaphelenchus xylophilus, the causative agent of pine wilt disease. Serratia sp. strain M24T3 has been identified as a bionematocide for B. xylophilus in vitro, and multiple genes potentially involved in virulence and nematotoxity were identified.

Proenca, Diogo Neves; Espirito Santo, Christophe; Grass, Gregor

2012-01-01

141

Draft genome sequence of Serratia sp. strain M24T3, isolated from pinewood disease nematode Bursaphelenchus xylophilus.  

PubMed

Here we report the draft genome sequence of Serratia sp. strain M24T3, which is associated with pinewood nematode Bursaphelenchus xylophilus, the causative agent of pine wilt disease. Serratia sp. strain M24T3 has been identified as a bionematocide for B. xylophilus in vitro, and multiple genes potentially involved in virulence and nematotoxity were identified. PMID:22740681

Proença, Diogo Neves; Espírito Santo, Christophe; Grass, Gregor; Morais, Paula V

2012-07-01

142

Draft genome sequence of Pseudomonas sp. strain M47T1, carried by Bursaphelenchus xylophilus isolated from Pinus pinaster.  

PubMed

The draft genome sequence of Pseudomonas sp. strain M47T1, carried by the Bursaphelenchus xylophilus pinewood nematode, the causative agent of pine wilt disease, is presented. In Pseudomonas sp. strain M47T1, genes that make this a plant growth-promoting bacterium, as well as genes potentially involved in nematotoxicity, were identified. PMID:22887683

Proença, Diogo Neves; Espírito Santo, Christophe; Grass, Gregor; Morais, Paula V

2012-09-01

143

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

144

Screening of mutant strain Streptomyces mediolani sp. AC37 for (-)-8-O-methyltetrangomycin production enhancement.  

PubMed

Streptomyces mediolani sp. AC37 was isolated from the root system of higher plant Taxus baccata and produced metabolite identified as (-)-8-O-methyltetrangomycin according to LC/MS/MS analysis. In our screening program for improvements of bioactive secondary metabolites from plant associate streptomycetes, mutation was used as a tool for the induction of genetic variations for selection of higher (-)-8-O-methyltetrangomycin producers of isolates. S. mediolani sp. AC37 was treated with UV irradiation and chemical mutagenic treatment (N-nitroso-N-methyl-urea). The radical scavenging and antioxidant capacity of (-)-8-O-methyltetrangomycin and extracts isolated from mutants were tested using EPR spin trapping technique and ABTS(·+) assay. Comparison of electron microscopic images of Streptomyces sp. AC37 and mutant strains of Streptomyces sp. AC37 revealed substantial differences in morphology and ultrastructure. PMID:23274989

Jiménez, Jakeline Trejos; Sturdíková, Maria; Brezová, Vlasta; Svajdlenka, Emil; Novotová, Marta

2012-12-01

145

[The cnr-like operon in strain Comamonas sp. encoding resistance to cobalt and nickel].  

PubMed

Plasmid pBS501 was detected in the strain Comamonas sp. BS501. This plasmid specifies high level of induced resistance (5 mM) to cobalt/nickel both in the host strain and in related strains C. testosteroni B-1241 and C. acidovorans B-1251. Hybridization analysis revealed a homology of pBS501 restriction fragments with the only well-characterized operon cnrXYHCBAT that resides in plasmid pMOL28 from Cupriavidus metallidurans CH34. Essential differences in the structural organization of the cobalt/nickel resistance determinant were found between plasmid pBS501 and the cnr-operon. PMID:19382684

Siunova, T V; Siunov, A V; Kochetkov, V V; Boronin, A M

2009-03-01

146

Purification and Properties of an Extracellular Agarase from Alteromonas sp. Strain C-1.  

PubMed

A marine bacterial strain isolated from the Bay of San Vicente, Chile, was identified as Alteromonas sp. strain C-1. In the presence of agar, this strain produced high levels of an extracellular agarase. The production of agarase was repressed by glucose, with a parallel decrease in bacterial growth. The enzyme was purified to homogeneity by anion-exchange chromatography and gel filtration, with an overall yield of 45%. The enzyme has a molecular weight of 52,000, is salt sensitive, and hydrolyzes agar, yielding neoagarotetraose as the main product, with an optimum pH of about 6.5. PMID:16348832

Leon, O; Quintana, L; Peruzzo, G; Slebe, J C

1992-12-01

147

Purification and Properties of an Extracellular Agarase from Alteromonas sp. Strain C-1  

PubMed Central

A marine bacterial strain isolated from the Bay of San Vicente, Chile, was identified as Alteromonas sp. strain C-1. In the presence of agar, this strain produced high levels of an extracellular agarase. The production of agarase was repressed by glucose, with a parallel decrease in bacterial growth. The enzyme was purified to homogeneity by anion-exchange chromatography and gel filtration, with an overall yield of 45%. The enzyme has a molecular weight of 52,000, is salt sensitive, and hydrolyzes agar, yielding neoagarotetraose as the main product, with an optimum pH of about 6.5. Images

Leon, Oscar; Quintana, Luis; Peruzzo, Gina; Slebe, Juan Carlos

1992-01-01

148

Evaluation of hexavalent chromium reduction by chromate-resistant moderately halophile, Nesterenkonia sp. strain MF2  

Microsoft Academic Search

A Gram-positive moderately halophilic chromate reducing bacterial strain was isolated from effluents of tanneries, and identified as Nesterenkonia sp. strain MF2 by phenotypic characterization and 16S rRNA analysis. The strain could tolerate up to 600mM of chromate and completely reduced 0.2mM highly toxic and soluble Cr(VI) (as CrO42?) into almost non-toxic and insoluble Cr(III) in 24h under aerobic condition.The maximum

Mohammad Ali Amoozegar; Ali Ghasemi; Mohammad Reza Razavi; Saied Naddaf

2007-01-01

149

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

Microsoft Academic Search

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.

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

2005-01-01

150

Sequence of the Ampullariella sp. strain 3876 gene coding for xylose isomerase.  

PubMed Central

The nucleotide sequence of the gene coding for xylose isomerase from Ampullariella sp. strain 3876, a gram-positive bacterium, has been determined. A clone of a fragment of strain 3876 DNA coding for a xylose isomerase activity was identified by its ability to complement a xylose isomerase-defective Escherichia coli strain. One such complementation positive fragment, 2,922 nucleotides in length, was sequenced in its entirety. There are two open reading frames 1,182 and 1,242 nucleotides in length, on opposite strands of this fragment, each of which could code for a protein the expected size of xylose isomerase. The 1,182-nucleotide open reading frame was identified as the coding sequence for the protein from the sequence analysis of the amino-terminal region and selected internal peptides. The gene initiates with GTG and has a high guanine and cytosine content (70%) and an exceptionally strong preference (97%) for guanine or cytosine in the third position of the codons. The gene codes for a 43,210-dalton polypeptide composed of 393 amino acids. The xylose isomerase from Ampullariella sp. strain 3876 is similar in size to other bacterial xylose isomerases and has limited amino acid sequence homology to the available sequences from E. coli, Bacillus subtilis, and Streptomyces violaceus-ruber. In all cases yet studied, the bacterial gene for xylulose kinase is downstream from the gene for xylose isomerase. We present evidence suggesting that in Ampullariella sp. strain 3876 these genes are similarly arranged.

Saari, G C; Kumar, A A; Kawasaki, G H; Insley, M Y; O'Hara, P J

1987-01-01

151

Genome sequence of the Ornithopus/Lupinus-nodulating Bradyrhizobium sp. strain WSM471  

PubMed Central

Bradyrhizobium sp. strain WSM471 is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from an effective nitrogen- (N2) fixing root nodule formed on the annual legume Ornithopus pinnatus (Miller) Druce growing at Oyster Harbour, Albany district, Western Australia in 1982. This strain is in commercial production as an inoculant for Lupinus and Ornithopus. Here we describe the features of Bradyrhizobium sp. strain WSM471, together with genome sequence information and annotation. The 7,784,016 bp high-quality-draft genome is arranged in 1 scaffold of 2 contigs, contains 7,372 protein-coding genes and 58 RNA-only encoding genes, and is one of 20 rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 Community Sequencing Program.

Reeve, Wayne; De Meyer, Sofie; Terpolilli, Jason; Melino, Vanessa; Ardley, Julie; Tian, Rui; Tiwari, Ravi; Howieson, John; Yates, Ronald; O'Hara, Graham; Ninawi, Mohamed; Lu, Megan; Bruce, David; Detter, Chris; Tapia, Roxanne; Han, Cliff; Wei, Chia-Lin; Huntemann, Marcel; Han, James; Chen, I-Min; Mavromatis, Konstantinos; Markowitz, Victor; Ivanova, Natalia; Pagani, Ioanna; Pati, Amrita; Goodwin, Lynne; Woyke, Tanja; Kyrpides, Nikos

2013-01-01

152

Genome sequence of the Ornithopus/Lupinus-nodulating Bradyrhizobium sp. strain WSM471.  

PubMed

Bradyrhizobium sp. strain WSM471 is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from an effective nitrogen- (N2) fixing root nodule formed on the annual legume Ornithopus pinnatus (Miller) Druce growing at Oyster Harbour, Albany district, Western Australia in 1982. This strain is in commercial production as an inoculant for Lupinus and Ornithopus. Here we describe the features of Bradyrhizobium sp. strain WSM471, together with genome sequence information and annotation. The 7,784,016 bp high-quality-draft genome is arranged in 1 scaffold of 2 contigs, contains 7,372 protein-coding genes and 58 RNA-only encoding genes, and is one of 20 rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 Community Sequencing Program. PMID:24976882

Reeve, Wayne; De Meyer, Sofie; Terpolilli, Jason; Melino, Vanessa; Ardley, Julie; Tian, Rui; Tiwari, Ravi; Howieson, John; Yates, Ronald; O'Hara, Graham; Ninawi, Mohamed; Lu, Megan; Bruce, David; Detter, Chris; Tapia, Roxanne; Han, Cliff; Wei, Chia-Lin; Huntemann, Marcel; Han, James; Chen, I-Min; Mavromatis, Konstantinos; Markowitz, Victor; Ivanova, Natalia; Pagani, Ioanna; Pati, Amrita; Goodwin, Lynne; Woyke, Tanja; Kyrpides, Nikos

2013-12-20

153

Isolation and Characterization of Novosphingobium sp. Strain MT1, a Dominant Polychlorophenol-Degrading Strain in a Groundwater Bioremediation System  

PubMed Central

A high-rate fluidized-bed bioreactor has been treating polychlorophenol-contaminated groundwater in southern Finland at 5 to 8°C for over 6 years. We examined the microbial diversity of the bioreactor using three 16S ribosomal DNA (rDNA)-based methods: denaturing gradient gel electrophoresis, length heterogeneity-PCR analysis, and restriction fragment length polymorphism analysis. The molecular study revealed that the process was dependent on a stable bacterial community with low species diversity. The dominant organism, Novosphingobium sp. strain MT1, was isolated and characterized. Novosphingobium sp. strain MT1 degraded the main contaminants of the groundwater, 2,4,6-trichlorophenol, 2,3,4,6-tetrachlorophenol, and pentachlorophenol, at 8°C. The strain carried a homolog of the pcpB gene, coding for the pentachlorophenol-4-monooxygenase in Sphingobium chlorophenolicum. Spontaneous deletion of the pcpB gene homolog resulted in the loss of degradation ability. Phenotypic dimorphism (planktonic and sessile phenotypes), low growth rate (0.14 to 0.15 h?1), and low-copy-number 16S rDNA genes (single copy) were characteristic of strain MT1 and other MT1-like organisms isolated from the bioreactor.

Tiirola, Marja A.; Mannisto, Minna K.; Puhakka, Jaakko A.; Kulomaa, Markku S.

2002-01-01

154

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

155

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

2011-01-01

156

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.

Tomioka, Noriko; Uchiyama, Hiroo; Yagi, Osami

1994-01-01

157

Decolorization of textile plant effluent by Citrobacter sp. strain KCTC 18061P.  

PubMed

Citrobacter sp. strain KCTC 18061P was found to be able to decolorize textile plant effluent containing different types of reactive dyes. Effects of physico-chemical parameters, such as aeration, nitrogen source, glucose and effluent concentrations on the color removal of real dye effluent by this strain were investigated. The observed changes in the visible spectra indicated color removal by the absorption of dye to cells during incubation with the strain. This strain showed higher decolorization ability under aerobic than static culture conditions. With 1% glucose, this strain removed 70% of effluent color within 5 days. Decolorization was not significantly dependent on the nitrogen sources tested. Chemical oxygen demand (COD) and biological oxygen demand (BOD) were decreased in proportion to incubation times, and their removal rates were about 35% and 50%, respectively, at 7 days of culture. PMID:18187889

Jang, Moon-Sun; Jung, Byung-Gil; Sung, Nak-Chang; Lee, Young-Choon

2007-12-01

158

Genome sequence of Halorubrum sp. strain T3, an extremely halophilic archaeon harboring a virus-like element.  

PubMed

Halorubrum sp. strain T3, harboring a virus-like element, was isolated from a sample collected from a solar saltern in Yunnan, China. Several strains of Halorubrum pleomorphic viruses were reported in this genus recently; however, the virus-host interaction in haloarchaea remains unclear. To explore this issue, here we present the genome sequence of Halorubrum sp. strain T3 (3,168,011 bp, 68.48% G+C content). PMID:23144373

Chen, Shaoxing; Wang, Chuanming; Zhao, Zhiwei; Yang, Zhu L

2012-12-01

159

Genome Sequence of Halorubrum sp. Strain T3, an Extremely Halophilic Archaeon Harboring a Virus-Like Element  

PubMed Central

Halorubrum sp. strain T3, harboring a virus-like element, was isolated from a sample collected from a solar saltern in Yunnan, China. Several strains of Halorubrum pleomorphic viruses were reported in this genus recently; however, the virus-host interaction in haloarchaea remains unclear. To explore this issue, here we present the genome sequence of Halorubrum sp. strain T3 (3,168,011 bp, 68.48% G+C content).

Chen, Shaoxing; Wang, Chuanming; Zhao, Zhiwei

2012-01-01

160

Isolation and Culture Characterization of a New Polyvinyl Alcohol-Degrading Strain: Penicillium sp. WSH02-21  

Microsoft Academic Search

A fungal strain able to grow on polyvinyl alcohol (PVA) as sole carbon source was isolated from activated sludge of a textile\\u000a factory. Morphological characteristics showed that this strain belonged to Penicillium sp., and, to our knowledge, this is the first report of PVA degradation by a strain of Penicillum sp. When 0.5% PVA was used as the carbon source

Ding Qian; Guocheng Du; Jian Chen

2004-01-01

161

Transmission dynamics of Bartonella sp. strain OE 1-1 in Sundevall's jirds (Meriones crassus).  

PubMed

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; Harrus, Shimon

2013-02-01

162

Simultaneous Fermentation of Glucose and Xylose to Butanol by Clostridium sp. Strain BOH3.  

PubMed

Cellulose and hemicellulose constitute the major components in sustainable feedstocks which could be used as substrates for biofuel generation. However, following hydrolysis to monomer sugars, the solventogenic Clostridium will preferentially consume glucose due to transcriptional repression of xylose utilization genes. This is one of the major barriers in optimizing lignocellulosic hydrolysates that produce butanol. Unlike studies on existing bacteria, this study demonstrates that newly reported Clostridium sp. strain BOH3 is capable of fermenting 60 g/liter of xylose to 14.9 g/liter butanol, which is similar to the 14.5 g/liter butanol produced from 60 g/liter of glucose. More importantly, strain BOH3 consumes glucose and xylose simultaneously, which is shown by its capability for generating 11.7 g/liter butanol from a horticultural waste cellulosic hydrolysate containing 39.8 g/liter glucose and 20.5 g/liter xylose, as well as producing 11.9 g/liter butanol from another horticultural waste hemicellulosic hydrolysate containing 58.3 g/liter xylose and 5.9 g/liter glucose. The high-xylose-utilization capability of strain BOH3 is attributed to its high xylose-isomerase (0.97 U/mg protein) and xylulokinase (1.16 U/mg protein) activities compared to the low-xylose-utilizing solventogenic strains, such as Clostridium sp. strain G117. Interestingly, strain BOH3 was also found to produce riboflavin at 110.5 mg/liter from xylose and 76.8 mg/liter from glucose during the fermentation process. In summary, Clostridium sp. strain BOH3 is an attractive candidate for application in efficiently converting lignocellulosic hydrolysates to biofuels and other value-added products, such as riboflavin. PMID:24858088

Xin, Fengxue; Wu, Yi-Rui; He, Jianzhong

2014-08-01

163

Identification of an Enzyme System for Daidzein-to-Equol Conversion in Slackia sp. Strain NATTS  

PubMed Central

An Escherichia coli library comprising 8,424 strains incorporating gene fragments of the equol-producing bacterium Slackia sp. strain NATTS was constructed and screened for E. coli strains having daidzein- and dihydrodaidzein (DHD)- metabolizing activity. We obtained 3 clones that functioned to convert daidzein to DHD and 2 clones that converted DHD to equol. We then sequenced the gene fragments inserted into plasmids contained by these 5 clones. All of the gene fragments were contiguous, encoding three open reading frames (ORF-1, -2, and -3). Analysis of E. coli strains containing an expression vector incorporating one of the orf-1, -2, or -3 genes revealed that (i) the protein encoded by orf-1 was involved in the conversion of cis/trans-tetrahydrodaidzein (cis/trans-THD) to equol, (ii) the protein encoded by orf-2 was involved in the conversion of DHD to cis/trans-THD, and (iii) the protein encoded by orf-3 was involved in the conversion of daidzein to DHD. ORF-1 had a primary amino acid structure similar to that of succinate dehydrogenase. ORF-2 was presumed to be an enzyme belonging to the short-chain dehydrogenase/reductase superfamily. ORF-3 was predicted to have 42% identity to the daidzein reductase of Lactococcus strain 20-92 and belonged to the NADH:flavin oxidoreductase family. These findings showed that the daidzein-to-equol conversion reaction in the Slackia sp. NATTS strain proceeds by the action of these three enzymes.

Moriyama, Kaoru; Nomoto, Koji; Akaza, Hideyuki

2012-01-01

164

Production of Proteasome Inhibitor Syringolin A by the Endophyte Rhizobium sp. Strain AP16.  

PubMed

Syringolin A, the product of a mixed nonribosomal peptide synthetase/polyketide synthase encoded by the syl gene cluster, is a virulence factor secreted by certain Pseudomonas syringae strains. Together with the glidobactins produced by a number of beta- and gammaproteobacterial human and animal pathogens, it belongs to the syrbactins, a structurally novel class of proteasome inhibitors. In plants, proteasome inhibition by syringolin A-producing P. syringae strains leads to the suppression of host defense pathways requiring proteasome activity, such as the ones mediated by salicylic acid and jasmonic acid. Here we report the discovery of a syl-like gene cluster with some unusual features in the alphaproteobacterial endophyte Rhizobium sp. strain AP16 that encodes a putative syringolin A-like synthetase whose components share 55% to 65% sequence identity (72% to 79% similarity) at the amino acid level. As revealed by average nucleotide identity (ANI) calculations, this strain likely belongs to the same species as biocontrol strain R. rhizogenes K84 (formely known as Agrobacterium radiobacter K84), which, however, carries a nonfunctional deletion remnant of the syl-like gene cluster. Here we present a functional analysis of the syl-like gene cluster of Rhizobium sp. strain AP16 and demonstrate that this endophyte synthesizes syringolin A and some related minor variants, suggesting that proteasome inhibition by syrbactin production can be important not only for pathogens but also for endophytic bacteria in the interaction with their hosts. PMID:24727275

Dudnik, Alexey; Bigler, Laurent; Dudler, Robert

2014-06-15

165

Methanobacterium paludis sp. nov. and a novel strain of Methanobacterium lacus isolated from northern peatlands.  

PubMed

Two mesophilic, hydrogenotrophic methanogens, designated strains SWAN1(T) and AL-21, were isolated from two contrasting peatlands: a near circumneutral temperate minerotrophic fen in New York State, USA, and an acidic boreal poor fen site in Alaska, USA, respectively. Cells of the two strains were rod-shaped, non-motile, stained Gram-negative and resisted lysis with 0.1?% SDS. Cell size was 0.6×1.5-2.8 µm for strain SWAN1(T) and 0.45-0.85×1.5-35 µm for strain AL-21. The strains used H2/CO2 but not formate or other substrates for methanogenesis, grew optimally around 32-37 °C, and their growth spanned through a slightly low to neutral pH range (4.7-7.1). Strain AL-21 grew optimally closer to neutrality at pH 6.2, whereas strain SWAN1(T) showed a lower optimal pH at 5.4-5.7. The two strains were sensitive to NaCl with a maximal tolerance at 160 mM for strain SWAN1(T) and 50 mM for strain AL-21. Na2S was toxic at very low concentrations (0.01-0.8 mM), resulting in growth inhibition above these values. The DNA G+C content of the genomes was 35.7 mol% for strain SWAN1(T) and 35.8 mol% for strain AL-21. Phylogenetic analysis of the 16S rRNA gene sequences showed that the strains are members of the genus Methanobacterium. Strain SWAN1(T) shared 94-97?% similarity with the type strains of recognized species of the genus Methanobacterium, whereas strain AL-21 shared 99?% similarity with Methanobacterium lacus 17A1(T). On the basis of phenotypic, genomic and phylogenetic characteristics, strain SWAN1(T) (?=?DSM 25820(T)?=?JCM 18151(T)) is proposed as the type strain of a novel species, Methanobacterium paludis sp. nov., while strain AL-21 is proposed as a second strain of Methanobacterium lacus. PMID:24449792

Cadillo-Quiroz, Hinsby; Bräuer, Suzanna L; Goodson, Noah; Yavitt, Joseph B; Zinder, Stephen H

2014-05-01

166

Carotenoid-containing outer membrane of Synechocystis sp. strain PCC6714.  

PubMed Central

Outer membranes, free of cytoplasmic or thylakoid membranes and peptidoglycan components, were obtained from Synechocystis sp. strain PCC6714. Electron microscope studies revealed double-track outer membrane vesicles with a smooth-appearing exoplasmic surface, an exoplasmic fracture face covered by closely packed particles and a corresponding plasmic fracture face with regularly distributed holes. Lipopolysaccharide, proteins, lipids, and carotenoids were the constituents of the outer membrane of Synechocystis sp. PCC6714. Twelve polypeptides were found in outer membrane fractions, among them two dominant outer membrane proteins (Mrs, 67,000 and 61,000). Lipopolysaccharide-specific components were GlcN and an unidentified heptose. Outer membrane lipid extracts contained phosphatidylglycerol, sulfolipid, phosphatidylcholine, and unknown lipids. The carotenoids, myxoxanthophyll, related carotenoid-glycosides, zeaxanthin, echinenone, and beta-carotene were found to be true constituents of the outer membrane of Synechocystis sp. PCC6714. Images

Jurgens, U J; Weckesser, J

1985-01-01

167

Simultaneous Degradation of Atrazine and Phenol by Pseudomonas sp. Strain ADP: Effects of Toxicity and Adaptation  

PubMed Central

The strain Pseudomonas sp. strain ADP is able to degrade atrazine as a sole nitrogen source and therefore needs a single source for both carbon and energy for growth. In addition to the typical C source for Pseudomonas, Na2-succinate, the strain can also grow with phenol as a carbon source. Phenol is oxidized to catechol by a multicomponent phenol hydroxylase. Catechol is degraded via the ortho pathway using catechol 1,2-dioxygenase. It was possible to stimulate the strain in order to degrade very high concentrations of phenol (1,000 mg/liter) and atrazine (150 mg/liter) simultaneously. With cyanuric acid, the major intermediate of atrazine degradation, as an N source, both the growth rate and the phenol degradation rate were similar to those measured with ammonia as an N source. With atrazine as an N source, the growth rate and the phenol degradation rate were reduced to ?35% of those obtained for cyanuric acid. This presents clear evidence that although the first three enzymes of the atrazine degradation pathway are constitutively present, either these enzymes or the uptake of atrazine is the bottleneck that diminishes the growth rate of Pseudomonas sp. strain ADP with atrazine as an N source. Whereas atrazine and cyanuric acid showed no significant toxic effect on the cells, phenol reduces growth and activates or induces typical membrane-adaptive responses known for the genus Pseudomonas. Therefore Pseudomonas sp. strain ADP is an ideal bacterium for the investigation of the regulatory interactions among several catabolic genes and stress response mechanisms during the simultaneous degradation of toxic phenolic compounds and a xenobiotic N source such as atrazine.

Neumann, Grit; Teras, Riho; Monson, Liis; Kivisaar, Maia; Schauer, Frieder; Heipieper, Hermann J.

2004-01-01

168

Draft Genome Sequence of Pandoraea sp. Strain SD6-2, Isolated from Lindane-Contaminated Australian Soil  

PubMed Central

Pandoraea sp. strain SD6-2 is a ?-hexachlorocyclohexane-degrading bacterial strain isolated from lindane-contaminated soil in Queensland, Australia. The genome of SD6-2 was sequenced to investigate its ability to degrade ?-hexachlorocyclohexane. Here we report the annotated genome sequence of this strain.

Pushiri, Hafizah; Pearce, Stephen L.; Oakeshott, John G.; Russell, Robyn J.

2013-01-01

169

Physiological characteristics of Thiomicrospira sp. Strain L-12 isolated from deep-sea hydrothermal vents.  

PubMed

Growth of the obligately chemolithotrophic Thiomicrospira sp. strain L-12, isolated from a hydrothermal vent at a depth of 2,550 m in the Galapagos Rift region, was optimal at pH 8 and required 200 mM Na+ and divalent ions (Ca2+ and Mg2+). The organism was microaerophilic and tolerated 300 microM sulfide without a decrease in the rate of CO2 incorporation. Growth and CO2 incorporation occurred within the temperature range of 10 to 35 degrees C, with both optimal at 25 degrees C. At the in situ pressure of 250 atm. the rate of CO2 incorporation was reduced by 25% relative to that measured at 1 atm: it was entirely suppressed at 500 atm. The results of this physiological characterization suggest that Thiomicrospira sp. strain L-12 can be an active autotroph in the hydrothermal environment. PMID:7054142

Ruby, E G; Jannasch, H W

1982-01-01

170

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

171

Unaltered Nodulation Competitiveness of a Strain of Bradyrhizobium sp. (Lotus) after a Decade in Soil.  

PubMed

A Bradyrhizobium sp. (Lotus) strain that formed a soil population that was highly competitive for nodulation of Lotus pedunculatus 11 years after its introduction into a field soil and a culture of the same strain stored lyophilized were compared with an antibiotic-resistant mutant in respect of their nodulation competitiveness. The mutant was less competitive than the wild-type strain it was isolated from and had to be present at a cell ratio of 5.76:1 in mixed inoculum in sand culture to form 50% of the nodules on L. pedunculatus (50% nodulation value, 5.76). The 50% nodulation values for a soil population of the mutant mixed with soil populations of the lyophilized and field soil strain were, respectively, 6.83 and 5.77, indicating that the field soil strain was not significantly different from the lyophilized strain in nodulation competitiveness. A 50% nodulation value of 11.18 obtained when soil containing a recently established mutant population was mixed with the field soil containing the population established 11 years before, indicating that the plant infection technique underestimated cell numbers of the field soil population by 100%. Nodulation competitiveness was unaffected by the size of the strain populations in the range of 100 to 1,000 cells per g of soil; at 10 cells per g a significant correlation between strain ratios in nodules and in soil was still evident. The results indicated that apparently superior nodulation competitiveness of a well-established soil population relative to that of a subsequently introduced strain may not necessarily reflect the intrinsic competitive abilites of the strain(s) involved. The soil strain did not differ from laboratory-maintained cultures in antigenic properties, effectiveness, or whole cell protein electrophoresis profiles. PMID:16348061

Lochner, H H; Strijdom, B W; Law, I J

1989-11-01

172

Unaltered Nodulation Competitiveness of a Strain of Bradyrhizobium sp. (Lotus) after a Decade in Soil  

PubMed Central

A Bradyrhizobium sp. (Lotus) strain that formed a soil population that was highly competitive for nodulation of Lotus pedunculatus 11 years after its introduction into a field soil and a culture of the same strain stored lyophilized were compared with an antibiotic-resistant mutant in respect of their nodulation competitiveness. The mutant was less competitive than the wild-type strain it was isolated from and had to be present at a cell ratio of 5.76:1 in mixed inoculum in sand culture to form 50% of the nodules on L. pedunculatus (50% nodulation value, 5.76). The 50% nodulation values for a soil population of the mutant mixed with soil populations of the lyophilized and field soil strain were, respectively, 6.83 and 5.77, indicating that the field soil strain was not significantly different from the lyophilized strain in nodulation competitiveness. A 50% nodulation value of 11.18 obtained when soil containing a recently established mutant population was mixed with the field soil containing the population established 11 years before, indicating that the plant infection technique underestimated cell numbers of the field soil population by 100%. Nodulation competitiveness was unaffected by the size of the strain populations in the range of 100 to 1,000 cells per g of soil; at 10 cells per g a significant correlation between strain ratios in nodules and in soil was still evident. The results indicated that apparently superior nodulation competitiveness of a well-established soil population relative to that of a subsequently introduced strain may not necessarily reflect the intrinsic competitive abilites of the strain(s) involved. The soil strain did not differ from laboratory-maintained cultures in antigenic properties, effectiveness, or whole cell protein electrophoresis profiles.

Lochner, Hester H.; Strijdom, Barend W.; Law, Ian J.

1989-01-01

173

Isolation and characterization of a white rot fungus Bjerkandera sp. strain capable of oxidizing phenanthrene.  

PubMed

Strain BOL13 was selected from 18 fungal strains isolated from an oil-spill contaminated site in Oruro, Bolivia. It was identified as a basidiomycete with high homology to Bjerkandera. The fungus degraded 100 mg phenanthrene l(-1) at 0.17 mg l(-1) d(-1) at 30 degrees C at pH 7. During phenanthrene degradation, a maximum manganese peroxidase activity of 100-120 U l(-1) was measured after 10 days of incubation. The ability of Bjerkandera sp. to produce lignin-modifying enzymes and to oxidize phenanthrene under various pH and temperature conditions was confirmed. PMID:16086246

Terrazas-Siles, Enrique; Alvarez, Teresa; Guieysse, Benoit; Mattiasson, Bo

2005-06-01

174

Aerobic degradation of 2-picolinic acid by a nitrobenzene-assimilating strain: Streptomyces sp. Z2  

Microsoft Academic Search

Streptomyces sp. Z2 was isolated from nitrobenzene contaminated activated sludge, which utilized nitrobenzene as a sole source of carbon, nitrogen, and energy under aerobic condition. It was found that besides nitrobenzene strain Z2 can degrade 2-picolinic acid. Strain Z2 completely degraded 2-picolinic acid with initial concentration of 500mg\\/L, 1000mg\\/L, 1500mg\\/L, 2000mg\\/L, 2500mg\\/L, and 3000mg\\/L within 36h, 50h, 72h, 100h, 136h,

Chunli Zheng; Jiti Zhou; Jing Wang; Baocheng Qu; Hong Lu; Hongxia Zhao

2009-01-01

175

An insertion element prevents phycobilisome synthesis in N2-fixing Synechocystis sp. strain BO 8402.  

PubMed

The unicellular diazotrophic cyanobacterium Synechocystis sp. strain BO 8402, isolated from Lake Constance, contains a novel insertion sequence, IS8402, in the apcA gene encoding a pigmented protein of phycobilisomes. IS8402 comprises 1,322 bp, flanked by two inverted repeats of 15 bp. Upon insertion in the target DNA, direct duplications of 8 nucleotides were generated. One open reading frame, potentially coding for a protein of 399 amino acids, was found. The deduced amino acid sequence shows homology to putative transposases of the IS4 family. Precise excision of the insertion element resulted in a spontaneous revertant, Synechocystis sp. strain BO 9201, that had regained the ability to form hemidiscoidal phycobilisomes. Apart from the unique insertion of IS8402 into apcA in strain BO 8402 both strains contain at least 12 further homologous insertion elements at corresponding sites in the genomes. The unique insertion in strain BO 8402 prevents the expression of apcABC operon and hence abolishes the formation of intact phycobilisomes. This decreases the quantum efficiency of photosystem II and promotes anaerobic N2 fixation in a unicellular cyanobacterium with a highly oxygen-sensitive nitrogenase. PMID:8787395

Brass, S; Ernst, A; Böger, P

1996-06-01

176

Desaturation, dioxygenation, and monooxygenation reactions catalyzed by naphthalene dioxygenase from Pseudomonas sp. strain 9816-4.  

PubMed Central

The stereospecific oxidation of indan and indene was examined with mutant and recombinant strains expressing naphthalene dioxygenase of Pseudomonas sp. strain 9816-4. Pseudomonas sp. strain 9816/11 and Escherichia coli JM109(DE3)[pDTG141] oxidized indan to (+)-(1S)-indanol, (+)-cis-(1R,2S)-indandiol, (+)-(1S)-indenol, and 1-indanone. The same strains oxidized indene to (+)-cis-(1R,2S)-indandiol and (+)-(1S)-indenol. Purified naphthalene dioxygenase oxidized indan to the same four products formed by strains 9816/11 and JM109(DE3)[pDTG141]. In addition, indene was identified as an intermediate in indan oxidation. The major products formed from indene by purified naphthalene dioxygenase were (+)-(1S)-indenol and (+)-(1R,2S)-indandiol. The results show that naphthalene dioxygenase catalyzes the enantiospecific monooxygenation of indan to (+)-(1S)-indanol and the desaturation of indan to indene, which then serves as a substrate for the formation of (+)-(1R,2S)-indandiol and (+)-(1S)-indenol. The relationship of the desaturase, monooxygenase, and dioxygenase activities of naphthalene dioxygenase is discussed with reference to reactions catalyzed by toluene dioxygenase, plant desaturases, cytochrome P-450, methane monooxygenase, and other bacterial monooxygenases.

Gibson, D T; Resnick, S M; Lee, K; Brand, J M; Torok, D S; Wackett, L P; Schocken, M J; Haigler, B E

1995-01-01

177

Two Distinct Monooxygenases for Alkane Oxidation in Nocardioides sp. Strain CF8  

PubMed Central

Alkane monooxygenases in Nocardioides sp. strain CF8 were examined at the physiological and genetic levels. Strain CF8 can utilize alkanes ranging in chain length from C2 to C16. Butane degradation by butane-grown cells was strongly inhibited by allylthiourea, a copper-selective chelator, while hexane-, octane-, and decane-grown cells showed detectable butane degradation activity in the presence of allylthiourea. Growth on butane and hexane was strongly inhibited by 1-hexyne, while 1-hexyne did not affect growth on octane or decane. A specific 30-kDa acetylene-binding polypeptide was observed for butane-, hexane-, octane-, and decane-grown cells but was absent from cells grown with octane or decane in the presence of 1-hexyne. These results suggest the presence of two monooxygenases in strain CF8. Degenerate primers designed for PCR amplification of genes related to the binuclear-iron-containing alkane hydroxylase from Pseudomonas oleovorans were used to clone a related gene from strain CF8. Reverse transcription-PCR and Northern blot analysis showed that this gene encoding a binuclear-iron-containing alkane hydroxylase was expressed in cells grown on alkanes above C6. These results indicate the presence of two distinct monooxygenases for alkane oxidation in Nocardioides sp. strain CF8.

Hamamura, Natsuko; Yeager, Chris M.; Arp, Daniel J.

2001-01-01

178

Organic solvent tolerance of halophilic a-amylase from a Haloarchaeon, Haloarcula sp. strain S-1  

Microsoft Academic Search

A halophilic archaeon, Haloarcula sp. strain S-1, produced extracellular organic solvent-tolerant ?-amylase. Molecular mass of the enzyme was estimated to be 70 kDa by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. This amylase exhibited maximal activity at 50°C in buffer containing 4.3 M NaCl, pH 7.0. Moreover, the enzyme was active and stable in various organic solvents (benzene, toluene, and chloroform, etc.). Activity was not

Tadamasa Fukushima; Toru Mizuki; Akinobu Echigo; Akira Inoue; Ron Usami

2005-01-01

179

Abenquines A–D: aminoquinone derivatives produced by Streptomyces sp. strain DB634  

Microsoft Academic Search

New bioactive secondary metabolites, called abenquines, were found in the fermentation broth of Streptomyces sp. strain DB634, which was isolated from the soils of the Chilean highland of the Atacama Desert. They are composed of an amino acid linked to an N-acetyl-aminobenzoquinone. Isolation of the abenquines (1–4), their structure elucidation by NMR analysis and MS, as well as the kinetics

Dirk Schulz; Pascal Beese; Birgit Ohlendorf; Arlette Erhard; Heidi Zinecker; Cristina Dorador; Johannes F Imhoff

2011-01-01

180

Substantially monodispersed poly(?- l -lysine)s frequently occurred in newly isolated strains of Streptomyces sp  

Microsoft Academic Search

The presence of poly(?-l-lysine) (?-PL) was found quite frequently by screening various strains of Streptomyces sp. Most of the ten newly obtained ?-PLs, when they were produced from glucose, showed a polydispersity index of M\\u000a w\\/M\\u000a n?=?1.01 using ion-pair chromatography analysis. The polymers were classified into five groups according to their chain lengths.\\u000a The average numbers of residues in the

Hideo Hirohara; Masayuki Saimura; Munenori Takehara; Masahiro Miyamoto; Atsushi Ikezaki

2007-01-01

181

Clustered Genes Required for the Synthesis of Heterocyst Envelope Polysaccharide in Anabaena sp. Strain PCC 7120  

Microsoft Academic Search

As demonstrated with alr2835 (hepA) and alr2834 (hepC) mutants, heterocysts of Anabaena sp. strain PCC 7120, a filamentous cyanobacterium, must have an envelope polysaccharide layer (the Hep phenotype) to fix dinitrogen in an oxygen-containing milieu (the Fox phenotype). Transpositions presumptively responsible for a Fox phenotype were localized in open reading frames (ORFs) near hepA and hepC. A mutation in each

Guocun Huang; Qing Fan; Sigal Lechno-Yossef; Elizabeth Wojciuch; C. Peter Wolk; Takakazu Kaneko; Satoshi Tabata

2005-01-01

182

Engineering the Genotype of Acinetobacter sp. Strain ADP1 To Enhance Biosynthesis of Cyanophycin  

Microsoft Academic Search

To study the importance of arginine provision and phosphate limitation for synthesis and accumulation of cyanophycin (CGP) in Acinetobacter sp. strain ADP1, genes encoding the putative arginine regulatory protein (argR) and the arginine succinyltransferase (astA) were inactivated, and the effects of these mutations on CGP synthesis were analyzed. The inactivation of these genes resulted in a 3.5- or 7-fold increase

Yasser Elbahloul; Alexander Steinbuchel

2006-01-01

183

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

184

Transcriptomic Analysis Reveals a Bifurcated Terephthalate Degradation Pathway in Rhodococcus sp. Strain RHA1  

Microsoft Academic Search

Phthalate isomers and their esters are important pollutants whose biodegradation is not well understood. Rhodococcus sp. strain RHA1 is notable for its ability to degrade a wide range of aromatic compounds. RHA1 was previously shown to degrade phthalate (PTH) and to have genes putatively encoding terephthalate (TPA) degradation. Transcriptomic analysis of 8,213 genes indicated that 150 were up-regulated during growth

Hirofumi Hara; Lindsay D. Eltis; Julian E. Davies; William W. Mohn

2007-01-01

185

Mineralization of phenol and its derivatives by Pseudomonas sp. strain CP4  

Microsoft Academic Search

A Pseudomonas sp. strain, CP4, was isolated that used phenol up to 1.5 g\\/l as sole source of carbon and energy. Optimal growth on 1.5 g phenol\\/l was at pH 6.5 to 7.0 and 30°C. Unadapted cells needed 72 h to decrease the chemical oxygen demand (COD) of about 2000 mg\\/l (from 1 g phenol\\/l) to about 200 mg\\/l. Adapted

K. S. Babu; P. V. Ajithkumar; A. A. M. Kunhi

1995-01-01

186

Purification and characterization of an antimicrobial peptide produced by Pseudomonas sp. strain 4B  

Microsoft Academic Search

An antimicrobial peptide produced by a bacterium isolated from the effluent pond of a bovine abattoir was purified and characterized.\\u000a The strain was characterized by biochemical profiling and 16S rDNA sequencing as Pseudomonas sp. The antimicrobial peptide was purified by ammonium sulfate precipitation, gel filtration, and ion exchange chromatography.\\u000a Direct activity on sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) was

Roberta Fontoura; Jordana Corralo Spada; Silvana Terra Silveira; Siu Mui Tsai; Adriano Brandelli

2009-01-01

187

Complexity of Gas Vesicle Biogenesis in Halobacterium sp. Strain NRC1: Identification of Five New Proteins  

Microsoft Academic Search

The genome of Halobacterium sp. strain NRC-1 contains a large gene cluster, gvpMLKJIHGFEDACNO, that is both necessary and sufficient for the production of buoyant gas-filled vesicles. Due to the resistance of gas vesicles to solubilization, only the major gas vesicle protein GvpA and a single minor protein, GvpC, were previously detected. Here, we used immunoblotting analysis to probe for the

Hem Dutt Shukla; Shiladitya DasSarma

2004-01-01

188

Middle-thermophilic sulfur-oxidizing bacteria Thiomonas sp. RAN5 strain for hydrogen sulfide removal  

Microsoft Academic Search

Hydrogen sulfide (H2S) is one of the most toxic and offensively odorous gases and is generated in anaerobic bioreactors. A middle-thermophilic sulfur-oxidizing bacterium (SOB), Thiomonas sp. strain RAN5, was isolated and applied for H2S removal from both artificial and anaerobically digested gas. When a bioreactor containing medium inoculated with RAN5 was aerated continuously with artificial gas (containing 100 ppm H2S)

Ryoki Asano; Kayako Hirooka; Yutaka Nakai

2012-01-01

189

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

190

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

Microsoft Academic Search

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\\u000a to 4-hydroxymuconic semialdehyde and the degradation of chlorinated and several alkylated hydroquinones. The activity of 1\\u000a mg of the purified enzyme with unsubstituted hydroquinone was 6.1 ?mol per minute, the apparent Km

Boris A Kolvenbach; Markus Lenz; Dirk Benndorf; Erdmann Rapp; Jan Fousek; Cestmir Vlcek; Andreas Schäffer; Frédéric LP Gabriel; Hans-Peter E Kohler; Philippe FX Corvini

2011-01-01

191

Isolation and Characterization of Pseudomonas sp. Strain ONBA-17 Degrading o -Nitriobenzaldehyde  

Microsoft Academic Search

Aerobic bacteria degrading o-nitrobenzaldehyde (ONBA) were isolated from activated sludges. One of the isolates, ONBA-17, was identified as Pseudomonas sp. The isolate could grow on ONBA as its sole source of carbon and nitrogen. Further studies demonstrated that the strain\\u000a was a moderately halophilic bacterium and capable of degrading benzoic acid, 2-nitrophenol, 2-aminophenol, 4-hydroxybenzoic\\u000a acid, and 4-dimetylaminobenzaldehyde. It could completely

Yu Fang-Bo; Shen Biao; Li Shun-Peng

2006-01-01

192

Isolation of Fenitrothion-degrading Strain Burkholderia sp. FDS-1 and Cloning of mpd Gene  

Microsoft Academic Search

A short rod shaped, gram-negative bacterium strain Burkholderia sp. FDS-1 was isolated from the sludge of the wastewater treating system of an organophosphorus pesticides manufacturer.\\u000a The isolate was capable of using fenitrothion as the sole carbon source for its growth. FDS-1 first hydrolyzed fenitrothion\\u000a to 3-methyl-4-nitrophenol, which was further metabolized to nitrite and methylhydroquinone. The addition of other carbon source

Zhonghui Zhang; Qing Hong; Jianghong Xu; Xiaozhou Zhang; Shunpeng Li

2006-01-01

193

Enhanced degradation of naphthalene by immobilization of Pseudomonas sp. strain NGK1 in polyurethane foam  

Microsoft Academic Search

A Pseudomonas sp. strain NGK1 (NCIM 5120) capable of degrading naphthalene was immobilized in polyurethane foam. The naphthalene-degrading activity of the freely suspended cells was compared with that of immobilized cells in batches in shaken culture and in a continuous culture system in a packed-bed reactor. Increasing concentrations of naphthalene were better tolerated and more quickly degraded by immobilized cell

S. Manohar; C. K. Kim; T. B. Karegoudar

2001-01-01

194

Molecular characterization of the cyanophycin synthetase from Synechocystis sp. strain PCC6308  

Microsoft Academic Search

A 3878-bp genomic region from the cyanobacterium Synechocystis sp. strain PCC6308, amplified by inverse PCR, harbored the structural genes cphA (2625 bp) and cphB (819 bp) encoding cyanophycin synthetase and cyanophycinase, respectively. Both primary structures exhibited a high degree of similarity to the corresponding translational products from other cyanobacteria. Five regions were localized in the cyanophycin synthetase consensus sequence by

Elsayed Aboulmagd; Fred Bernd Oppermann-Sanio; Alexander Steinbüchel

2000-01-01

195

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.

Gilbert, E S; Crowley, D E

1997-01-01

196

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.

2009-01-01

197

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.

Hage, Jacobus C.; Hartmans, Sybe

1999-01-01

198

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

199

Dynamic metabolic and transcriptional profiling of Rhodococcus sp. strain YYL during the degradation of tetrahydrofuran.  

PubMed

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 (1)H 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; Lu, Zhenmei; Ye, Yangfang

2014-05-01

200

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

201

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.

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

202

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.

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

2012-01-01

203

Circadian expression of the dnaK gene in the cyanobacterium Synechocystis sp. strain PCC 6803.  

PubMed Central

The expression of the dnaK gene in the cyanobacterium Synechocystis sp. strain PCC 6803 was continuously monitored as bioluminescence by an automated monitoring system, using the bacterial luciferase genes (luxAB) of Vibrio harveyi as a reporter of promoter activity. A dnaK-reporting bioluminescent Synechocystis strain was constructed by fusing a promoterless segment of the luxAB gene set downstream of the promoter region of the Synechocystis dnaK gene and introduction of this gene fusion into a BglII site downstream of the ndhB gene in the Synechocystis chromosome. Bioluminescence from this strain was continuously monitored and oscillated with a period of about 22 h for at least 5 days in continuous light. The phase of the rhythm was reset by the timing of the 12-h dark period administered prior to the continuous light. The period of the rhythm was temperature compensated between 25 and 35 degrees C. Thus, the bioluminescence rhythm satisfied the three criteria of circadian rhythms. Furthermore, the abundance of dnaK mRNA also oscillated with a period of about 1 day for at least 2 days in continuous light conditions, indicating circadian control of dnaK gene expression in Synechocystis sp. strain PCC 6803.

Aoki, S; Kondo, T; Ishiura, M

1995-01-01

204

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.

2011-01-01

205

Reduction of molybdate to molybdenum blue by Klebsiella sp. strain hkeem.  

PubMed

A novel molybdate-reducing bacterium, tentatively identified as Klebsiella sp. strain hkeem and based on partial 16s rDNA gene sequencing and phylogenetic analysis, has been isolated. Strain hkeem produced 3 times more molybdenum blue than Serratia sp. strain Dr.Y8; the most potent Mo-reducing bacterium isolated to date. Molybdate was optimally reduced to molybdenum blue using 4.5 mM phosphate, 80 mM molybdate and using 1% (w/v) fructose as a carbon source. Molybdate reduction was optimum at 30 °C and at pH 7.3. The molybdenum blue produced from cellular reduction exhibited absorption spectrum with a maximum peak at 865 nm and a shoulder at 700 nm. Inhibitors of electron transport system such as antimycin A, rotenone, sodium azide, and potassium cyanide did not inhibit the molybdenum-reducing enzyme. Mercury, silver, and copper at 1 ppm inhibited molybdenum blue formation in whole cells of strain hkeem. PMID:22052341

Lim, H K; Syed, M A; Shukor, M Y

2012-06-01

206

Dechlorination of lindane by the cyanobacterium Anabaena sp. strain PCC7120 depends on the function of the nir operon.  

PubMed Central

Nitrate is essential for lindane dechlorination by the cyanobacteria Anabaena sp. strain PCC7120 and Nostoc ellipsosporum, as it is for dechlorination of other organic compounds by heterotrophic microorganisms. Based on analyses of mutants and effects of environmental factors, we conclude that lindane dechlorination by Anabaena sp. requires a functional nir operon that encodes the enzymes for nitrate utilization.

Kuritz, T; Bocanera, L V; Rivera, N S

1997-01-01

207

Draft genome sequence of Salimicrobium sp. strain MJ3, isolated from Myulchi-Jeot, Korean fermented seafood.  

PubMed

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; Jeon, Che Ok

2012-12-01

208

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.

Lee, Se Hee; Jung, Ji Young

2012-01-01

209

Genome sequence of Pseudomonas sp. Strain S9, an extracellular arylsulfatase-producing bacterium isolated from Mangrove Soil.  

PubMed

Pseudomonas sp. strain S9 was originally isolated from mangrove soil in Xiamen, China. It is an aerobic bacterium which shows extracellular arylsulfatase activity. Here, we describe the 4.8-Mb draft genome sequence of Pseudomonas sp. S9, which exhibits novel cysteine-type sulfatases. PMID:21622746

Long, Mengxian; Ruan, Lingwei; Yu, Ziniu; Xu, Xun

2011-08-01

210

Circadian Rhythm of Nitrogenase Gene Expression in the Diazotrophic Filamentous Nonheterocystous Cyanobacterium Trichodesmium sp. Strain IMS 101  

Microsoft Academic Search

Recent studies suggested that the daily cycle of nitrogen fixation activity in the marine filamentous nonhet- erocystous cyanobacterium Trichodesmium sp. is controlled by a circadian rhythm. In this study, we evaluated the rhythm of nitrogen fixation in Trichodesmium sp. strain IMS 101 by using the three criteria for an endogenous rhythm. Nitrogenase transcript abundance oscillated with a period of approximately

YI-BU CHEN; BENNY DOMINIC; MARK T. MELLON; JONATHAN P. ZEHR

1998-01-01

211

Draft Genome Sequence of Pedobacter sp. Strain V48, Isolated from a Coastal Sand Dune in the Netherlands  

PubMed Central

Pedobacter sp. strain V48 participates in an interaction with Pseudomonas fluorescens which elicits interaction-induced phenotypes. We report the draft genome sequence of Pedobacter sp. V48, consisting of 6.46 Mbp. The sequence will contribute to improved understanding of the genus and facilitate genomic analysis of the model interspecies interaction with P. fluorescens.

Bitzer, Adam S.; Garbeva, Paolina

2014-01-01

212

Oxygen-Dependent Regulation of the Central Pathway for the Anaerobic Catabolism of Aromatic Compounds in Azoarcus sp. Strain CIB  

Microsoft Academic Search

The role of oxygen in the transcriptional regulation of the PN promoter that controls the bzd operon involved in the anaerobic catabolism of benzoate in the denitrifying Azoarcus sp. strain CIB has been investigated. In vivo experiments using PN::lacZ translational fusions, in both Azoarcus sp. strain CIB and Escherichia coli cells, have shown an oxygen-dependent repression effect on the transcription

G. Durante-Rodriguez; M. T. Zamarro; J. L. Garcia; E. Diaz; Manuel Carmona

2006-01-01

213

Extracellular Signal Molecule(s) Involved in the Carbon Starvation Response of Marine Vibrio sp. Strain S14  

Microsoft Academic Search

The role of exogenous metabolites as putative signal molecules mediating and\\/or regulating the carbon starvation adaptation program in Vibrio sp. strain S14 was investigated. Addition of the stationary-phase supernatant extract (SSE) of Vibrio sp. strain S14 to logarithmic-phase cells resulted in a significant number of carbon starvation-induced proteins being up-regulated. Halogenated furanones, putative antagonists of acylated homoserine lactones (AHLs), inhibited

SUJATHA SRINIVASAN; JORGEN OSTLING; TIMOTHY CHARLTON; ROCKY DE NYS; KATHY TAKAYAMA; STAFFAN KJELLEBERG

1998-01-01

214

Evaluation of insecticidal activity of a bacterial strain, Serratia sp. EML-SE1 against diamondback moth  

Microsoft Academic Search

To identify novel bioinsecticidal agents, a bacterial strain, Serratia sp. EML-SE1, was isolated from a dead larva of the lepidopteran diamondback moth (Plutella xylostella) collected from a cabbage field in Korea. In this study, the insecticidal activity of liquid cultures in Luria-Bertani broth\\u000a (LBB) and nutrient broth (NB) of a bacterial strain, Serratia sp. EML-SE1 against thirty 3rd and 4th

Hyung Uk Jeong; Hye Yeon Mun; Hyung Keun Oh; Seung Bum Kim; Kwang Yeol Yang; Iksoo Kim; Hyang Burm Lee

2010-01-01

215

Biodegradation of phenanthrene with biosurfactant production by a new strain of Brevibacillus sp.  

PubMed

In this work, a phenanthrene-degrading bacterial strain was isolated by enrichment method from hydrocarbon contaminated sludge samples and identified as Brevibacillus sp. PDM-3 based on morphological, biochemical, chemotaxonomic (FAMEs analysis) and molecular (16S rDNA sequencing) analysis. Growth parameters for efficient degradation of phenanthrene such as nutrient medium, pH, temperature, rpm and inoculum size were standardized and 93% of phenanthrene was degraded in 6 days as analysed by HPLC. The bacterial strain PDM-3 also has the ability to produce biosurfactant during phenanthrene degradation as detected by the surface tension measurements of the culture supernatant and the emulsification index (EI??). The biosurfactant was identified by its functional groups through FT-IR spectroscopy. Phenanthrene degradation and biosurfactant production are associated with each other and can be used in environmental biotechnology. Further, the strain has the ability to degrade other PAHs such as anthracene and fluorene by utilizing them as sole carbon and energy source. PMID:20627713

Reddy, M Srikanth; Naresh, B; Leela, T; Prashanthi, M; Madhusudhan, N Ch; Dhanasri, G; Devi, Prathibha

2010-10-01

216

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.

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

2009-01-01

217

Degradation of Chlorinated Dibenzofurans and Dibenzo-p-Dioxins by Sphingomonas sp. Strain RW1  

PubMed Central

The ability of the dibenzofuran- and dibenzo-p-dioxin-mineralizing bacterium Sphingomonas sp. strain RW1 (R.-M. Wittich, H. Wilkes, V. Sinnwell, W. Francke, and P. Fortnagel, Appl. Environ. Microbiol. 58:1005-1010, 1992) to oxidize chlorinated derivatives of dibenzofuran and dibenzo-p-dioxin was analyzed. Strain RW1 degraded several mono- and dichlorinated dibenzofurans and dibenzo-p-dioxins, but it did not degrade more highly chlorinated congeners. Most mono- and dichlorinated dibenzofurans and dibenzo-p-dioxins investigated in this study were degraded to the corresponding mono- and dichlorinated salicylates and catechols, respectively, together with salicylate and catechol. This indicates an initial dioxygenolytic attack on the substituted as well as on the nonsubstituted aromatic nucleus of most of the target compounds. Strain RW1 could not grow at the expense of monochlorinated dibenzo-p-dioxins and dibenzofurans as carbon sources, with the exception of 4-chlorodibenzofuran, which was stoichiometrically converted to 3-chlorosalicylate.

Wilkes, H.; Wittich, R.; Timmis, K. N.; Fortnagel, P.; Francke, W.

1996-01-01

218

Effects of modified Phycobilin biosynthesis in the Cyanobacterium Synechococcus sp. Strain PCC 7002.  

PubMed

The pathway for phycocyanobilin biosynthesis in Synechococcus sp. strain PCC 7002 comprises two enzymes: heme oxygenase and phycocyanobilin synthase (PcyA). The phycobilin content of cells can be modified by overexpressing genes encoding alternative enzymes for biliverdin reduction. Overexpression of the pebAB and HY2 genes, encoding alternative ferredoxin-dependent biliverdin reductases, caused unique effects due to the overproduction of phycoerythrobilin and phytochromobilin, respectively. Colonies overexpressing pebAB became reddish brown and visually resembled strains that naturally produce phycoerythrin. This was almost exclusively due to the replacement of phycocyanobilin by phycoerythrobilin on the phycocyanin ?-subunit. This phenotype was unstable, and such strains rapidly reverted to the wild-type appearance, presumably due to strong selective pressure to inactivate pebAB expression. Overproduction of phytochromobilin, synthesized by the Arabidopsis thaliana HY2 product, was tolerated much better. Cells overexpressing HY2 were only slightly less pigmented and blue-green than the wild type. Although the pcyA gene could not be inactivated in the wild type, pcyA was easily inactivated when cells expressed HY2. These results indicate that phytochromobilin can functionally substitute for phycocyanobilin in Synechococcus sp. strain PCC 7002. Although functional phycobilisomes were assembled in this strain, the overall phycobiliprotein content of cells was lower, the efficiency of energy transfer by these phycobilisomes was lower than for wild-type phycobilisomes, and the absorption cross-section of the cells was reduced relative to that of the wild type because of an increased spectral overlap of the modified phycobiliproteins with chlorophyll a. As a result, the strain producing phycobiliproteins carrying phytochromobilin grew much more slowly at low light intensity. PMID:21296968

Alvey, Richard M; Biswas, Avijit; Schluchter, Wendy M; Bryant, Donald A

2011-04-01

219

Plant-microbe association for rhizoremediation of chloronitroaromatic pollutants with Comamonas sp. strain CNB-1.  

PubMed

Comamonas sp. strain CNB-1, isolated from activated sludge and having a strong ability to degrade 4-chloronitrobenzene (4CNB), was applied for rhizoremediation of 4CNB-polluted soil through association with alfalfa. Confocal laser scanning microscopy revealed that strain CNB-1 successfully colonized alfalfa roots. Determination of strain CNB-1 populations by cultivation method and by quantitative competitive PCR technique targeting the chloronitrobenzene nitroreductase gene showed that the population of strain CNB-1 in the rhizosphere was about 10-100 times higher than that in the bulk soil. Gnotobiotic and outdoor experiments showed that pollutant 4CNB was completely removed within 1 or 2 days after 4CNB application into soil, and that its phytotoxicity to alfalfa was eliminated by inoculation of strain CNB-1. Results from PCR-denaturing gradient gel electrophoresis and analysis of 16S rRNA gene libraries revealed that the indigenous soil microbial community mainly consisted of alphaproteobacteria, betaproteobacteria, gammaproteobacteria, the CFB bacteria (Cytophaga-Flavabacterium-Bacteriodes), and Acidobacteria. This microbial community was not significantly influenced by inoculation of strain CNB-1. Thus, this study has developed a Comamonas-alfalfa system for rhizoremediation of 4CNB. PMID:17222144

Liu, Lei; Jiang, Cheng-Ying; Liu, Xing-Yu; Wu, Jian-Feng; Han, Ji-Gang; Liu, Shuang-Jiang

2007-02-01

220

Biodegradation of polycyclic aromatic hydrocarbons by a halotolerant bacterial strain Ochrobactrum sp. VA1.  

PubMed

Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous pollutants in the environment and are derived from both man-made and natural resources. The present study is focused on the degradation of PAHs by a halotolerant bacterial strain under saline conditions. The bacterial strain VA1 was isolated from a PAH-degrading consortium that was enriched from marine water samples that were collected from different sites at Chennai, India. In the present study, a clearing zone formed on PAH-amended mineral salt agar media confirmed the utilization of PAH by the bacterial strain VA1. The results show that the strain VA1 was able to degrade anthracene (88%), phenanthrene (98%), naphthalene (90%), fluorene (97%), pyrene (84%), benzo(k)fluoranthene (57%) and benzo(e)pyrene (50%) at a 30 g/L NaCl concentration. The present study reveals that the VA1 strain was able to degrade PAHs in petroleum wastewater under saline conditions. The promising PAH-degrading halotolerant bacterial strain, VA1, was identified as Ochrobactrum sp. using biochemical and molecular techniques. PMID:20934193

Arulazhagan, P; Vasudevan, N

2011-02-01

221

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

222

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.

Trautner, Christoph

2013-01-01

223

The pacL gene of Synechococcus sp. strain PCC 7942 encodes a Ca(2+)-transporting ATPase.  

PubMed Central

An ATP-dependent Ca2+ uptake activity was identified in plasma membrane vesicles prepared from Synechococcus sp. strain PCC 7942. This activity was insensitive to agents which collapse pH gradients and membrane potentials but sensitive to vanadate, indicating that the activity is catalyzed by a P-type Ca(2+)-ATPase. A gene was cloned from Synechococcus sp. strain PCC 7942 by using a degenerate oligonucleotide based on a sequence conserved among P-type ATPases. This gene (pacL) encodes a product similar in structure to eukaryotic Ca(2+)-ATPases. We have shown that pacL encodes a Ca(2+)-ATPase by demonstrating that a strain in which pacL is disrupted has no Ca(2+)-ATPase activity associated with its plasma membrane. In addition, Ca(2+)-ATPase activity was restored to the delta pacL strain by introducing pacL into a second site in the Synechococcus sp. strain PCC 7942 chromosome. Images

Berkelman, T.; Garret-Engele, P.; Hoffman, N. E.

1994-01-01

224

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

PubMed Central

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).

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

2011-01-01

225

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

226

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

227

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

PubMed Central

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.

Rajgarhia, V B; Strohl, W R

1997-01-01

228

Molecular Characterization and Substrate Specificity of Nitrobenzene Dioxygenase from Comamonas sp. Strain JS765  

PubMed Central

Comamonas sp. strain JS765 can grow with nitrobenzene as the sole source of carbon, nitrogen, and energy. We report here the sequence of the genes encoding nitrobenzene dioxygenase (NBDO), which catalyzes the first step in the degradation of nitrobenzene by strain JS765. The components of NBDO were designated ReductaseNBZ, FerredoxinNBZ, OxygenaseNBZ?, and OxygenaseNBZ?, with the gene designations nbzAa, nbzAb, nbzAc, and nbzAd, respectively. Sequence analysis showed that the components of NBDO have a high level of homology with the naphthalene family of Rieske nonheme iron oxygenases, in particular, 2-nitrotoluene dioxygenase from Pseudomonas sp. strain JS42. The enzyme oxidizes a wide range of substrates, and relative reaction rates with partially purified OxygenaseNBZ revealed a preference for 3-nitrotoluene, which was shown to be a growth substrate for JS765. NBDO is the first member of the naphthalene family of Rieske nonheme iron oxygenases reported to oxidize all of the isomers of mono- and dinitrotoluenes with the concomitant release of nitrite.

Lessner, Daniel J.; Johnson, Glenn R.; Parales, Rebecca E.; Spain, Jim C.; Gibson, David T.

2002-01-01

229

Production of S-(+)-ibuprofen from a nitrile compound by Acinetobacter sp. strain AK226.  

PubMed Central

S-(+)-2-(4'-Isobutylphenyl)propionic acid [S-(+)-ibuprofen] was produced from racemic 2-(4'-isobutylphenyl)propionitrile (Ibu-CN) by an isolated bacterial strain, Acinetobacter sp. strain AK226. Ammonium acetate, acetonitrile, or n-butyronitrile as a carbon source in the culture medium was effective for bacterial growth and induction of this activity. The optimum pH of the reaction was around 8.0. S-(+)-Ibuprofen formed from Ibu-CN by resting cells was present in a 95% enantiomeric excess. Acinetobacter sp. strain AK226 appeared to possess a nitrilase for Ibu-CN because 2-(4'-isobutylphenyl)propionamide was not detected in the reaction mixture and 2-(4'-isobutylphenyl)propionamide was not hydrolyzed to S-(+)-ibuprofen. Since S-(+)-ibuprofen was preferentially produced while the R enantiomer of Ibu-CN was left almost intact over the time course of the reaction, the putative nitrilase appeared to be highly specific for the S enantiomer of Ibu-CN.

Yamamoto, K; Ueno, Y; Otsubo, K; Kawakami, K; Komatsu, K

1990-01-01

230

Pseudomonas sp. strain 273, and aerobic {alpha},{omega}-dichloroalkane-degrading bacterium  

SciTech Connect

A gram-negative, aerobic bacterium was isolated from soil; this bacterium grew in 50% (vol/vol) suspensions of 1,10-dichlorodecane (1,10-DCD) as the sole source of carbon and energy. Phenotypic and small-subunit ribosomal RNA characterizations identified the organism, designated strain 273, as a member of the genus Pseudomonas. After induction with 1,10-DCD, Pseudomonas sp. strain 273 released stoichiometric amounts of chloride from C{sub 5} to C{sub 12} {alpha},{omega}-dichloroalkanes in the presence of oxygen. No dehalogenation occurred under anaerobic conditions. The best substrates for dehalogenation and growth were C{sub 9} to C{sub 12} chloroalkanes. The isolate also grew with nonhalogenated aliphatic compounds, and decane-grown cells dechlorinated 1,10-DCD without a lag phase. In addition, cells grown on decane dechlorinated 1,10-DCD in the presence of chloramphenicol, indicating that the 1,10-DCD-dechlorinating enzyme system was also induced by decane. Other known alkane-degrading Pseudomonas species did not grow with 1,10-DCD as a carbon source. Dechlorination of 1,10-DCD was demonstrated in cell extracts of Pseudomonas sp. strain 273. Cell-free activity was strictly oxygen dependent, and NADH stimulated dechlorination, whereas EDTA had an inhibitory effect.

Wischnak, C.; Mueller, R. [Technische Univ. Hamburg-Harburg (Germany). Arbeitsbereich Biotechnologie II; Loeffler, F.E. [Technische Univ. Hamburg-Harburg (Germany). Arbeitsbereich Biotechnologie II]|[Michigan State Univ., East Lansing, MI (United States). Center for Microbial Ecology; Li, J.; Urbance, J.W. [Michigan State Univ., East Lansing, MI (United States). Center for Microbial Ecology

1998-09-01

231

Novel Acetone Metabolism in a Propane-Utilizing Bacterium, Gordonia sp. Strain TY-5?  

PubMed Central

In the propane-utilizing bacterium Gordonia sp. strain TY-5, propane was shown to be oxidized to 2-propanol and then further oxidized to acetone. In this study, the subsequent metabolism of acetone was studied. Acetone-induced proteins were found in extracts of cells induced by acetone, and a gene cluster designated acmAB was cloned on the basis of the N-terminal amino acid sequences of acetone-induced proteins. The acmA and acmB genes encode a Baeyer-Villiger monooxygenase (BVMO) and esterase, respectively. The BVMO encoded by acmA was purified from acetone-induced cells of Gordonia sp. strain TY-5 and characterized. The BVMO exhibited NADPH-dependent oxidation activity for linear ketones (C3 to C10) and cyclic ketones (C4 to C8). Escherichia coli expressing the acmA gene oxidized acetone to methyl acetate, and E. coli expressing the acmB gene hydrolyzed methyl acetate. Northern blot analyses revealed that polycistronic transcription of the acmAB gene cluster was induced by propane, 2-propanol, and acetone. These results indicate that the acmAB gene products play an important role in the metabolism of acetone derived from propane oxidation and clarify the propane metabolism pathway of strain TY-5 (propane ? 2-propanol ? acetone ? methyl acetate ? acetic acid + methanol). This paper provides the first evidence for BVMO-dependent acetone metabolism.

Kotani, Tetsuya; Yurimoto, Hiroya; Kato, Nobuo; Sakai, Yasuyoshi

2007-01-01

232

Bacillus mesophilum sp. nov., strain IITR-54(T), a novel 4-chlorobiphenyl dechlorinating bacterium.  

PubMed

The taxonomic position of a Gram-positive, endospore-forming bacterium isolated from soil sample collected from an industrial site was analyzed by a polyphasic approach. The strain designated as IITR-54(T) matched most of the phenotypic and chemical characteristics of the genus Bacillus and represents a novel species. It was found to biodegrade 4-chlorobiphenyl through dechlorination and was isolated through enrichment procedure from an aged polychlorinated biphenyl-contaminated soil. Both resting cell assay and growth under aerobic liquid conditions using 4-chlorobiphenyl as sole source of carbon along with 0.01 % yeast extract, formation of chloride ions was measured. 16S rRNA (1,489 bases) nucleotide sequence of isolated strain was compared with those of closely related Bacillus type strains and confirmed that the strain belongs to the genus Bacillus. Strain IITR-54(T) differs from all other species of Bacillus by at least 2.1 % at the 16S rRNA level, and the moderately related species are Bacillus oceanisediminis (97.9 %) followed by Bacillus infantis (97.7 %), Bacillus firmus (97.4 %), Bacillus drentensis (97.3 %), Bacillus circulans (97.2 %), Bacillus soli (97.1 %), Bacillus horneckiae (97.1 %), Bacillus pocheonensis (97.1 %) and Bacillus bataviensis (97.1 %), respectively. The cell wall peptidoglycan contained meso-diaminopimelic acid and the major isoprenoid quinone was MK-7. Major fatty acids are iso-C15:0 (32.4 %) and anteiso-C15:0 (27.4 %). Predominant polar lipids are diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The results of physiological and biochemical tests allowed the genotypic and phenotypic distinctiveness of strain IITR-54(T) with its phylogenetic relatives and suggest that the strain IITR-54(T) should be recognized as a novel species, for which the name Bacillus mesophilum sp. nov. is proposed. The type strain is IITR-54(T) (= MTCC 11060(T) = JCM 19208(T)). PMID:24807729

Manickam, Natesan; Singh, Nitin Kumar; Bajaj, Abhay; Kumar, Rajendran Mathan; Kaur, Gurwinder; Kaur, Navjot; Bala, Monu; Kumar, Anand; Mayilraj, Shanmugam

2014-07-01

233

Engineering pyruvate decarboxylase-mediated ethanol production in the thermophilic host Geobacillus thermoglucosidasius.  

PubMed

This study reports the expression, purification, and kinetic characterization of a pyruvate decarboxylase (PDC) from Gluconobacter oxydans. Kinetic analyses showed the enzyme to have high affinity for pyruvate (120 ?M at pH 5), high catalytic efficiency (4.75?×?10(5) M(-1) s(-1) at pH 5), a pHopt of approximately 4.5 and an in vitro temperature optimum at approximately 55 °C. Due to in vitro thermostablity (approximately 40 % enzyme activity retained after 30 min at 65 °C), this PDC was considered to be a suitable candidate for heterologous expression in the thermophile Geobacillus thermoglucosidasius for ethanol production. Initial studies using a variety of methods failed to detect activity at any growth temperature (45-55 °C). However, the application of codon harmonization (i.e., mimicry of the heterogeneous host's transcription and translational rhythm) yielded a protein that was fully functional in the thermophilic strain at 45 °C (as determined by enzyme activity, Western blot, mRNA detection, and ethanol productivity). Here, we describe the first successful expression of PDC in a true thermophile. Yields as high as 0.35?±?0.04 g/g ethanol per gram of glucose consumed were detected, highly competitive to those reported in ethanologenic thermophilic mutants. Although activities could not be detected at temperatures approaching the growth optimum for the strain, this study highlights the possibility that previously unsuccessful expression of pdcs in Geobacillus spp. may be the result of ineffective transcription/translation coupling. PMID:24276622

Van Zyl, L J; Taylor, M P; Eley, K; Tuffin, M; Cowan, D A

2014-02-01

234

Chemoheterotrophic Growth of the Cyanobacterium Anabaena sp. Strain PCC 7120 Dependent on a Functional Cytochrome c Oxidase  

PubMed Central

Anabaena sp. strain PCC 7120 is a filamentous cyanobacterium commonly used as a model organism for studying cyanobacterial cell differentiation and nitrogen fixation. For many decades, this cyanobacterium was considered an obligate photo-lithoautotroph. We now discovered that this strain is also capable of mixotrophic, photo-organoheterotrophic, and chemo-organoheterotrophic growth if high concentrations of fructose (at least 50 mM and up to 200 mM) are supplied. Glucose, a substrate used by some facultatively organoheterotrophic cyanobacteria, is not effective in Anabaena sp. PCC 7120. The gtr gene from Synechocystis sp. PCC 6803 encoding a glucose carrier was introduced into Anabaena sp. PCC 7120. Surprisingly, the new strain containing the gtr gene did not grow on glucose but was very sensitive to glucose, with a 5 mM concentration being lethal, whereas the wild-type strain tolerated 200 mM glucose. The Anabaena sp. PCC 7120 strain containing gtr can grow mixotrophically and photo-organoheterotrophically, but not chemo-organoheterotrophically with fructose. Anabaena sp. PCC 7120 contains five respiratory chains ending in five different respiratory terminal oxidases. One of these enzymes is a mitochondrial-type cytochrome c oxidase. As in almost all cyanobacteria, this enzyme is encoded by three adjacent genes called coxBAC1. When this locus was disrupted, the cells lost the capability for chemo-organoheterotrophic growth.

Stebegg, Ronald; Wurzinger, Bernhard; Mikulic, Markus

2012-01-01

235

Lipase modulator protein (LimL) of Pseudomonas sp. strain 109.  

PubMed Central

Plasmids containing a Pseudomonas sp. strain 109 extracellular lipase gene (lipL) lacking NH2-terminal sequence and a lipase modulator gene (limL) lacking the NH2-terminal hydrophobic region were constructed and expressed independently in Escherichia coli by using the T7 promoter expression vector system. Recombinant LipL (rLipL) was produced as inclusion bodies, whereas recombinant LimL (rLimL) was present as a soluble protein. During in vitro renaturation of the purified rLipL inclusion bodies after they had been dissolved in 8 M urea, addition of rLimL was essential to solubilize and modulate rLipL. The solubility and activity of rLipL were influenced by the rLimL/rLipL molar ratio; the highest level of solubility was obtained at an rLimL/rLipL ratio of 4:5, whereas the highest activity level was obtained at an rLimL/rLipL ratio of 4:1. After renaturation, rLipL and rLimL were coprecipitated with anti-rLipL antibody, indicating the formation of an rLipL-rLimL complex. Activity of the native lipase purified from Pseudomonas sp. strain 109 was also inhibited by rLimL. By Western blotting (immunoblotting) with anti-rLimL antibody, native LimL was detected in Pseudomonas cells solubilized by sarcosyl treatment. LimL was purified from Pseudomonas sp. strain 109, and the NH2-terminal amino acid sequence was determined to be NH2-Leu-Glu-Pro-Ser-Pro-Ala-Pro-. We propose that to prevent membrane degradation, LimL weakens lipase activity inside the cell, especially in the periplasm, in addition to modulating lipase folding.

Ihara, F; Okamoto, I; Akao, K; Nihira, T; Yamada, Y

1995-01-01

236

Protein tyrosine phosphorylation in the cyanobacterium Anabaena sp. strain PCC 7120.  

PubMed

Components of a protein tyrosine phosphorylation/dephosphorylation network were identified in the cyanobacterium Anabaena sp. strain PCC 7120. Three phosphotyrosine (P-Tyr) proteins of 27, 36, and 52 kDa were identified through their conspicuous immunoreactions with RC20H monoclonal antibodies specific for P-Tyr. These immunoreactions were outcompeted completely by free P-Tyr (5 mM) but not by phosphoserine or phosphothreonine. The P-Tyr content of the three major P-Tyr proteins and several minor proteins increased with their time of incubation in the presence of Mg-ATP and the protein phosphatase inhibitors sodium orthovanadate and sodium fluoride. Incubation of the same extracts with [gamma-32P]ATP but not [alpha-32P]ATP led to the phosphorylation of five polypeptides with molecular masses of 20, 27, 52, 85, and 100 kDa. Human placental protein tyrosine phosphatase 1B, with absolute specificity for P-Tyr, liberated significant quantities of 32Pi from four of the polypeptides, confirming that a portion of the protein-bound phosphate was present as 32P-Tyr. Alkaline phosphatase and the dual-specificity protein phosphatase IphP from the cyanobacterium Nostoc commune UTEX 584 also dephosphorylated these proteins and did so with greater apparent efficiency. Two of the polypeptides were partially purified, and phosphoamino analysis identified 32P-Tyr, [32P]phosphoserine, and [32P]phosphothreonine. Anabaena sp. strain PCC 7120 cell extracts contained a protein tyrosine phosphatase activity that was abolished in the presence of sodium orthovanadate and inhibited significantly by the sulfhydryl-modifying agents p-hydroxymercuriphenylsulfonic acid and p-hydroxymercuribenzoate as well as by heparin. In Anabaena sp. strain PCC 7120 the presence and/or phosphorylation status of P-Tyr proteins was influenced by incident photon flux density. PMID:9079918

McCartney, B; Howell, L D; Kennelly, P J; Potts, M

1997-04-01

237

Protein tyrosine phosphorylation in the cyanobacterium Anabaena sp. strain PCC 7120.  

PubMed Central

Components of a protein tyrosine phosphorylation/dephosphorylation network were identified in the cyanobacterium Anabaena sp. strain PCC 7120. Three phosphotyrosine (P-Tyr) proteins of 27, 36, and 52 kDa were identified through their conspicuous immunoreactions with RC20H monoclonal antibodies specific for P-Tyr. These immunoreactions were outcompeted completely by free P-Tyr (5 mM) but not by phosphoserine or phosphothreonine. The P-Tyr content of the three major P-Tyr proteins and several minor proteins increased with their time of incubation in the presence of Mg-ATP and the protein phosphatase inhibitors sodium orthovanadate and sodium fluoride. Incubation of the same extracts with [gamma-32P]ATP but not [alpha-32P]ATP led to the phosphorylation of five polypeptides with molecular masses of 20, 27, 52, 85, and 100 kDa. Human placental protein tyrosine phosphatase 1B, with absolute specificity for P-Tyr, liberated significant quantities of 32Pi from four of the polypeptides, confirming that a portion of the protein-bound phosphate was present as 32P-Tyr. Alkaline phosphatase and the dual-specificity protein phosphatase IphP from the cyanobacterium Nostoc commune UTEX 584 also dephosphorylated these proteins and did so with greater apparent efficiency. Two of the polypeptides were partially purified, and phosphoamino analysis identified 32P-Tyr, [32P]phosphoserine, and [32P]phosphothreonine. Anabaena sp. strain PCC 7120 cell extracts contained a protein tyrosine phosphatase activity that was abolished in the presence of sodium orthovanadate and inhibited significantly by the sulfhydryl-modifying agents p-hydroxymercuriphenylsulfonic acid and p-hydroxymercuribenzoate as well as by heparin. In Anabaena sp. strain PCC 7120 the presence and/or phosphorylation status of P-Tyr proteins was influenced by incident photon flux density.

McCartney, B; Howell, L D; Kennelly, P J; Potts, M

1997-01-01

238

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.

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

2010-01-01

239

Metabolic engineering of Synechocystis sp. strain PCC 6803 for isobutanol production.  

PubMed

Global warming and decreasing fossil fuel reserves have prompted great interest in the synthesis of advanced biofuels from renewable resources. In an effort to address these concerns, we performed metabolic engineering of the cyanobacterium Synechocystis sp. strain PCC 6803 to develop a strain that can synthesize isobutanol under both autotrophic and mixotrophic conditions. With the expression of two heterologous genes from the Ehrlich pathway, the engineered strain can accumulate 90 mg/liter of isobutanol from 50 mM bicarbonate in a gas-tight shaking flask. The strain does not require any inducer (i.e., isopropyl ?-d-1-thiogalactopyranoside [IPTG]) or antibiotics to maintain its isobutanol production. In the presence of glucose, isobutanol synthesis is only moderately promoted (titer = 114 mg/liter). Based on isotopomer analysis, we found that, compared to the wild-type strain, the mutant significantly reduced its glucose utilization and mainly employed autotrophic metabolism for biomass growth and isobutanol production. Since isobutanol is toxic to the cells and may also be degraded photochemically by hydroxyl radicals during the cultivation process, we employed in situ removal of the isobutanol using oleyl alcohol as a solvent trap. This resulted in a final net concentration of 298 mg/liter of isobutanol under mixotrophic culture conditions. PMID:23183979

Varman, Arul M; Xiao, Yi; Pakrasi, Himadri B; Tang, Yinjie J

2013-02-01

240

[Identification and degradation capability of three pyrene-degrading Gordonia sp. strains].  

PubMed

Three pyrene-degrading bacterial strains named D44, D82S and D82Q were isolated from PAHs-contaminated soil in Shenfu Irrigation Area of Shenyang, Northeast China. The strains were identified as Gordonia sp., based on the morphological observation, physiological and biochemical identification, and phylogenetical analysis of 16S rDNA sequences. For all the three stains, their optimal pH was 7, and their growth was obviously inhibited when the pH was lower than 5 or higher than 9. The three strains were capable of utilizing pyrene, benzo[a] pyrene, anthracene, naphthalene, phenanthrene, and fluoranthene as the sole source of carbon and energy. After seven days incubation, the three strains could degrade more than 65% of pyrene with an initial concentration 100 mg x L(-1), and the D44, D82S, and D82Q could degrade 79.6%, 91.3%, and 62.8% of benzo[a] pyrene with an initial concentration 50 mg x L(-1), respectively. PCR amplification indicated that the strains D82Q and D82S possessed alkane monooxygenase gene alkB. PMID:22007465

Hu, Feng-chai; Li, Xin-yu; Su, Zhen-cheng; Wang, Xiu-juan; Zhang, Hui-wen; Sun, Jun-de

2011-07-01

241

Biodegradation of fomesafen by strain Lysinibacillus sp. ZB-1 isolated from soil.  

PubMed

The fomesafen degrading bacterium ZB-1 was isolated from contaminated agricultural soil, and identified as Lysinibacillus sp. based on the comparative analysis of 16S rRNA gene. The strain could utilize fomesafen as the sole carbon source for growth, and the total degradation rate was 81.32% after 7 d of inoculation in mineral salts medium. Strain ZB-1 could also degrade other diphenyl ethers including lactofen and fluoroglycofen. The optimum temperature for fomesafen degradation by strain ZB-1 was 30 degrees C. The effect of fomesafen concentration on degradation was also examined. Cell-free extract of strain ZB-1 was able to degrade fomesafen and other diphenyl ethers. Metabolism of fomesafen was accompanied by a transient accumulation of a metabolite identified as [N-[4-{4-(trifluoromethyl)phenoxy}-2-methanamidephenyl]acetamide] using liquid chromatography-mass spectrometry, thus indicating a metabolic pathway involving reduction, acetylation of nitro groups and dechlorination. The inoculation of strain ZB-1 to soil treated with fomesafen resulted in a higher degradation rate than in noninoculated soil regardless of the soil sterilized or nonsterilized. PMID:19846192

Liang, Bo; Lu, Peng; Li, Huihui; Li, Rong; Li, Shunpeng; Huang, Xing

2009-12-01

242

Whole-Genome Sequence of Burkholderia sp. Strain RPE67, a Bacterial Gut Symbiont of the Bean Bug Riptortus pedestris.  

PubMed

Burkholderia sp. strain RPE67 is a bacterial symbiont isolated from a field-collected bean bug, Riptortus pedestris. To understand the genetic basis of the insect-microbe symbiosis, we performed whole-genome sequencing of the Burkholderia strain, revealing an 8.69-Mb genome consisting of three chromosomes and three plasmids. PMID:24948758

Takeshita, Kazutaka; Shibata, Tomoko F; Nikoh, Naruo; Nishiyama, Tomoaki; Hasebe, Mitsuyasu; Fukatsu, Takema; Shigenobu, Shuji; Kikuchi, Yoshitomo

2014-01-01

243

Genome Sequence of Methylobacterium sp. Strain GXF4, a Xylem-Associated Bacterium Isolated from Vitis vinifera L. Grapevine  

PubMed Central

Methylobacterium sp. strain GXF4 is an isolate from grapevine. Here we present the sequence, assembly, and annotation of its genome, which may shed light on its role as a grapevine xylem inhabitant. To our knowledge, this is the first genome announcement of a plant xylem-associated strain of the genus Methylobacterium.

Gan, Han Ming; Chew, Teong Han; Hudson, Andre O.

2012-01-01

244

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

245

Whole-Genome Sequence of Fish-Pathogenic Mycobacterium sp. Strain 012931, Isolated from Yellowtail (Seriola quinqueradiata)  

PubMed Central

The genus Mycobacterium comprises a large number of well-characterized species, several of which are human and animal pathogens. Here, we report the whole-genome sequence of Mycobacterium sp. strain 012931, a fish pathogen responsible for huge losses in aquaculture farms in Japan. The strain was isolated from a marine fish, yellowtail (Seriola quinqueradiata).

Kurokawa, Satoru; Kabayama, Jun; Nho, Seong Won; Hwang, Seong Don; Hikima, Jun-ichi; Jung, Tae Sung; Kondo, Hidehiro; Hirono, Ikuo; Takeyama, Haruko

2013-01-01

246

Plant growth-promoting bacterium Pseudomonas sp. strain GRP 3 influences iron acquisition in mung bean ( Vigna radiata L. Wilzeck)  

Microsoft Academic Search

Siderophores produced by Pseudomonas sp. may be used by the bacteria (homologously) or in effecting plant nutrition (heterologously). The problem of iron non-availability particularly in calcareous soils may be overcome by incorporation of siderophore producing strains of fluorescent psuedomonads (FLPs). Siderophore producing bacterium Pseudomonas strain GRP3 was used in a pot experiment to assess the role of microbial siderophores in

A Sharma; B. N Johri; B. R Glick

2003-01-01

247

Complete Genome Sequence of Hyperthermophilic Pyrococcus sp. Strain NA2, Isolated from a Deep-Sea Hydrothermal Vent Area ?  

PubMed Central

Pyrococcus sp. strain NA2, isolated from a deep-sea hydrothermal vent sample, is a novel marine hyperthermophilic archaeon that grows optimally at 93°C. The complete genome sequence of the strain contains all the genes for the tricarboxylic acid cycle except for succinate dehydrogenase/fumarate reductase, but the genome does not encode proteins involved in polysaccharide utilization.

Lee, Hyun Sook; Bae, Seung Seob; Kim, Min-Sik; Kwon, Kae Kyoung; Kang, Sung Gyun; Lee, Jung-Hyun

2011-01-01

248

Draft Genome Sequence of the Actinomycete Rhodococcus sp. Strain AW25M09, Isolated from the Hadsel Fjord, Northern Norway  

PubMed Central

The cold-adapted Rhodococcus sp. strain AW25M09 was isolated from an Atlantic hagfish caught off the shore of northern Norway as part of an ongoing bioprospecting project that aims to identify novel bacteria with biotechnological potential. Here, we present the 5.8-Mb draft genome sequence, together with details regarding the origin of the strain and its sequence assembly.

Hjerde, Erik; Pierechod, Marcin M.; Williamson, Adele K.; Bjerga, Gro E. K.; Willassen, Nils P.; Smalas, Arne O.

2013-01-01

249

Pathways in the Degradation of Hydrolyzed Alcohols of Butyl Benzyl Phthalate in Metabolically Diverse Gordonia sp.Strain MTCC 4818  

Microsoft Academic Search

In the present study, the metabolic pathways involved in the degradation of benzyl alcohol and 1-butanol, the hydrolyzed products of butyl benzyl phthalate, were investigated by the Gordonia sp. strain MTCC 4818. The strain can utilize both benzyl alcohol and 1-butanol individually as sole carbon sources, where benzyl alcohol was found to be metabolized via benzaldehyde, benzoic acid and catechol,

Subhankar Chatterjee; Somnath Mallick; Tapan K. Dutta

2005-01-01

250

Whole-Genome Sequence of Burkholderia sp. Strain RPE67, a Bacterial Gut Symbiont of the Bean Bug Riptortus pedestris  

PubMed Central

Burkholderia sp. strain RPE67 is a bacterial symbiont isolated from a field-collected bean bug, Riptortus pedestris. To understand the genetic basis of the insect-microbe symbiosis, we performed whole-genome sequencing of the Burkholderia strain, revealing an 8.69-Mb genome consisting of three chromosomes and three plasmids.

Takeshita, Kazutaka; Shibata, Tomoko F.; Nikoh, Naruo; Nishiyama, Tomoaki; Hasebe, Mitsuyasu; Fukatsu, Takema; Shigenobu, Shuji

2014-01-01

251

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.

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

2014-01-01

252

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.

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

2014-01-01

253

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

PubMed

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; Dong, Qunfeng

2014-01-01

254

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.

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

2014-01-01

255

Complete Genome Sequence of Methylocystis sp. Strain SC2, an Aerobic Methanotroph with High-Affinity Methane Oxidation Potential  

PubMed Central

Methylocystis sp. strain SC2 is an aerobic type II methanotroph isolated from a highly polluted aquifer in Germany. A specific trait of the SC2 strain is the expression of two isozymes of particulate methane monooxygenase with different methane oxidation kinetics. Here we report the complete genome sequence of this methanotroph that contains not only a circular chromosome but also two large plasmids.

Dam, Bomba; Dam, Somasri; Kube, Michael; Reinhardt, Richard

2012-01-01

256

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

PubMed

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; Manna, Sanjib K

2014-01-01

257

Genome Sequence of the ethene- and vinyl chloride-oxidizing actinomycete Nocardioides sp. strain JS614.  

PubMed

Nocardioides sp. strain JS614 grows on ethene and vinyl chloride (VC) as sole carbon and energy sources and is of interest for bioremediation and biocatalysis. Sequencing of the complete genome of JS614 provides insight into the genetic basis of alkene oxidation, supports ongoing research into the physiology and biochemistry of growth on ethene and VC, and provides biomarkers to facilitate detection of VC/ethene oxidizers in the environment. This is the first genome sequence from the genus Nocardioides and the first genome of a VC/ethene-oxidizing bacterium. PMID:21551312

Coleman, Nicholas V; Wilson, Neil L; Barry, Kerrie; Brettin, Thomas S; Bruce, David C; Copeland, Alex; Dalin, Eileen; Detter, John C; Del Rio, Tijana Glavina; Goodwin, Lynne A; Hammon, Nancy M; Han, Shunsheng; Hauser, Loren J; Israni, Sanjay; Kim, Edwin; Kyrpides, Nikolaos; Land, Miriam L; Lapidus, Alla; Larimer, Frank W; Lucas, Susan; Pitluck, Sam; Richardson, Paul; Schmutz, Jeremy; Tapia, Roxanne; Thompson, Sue; Tice, Hope N; Spain, Jim C; Gossett, James G; Mattes, Timothy E

2011-07-01

258

Degradation of toxaphene by Bjerkandera sp. strain BOL13 using waste biomass as a cosubstrate.  

PubMed

The white-rot fungus Bjerkandera sp. strain BOL13 was capable of degrading toxaphene when supplied with wood chips, wheat husk or cane molasses as cosubstrates in batch culture experiments. Approximately 85% of toxaphene was removed when wheat husk was the main substrate. The production of lignin peroxidase was only stimulated when wheat husk was present in the liquid medium. Although xylanase was always detected, wheat husk supported the highest xylanase production. A negligible amount of beta-glucosidase and cellulase were found in the batch culture medium. To the best of our knowledge, this is the first reported case of toxaphene degradation by white-rot fungi. PMID:16283301

Lacayo Romero, Martha; Terrazas, Enrique; van Bavel, Bert; Mattiasson, Bo

2006-07-01

259

Genome Sequence of the Ethene- and Vinyl Chloride-Oxidizing Actinomycete Nocardioides sp Strain JS614  

SciTech Connect

Nocardioides sp. strain JS614 grows on ethene and vinyl chloride (VC) as sole carbon and energy sources and is of interest for bioremediation and biocatalysis. Sequencing of the complete genome of JS614 provides insight into the genetic basis of alkene oxidation, supports ongoing research into the physiology and biochemistry of growth on ethene and VC, and provides biomarkers to facilitate detection of VC/ethene oxidizers in the environment. This is the first genome sequence from the genus Nocardioides and the first genome of a VC/ethene-oxidizing bacterium.

Coleman, Nicholas V [University of Sydney, Australia; Wilson, Neil L [University of Sydney, Australia; Barry, Kerrie [U.S. Department of Energy, Joint Genome Institute; Bruce, David [Los Alamos National Laboratory (LANL); Copeland, A [U.S. Department of Energy, Joint Genome Institute; Dalin, Eileen [U.S. Department of Energy, Joint Genome Institute; Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Glavina Del Rio, Tijana [U.S. Department of Energy, Joint Genome Institute; Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Hammon, Nancy [U.S. Department of Energy, Joint Genome Institute; Han, Shunsheng [Los Alamos National Laboratory (LANL); Hauser, Loren John [ORNL; Israni, Sanjay [U.S. Department of Energy, Joint Genome Institute; Kim, Edwin [U.S. Department of Energy, Joint Genome Institute; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute; Land, Miriam L [ORNL; Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute; Larimer, Frank W [ORNL; Lucas, Susan [U.S. Department of Energy, Joint Genome Institute; Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Richardson, Paul [U.S. Department of Energy, Joint Genome Institute; Schmutz, Jeremy [Stanford University; Tapia, Roxanne [Los Alamos National Laboratory (LANL); Thompson, Sue [Los Alamos National Laboratory (LANL); Tice, Hope [U.S. Department of Energy, Joint Genome Institute; Spain, Jim C [Georgia Institute of Technology; Gossett, James G [Cornell University; Mattes, Timothy E [University of Iowa

2011-01-01

260

Antimicrobial evaluation of fungal extracts produced by endophytic strains of Phomopsis sp.  

PubMed

Crude extract of cultures of 13 fungal strains identified as Phomopsis sp. and isolated as endophytes from the leaves of Aspidosperma tomentosum and twigs of Spondias mombin were examined for their antibacterial and antifungal activities. The screening was conducted using the bioautographic TLC agar-overlay technique against bacteria (E. coli, P. aeruginosa, S. aureus), yeast (C. albicans, S. cerevisiae), and readily adapted for use with filamentous fungi (A. niger, F. oxysporum). Three of the 13 extracts effectively inhibited the growth of all test-organisms, indicating that they may represent a potential for pharmaceutical and/or agricultural applications and are worthy of further study. PMID:15069675

Corrado, Marcia; Rodrigues, Katia F

2004-01-01

261

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

PubMed

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

2011-10-15

262

Genome Sequence of the Ethene- and Vinyl Chloride-Oxidizing Actinomycete Nocardioides sp. Strain JS614?  

PubMed Central

Nocardioides sp. strain JS614 grows on ethene and vinyl chloride (VC) as sole carbon and energy sources and is of interest for bioremediation and biocatalysis. Sequencing of the complete genome of JS614 provides insight into the genetic basis of alkene oxidation, supports ongoing research into the physiology and biochemistry of growth on ethene and VC, and provides biomarkers to facilitate detection of VC/ethene oxidizers in the environment. This is the first genome sequence from the genus Nocardioides and the first genome of a VC/ethene-oxidizing bacterium.

Coleman, Nicholas V.; Wilson, Neil L.; Barry, Kerrie; Brettin, Thomas S.; Bruce, David C.; Copeland, Alex; Dalin, Eileen; Detter, John C.; del Rio, Tijana Glavina; Goodwin, Lynne A.; Hammon, Nancy M.; Han, Shunsheng; Hauser, Loren J.; Israni, Sanjay; Kim, Edwin; Kyrpides, Nikolaos; Land, Miriam L.; Lapidus, Alla; Larimer, Frank W.; Lucas, Susan; Pitluck, Sam; Richardson, Paul; Schmutz, Jeremy; Tapia, Roxanne; Thompson, Sue; Tice, Hope N.; Spain, Jim C.; Gossett, James G.; Mattes, Timothy E.

2011-01-01

263

Substrate Preferences in Biodesulfurization of Diesel Range Fuels by Rhodococcus sp. Strain ECRD-1  

PubMed Central

The range of sulfur compounds in fuel oil and the substrate range and preference of the biocatalytic system determine the maximum extent to which sulfur can be removed by biodesulfurization. We show that the biodesulfurization apparatus in Rhodococcus sp. strain ECRD-1 is able to attack all isomers of dibenzothiophene including those with at least four pendant carbons, with a slight preference for those substituted in the ?-position. With somewhat less avidity, this apparatus is also able to attack substituted benzothiophenes with between two and seven pendant carbons. Some compounds containing sulfidic sulfur are also susceptible to desulfurization, although we have not yet been able to determine their molecular identities.

Prince, Roger C.; Grossman, Matthew J.

2003-01-01

264

Anabaena sp. Strain PCC 7120 hetY Gene Influences Heterocyst Development  

PubMed Central

The filamentous cyanobacterium Anabaena (Nostoc) sp. strain PCC 7120 responds to starvation for fixed nitrogen by producing a semiregular pattern of nitrogen-fixing cells called heterocysts. Overexpression of the hetY gene partially suppressed heterocyst formation, resulting in an abnormal heterocyst pattern. Inactivation of hetY increased the time required for heterocyst maturation and caused defects in heterocyst morphology. The 489-bp hetY gene (alr2300), which is adjacent to patS (asl2301), encodes a protein that belongs to a conserved family of bacterial hypothetical proteins that contain an ATP-binding motif.

Yoon, Ho-Sung; Lee, Martin H.; Xiong, Jin; Golden, James W.

2003-01-01

265

Complete Genomic Sequence of the Filamentous Nitrogen-fixing Cyanobacterium Anabaena sp. Strain PCC 7120  

Microsoft Academic Search

The nucleotide sequence of the entire genome of a filamentous cyanobacterium, Anabaena sp. strain PCC 7120, was determined. The genome of Anabaena consisted of a single chromosome (6,413,771 bp) and six plasmids, designated pCC7120? (408,101 bp), pCC7120? (186,614 bp), pCC7120? (101,965 bp), pCC7120? (55,414 bp), pCC7120? (40,340 bp), and pCC7120? (5,584 bp). The chromosome bears 5368 po- tential protein-encoding genes,

Takakazu Kaneko; Yasukazu Nakamura; C. Peter Wolk; Tanya Kuritz; Shigemi Sasamoto; Akiko Watanabe; Mayumi Iriguchi; Atsuko Ishikawa; Kumiko Kawashima; Takaharu Kimura; Yoshie Kishida; Mitsuyo Kohara; Midori Matsumoto; Ai Matsuno; Akiko Muraki; Naomi Nakazaki; Sayaka Shimpo; Masako Sugimoto; Masaki Takazawa; Manabu Yamada; Miho Yasuda; Satoshi Tabata

2001-01-01

266

Reclassification of strain CCM 132, previously classified as Kocuria varians, as Kocuria carniphila sp. nov.  

PubMed

A Gram-positive actinobacterium, previously classified as Kocuria varians, was subjected to a polyphasic taxonomic study. The bacterium showed the peptidoglycan type Lys-Ala3 (variation A3alpha), MK-7(H2) was the major menaquinone and anteiso-C(15 : 0) and anteiso-C(17 : 0) were the major fatty acids. On the basis of the phylogenetic and phenotypic characteristics of the actinobacterium, a novel species, Kocuria carniphila sp. nov. (type strain, CCM 132T=DSM 16004T), is proposed. PMID:15653866

Tvrzová, Ludmila; Schumann, Peter; Sedlácek, Ivo; Pácová, Zdena; Spröer, Cathrin; Verbarg, Susanne; Kroppenstedt, Reiner M

2005-01-01

267

Cloning and nucleotide sequence of the isoamylase gene from a strain of Pseudomonas sp.  

PubMed

A strain of Pseudomonas sp., SMP1, isolated from a soil sample collected in the Monterotondo area (Rome), secreted isoamylase activity into the culture medium. The enzyme was purified and optimal reaction and stability conditions were determined by varying pH and temperature. The chemico-physical properties of the enzyme were similar to those of the isoamylase purified in Japan more than 20 years ago from 'Pseudomonas amyloderamosa' strain SB15. A genomic library of SMP1 was prepared in Escherichia coli using pUC12 as vector. Two isoamylase-producing colonies were identified out of 6300 screened. The hybrid plasmids isolated from the two clones showed common restriction patterns. The chromosomal portion of one of these plasmids (pSM257) was completely sequenced. Comparison between the deduced amino acid sequence of the isoamylase and the published sequences of other amylolytic enzymes showed the presence of conserved domains. PMID:2778432

Tognoni, A; Carrera, P; Galli, G; Lucchese, G; Camerini, B; Grandi, G

1989-01-01

268

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

SciTech Connect

A mutant ( 5) of Synechocystis sp. strain PCC 6803 constructed by inactivating five inorganic carbon sequestration systems did not take up CO2 or HCO3– and was unable to grow in air with or without glucose. The 4 mutant in which BicA is the only active inorganic carbon sequestration system showed low activity of HCO3– uptake and grew under these conditions but more slowly than the wild-type strain. The 5 mutant required 1.7% CO2 to attain half the maximal growth rate. Electron transport activity of the mutants was strongly inhibited under high light intensities, with the 5 mutant more susceptible to high light than the 4 mutant. The results implicated the significance of carbon sequestration in dissipating excess light energy.

Xu, Min; Bernat, Gabor; Singh, Abhay K.; Mi, Hualing; Rogner, Matthias; Pakrasi, Himadri B.; Ogawa, Teruo

2008-09-10

269

Purification and properties of formate dehydrogenase from Moraxella sp. strain C-1.  

PubMed Central

NAD+-dependent formate dehydrogenase was screened in various bacterial strains. Facultative methanol-utilizing bacteria isolated from soil samples, acclimated to a medium containing methanol and formate at pH 9.5, were classified as members of the genus Moraxella. From a crude extract of Moraxella sp. strain C-1, formate dehydrogenase was purified to homogeneity, as judged by disc gel electrophoresis. The enzyme has an isoelectric point of 3.9 and a molecular weight of approximately 98,000. The enzyme is composed of two identical subunits with molecular weights of about 48,000. The apparent Km values for sodium formate and NAD+ were calculated to be 13 mM and 0.068 mM, respectively. Images

Asano, Y; Sekigawa, T; Inukai, H; Nakazawa, A

1988-01-01

270

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

271

Chemotaxis of Burkholderia sp. Strain SJ98 towards chloronitroaromatic compounds that it can metabolise  

PubMed Central

Background Burkholderia sp. strain SJ98 is known for its chemotaxis towards nitroaromatic compounds (NACs) that are either utilized as sole sources of carbon and energy or co-metabolized in the presence of alternative carbon sources. Here we test for the chemotaxis of this strain towards six chloro-nitroaromatic compounds (CNACs), namely 2-chloro-4-nitrophenol (2C4NP), 2-chloro-3-nitrophenol (2C3NP), 4-chloro-2-nitrophenol (4C2NP), 2-chloro-4-nitrobenzoate (2C4NB), 4-chloro-2-nitrobenzoate (4C2NB) and 5-chloro-2-nitrobenzoate (5C2NB), and examine its relationship to the degradation of such compounds. Results Strain SJ98 could mineralize 2C4NP, 4C2NB and 5C2NB, and co-metabolically transform 2C3NP and 2C4NB in the presence of an alternative carbon source, but was unable to transform 4C2NP under these conditions. Positive chemotaxis was only observed towards the five metabolically transformed CNACs. Moreover, the chemotaxis was induced by growth in the presence of the metabolisable CNAC. It was also competitively inhibited by the presence of nitroaromatic compounds (NACs) that it could metabolise but not by succinate or aspartate. Conclusions Burkholderia sp. strain SJ98 exhibits metabolic transformation of, and inducible chemotaxis towards CNACs. Its chemotactic responses towards these compounds are related to its previously demonstrated chemotaxis towards NACs that it can metabolise, but it is independently inducible from its chemotaxis towards succinate or aspartate.

2012-01-01

272

Characterization of Gordonia sp. strain F.5.25.8 capable of dibenzothiophene desulfurization and carbazole utilization  

Microsoft Academic Search

A dibenzothiophene (DBT)-degrading bacterial strain able to utilize carbazole as the only source of nitrogen was identified as Gordonia sp. F.5.25.8 due to its 16S rRNA gene sequence and phenotypic characteristics. Gas chromatography (GC) and GC–mass spectroscopy analyses showed that strain F.5.25.8 transformed DBT into 2-hydroxybiphenyl (2-HBP). This strain was also able to grow using various organic sulfur or nitrogen

S. C. C. Santos; D. S. Alviano; C. S. Alviano; M. Pádula; A. C. Leitão; O. B. Martins; C. M. S. Ribeiro; M. Y. M. Sassaki; C. P. S. Matta; J. Bevilaqua; G. V. Sebastián; L. Seldin

2006-01-01

273

Plasmid-borne catabolism of methyl parathion and p-nitrophenol in Pseudomonas sp. strain WBC3  

Microsoft Academic Search

Pseudomonas sp. strain WBC-3 utilises methyl parathion (MP) or p-nitrophenol (PNP) as the sole source of carbon, nitrogen, and energy. A plasmid designated pZWL0 of ?70kb in this strain was found to be responsible for MP and PNP degradation. This was based on the fact that the plasmid-cured strains showed PNP?MP? phenotype and the PNP+MP+ phenotype could be conjugally transferred.

Hong Liu; Jun-Jie Zhang; Su-Jun Wang; Xian-En Zhang; Ning-Yi Zhou

2005-01-01

274

High-level chromate resistance in Arthrobacter sp. strain FB24 requires previously uncharacterized accessory genes  

PubMed Central

Background The genome of Arthrobacter sp. strain FB24 contains a chromate resistance determinant (CRD), consisting of 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. To delineate the contribution of the CRD genes to the FB24 chromate [Cr(VI)] response, we evaluated the growth of mutant strains bearing regions of the CRD and transcript expression levels in response to Cr(VI) challenge. Results 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 possible regulatory roles. Conclusion Our findings indicate that chromate resistance in Arthrobacter sp. strain FB24 is due to chromate efflux through the ChrA transport protein. More importantly, new genes have been identified as having significant roles in chromate resistance. Collectively, the functional predictions of these additional genes suggest the involvement of a signal transduction system in the regulation of chromate efflux and warrants further study.

2009-01-01

275

Antibacterial activity of wild Xylaria sp. strain R005 (Ascomycetes) against multidrug-resistant Staphylococcus aureus and Pseudomonas aeruginosa.  

PubMed

There is a growing need for new and effective antibiotic agents due to the recent emergence of life-threatening, multidrug-resistant bacterial infections such as methicillin-resistant Staphylococcus aureus and Pseudomonas aeruginosa. In the present study, the antimicrobial potential of mushroom was investigated against multidrug-resistant bacterial strains. The mushroom was identified as Xylaria sp. strain R005 based on the morphological characteristics and confirmed by 18S ribosomal RNA sequence comparisons. The crude ethyl acetate extracts of culture filtrate and fruiting bodies of Xylaria sp. showed significant antibacterial activity against multidrug-resistant S. aureus strains (1-10) and P. aeruginosa strains (1-8). The minimum inhibitory concentration of the ethyl acetate extracts of culture filtrate and fruiting bodies ranged from 225 µg/mL to 625 µg/mL, and 120 µg/mL to 625 µg/mL, respectively, against clinical strains of S. aurues and P. aeruginosa. The synergistic action of extracts of Xylaria sp. with vancomycin and ciprofloxacin was observed against S. aureus strain 6 and P. aeruginosa strain 3, respectively. The fractional inhibitory concentration indices (FICIs) of culture filtrate extract with vancomycin and ciprofloxacin were 0.5 and 0.18, respectively. The FICI of fruiting body extract with vancomycin and ciprofloxacin were 0.5 and 0.375, respectively. These results clearly indicate that the metabolites of culture filtrate and fruiting bodies of Xylaria sp. are the potential source for production of new antimicrobial compounds. PMID:22339707

Ramesh, Veluchamy; Arivudainambi, U; Thalavaipandian, Annamalai; Karunakaran, Chandran; Rajendran, Ayyappan

2012-01-01

276

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.

2014-01-01

277

Molecular Characterization of the PceA Reductive Dehalogenase of Desulfitobacterium sp. Strain Y51  

PubMed Central

The tetrachloroethene (PCE) reductive dehalogenase (encoded by the pceA gene and designated PceA dehalogenase) of Desulfitobacterium sp. strain Y51 was purified and characterized. The expression of the enzyme was highly induced in the presence of PCE and trichloroethene (TCE). The purified enzyme catalyzed the reductive dehalogenation of PCE via TCE to cis-1,2-dichloroethene at a specific activity of 113.6 nmol?·?min?1?· mg of protein?1. The apparent Km values for PCE and TCE were 105.7 and 535.3 ?M, respectively. Chlorinated ethenes other than PCE and TCE were not dehalogenated. However, the enzyme exhibited dehalogenation activity for various chlorinated ethanes such as hexachloroethane, pentachloroethane, 1,1,1,2-tetrachloroethane, and 1,1,2,2-tetrachloroethane. The pceA gene of Desulfitobacterium sp. strain Y51 was identified in a 2.8-kb DNA fragment and used to express the protein in Escherichia coli for the preparation of antibodies. Immunoblot analyses located PceA in the periplasm of the cell.

Suyama, Akiko; Yamashita, Masaki; Yoshino, Sadazo; Furukawa, Kensuke

2002-01-01

278

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

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

1985-01-01

279

Physiological factors affecting carbon tetrachloride dehalogenation by the denitrifying bacterium Pseudomonas sp. strain KC.  

PubMed Central

Pseudomonas sp. strain KC was grown on a medium with a low content of transition metals in order to examine the conditions for carbon tetrachloride (CT) transformation. Several carbon sources, including acetate, glucose, glycerol, and glutamate, were able to support CT transformation. The chelators 2,2'-dipyridyl and 1,10-phenanthroline stimulated CT transformation in a rich medium that otherwise did not support this activity. Low (< 10 microM) additions of dissolved iron(II), iron(III), and cobalt(II), as well as an insoluble iron(III) compound, ferric oxyhydroxide, inhibited CT transformation. The addition of 50 microM iron to actively growing cultures resulted in delayed inhibition of CT transformation. CT transformation was seen in aerobic cultures of KC, but with reduced efficiency compared with denitrifying cultures. Inhibition of CT transformation by iron was also seen in aerobically grown cultures. Optimal conditions were used in searching for effective CT transformation activity among denitrifying enrichments grown from samples of aquifer material. No activity comparable to that of Pseudomonas sp. strain KC was found among 16 samples tested.

Lewis, T A; Crawford, R L

1993-01-01

280

Degradation of Phenanthrene and Anthracene by Cell Suspensions of Mycobacterium sp. Strain PYR-1  

PubMed Central

Cultures of Mycobacterium sp. strain PYR-1 were dosed with anthracene or phenanthrene and after 14 days of incubation had degraded 92 and 90% of the added anthracene and phenanthrene, respectively. The metabolites were extracted and identified by UV-visible light absorption, high-pressure liquid chromatography retention times, mass spectrometry, 1H and 13C nuclear magnetic resonance spectrometry, and comparison to authentic compounds and literature data. Neutral-pH ethyl acetate extracts from anthracene-incubated cells showed four metabolites, identified as cis-1,2-dihydroxy-1,2-dihydroanthracene, 6,7-benzocoumarin, 1-methoxy-2-hydroxyanthracene, and 9,10-anthraquinone. A novel anthracene ring fission product was isolated from acidified culture media and was identified as 3-(2-carboxyvinyl)naphthalene-2-carboxylic acid. 6,7-Benzocoumarin was also found in that extract. When Mycobacterium sp. strain PYR-1 was grown in the presence of phenanthrene, three neutral metabolites were identified as cis- and trans-9,10-dihydroxy-9,10-dihydrophenanthrene and cis-3,4-dihydroxy-3,4-dihydrophenanthrene. Phenanthrene ring fission products, isolated from acid extracts, were identified as 2,2?-diphenic acid, 1-hydroxynaphthoic acid, and phthalic acid. The data point to the existence, next to already known routes for both gram-negative and gram-positive bacteria, of alternative pathways that might be due to the presence of different dioxygenases or to a relaxed specificity of the same dioxygenase for initial attack on polycyclic aromatic hydrocarbons.

Moody, Joanna D.; Freeman, James P.; Doerge, Daniel R.; Cerniglia, Carl E.

2001-01-01

281

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.

Dodge, Anthony G.; Wackett, Lawrence P.

2012-01-01

282

Enhanced degradation of 2-nitrotoluene by immobilized cells of Micrococcus sp. strain SMN-1.  

PubMed

Nitrotoluenes are the toxic pollutants of the environment because of their large scale use in the production of explosives. Biodegradation of such chemicals by microorganisms may provide an effective method for their detoxification. We have studied the degradation of 2-nitrotoluene by cells of Micrococcus sp. strain SMN-1 immobilized in various matrices such as polyurethane foam (PUF), sodium alginate (SA), sodium alginate-polyvinyl alcohol (SA-PVA), agar and polyacrylamide. The rate of degradation of 15 and 30 mM 2-nitrotoluene by freely suspended cells and immobilized cells in batches and fed-batch with shaken cultures were compared. The PUF-immobilized cells achieved higher degradation of 15 and 30 mM 2-nitrotoluene than freely suspended cells and the cells immobilized in SA-PVA, polyacrylamide, SA and agar. The PUF-immobilized cells could be reused more than 24 cycles without loosing their degradation capacity and showed more tolerance to pH and temperature changes than freely suspended cells. These results revealed the enhanced rate of degradation of 2-nitrotoluene by PUF-immobilized cells of Micrococcus sp. strain SMN-1. PMID:23153775

Mulla, Sikandar I; Talwar, Manjunatha P; Bagewadi, Zabin K; Hoskeri, Robertcyril S; Ninnekar, Harichandra Z

2013-02-01

283

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

PubMed

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. PMID:3009412

Nunn, D N; Lidstrom, M E

1986-05-01

284

Characterization of the desulfurization genes from Rhodococcus sp. strain IGTS8.  

PubMed Central

Rhodococcus sp. strain IGTS8 possesses an enzymatic pathway that can remove covalently bound sulfur from dibenzothiophene (DBT) without breaking carbon-carbon bonds. The DNA sequence of a 4.0-kb BstBI-BsiWI fragment that carries the genes for this pathway was determined. Frameshift and deletion mutations established that three open reading frames were required for DBT desulfurization, and the genes were designated soxABC (for sulfur oxidation). Each sox gene was subcloned independently and expressed in Escherichia coli MZ1 under control of the inducible lambda pL promoter with a lambda cII ribosomal binding site. SoxC is an approximately 45-kDa protein that oxidizes DBT to DBT-5,5'-dioxide. SoxA is an approximately 50-kDa protein responsible for metabolizing DBT-5,5'-dioxide to an unidentified intermediate. SoxB is an approximately 40-kDa protein that, together with the SoxA protein, completes the desulfurization of DBT-5,5'-dioxide to 2-hydroxybiphenyl. Protein sequence comparisons revealed that the predicted SoxC protein is similar to members of the acyl coenzyme A dehydrogenase family but that the SoxA and SoxB proteins have no significant identities to other known proteins. The sox genes are plasmidborne and appear to be expressed as an operon in Rhodococcus sp. strain IGTS8 and in E. coli. Images

Denome, S A; Oldfield, C; Nash, L J; Young, K D

1994-01-01

285

Characterization of the Gene Cluster Involved in Isoprene Metabolism in Rhodococcus sp. Strain AD45  

PubMed Central

The genes involved in isoprene (2-methyl-1,3-butadiene) utilization in Rhodococcus sp. strain AD45 were cloned and characterized. Sequence analysis of an 8.5-kb DNA fragment showed the presence of 10 genes of which 2 encoded enzymes which were previously found to be involved in isoprene degradation: a glutathione S-transferase with activity towards 1,2-epoxy-2-methyl-3-butene (isoI) and a 1-hydroxy-2-glutathionyl-2-methyl-3-butene dehydrogenase (isoH). Furthermore, a gene encoding a second glutathione S-transferase was identified (isoJ). The isoJ gene was overexpressed in Escherichia coli and was found to have activity with 1-chloro-2,4-dinitrobenzene and 3,4-dichloro-1-nitrobenzene but not with 1,2-epoxy-2-methyl-3-butene. Downstream of isoJ, six genes (isoABCDEF) were found; these genes encoded a putative alkene monooxygenase that showed high similarity to components of the alkene monooxygenase from Xanthobacter sp. strain Py2 and other multicomponent monooxygenases. The deduced amino acid sequence encoded by an additional gene (isoG) showed significant similarity with that of ?-methylacyl-coenzyme A racemase. The results are in agreement with a catabolic route for isoprene involving epoxidation by a monooxygenase, conjugation to glutathione, and oxidation of the hydroxyl group to a carboxylate. Metabolism may proceed by fatty acid oxidation after removal of glutathione by a still-unknown mechanism.

van Hylckama Vlieg, Johan E. T.; Leemhuis, Hans; Spelberg, Jeffrey H. Lutje; Janssen, Dick B.

2000-01-01

286

A Gene Cluster Involved in Metal Homeostasis in the Cyanobacterium Synechocystis sp. Strain PCC 6803  

PubMed Central

A gene cluster composed of nine open reading frames (ORFs) involved in Ni2+, Co2+, and Zn2+ sensing and tolerance in the cyanobacterium Synechocystis sp. strain PCC 6803 has been identified. The cluster includes an Ni2+ response operon and a Co2+ response system, as well as a Zn2+ response system previously described. Expression of the Ni2+ response operon (nrs) was induced in the presence of Ni2+ and Co2+. Reduced Ni2+ tolerance was observed following disruption of two ORFs of the operon (nrsA and nrsD). We also show that the nrsD gene encodes a putative Ni2+ permease whose carboxy-terminal region is a metal binding domain. The Co2+ response system is composed of two divergently transcribed genes, corR and corT, mutants of which showed decreased Co2+ tolerance. Additionally, corR mutants showed an absence of Co2+-dependent induction of corT, indicating that CorR is a transcriptional activator of corT. To our knowledge, CorR is the first Co2+-sensing transcription factor described. Our data suggest that this region of the Synechocystis sp. strain PCC 6803 genome is involved in sensing and homeostasis of Ni2+, Co2+, and Zn2+.

Garcia-Dominguez, Mario; Lopez-Maury, Luis; Florencio, Francisco J.; Reyes, Jose C.

2000-01-01

287

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

288

Biodegradation of crude oil by a newly isolated strain Rhodococcus sp. JZX-01.  

PubMed

A highly efficient oil-degrading bacteria JZX-01 was isolated from the oil-contaminated soil of the seacoast near the Boxi Offshore Oil Field of China. Morphological, physiological, and 16S rDNA gene sequence analyses indicated that JZX-01 was assigned to the genus Rhodococcus sp. This strain decomposed 65.27 ± 5.63 % of the crude oil in 9 days. Gas chromatography-mass spectrometry analysis showed that even the long-chain hydrocarbons (C31-C38) and branched alkanes (pristine and phytane), which were regarded as the stubborn ones, could be degraded. Further study showed that the bacteria still has good oil degradation ability at low temperatures as well as under high salt conditions. Moreover, JZX-01 was found to have a biosurfactant-producing capacity, which significantly favors the surface tension reduction and crude oil degradation. The promising isolated strain Rhodococcus sp. JZX-01 could be further used for the bioremediation of oil-polluted soil or seawater in a wide range of temperatures and high salt conditions. PMID:23996118

Li, Chen; Zhou, Zheng-Xi; Jia, Xiao-Qiang; Chen, Yu; Liu, Jiao; Wen, Jian-Ping

2013-12-01

289

Isolation of fenitrothion-degrading strain Burkholderia sp. FDS-1 and cloning of mpd gene.  

PubMed

A short rod shaped, gram-negative bacterium strain Burkholderia sp. FDS-1 was isolated from the sludge of the wastewater treating system of an organophosphorus pesticides manufacturer. The isolate was capable of using fenitrothion as the sole carbon source for its growth. FDS-1 first hydrolyzed fenitrothion to 3-methyl-4-nitrophenol, which was further metabolized to nitrite and methylhydroquinone. The addition of other carbon source and omitting phosphorus source had little effect on the hydrolysis of fenitrothion. The gene encoding the organophosphorus hydrolytic enzyme was cloned and sequenced. The sequence was similar to mpd, a gene previously shown to encode a parathion-methyl-hydrolyzing enzyme in Plesiomonas sp. M6. The inoculation of strain FDS-1 (10(6) cells g(-1)) to soil treated with 100 mg fenitrothion emulsion kg(-1) resulted in a higher degradation rate than in noninoculated soils regardless of the soil sterilized or nonsterilized. These results highlight the potential of this bacterium to be used in the cleanup of contaminated pesticide waste in the environment. PMID:16715406

Zhang, Zhonghui; Hong, Qing; Xu, Jianghong; Zhang, Xiaozhou; Li, Shunpeng

2006-06-01

290

Rapid Aggregation of Biofuel-Producing Algae by the Bacterium Bacillus sp. Strain RP1137  

PubMed Central

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.

Powell, Ryan J.

2013-01-01

291

Isolation and transcriptional analysis of novel tetrachloroethene reductive dehalogenase gene from Desulfitobacterium sp. strain KBC1.  

PubMed

Strain KBC1, an anaerobic bacterium, that dechlorinates tetrachloroethene (PCE) to trichloroethene was isolated. This strain also dechlorinated high concentrations of PCE at a temperature range of 10 to 40 degrees C and showed high oxygen tolerance. Based on the 16S rRNA gene sequence analysis, this microorganism was identified as a species of the genus Desulfitobacterium. Several species of this genus have been reported to be potent ortho-chlorophenol and PCE dechlorinators; however, the gene coding PCE-specific dehalogenase had not been cloned thus far. In this report, we identified a novel PCE reductive dehalogenase (PrdA) gene from the Desulfitobacterium sp. strain KBC1. These prd genes, including putative membrane anchor protein, were classified as novel type of PCE reductive dehalogenase (approximately 40% homology with the general PCE dehalogenase). It was revealed that the two open reading frames had been transcribed as identical mRNA and were induced strictly in the presence of PCE. This transcriptional regulation appeared to be controlled by the transcriptional activator located downstream of prdAB operon. According to the substrate utility of the strain KBC1 and phylogenetic analysis of PrdA, this microorganism may be expected to play the role of a primary dechlorinator of PCE in the environment. PMID:16172885

Tsukagoshi, Norihiko; Ezaki, Satoshi; Uenaka, Tetsuya; Suzuki, Nobukazu; Kurane, Ryuichiro

2006-01-01

292

Biodegradation of triazine herbicide metribuzin by the strain Bacillus sp. N1.  

PubMed

By enrichment culturing of soil contaminated with metribuzin, a highly efficient metribuzin degrading bacterium, Bacillus sp. N1, was isolated. This strain grows using metribuzin at 5.0% (v/v) as the sole nitrogen source in a liquid medium. Optimal metribuzin degradation occurred at a temperature of 30ºC and at pH 7.0. With an initial concentration of 20 mg L(-1), the degradation rate was 73.5% in 120 h. If the initial concentrations were higher than 50 mg L(-1), the biodegradation rates decreased as the metribuzin concentrations increased. When the concentration was 100 mg L(-1), the degradation rate was only 45%. Degradation followed the pesticide degradation kinetic equation at initial concentrations between 5 mg L(-1) and 50 mg L(-1). When the metribuzin contaminated soil was mixed with strain N1 (with the concentration of metribuzin being 20 mg L(-1) and the inoculation rate of 10(11) g(-1) dry soil), the degradation rate of the metribuzin was 66.4% in 30 days, while the degradation rate of metribuzin was only 19.4% in the control soil without the strain N1. These results indicate that the strain N1 can significantly increase the degradation rate of metribuzin in contaminated soil. PMID:24328539

Zhang, Hao; Zhang, Yubin; Hou, Zhiguang; Wu, Xian; Gao, Henan; Sun, Fengjie; Pan, Hongyu

2014-01-01

293

Biodegradation of the neonicotinoid insecticide Acetamiprid by bacterium Pigmentiphaga sp. strain AAP-1 isolated from soil.  

PubMed

The Acetamiprid-degrading bacterium AAP-1 was isolated from contaminated soil, and identified as Pigmentiphaga sp. combined traditionary categorization method with modern molecule method. The strain could utilize Acetamiprid as the sole carbon, nitrogen and energy source for growth and metabolized 100 mgL(-1) Acetamiprid within 2.5h. During the degradation of Acetamiprid, one N-deacetylation metabolite, was characterized by FT-IR, GC-MS and NMR analysis. A novel microbial biodegradation pathway for Acetamiprid was proposed on the basis of the metabolite. Compared with uninoculated soils, the addition of the AAP-1 strain into soils treated with Acetamiprid gained a higher degradation rate, and the bacteria community analysis by T-RFLP in contaminated soil recovered after inoculation of the AAP-1 strain. On the basis of these results, strain AAP-1 has the potential to be used in the bioremediation of Acetamiprid-contaminated environments. This is the first report of Acetamiprid-degrading isolate from the genus of Pigmentiphaga. PMID:23624055

Wang, Guangli; Yue, Wenlong; Liu, Yuan; Li, Feng; Xiong, Minhua; Zhang, Hui

2013-06-01

294

Continuous degradation of trichloroethylene by Xanthobacter sp. strain Py2 during growth on propene.  

PubMed Central

Propene-grown Xanthobacter sp. strain Py2 cells can degrade trichloroethylene (TCE), but the transformation capacity of such cells was limited and depended on both the TCE concentration and the biomass concentration. Toxic metabolites presumably accumulated extracellularly, because the fermentation of glucose by yeast cells was inhibited by TCE degradation products formed by strain Py2. The affinity of the propene monooxygenase for TCE was low, and this allowed strain Py2 to grow on propene in the presence of TCE. During batch growth with propene and TCE, the TCE was not degraded before most of the propene had been consumed. Continuous degradation of TCE in a chemostat culture of strain Py2 growing with propene was observed with TCE concentrations up to 206 microns in the growth medium without washout of the fermentor occurring. At this TCE concentration the specific degradation rate was 1.5 nmol/min/mg of biomass. The total amount of TCE that could be degraded during simultaneous growth on propene depended on the TCE concentration and ranged from 0.03 to 0.34g of TCE per g of biomass. The biomass yield on propene was not affected by the cometabolic degradation of TCE.

Reij, M W; Kieboom, J; de Bont, J A; Hartmans, S

1995-01-01

295

A Novel Transformation of Polychlorinated Biphenyls by Rhodococcus sp. Strain RHA1  

PubMed Central

We have characterized a biphenyl degrader, Rhodococcus sp. strain RHA1. Biphenyl-grown cells of strain RHA1 efficiently transformed 45 components in the 62 major peaks of a polychlorinated biphenyl (PCB) mixture of Kanechlors 200, 300, 400, and 500 within 3 days, which includes mono- to octachlorobiphenyls. Among the intermediate metabolites of PCB transformation, di- and trichlorobenzoic acids were identified. The gradual decrease of these chlorobenzoic acids during incubation indicated that these chlorobenzoic acids would also be degraded by this strain. The effect of the position of chlorine substitution was determined by using PCB mixtures that have chlorine substitutions mainly at either the ortho or the meta position. This strain transformed both types of congeners, and strong PCB transformation activity of RHA1 was indicated. RHA1 accumulated 4-chlorobenzoic acid temporally during the transformation of 4-chlorobiphenyl. The release of most chloride in the course of 2,2(prm1)-dichlorobiphenyl degradation was observed. These results suggested that RHA1 would break down at least some PCB congeners into smaller molecules to a considerable extent.

Seto, M.; Kimbara, K.; Shimura, M.; Hatta, T.; Fukuda, M.; Yano, K.

1995-01-01

296

Molecular structure and enzymatic function of lycopene cyclase from the cyanobacterium Synechococcus sp strain PCC7942.  

PubMed Central

A gene encoding the enzyme lycopene cyclase in the cyanobacterium Synechococcus sp strain PCC7942 was mapped by genetic complementation, cloned, and sequenced. This gene, which we have named crtL, was expressed in strains of Escherichia coli that were genetically engineered to accumulate the carotenoid precursors lycopene, neurosporene, and zeta-carotene. The crtL gene product converts the acyclic hydrocarbon lycopene into the bicyclic beta-carotene, an essential component of the photosynthetic apparatus in oxygen-evolving organisms and a source of vitamin A in human and animal nutrition. The enzyme also converts neurosporene to the monocyclic beta-zeacarotene but does not cyclize zeta-carotene, indicating that desaturation of the 7-8 or 7'-8' carbon-carbon bond is required for cyclization. The bleaching herbicide 2-(4-methylphenoxy)triethylamine hydrochloride (MPTA) effectively inhibits both cyclization reactions. A mutation that confers resistance to MPTA in Synechococcus sp PCC7942 was identified as a point mutation in the promoter region of crtL. The deduced amino acid sequence of lycopene cyclase specifies a polypeptide of 411 amino acids with a molecular weight of 46,125 and a pI of 6.0. An amino acid sequence motif indicative of FAD utilization is located at the N terminus of the polypeptide. DNA gel blot hybridization analysis indicated a single copy of crtL in Synechococcus sp PCC7942. Other than the FAD binding motif, the predicted amino acid sequence of the cyanobacterial lycopene cyclase bears little resemblance to the two known lycopene cyclase enzymes from nonphotosynthetic bacteria. Preliminary results from DNA gel blot hybridization experiments suggest that, like two earlier genes in the pathway, the Synechococcus gene encoding lycopene cyclase is homologous to plant and algal genes encoding this enzyme.

Cunningham, F X; Sun, Z; Chamovitz, D; Hirschberg, J; Gantt, E

1994-01-01

297

Plasmid-Borne Genes Code for an Angular Dioxygenase Involved in Dibenzofuran Degradation by Terrabacter sp. Strain YK3  

PubMed Central

The genes responsible for angular dioxygenation of dibenzofuran in actinomycetes were cloned by using a degenerate set of PCR primers designed by using conserved sequences of the dioxygenase alpha subunit genes. One sequence of alpha subunit genes was commonly amplified from four dibenzofuran-utilizing actinomycetes: Terrabacter sp. strains YK1 and YK3, Rhodococcus sp. strain YK2, and Microbacterium sp. strain YK18. A 5.2-kb PstI fragment encoding the alpha and beta subunits of the terminal dioxygenase, ferredoxin, and ferredoxin reductase (designated dfdA1 to dfdA4, respectively) was cloned from the large circular plasmid pYK3 isolated from Terrabacter sp. strain YK3. We confirmed that transcription of the dfdA1 gene was induced by dibenzofuran in Terrabacter sp. strain YK3. Southern blot hybridization analysis revealed that this type of dioxygenase gene is distributed among diverse dibenzofuran-utilizing actinomycetes. However, genes homologous to dfdA1 were not detected in dibenzofuran utilization-deficient mutants of Terrabacter, Rhodococcus, and Microbacterium species. When the dfdA1 to dfdA4 genes were introduced into a non-dibenzofuran-degrading mutant of Rhodococcus sp. strain YK2, strain YK2-RD2, which had spontaneously lost the gene homologous to dfdA1, the ability to degrade dibenzofuran was restored. Analysis of the breakdown products indicated that DfdA has angular dioxygenase activity. This dfdA transformant degraded several aromatic compounds, indicating that the novel angular dioxygenase possesses broad substrate specificity.

Iida, Toshiya; Mukouzaka, Yuki; Nakamura, Kaoru; Kudo, Toshiaki

2002-01-01

298

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

299

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.

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

1997-01-01

300

Multiple Mechanisms of Uranium Immobilization by Cellulomonas sp. strain ES6  

SciTech Connect

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 near edge structure (XANES) analysis showed U precipitates containing nearly equal fractions of U(IV) and U(VI), whereas in PIPES buffer, U precipitates consisted primarily of U(VI). Mass balance calculations for U and P corroborate these observations. High-resolution transmission electron microscopy (HR42TEM) and energy dispersive X-ray spectroscopy (EDS) showed both extracellular and intracellular accumulation of U solids. The U(VI)-phosphate precipitates, confirmed by EDS as containing U and P in equimolar concentrations, had nanometer sized lath structure. When anthraquinone-2,6-disulfonate (AQDS), a known electron shuttle, was added to the experimental reactors, U reduction became the dominant removal mechanism, in contrast to primarily phosphate-mediated precipitation observed in the absence of AQDS. Uranium immobilization by abiotic precipitation or microbial reduction has been extensively reported; however, 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, t 52 he presence of multiple U immobilization mechanisms within one organism is reported using Cellulomonas sp. strain ES6.

Sivaswamy, Vaideeswaran; Brent Peyton; Viamajala, Sridhar; Robin Gerlach; William Apel; Rajesh Sani; Alice Dohnalkova; Thomas Borch

2011-02-01

301

Cloning and Expression of the Benzoate Dioxygenase Genes from Rhodococcus sp. Strain 19070  

PubMed Central

The bopXYZ genes from the gram-positive bacterium Rhodococcus sp. strain 19070 encode a broad-substrate-specific benzoate dioxygenase. Expression of the BopXY terminal oxygenase enabled Escherichia coli to convert benzoate or anthranilate (2-aminobenzoate) to a nonaromatic cis-diol or catechol, respectively. This expression system also rapidly transformed m-toluate (3-methylbenzoate) to an unidentified product. In contrast, 2-chlorobenzoate was not a good substrate. The BopXYZ dioxygenase was homologous to the chromosomally encoded benzoate dioxygenase (BenABC) and the plasmid-encoded toluate dioxygenase (XylXYZ) of gram-negative acinetobacters and pseudomonads. Pulsed-field gel electrophoresis failed to identify any plasmid in Rhodococcus sp. strain 19070. Catechol 1,2- and 2,3-dioxygenase activity indicated that strain 19070 possesses both meta- and ortho-cleavage degradative pathways, which are associated in pseudomonads with the xyl and ben genes, respectively. Open reading frames downstream of bopXYZ, designated bopL and bopK, resembled genes encoding cis-diol dehydrogenases and benzoate transporters, respectively. The bop genes were in the same order as the chromosomal ben genes of P. putida PRS2000. The deduced sequences of BopXY were 50 to 60% identical to the corresponding proteins of benzoate and toluate dioxygenases. The reductase components of these latter dioxygenases, BenC and XylZ, are 201 residues shorter than the deduced BopZ sequence. As predicted from the sequence, expression of BopZ in E. coli yielded an approximately 60-kDa protein whose presence corresponded to increased cytochrome c reductase activity. While the N-terminal region of BopZ was approximately 50% identical in sequence to the entire BenC or XylZ reductases, the C terminus was unlike other known protein sequences.

Haddad, Sandra; Eby, D. Matthew; Neidle, Ellen L.

2001-01-01

302

Draft Genome Sequence of Marine Actinomycete Streptomyces sp. Strain NTK 937, Producer of the Benzoxazole Antibiotic Caboxamycin  

PubMed Central

Streptomyces sp. strain NTK 937 is the producer of the benzoxazole antibiotic caboxamycin, which has been shown to exert inhibitory activity against Gram-positive bacteria, cytotoxic activity against several human tumor cell lines, and inhibition of the enzyme phosphodiesterase. In this genome announcement, we present a draft genome sequence of Streptomyces sp. NTK 937 in which we identified at least 35 putative secondary metabolite biosynthetic gene clusters.

Olano, Carlos; Cano-Prieto, Carolina; Losada, Armando A.; Bull, Alan T.; Goodfellow, Michael; Fiedler, Hans-Peter; Mendez, Carmen

2014-01-01

303

Complete Genome Sequence of Thermococcus sp. Strain 4557, a Hyperthermophilic Archaeon Isolated from a Deep-Sea Hydrothermal Vent Area  

PubMed Central

Thermococcus sp. strain 4557 is a hyperthermophilic anaerobic archaeon isolated from the deep-sea hydrothermal vent Guaymas Basin site in the Gulf of California at a depth of 2,000 m. Here, we present the complete genome sequence of Thermococcus sp. 4557, which consists of a single circular chromosome of 2,011,320 bp with a G+C content of 56.08%.

Wang, Xingna; Gao, Zhaoming; Xu, Xun; Ruan, Lingwei

2011-01-01

304

Draft Genome Sequence of Marine Actinomycete Streptomyces sp. Strain NTK 937, Producer of the Benzoxazole Antibiotic Caboxamycin.  

PubMed

Streptomyces sp. strain NTK 937 is the producer of the benzoxazole antibiotic caboxamycin, which has been shown to exert inhibitory activity against Gram-positive bacteria, cytotoxic activity against several human tumor cell lines, and inhibition of the enzyme phosphodiesterase. In this genome announcement, we present a draft genome sequence of Streptomyces sp. NTK 937 in which we identified at least 35 putative secondary metabolite biosynthetic gene clusters. PMID:24994793

Olano, Carlos; Cano-Prieto, Carolina; Losada, Armando A; Bull, Alan T; Goodfellow, Michael; Fiedler, Hans-Peter; Méndez, Carmen; Salas, José A

2014-01-01

305

Complete Genome Sequence of the Sesbania Symbiont and Rice Growth-Promoting Endophyte Rhizobium sp. Strain IRBG74.  

PubMed

Rhizobium sp. strain IRBG74 is the first known nitrogen-fixing symbiont in the Agrobacterium/Rhizobium clade that nodulates the aquatic legume Sesbania sp. and is also a growth-promoting endophyte of wetland rice. Here, we present the sequence of the IRBG74 genome, which is composed of a circular chromosome, a linear chromosome, and a symbiotic plasmid, pIRBG74a. PMID:24265489

Crook, Matthew B; Mitra, Shubhajit; Ané, Jean-Michel; Sadowsky, Michael J; Gyaneshwar, Prasad

2013-01-01

306

Draft Genome Sequence of Rhodococcus sp. Strain P14, a Biodegrader of High-Molecular-Weight Polycyclic Aromatic Hydrocarbons  

PubMed Central

The genus Rhodococcus is known for its ability to degrade various xenobiotic compounds. Rhodococcus sp. strain P14 isolated from crude oil-contaminated sediments can degrade mineral oil and polycyclic aromatic hydrocarbons (PAHs). The draft genome sequence of Rhodococcus sp. P14 was obtained using Solexa technology, which provided an invaluable genetic background for further investigation of the ability of P14 to degrade xenobiotic compounds.

Zhang, Ying; Qin, Fujun; Qiao, Jing; Li, Gangmin; Shen, Chenghui; Huang, Tongwang

2012-01-01

307

Endophytic and entomopathogenic strains of Beauveria sp to control the bovine tick Rhipicephalus (Boophilus) microplus.  

PubMed

Pathogenicity of strains of the entomopathogenic fungus Beauveria bassiana and endophytic strains of Beauveria sp against the bovine tick Rhipicephalus (Boophilus) microplus was tested in laboratory bioassays and under field conditions. Suspensions containing 10(5), 10(7) and 10(9) conidia/mL were prepared of each fungal strain for laboratory bioassays. The ticks were maintained at 28 degrees C, 90 +/- 5% relative humidity, and the following variables were evaluated: initial female weight, egg weight, hatching percentage, reproductive efficiency, and percentage control. For tests under field conditions, a Beauveria suspension containing 10(6) conidia/mL was sprayed on tick-infested cows. After 72 h, the ticks were collected to estimate mortality under field conditions. Laboratory bioassays showed a mortality of 20 to 50% of the ticks seven days after inoculation with 10(7) Beauveria conidia/mL. Under field conditions 10(6) Beauveria conidia/mL induced 18-32% mortality. All Beauveria strains were effective in biological control of R. (Boophilus) microplus under laboratory and field test conditions. This is the first demonstration that endophytic fungi can be used for biological control of the cattle tick; this could help reduce environmental contamination by diminishing the need for chemical acaricides. Two endophytic strains were isolated from maize leaves and characterized by molecular sequencing of 5.8S rDNA ITS1 and ITS2 and morphological analyses of conidia. We found that these two endophytic Beauveria isolates, designated B95 and B157, are close to Beauveria amorpha. PMID:20662157

Campos, R A; Boldo, J T; Pimentel, I C; Dalfovo, V; Araújo, W L; Azevedo, J L; Vainstein, M H; Barros, N M

2010-01-01

308

Metabolic ability and gene characteristics of Arthrobacter sp. strain DNS10, the sole atrazine-degrading strain in a consortium isolated from black soil  

Microsoft Academic Search

Strain DNS10 was the only member that could utilize atrazine as the sole nitrogen source for growth in an atrazine-degrading consortium which was isolated from black soil previously in our laboratory. It belongs to the genus Arthrobacter according to the sequence of 16S rRNA gene and is designated as Arthrobacter sp. DNS10. 16S rRNA gene phylogenetic analysis showed that strain

Ying Zhang; Zhao Jiang; Bo Cao; Miao Hu; Zhigang Wang; Xiaonan Dong

2011-01-01

309

Rhizosphere colonization and arsenic translocation in sunflower (Helianthus annuus L.) by arsenate reducing Alcaligenes sp. strain Dhal-L.  

PubMed

In the present study, six arsenic-resistant strains previously isolated were tested for their plant growth promoting characteristics and heavy metal resistance, in order to choose one model strain as an inoculum for sunflower plants in pot experiments. The aim was to investigate the effect of arsenic-resistant strain on sunflower growth and on arsenic uptake from arsenic contaminated soil. Based on plant growth promoting characteristics and heavy metal resistance, Alcaligenes sp. strain Dhal-L was chosen as an inoculum. Beside the ability to reduce arsenate to arsenite via an Ars operon, the strain exhibited 1-amino-cyclopropane-1-carboxylic acid deaminase activity and it was also able to produce siderophore and indole acetic acid. Pot experiments were conducted with an agricultural soil contaminated with arsenic (214 mg kg?¹). A real time PCR method was set up based on the quantification of ACR3(2) type of arsenite efflux pump carried by Alcaligenes sp. strain Dhal-L, in order to monitor presence and colonisation of the strain in the bulk and rhizospheric soil. As a result of strain inoculation, arsenic uptake by plants was increased by 53 %, whereas ACR3(2) gene copy number in rhizospheric soil was 100 times higher in inoculated than in control pots, indicating the colonisation of strain. The results indicated that the presence of arsenate reducing strains in the rhizosphere of sunflower influences arsenic mobilization and promotes arsenic uptake by plant. PMID:23632906

Cavalca, Lucia; Corsini, Anna; Bachate, Sachin Prabhakar; Andreoni, Vincenza

2013-10-01

310

Combined bioremediation of atrazine-contaminated soil by Pennisetum and Arthrobacter sp. strain DNS10.  

PubMed

Strain DNS10 was isolated from the black soil collected from the northeast of China which had been cultivated with atrazine as the sole nitrogen source. Pennisetum is a common plant in Heilongjiang Province of China. The main objective of this paper was to evaluate the efficiency of plant-microbe joint interactions (Arthrobacter sp. DNS10 + Pennisetum) in atrazine degradation compared with single-strain and single-plant effects. Plant-microbe joint interactions degraded 98.10 % of the atrazine, while single strain and single plant only degraded 87.38 and 66.71 % after a 30-day experimental period, respectively. The results indicated that plant-microbe joint interactions had a better degradation effect. Meanwhile, we found that plant-microbe joint interactions showed a higher microbial diversity. The results of microbial diversity illustrated that the positive effects of cropping could improve soil microbial growth and activity. In addition, we planted atrazine-sensitive plants (soybean) in the soil after repair. The results showed that soybean growth in soil previously treated with the plant-microbe joint interactions treatment was better compared with other treatments after 20 days of growth. This was further proved that the soil is more conducive for crop cultivation. Hence, plant-microbe joint interactions are considered to be a potential tool in the remediation of atrazine-contaminated soil. PMID:24352545

Zhang, Ying; Ge, Shijie; Jiang, Mingyue; Jiang, Zhao; Wang, Zhigang; Ma, Bingbing

2014-05-01

311

Rapid decolorization of methyl orange by a novel Aeromonas sp. strain DH-6.  

PubMed

Azo dyes are extensively used, but are recalcitrant and refractory. In this study, an indigenous strain DH-6 was isolated and identified as Aeromonas sp. based on 16S rDNA analysis for its excellent methyl orange (MO) decolorizing capability. Plackett-Burman design and response surface methodology (RSM) were employed to investigate the effect of operational parameters on decolorization and to optimize the decolorization process. Based on the results the concentrations of glucose, Na2HPO4 and MO and temperature were selected as the four significant parameters of RSM. The optimal conditions for MO decolorization by the strain were as follows: 3.0 g/L glucose, 4.9 g/L Na2HPO4, 100 mg/L MO, and at 40 °C. The verification tests showed that 95.5% decolorization was observed after incubation for 2 h, which is within the confidence interval. Under the optimal conditions, the kinetics of the decolorization fitted the first-order model well (R(2) = 0.969). As the strain DH-6 still showed a good decolorizing capability at a relatively high temperature, it is considered a candidate for azo dye bioremediation in some tropical or subtropical regions. PMID:24845314

Du, Lin-Na; Li, Gang; Xu, Fang-Cheng; Pan, Xiu; Wen, Ling-Ning; Wang, Yang

2014-01-01

312

[Construction and evaluation of efficient gene expression platforms in Synechocystis sp. strain PCC6803].  

PubMed

For metabolic engineering of cyanobacteria, there is an urgent need to construct a group of efficient heterologous gene expression platforms and to evaluate their expression efficiencies. Here we constructed three integrative vectors, the pKW1188-derived pFQ9F, pFQ9R and pFQ20, for integration of heterologous genes into the genome of the model cyanobacteria strain Synechocystis sp. strain PCC6803. The pFQ16, an RSF1010-derived broad host range shuttle vector, was constructed for conjugative transfer of genes to various cyanobacteria strains. All the four platforms constructed here applied the rbc (encodes Ribulose-1, 5-bisphosphate carboxylase/oxygenase) and the rbc terminator to promote and terminate the gene transcription. Besides, a "Shine-Dalgarno -AUG" fusion translation strategy was used to keep the high protein translation efficiency. Using lacZ as a reporter gene, the expression efficiency of pFQ20 was evaluated and showed a strong beta-galactosidase expression (109 Miller). Furthermore, the platform pFQ20 was used to express the E. coli tesA' gene and showed significant protein bands through the Western Blot test. The expression platforms constructed in this study offer useful molecular tools for metabolic engineering of cyanobacteria in the future. PMID:24409696

Qi, Fengxia; Tan, Xiaoming; Lü, Xuefeng

2013-09-01

313

Modification of Norfloxacin by a Microbacterium sp. Strain Isolated from a Wastewater Treatment Plant?  

PubMed Central

Antimicrobial residues found in municipal wastewater may increase selective pressure on microorganisms for development of resistance, but studies with mixed microbial cultures derived from wastewater have suggested that some bacteria are able to inactivate fluoroquinolones. Medium containing N-phenylpiperazine and inoculated with wastewater was used to enrich fluoroquinolone-modifying bacteria. One bacterial strain isolated from an enrichment culture was identified by 16S rRNA gene sequence analysis as a Microbacterium sp. similar to a plant growth-promoting bacterium, Microbacterium azadirachtae (99.70%), and a nematode pathogen, “M. nematophilum” (99.02%). During growth in medium with norfloxacin, this strain produced four metabolites, which were identified by liquid chromatography-tandem mass spectrometry (LC-MS/MS) and nuclear magnetic resonance (NMR) analyses as 8-hydroxynorfloxacin, 6-defluoro-6-hydroxynorfloxacin, desethylene norfloxacin, and N-acetylnorfloxacin. The production of the first three metabolites was enhanced by ascorbic acid and nitrate, but it was inhibited by phosphate, amino acids, mannitol, formate, and thiourea. In contrast, N-acetylnorfloxacin was most abundant in cultures supplemented with amino acids. This is the first report of defluorination and hydroxylation of a fluoroquinolone by an isolated bacterial strain. The results suggest that some bacteria may degrade fluoroquinolones in wastewater to metabolites with less antibacterial activity that could be subject to further degradation by other microorganisms.

Kim, Dae-Wi; Heinze, Thomas M.; Kim, Bong-Soo; Schnackenberg, Laura K.; Woodling, Kellie A.; Sutherland, John B.

2011-01-01

314

Production of an extracellular thermohalophilic lipase from a moderately halophilic bacterium, Salinivibrio sp. strain SA-2.  

PubMed

Fifty strains of moderately halophilic bacteria were isolated from various salty environments in Iran. A strain designated as SA-2 was shown to be the best producer of extracellular lipase and was selected for further studies. Biochemical and physiological characterization along with 16S rDNA sequence analysis placed SA-2 in the genus Salinivibrio. The optimum salt, pH, temperature and aeration for enzyme production were 0.1 M KCl, pH 8, 35 degrees C and 150 rpm, respectively. The enzyme production was synchronized bacterial growth and reached a maximum level during the early-stationary phase in the basal medium containing 1 M NaCl. Triacylglycerols enhanced lipase production, while carbohydrates had inhibitory effects on it. The maximum lipase activity was obtained at pH 7.5, 50 degrees C and CaCl(2) concentration of 0.01 M. The enzyme was stable at pH range of 7.5-8 and retained 90% of its activity at 80 degrees C for 30 min. Different concentrations of NaNO(3), Na(2)SO(4), KCl and NaCl had no affect on lipase stability for 3 h. These results suggest that the lipase secreted by Salinivibrio sp. strain SA-2 is industrially important from the perspective of its tolerance to a broad temperature range, its moderate thermoactivity and its high tolerance to a wide range of salt concentrations (0-3 M NaCl). PMID:18506896

Amoozegar, Mohammad Ali; Salehghamari, Ensieh; Khajeh, Khosro; Kabiri, Mahbube; Naddaf, Saied

2008-06-01

315

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

2013-12-01

316

Isolation and characterization of a Sphingomonas sp. strain F-7 degrading fenvalerate and its use in bioremediation of contaminated soil.  

PubMed

A fenvalerate-degrading bacterial strain F-7 was isolated from long-term contaminated sludge. Based on morphological, physiological and biochemical characterization, and phylogenetic analysis of 16S rRNA gene sequence, strain F-7 was identified as Sphingomonas sp. The bacterium could utilize fenvalerate as the sole source of carbon. An amount measuring 100 mg L(-1) fenvalerate was completely degraded within 72 h and 3-phenoxybenzoic acid (3-PBA) was detected as a major metabolite. The result indicates that S. sp. F-7 might metabolize fenvalerate by hydrolysis of carboxylester linkage. It was capable of degrading permethrin, fenpropathrin, beta-cypermethrin, cyhalothrin, deltamethrin, bifenthrin and 3-PBA. Further studies demonstrated that the strain was multi-resistant to heavy metals and antibiotics. In addition, degradative enzymes involved were confirmed as intracellular distributed and constitutively expressed. Furthermore, application of the strain was found to accelerate the removal of fenvalerate in soil. This is the first report of fenvalerate degrading strain isolated from S. sp. These results might help with future research in better understanding of pyrethroid biodegradation and highlight S. sp. F-7 might have potential for practical application in bioremediation of fenvalerate-contaminated sites. PMID:23356341

Yu, Fang B; Shan, Sheng D; Luo, Lin P; Guan, Li B; Qin, Hua

2013-01-01

317

Genome Sequence of Lactobacillus saerimneri 30a (Formerly Lactobacillus sp. Strain 30a), a Reference Lactic Acid Bacterium Strain Producing Biogenic Amines  

PubMed Central

Lactobacillus sp. strain 30a (Lactobacillus saerimneri) produces the biogenic amines histamine, putrescine, and cadaverine by decarboxylating their amino acid precursors. We report its draft genome sequence (1,634,278 bases, 42.6% G+C content) and the principal findings from its annotation, which might shed light onto the enzymatic machineries that are involved in its production of biogenic amines.

Romano, Andrea; Trip, Hein; Campbell-Sills, Hugo; Bouchez, Olivier; Sherman, David; Lolkema, Juke S.

2013-01-01

318

Genomics of the Proteorhodopsin-Containing Marine Flavobacterium Dokdonia sp. Strain MED134?†  

PubMed Central

Proteorhodopsin phototrophy is expected to have considerable impact on the ecology and biogeochemical roles of marine bacteria. However, the genetic features contributing to the success of proteorhodopsin-containing bacteria remain largely unknown. We investigated the genome of Dokdonia sp. strain MED134 (Bacteroidetes) for features potentially explaining its ability to grow better in light than darkness. MED134 has a relatively high number of peptidases, suggesting that amino acids are the main carbon and nitrogen sources. In addition, MED134 shares with other environmental genomes a reduction in gene copies at the expense of important ones, like membrane transporters, which might be compensated by the presence of the proteorhodopsin gene. The genome analyses suggest Dokdonia sp. MED134 is able to respond to light at least partly due to the presence of a strong flavobacterial consensus promoter sequence for the proteorhodopsin gene. Moreover, Dokdonia sp. MED134 has a complete set of anaplerotic enzymes likely to play a role in the adaptation of the carbon anabolism to the different sources of energy it can use, including light or various organic matter compounds. In addition to promoting growth, proteorhodopsin phototrophy could provide energy for the degradation of complex or recalcitrant organic matter, survival during periods of low nutrients, or uptake of amino acids and peptides at low concentrations. Our analysis suggests that the ability to harness light potentially makes MED134 less dependent on the amount and quality of organic matter or other nutrients. The genomic features reported here may well be among the keys to a successful photoheterotrophic lifestyle.

Gonzalez, Jose M.; Pinhassi, Jarone; Fernandez-Gomez, Beatriz; Coll-Llado, Montserrat; Gonzalez-Velazquez, Monica; Puigbo, Pere; Jaenicke, Sebastian; Gomez-Consarnau, Laura; Fernandez-Guerra, Antoni; Goesmann, Alexander; Pedros-Alio, Carlos

2011-01-01

319

Kinetics study of pyridine biodegradation by a novel bacterial strain, Rhizobium sp. NJUST18.  

PubMed

Biodegradation of pyridine by a novel bacterial strain, Rhizobium sp. NJUST18, was studied in batch experiments over a wide concentration range (from 100 to 1,000 mg l(-1)). Pyridine inhibited both growth of Rhizobium sp. NJUST18 and biodegradation of pyridine. The Haldane model could be fitted to the growth kinetics data well with the kinetic constants ?* = 0.1473 h(-1), K s = 793.97 mg l(-1), K i = 268.60 mg l(-1) and S m = 461.80 mg l(-1). The true ? max, calculated from ?*, was found to be 0.0332 h(-1). Yield coefficient Y X/S depended on S i and reached a maximum of 0.51 g g(-1) at S i of 600 mg l(-1). V max was calculated by fitting the pyridine consumption data with the Gompertz model. V max increased with initial pyridine concentration up to 14.809 mg l(-1) h(-1). The q S values, calculated from [Formula: see text], were fitted with the Haldane equation, yielding q Smax = 0.1212 g g(-1) h(-1) and q* = 0.3874 g g(-1) h(-1) at S m' = 507.83 mg l(-1), K s' = 558.03 mg l(-1), and K i' = 462.15 mg l(-1). Inhibition constants for growth and degradation rate value were in the same range. Compared with other pyridine degraders, ? max and S m obtained for Rhizobium sp. NJUST18 were relatively high. High K i and K i' values and extremely high K s and K s' values indicated that NJUST18 was able to grow on pyridine within a wide concentration range, especially at relatively high concentrations. PMID:24425539

Shen, Jinyou; Zhang, Xin; Chen, Dan; Liu, Xiaodong; Zhang, Libin; Sun, Xiuyun; Li, Jiansheng; Bi, Huiping; Wang, Lianjun

2014-06-01

320

Cloning, sequencing, and analysis of aklaviketone reductase from Streptomyces sp. strain C5.  

PubMed Central

DNA sequence analysis of a region of the Streptomyces sp. strain C5 daunomycin biosynthesis gene cluster, located just upstream of the daunomycin polyketide biosynthesis genes, revealed the presence of six complete genes. The two genes reading right to left include genes encoding the potentially translationally coupled gene products, an acyl carrier protein and a ketoreductase, and the four genes reading divergently, left to right, include two open reading frames of unknown function followed by a gene encoding an apparent glycosyltransferase and dauE, encoding aklaviketone reductase. Extracts of Streptomyces lividans TK24 containing recombinant DauE catalyzed the NADPH-specific conversion of aklaviketone, maggiemycin, and 7-oxodaunomycinone to aklavinone, epsilon-rhodomycinone, and daunomycinone, respectively. Neither the product of dauB nor that of the ketoreductase gene directly downstream of the acyl carrier protein gene demonstrated aklaviketone reductase activity.

Dickens, M L; Ye, J; Strohl, W R

1996-01-01

321

Reduction of conjugal transfer efficiency by three restriction activities of Anabaena sp. strain PCC 7120.  

PubMed Central

The efficiency of conjugal transfer of plasmids from Escherichia coli to the cyanobacterium Anabaena sp. strain PCC 7120 was quantitated as a function of the number of restriction sites for the restriction enzymes carried by the recipient. In addition to the previously recognized isoschizomers of AvaI and AvaII, PCC 7120 was found to possess an isoschizomer of AvaIII. Plasmids modified in E. coli with methylases that protect in vitro against restriction by the three enzymes were transferred with high efficiency, nearly independent of the number of restriction sites on the plasmid. Plasmids left unprotected against one of the three restriction enzymes were transferred with lower efficiencies. For low numbers of sites, the efficiency of conjugal transfer decreased as an exponential function of the number of unprotected sites. The methods presented may be used to increase the efficiency of conjugal transfer into restriction-competent bacteria.

Elhai, J; Vepritskiy, A; Muro-Pastor, A M; Flores, E; Wolk, C P

1997-01-01

322

Biodegradation of 3-nitrotyrosine by Burkholderia sp. strain JS165 and Variovorax paradoxus JS171.  

PubMed

The cascade of reactive nitrogen species generated from nitric oxide causes modification of proteins, lipids, and nucleic acids in a wide range of organisms. 3-Nitrotyrosine is one of the most common products of the action of reactive nitrogen species on proteins. Although a great deal is known about the formation of 3-nitrotyrosine, the subsequent metabolism of this compound is a mystery. Variovorax paradoxus JS171 and Burkholderia sp. strain JS165 were isolated from soil slurries when 3-nitrotyrosine was provided as the sole carbon, nitrogen, and energy source. During growth on 3-nitrotyrosine stoichiometric amounts of nitrite were released along with approximately one-half of the theoretically available ammonia. The catabolic pathway involving oxidative denitration is distinct from the pathway for tyrosine metabolism. The facile isolation and the specific, regulated pathway for 3-nitrotyrosine degradation in natural ecosystems suggest that there is a significant flux of 3-nitrotyrosine in such environments. PMID:16461647

Nishino, Shirley F; Spain, Jim C

2006-02-01

323

Identification and cloning of genes involved in specific desulfurization dibenzothiophene by Rhodococcus sp. strain IGTS8  

SciTech Connect

The presence of sulfur in coal and petroleum contributes to corrosion of production and refining equipment and burning these high-sulfur products emits sulfur oxides to the atmosphere. Microorganisms that can enzymatically release organically bound sulfur from organic components of coal or petroleum or from dibenzothiophene (DBT) could reduce the sulfur content of high sulfur fuels without depleting their British thermal unit value. Two major pathways for microbial metabolism of DBT have been proposed. Some of the genes for the DPT degradative pathway have been isolated and characterized. However, no genes for the desulfurization pathway have been identified. This paper reports the isolation from Rhodoccus sp. strain IGTS8 pf a set of genes that confer a specific desulfurization phenotype to mutants and to a related organism, R. fascians D188-5, that is normally unable to desulfurize DBT. 38 refs., 2 figs., 1 tab.

Denome, S.A.; Young, K.D.; Olson, E.S. (Univ. of North Dakota School of Medicine, Energy and Environmental Research Center, Grand Forks, ND (United States))

1993-09-01

324

Unique modification of adenine in genomic DNA of the marine cyanobacterium Trichodesmium sp. strain NIBB 1067.  

PubMed Central

The genomic DNA of the marine nonheterocystous nitrogen-fixing cyanobacterium Trichodesmium sp. strain NIBB 1067 was found to be highly resistant to DNA restriction endonucleases. The DNA was digested extensively by the restriction enzyme DpnI, which requires adenine methylation for activity. The DNA composition, determined by high-performance liquid chromatography (HPLC), was found to be 69% AT. Surprisingly, it was found that a modified adenine which was not methylated at the usual N6 position was present and made up 4.7 mol% of the nucleosides in Trichodesmium DNA (15 mol% of deoxyadenosine). In order for adenine residues to be modified at this many positions, there must be many modifying enzymes or at least one of the modifying enzymes must have a degenerate recognition site. The reason(s) for this extensive methylation has not yet been determined but may have implications for the ecological success of this microorganism in nature. Images FIG. 1 FIG. 2

Zehr, J P; Ohki, K; Fujita, Y; Landry, D

1991-01-01

325

Fluoranthene metabolism in Mycobacterium sp. strain KR20: identity of pathway intermediates during degradation and growth.  

PubMed

Mycobacterium sp. strain KR20, which was isolated from a polycyclic aromatic hydrocarbon (PAH) contaminated soil of a former gaswork plant site, metabolized about 60% of the fluoranthene added (0.5 mg ml(-1)) to batch cultures in mineral salts medium within 10 d at 20 degrees C. It thereby increased its cell number about 30-fold and produced at least seven metabolites. Five metabolites, namely cis-2,3-fluoranthene dihydrodiol, Z-9-carboxymethylene-fluorene-1-carboxylic acid, cis-1,9a-dihydroxy-1-hydro-fluorene-9-one-8-carboxylic acid, 4-hydroxybenzochromene-6-one-7-carboxylic acid and benzene-1,2,3-tricarboxylic acid, could be identified by NMR and MS spectroscopic techniques and ascribed to an alternative fluoranthene degradation pathway. Besides fluoranthene, the isolate could not use any of the PAHs tested as a sole source of carbon and energy. PMID:11577157

Rehmann, K; Hertkorn, N; Kettrup, A A

2001-10-01

326

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

PubMed Central

Pseudomonas sp. strain HBP1 was found to grow on 2-hydroxy- and 2,2'-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',3-trihydroxybiphenyl when acting on 2,2'-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',3-trihydroxybiphenyl involved meta cleavage, with subsequent formation of benzoate and salicylate, respectively.

Kohler, H P; Kohler-Staub, D; Focht, D D

1988-01-01

327

A cryptic miniplasmid from the hyperthermophilic bacterium Thermotoga sp. strain RQ7.  

PubMed Central

An 846-bp cryptic plasmid has been discovered in the hyperthermophilic bacterium Thermotoga sp. strain RQ7. This is the first plasmid described for an organism from this ancient bacterial lineage and the smallest plasmid described to date for any organism. Nucleotide sequencing revealed a single open reading frame possibly encoding a 25,460-Da basic protein (212 amino acids). Upstream of the putative promoter lie five 11-bp direct repeats, each separated by 1 to 4 bp, while between the promoter and the open reading frame lies an 11-bp palindromic sequence. Its mode of replication is unknown, but its sequence bears similarities to those of plasmids which replicate by a rolling-circle mechanism. Images

Harriott, O T; Huber, R; Stetter, K O; Betts, P W; Noll, K M

1994-01-01

328

Xanthan Lyase of Bacillus sp. Strain GL1 Liberates Pyruvylated Mannose from Xanthan Side Chains  

PubMed Central

When the bacterium Bacillus sp. strain GL1 was grown in a medium containing xanthan as the carbon source, the viscosity of the medium decreased in association with growth, showing that the bacterium had xanthan-depolymerizing enzymes. One of the xanthan-depolymerizing enzymes (xanthan lyase) was present in the medium and was found to be induced by xanthan. The xanthan lyase purified from the culture fluid was a monomer with a molecular mass of 75 kDa, and was most active at pH 5.5 and 50°C. The enzyme was highly specific for xanthan and produced pyruvylated mannose. The result indicates that the enzyme cleaved the linkage between the terminal pyruvylated mannosyl and glucuronyl residues in the side chain of xanthan.

Hashimoto, Wataru; Miki, Hikaru; Tsuchiya, Noriaki; Nankai, Hirokazu; Murata, Kousaku

1998-01-01

329

Purification and properties of glutathione reductase from the cyanobacterium Anabaena sp. strain 7119  

SciTech Connect

An NADPH-glutathione reductase (EC 1.6.4.2) has been purified 6000-fold to electrophoretic homogeneity from the filamentous cyanobacterium Anabaena sp. strain 7119. The purified enzyme exhibits a specific activity of 249 U/mg and is characterized by being a dimeric flavin adenine dinucleotide-containing protein with a ratio of absorbance at 280 nm to absorbance at 462 nm of 5.8, a native molecular weight of 104,000, a Stokes radius of 4.13 nm, and a pI of 4.02. The enzyme activity is inhibited by sulfhydryl reagents and heavy-metal ions, especially in the presence of NADPH, with oxidized glutathione behaving as a protective agent. As is the case with the same enzyme from other sources, the kinetic data are consistent with a branched mechanism. Nevertheless, the cyanobacterial enzyme presents three distinctive

Serrano, A.; Rivas, J.; Losada, M.

1984-04-01

330

Cell Surface-Associated Proteins in the Filamentous Cyanobacterium Anabaena sp. strain PCC 7120  

PubMed Central

The cell surface senses environmental changes first and transfers signals into the cell. To understand the response to environmental changes, it is necessary to analyze cell surface components, particularly cell surface-associated proteins. We therefore investigated cell surface-associated proteins from the filamentous cyanobacterium Anabaena sp. strain PCC 7120. The cell surface-associated proteins extracted by an acidic buffer were resolved by SDS-PAGE. Eighteen proteins were identified from resolved bands by amino-terminal sequencing. Analysis of cell surface-associated proteins indicated that several proteins among them were involved in nucleic acid binding, protein synthesis, proteolytic activity and electron transfer, and other proteins were involved in the stress response.

Yoshimura, Hidehisa; Ikeuchi, Masahiko; Ohomori, Masayuki

2012-01-01

331

Genome-wide responses of the model archaeon Halobacterium sp. strain NRC-1 to oxygen limitation.  

PubMed

As part of a comprehensive postgenomic investigation of the model archaeon Halobacterium sp. strain NRC-1, we used whole-genome DNA microarrays to compare transcriptional profiles of cells grown under anaerobic or aerobic conditions. When anaerobic growth supported by arginine fermentation was compared to aerobic growth, genes for arginine fermentation (arc) and anaerobic respiration (dms), using trimethylamine N-oxide (TMAO) as the terminal electron acceptor, were highly upregulated, as was the bop gene, required for phototrophic growth. When arginine fermentation was compared to anaerobic respiration with TMAO, the arc and dms genes were both induced with arginine, while TMAO induced the bop gene and major gas vesicle protein (gvpAC) genes specifying buoyant gas vesicles. Anaerobic conditions with either TMAO or arginine also upregulated the cba genes, encoding one of three cytochrome oxidases. In-frame deletion of two COG3413 family regulatory genes, bat and dmsR, showed downregulation of the bop gene cluster and loss of purple membrane synthesis and downregulation of the dms operon and loss of anaerobic respiration capability, respectively. Bioinformatic analysis identified additional regulatory and sensor genes that are likely involved in the full range of cellular responses to oxygen limitation. Our results show that the Halobacterium sp. has evolved a carefully orchestrated set of responses to oxygen limitation. As conditions become more reducing, cells progressively increase buoyancy, as well as capabilities for phototrophy, scavenging of molecular oxygen, anaerobic respiration, and fermentation. PMID:22865851

DasSarma, Priya; Zamora, Regie C; Müller, Jochen A; DasSarma, Shiladitya

2012-10-01

332

Biomass production and nutrients removal by a new microalgae strain Desmodesmus sp. in anaerobic digestion wastewater.  

PubMed

Anaerobic digestion wastewater (ADW), which contains large amount of nitrogen and phosphorus, particularly high concentration of ammonium, might lead to severely environmental pollution. A new unicellular green microalgae species from a wetland at the Olympic Forest Park, Beijing, China was screened based on its growth rates and nutrients removal capability under ADW. Results of 18s rDNA and ITS1 analysis indicated that this strain have a close relationship with Desmodesmus sp., named as EJ9-6. Desmodesmus sp. EJ9-6 could remove 100% NH4-N (68.691mg/L), TP (4.565mg/L) and PO4-P (4.053mg/L), and 75.50% TN (84.236mg/L) at 10.0% ADW, which the highest biomass production was 0.412g/L after 14d cultivation. Maximum nutrients removal was observed at 10.0% ADW with daily removal rates of TN, NH4-N, TP and PO4-P at 4.542, 5.284, 0.326 and 0.290mg/L/d, respectively. PMID:24704885

Ji, Fang; Liu, Ying; Hao, Rui; Li, Gang; Zhou, Yuguang; Dong, Renjie

2014-06-01

333

Efficient biotransformation of herbicide diuron by bacterial strain Micrococcus sp. PS-1.  

PubMed

A Gram-positive, Micrococcus sp. strain PS-1 capable of utilizing phenylurea herbicide diuron as a sole carbon source at a high concentration (up to 250 ppm) was isolated from diuron storage site by selective enrichment study. The taxonomic characterization with 16S rRNA gene sequencing (1,477 bp) identified PS-1 as a member of Micrococcus sp. It was studied for the degradation of diuron and a range of its analogues (monuron, linuron, monolinuron, chlortoluron and fenuron). The shake flasks experiments demonstrated fast degradation of diuron (up to 96% at 250 ppm within 30 h incubation) with the addition of small quantity (0.01%) of non-ionic detergent. The relative degradation profile by the isolate was in the order of fenuron > monuron > diuron > linuron > monolinuron > chlortoluron. Further, the biochemical characterization of catabolic pathway by spectroscopic and chromatographic techniques demonstrated that the degradation proceeded via formation of dealkylated metabolites to form 3,4-dichloroaniline (3,4-DCA). It was the major metabolite formed, associated with profound increase in degradation kinetics in presence of appropriate additive. PMID:20401520

Sharma, Priyanka; Chopra, Adity; Cameotra, Swaranjit Singh; Suri, C Raman

2010-11-01

334

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

335

Distinct actions by Paenibacillus sp. strain E18 ?-L-arabinofuranosidases and xylanase in xylan degradation.  

PubMed

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; Yao, Bin

2013-03-01

336

Soluble cytochromes from the marine methanotroph Methylomonas sp. strain A4.  

PubMed Central

Soluble c-type cytochromes are central to metabolism of C1 compounds in methylotrophic bacteria. In order to characterize the role of c-type cytochromes in methane-utilizing bacteria (methanotrophs), we have purified four different cytochromes, cytochromes c-554, c-553, c-552, and c-551, from the marine methanotroph Methylomonas sp. strain A4. The two major species, cytochromes c-554 and c-552, were monoheme cytochromes and accounted for 57 and 26%, respectively, of the soluble c-heme. The approximate molecular masses were 8,500 daltons (Da) (cytochrome c-554) and 14,000 Da (cytochrome c-552), and the isoelectric points were pH 6.4 and 4.7, respectively. Two possible diheme c-type cytochromes were also isolated in lesser amounts from Methylomonas sp. strain A4, cytochromes c-551 and c-553. These were 16,500 and 34,000 Da, respectively, and had isoelectric points at pH 4.75 and 4.8, respectively. Cytochrome c-551 accounted for 9% of the soluble c-heme, and cytochrome c-553 accounted for 8%. All four cytochromes differed in their oxidized versus reduced absorption maxima and their extinction coefficients. In addition, cytochromes c-554, c-552, and c-551 were shown to have different electron paramagnetic spectra and N-terminal amino acid sequences. None of the cytochromes showed significant activity with purified methanol dehydrogenase in vitro, but our data suggested that cytochrome c-552 is probably the in vivo electron acceptor for the methanol dehydrogenase. Images

DiSpirito, A A; Lipscomb, J D; Lidstrom, M E

1990-01-01

337

Genes encoding two isocitrate dehydrogenase isozymes of a psychrophilic bacterium, Vibrio sp. strain ABE-1.  

PubMed Central

The genes coding for two structurally different isocitrate dehydrogenase isozymes (IDH-I and IDH-II) of a psychrophilic bacterium, Vibrio sp. strain ABE-1, were cloned and sequenced. Open reading frames of the genes (icdI and icdII) are 1,248 and 2,229 bp in length, respectively. The amino acid sequences predicted from the open reading frames of icdI and icdII corresponded to the N-terminal amino acid sequences of the purified IDH-I and IDH-II, respectively. No homology was found between the deduced amino acid sequences of the isozymes; however, the IDH-I, a dimeric enzyme, had a high amino acid sequence identity (74.3%) to the Escherichia coli IDH. The deduced amino acid sequence of the IDH-II, a monomeric enzyme, was not related to any known sequence. However, the IDH-II had an amino acid sequence homologous to that of a cyanogen bromide-cleaved peptide containing a putative active-site methionyl residue of the monomeric IDH of Azotobacter vinelandii. The two genes (icdlI and icdII) were found to be tandemly located in the same orientation. Northern (RNA) blot analyses showed that the two genes are transcribed independently. Primer extension experiments located single transcriptional start sites 39 and 96 bp upstream of the start codons of icdI and icdII, respectively. The amount of icdI transcript but not icdII increased when Vibrio sp. strain ABE-1 cells were cultured in acetate minimal medium. Images

Ishii, A; Suzuki, M; Sahara, T; Takada, Y; Sasaki, S; Fukunaga, N

1993-01-01

338

[14C]methylammonium transport by Frankia sp. strain CpI1.  

PubMed

We describe an NH4+-specific transport system in the N2-fixing symbiotic actinomycete Frankia sp. strain CpI1. [14C]methylammonium was used as an NH4+ analog. No specific transport process was detected when cells were grown on high concentrations of NH4+. A transport system with a high affinity for CH3NH3+ was synthesized after 3 to 4 h of nitrogen starvation. Methylammonium transport was not significantly inhibited by a variety of amino acids, primary amines, and polyamines. Ammonium completely eliminated CH3NH3+ transport. The Km for CH3NH3+ transport was around 2 +/- 1.8 microM with a Vmax of 4 to 5 nmol/min per mg of protein. The electron transport inhibitors cyanide and azide eliminated uptake, as did the uncoupler carbonyl cyanide-m-chlorophenylhydrazone. The sulfydryl reagent p-chloromercuribenzoic acid and the heavy metal thallium also inhibited uptake, suggesting the presence of an NH4+-specific permease. Concentration of CH3NH3+ across the membrane was demonstrated by conducting uptakes at low temperature to slow the metabolism of CH3NH3+ by glutamine synthetase. At 7 degrees C most of the label was concentrated inside the cells in a form that could be chased from the cells by adding excess NH4+ to the medium. At 30 degrees C most of the label was present as an impermeant metabolite. Thin-layer chromatography of cell extracts confirmed that the radioactivity inside the cells was mainly in the form of CH3NH3+ at 7 degrees C but was present as an unidentified metabolite at 30 degrees C. These studies demonstrate that Frankia sp. strain CpI1 has a high-affinity NH4+ transport system that is synthesized in response to NH4+ starvation. PMID:6501218

Mazzucco, C E; Benson, D R

1984-11-01

339

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

SciTech Connect

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-(/sup 14/C)glutamate from 2-keto-(1-/sup 14/C)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 (/sup 14/C)bicarbonate and L-(1-/sup 14/C)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.

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

1987-03-01

340

Characterization and Implications of the Cell Surface Reactivity of Calothrix sp. Strain KC97  

PubMed Central

The cell surface reactivity of the cyanobacterium Calothrix sp. strain KC97, an isolate from the Krisuvik hot spring, Iceland, was investigated in terms of its proton binding behavior and charge characteristics by using acid-base titrations, electrophoretic mobility analysis, and transmission electron microscopy. Analysis of titration data with the linear programming optimization method showed that intact filaments were dominated by surface proton binding sites inferred to be carboxyl groups (acid dissociation constants [pKa] between 5.0 and 6.2) and amine groups (mean pKa of 8.9). Sheath material isolated by using lysozyme and sodium dodecyl sulfate generated pKa spectra similarly dominated by carboxyls (pKa of 4.6 to 6.1) and amines (pKa of 8.1 to 9.2). In both intact filaments and isolated sheath material, the lower ligand concentrations at mid-pKa values were ascribed to phosphoryl groups. Whole filaments and isolated sheath material displayed total reactive-site densities of 80.3 × 10?5 and 12.3 × 10?5 mol/g (dry mass) of cyanobacteria, respectively, implying that much of the surface reactivity of this microorganism is located on the cell wall and not the sheath. This is corroborated by electrophoretic mobility measurements that showed that the sheath has a net neutral charge at mid-pHs. In contrast, unsheathed cells exhibited a stronger negative-charge characteristic. Additionally, transmission electron microscopy analysis of ultrathin sections stained with heavy metals further demonstrated that most of the reactive binding sites are located upon the cell wall. Thus, the cell surface reactivity of Calothrix sp. strain KC97 can be described as a dual layer composed of a highly reactive cell wall enclosed within a poorly reactive sheath.

Phoenix, V. R.; Martinez, R. E.; Konhauser, K. O.; Ferris, F. G.

2002-01-01

341

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.

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

2013-01-01

342

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.

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

2011-01-01

343

Strain improvement of Aspergillus sp. and Penicillium sp. by induced mutation for biotransformation of alpha-pinene to verbenol.  

PubMed

Variants of Aspergillus sp. and Penicillium sp. obtained after treatment with colchicine, ethyl methanesulphonate (EMS), or ultraviolet (UV) irradiation indicated varying levels of significant increases in their efficiency to transform alpha-pinene to verbenol. In case of Aspergillus sp. the UV-induced variant was the best performer with a 15-fold increase in biotransformation efficiency compared to the wild type. In case of colchicine and EMS-induced variants the biotransformation increases were 2- and 8-fold, respectively. The UV-induced variant of Penicillium sp. was capable of eight fold increase in efficiency while the colchicine- and EMS-induced variants were 1.5- and 2-fold, respectively. The variants were characterised with respect to changes in colony morphology, spore dimension, DNA content, and products formed, viz. verbenol and verbenone. PMID:10099602

Agrawal, R; Deepika, N U; Joseph, R

1999-04-20

344

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

345

An Evolutionary Hot Spot: the pNGR234b Replicon of Rhizobium sp. Strain NGR234  

Microsoft Academic Search

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

W. R. Streit; R. A. Schmitz; X. Perret; C. Staehelin; W. J. Deakin; C. Raasch; H. Liesegang; W. J. Broughton

2004-01-01

346

Permeable Reactive Biobarriers for In Situ Cr(VI) Reduction: Bench Scale Tests Using Cellulomonas sp. Strain ES6  

Microsoft Academic Search

Chromate (Cr(VI)) reduction studies were performed in bench scale flow columns using the fermentative subsurface isolate Cellulomonas sp. strain ES6. In these tests, columns packed with either quartz sand or hydrous ferric oxide (HFO)-coated quartz sand, were inoculated with strain ES6 and fed nutrients to stimulate growth before nutrient-free Cr(VI) solutions were injected. Results show that in columns containing quartz

Sridhar Viamajala; Brent M. Peyton; Robin Gerlach; Vaideeswaran; William A. Apel; James N. Petersen

2008-01-01

347

Draft Genome Sequence of Marine-Derived Actinomycete Nocardiopsis sp. Strain TP-A0876, a Producer of Polyketide Pyrones.  

PubMed

Here we report the draft genome sequence of Nocardiopsis sp. strain TP-A0876, isolated from marine sediment, which produces polyketide-derived pyrones called nocapyrones. The genome contains three polyketide synthase (PKS) gene clusters, one of which was proposed to be responsible for nocapyrone biosynthesis. This genome sequence will facilitate the study of the potential for secondary metabolism in Nocardiopsis strains. PMID:25013138

Komaki, Hisayuki; Ichikawa, Natsuko; Hosoyama, Akira; Fujita, Nobuyuki; Igarashi, Yasuhiro

2014-01-01

348

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

349

Formamicin, a novel antifungal antibiotic produced by a strain of Saccharothrix sp. I. Taxonomy, production, isolation and biological properties.  

PubMed

Formamicin, an antifungal antibiotic, was isolated from the cultured broth of an actinomycete strain. The strain was isolated from a soil collected at Setagaya-ku, Tokyo, Japan, and identified as Saccharothrix sp. MK27-91F2. Formamicin was extracted with acetone from cultured mycelia and purified by silicagel and Sephadex LH-20 column chromatographies and CPC (Centrifugal liquid-liquid Partition Chromatography). Formamicin showed strong antimicrobial activity against phytopathogenic fungi. PMID:9592565

Igarashi, M; Kinoshita, N; Ikeda, T; Nakagawa, E; Hamada, M; Takeuchi, T

1997-11-01

350

Draft Genome Sequence of the Actinomycete Rhodococcus sp. Strain AW25M09, Isolated from the Hadsel Fjord, Northern Norway.  

PubMed

The cold-adapted Rhodococcus sp. strain AW25M09 was isolated from an Atlantic hagfish caught off the shore of northern Norway as part of an ongoing bioprospecting project that aims to identify novel bacteria with biotechnological potential. Here, we present the 5.8-Mb draft genome sequence, together with details regarding the origin of the strain and its sequence assembly. PMID:23516194

Hjerde, Erik; Pierechod, Marcin M; Williamson, Adele K; Bjerga, Gro E K; Willassen, Nils P; Smalås, Arne O; Altermark, Bjørn

2013-01-01

351

Identification of a Third Sulfate Activation System in Sinorhizobium sp. Strain BR816: the CysDN Sulfate Activation Complex  

Microsoft Academic Search

Sinorhizobium sp. strain BR816 possesses two nodPQ copies, providing activated sulfate (3-phosphoade- nosine-5-phosphosulfate (PAPS)) needed for the biosynthesis of sulfated Nod factors. It was previously shown that the Nod factors synthesized by a nodPQ double mutant are not structurally different from those of the wild-type strain. In this study, we describe the characterization of a third sulfate activation locus. Two

Carla Snoeck; Christel Verreth; Ismael Hernandez-Lucas; Esperanza Martínez-Romero; Jos Vanderleyden

2006-01-01

352

Isolation, Identification, and Degradation Characteristics of Phenazine1Carboxylic Acid–Degrading Strain Sphingomonas sp. DP58  

Microsoft Academic Search

A phenazine-1-carboxylic acid (PCA)–degrading bacterium, strain DP58, was isolated from pimiento rhizosoil. Based on morphology,\\u000a physiologic tests, 16S rDNA sequence, and phylogenetic characteristics, it was identified as Sphingomonas sp. The PCA-degradation experiments were conducted both in Luria-Bertani and inorganic salt medium at 28?C. The relationship\\u000a between bacterium growth and PCA degradation suggested that strain DP58 could use PCA as the

Zhi-Jian Yang; Wei Wang; Ying Jin; Hong-Bo Hu; Xue-Hong Zhang; Yu-Quan Xu

2007-01-01

353

Mutation breeding of chitosanase-producing strain Bacillus sp. S65 by low-energy ion implantation  

Microsoft Academic Search

In order to obtain an industrial strain with higher chitosanase yield, the wild strain Bacillus sp. S65 cells were mutated by a novel mutagen, nitrogen ion beam, with energy of 15 keV and dose ranging from 2.6 × 1014 to 5.2 × 1015 ions\\/cm2. One mutant, s65F5 with high yield of chitosanase was isolated. Results showed that the production of chitosanase of s65F5 was dramatically increased

Caixin Su; Wei Zhou; Yonghong Fan; Li Wang; Shiguang Zhao; Zengliang Yu

2006-01-01

354

Ecotoxicological assessment of pesticides towards the plant growth promoting activities of Lentil ( Lens esculentus )-specific Rhizobium sp. strain MRL3  

Microsoft Academic Search

This study was designed to evaluate the effect of the selected pesticides [herbicides (metribuzin and glyphosate), insecticides\\u000a (imidacloprid and thiamethoxam) and fungicides (hexaconazole, metalaxyl and kitazin)] at the recommended and the higher dose\\u000a rates on plant growth promoting traits of Rhizobium sp. strain MRL3 isolated from lentil-nodules. Strain MRL3 was explicitly selected owing to its high pesticide-tolerance ability\\u000a and substantial

Munees Ahemad; Mohammad Saghir Khan

2011-01-01

355

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

356

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 Central

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.

Oliveira, Juliana Velasco de Castro; dos Santos, Renato Augusto Correa; Borges, Thuanny A.

2013-01-01

357

Enzymatic reactions and synthesis of n?butyl caproate: esterification, transesterification and aminolysis using a recombinant lipase from Geobacillus thermoleovorans CCR11  

Microsoft Academic Search

The recombinant lipase LipMatCCR11 from the thermophilic strain Geobacillus thermoleovorans CCR11 was applied in the synthesis of n?butyl caproate via transesterification in hexane and xylene. The short chain flavour ester was obtained by alcoholysis from ethyl caproate and n?butyl alcohol and acidolysis from n?butyl butyrate and caproic acid. This enzyme was also used in the condensation reaction from caproic acid

2010-01-01

358

Reinvestigation of Brevibacterium sp. Strain KY-4313 as a Source of Canthaxanthin  

PubMed Central

The hydrocarbon-utilizing Brevibacterium sp. strain KY-4313 was reevaluated for its potential to produce canthaxanthin, a carotenoid pigment of strong commercial interest. Three approaches were used to optimize the canthaxanthin yield from this organism, i.e., the preparation of mutants, the addition of supposedly carotenogenic chemicals to the growth medium, and growth promotion. Following treatment of the parent strain with N-nitrosomethylurea, a presumed mutant was isolated which showed a 32% increase in cellular canthaxanthin content. No effective carotenogenic chemicals were found in connection with hydrocarbon fermentations, in which mainly growth promotion through periodic medium renewal proved conducive to enhanced pigment production. Carotenogenesis could be stimulated in brain heart infusion broth by adding alcohols or retinol. Improved growth in this medium was generally not associated with higher canthaxanthin yields. Both superior growth and pigment levels were obtained in a newly designed medium based on fumaric acid-molasses. The maximum yields of canthaxanthin in shake flasks were (in milligrams per liter) 4.2 (brain heart infusion broth plus propanol-zinc sulfate), 3.6 (hydrocarbon medium), and 9.3 (fumaric acid-molasses), which represent a significant improvement over the originally reported optimal result (1 mg/liter). The corresponding yields of echinenone, the direct precursor of canthaxanthin, were 1.2, 1.6, and 2.3 mg/liter, respectively. Two-liter hydrocarbon batch fermentations involving medium renewal maximally produced 7.2 mg of canthaxanthin and 3.7 mg of echinenone per liter.

Nelis, H. J.; De Leenheer, A. P.

1989-01-01

359

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.

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

2013-01-01

360

Ageing of atrazine in manure amended soils assessed by bioavailability to Pseudomonas sp. strain ADP.  

PubMed

Animal manure is applied to agricultural land in areas of high livestock production. In the present study, we evaluated ageing of atrazine in two topsoils with and without addition of manure and in one subsoil. Ageing was assessed as the bioavailability of atrazine to the atrazine mineralizing bacteria Pseudomonas sp. strain ADP. Throughout an ageing period of 90 days bioavailability was investigated at days 1, 10, 32, 60 and 90, where ~10(8) cells g(-1) of the ADP strain was inoculated to the (14)C-atrazine exposed soil and (14)CO2 was collected over 7 days as a measure of mineralized atrazine. Even though the bioavailable residue decreased in all of the three soils as time proceeded, we found that ageing occurred faster in the topsoils rich in organic carbon than in subsoil. For one topsoil rich in organic carbon content, Simmelkær, we observed a higher degree of ageing when treated with manure. Contrarily, sorption experiments showed less sorption to Simmelkær treated with manure than the untreated soil indicating that sorption processes are not the only mechanisms of ageing. The other topsoil low in organic carbon content, Ringe, showed no significant difference in ageing between the manure-treated and untreated soil. The present study illustrates that not simply the organic carbon content influences adsorption and ageing of atrazine in soil but the origin and composition of organic matter plays an important role. PMID:23824341

Glæsner, Nadia; Bælum, Jacob; Strobel, Bjarne W; Jacobsen, Carsten S

2014-04-01

361

Using transcriptomics to improve butanol tolerance of Synechocystis sp. strain PCC 6803.  

PubMed

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; Hallström, Björn; Nielsen, Jens; Uhlén, Mathias; Hudson, Elton P

2013-12-01

362

Differential Degradation of Bicyclics with Aromatic and Alicyclic Rings by Rhodococcus sp. Strain DK17 ?  

PubMed Central

The metabolically versatile Rhodococcus sp. strain DK17 is able to grow on tetralin and indan but cannot use their respective desaturated counterparts, 1,2-dihydronaphthalene and indene, as sole carbon and energy sources. Metabolite analyses by gas chromatography-mass spectrometry and nuclear magnetic resonance spectrometry clearly show that (i) the meta-cleavage dioxygenase mutant strain DK180 accumulates 5,6,7,8-tetrahydro-1,2-naphthalene diol, 1,2-indene diol, and 3,4-dihydro-naphthalene-1,2-diol from tetralin, indene, and 1,2-dihydronaphthalene, respectively, and (ii) when expressed in Escherichia coli, the DK17 o-xylene dioxygenase transforms tetralin, indene, and 1,2-dihydronaphthalene into tetralin cis-dihydrodiol, indan-1,2-diol, and cis-1,2-dihydroxy-1,2,3,4-tetrahydronaphthalene, respectively. Tetralin, which is activated by aromatic hydroxylation, is degraded successfully via the ring cleavage pathway to support growth of DK17. Indene and 1,2-dihydronaphthalene do not serve as growth substrates because DK17 hydroxylates them on the alicyclic ring and further metabolism results in a dead-end metabolite. This study reveals that aromatic hydroxylation is a prerequisite for proper degradation of bicyclics with aromatic and alicyclic rings by DK17 and confirms the unique ability of the DK17 o-xylene dioxygenase to perform distinct regioselective hydroxylations.

Kim, Dockyu; Yoo, Miyoun; Choi, Ki Young; Kang, Beom Sik; Kim, Tai Kyoung; Hong, Soon Gyu; Zylstra, Gerben J.; Kim, Eungbin

2011-01-01

363

Differential degradation of bicyclics with aromatic and alicyclic rings by Rhodococcus sp. strain DK17.  

PubMed

The metabolically versatile Rhodococcus sp. strain DK17 is able to grow on tetralin and indan but cannot use their respective desaturated counterparts, 1,2-dihydronaphthalene and indene, as sole carbon and energy sources. Metabolite analyses by gas chromatography-mass spectrometry and nuclear magnetic resonance spectrometry clearly show that (i) the meta-cleavage dioxygenase mutant strain DK180 accumulates 5,6,7,8-tetrahydro-1,2-naphthalene diol, 1,2-indene diol, and 3,4-dihydro-naphthalene-1,2-diol from tetralin, indene, and 1,2-dihydronaphthalene, respectively, and (ii) when expressed in Escherichia coli, the DK17 o-xylene dioxygenase transforms tetralin, indene, and 1,2-dihydronaphthalene into tetralin cis-dihydrodiol, indan-1,2-diol, and cis-1,2-dihydroxy-1,2,3,4-tetrahydronaphthalene, respectively. Tetralin, which is activated by aromatic hydroxylation, is degraded successfully via the ring cleavage pathway to support growth of DK17. Indene and 1,2-dihydronaphthalene do not serve as growth substrates because DK17 hydroxylates them on the alicyclic ring and further metabolism results in a dead-end metabolite. This study reveals that aromatic hydroxylation is a prerequisite for proper degradation of bicyclics with aromatic and alicyclic rings by DK17 and confirms the unique ability of the DK17 o-xylene dioxygenase to perform distinct regioselective hydroxylations. PMID:21965391

Kim, Dockyu; Yoo, Miyoun; Choi, Ki Young; Kang, Beom Sik; Kim, Tai Kyoung; Hong, Soon Gyu; Zylstra, Gerben J; Kim, Eungbin

2011-12-01

364

Unique ultrastructure in the elementary body of Chlamydia sp. strain TWAR.  

PubMed Central

The ultrastructure of two prototype strains (TW-183 and AR-39) of Chlamydia sp. strain TWAR was described. The TWAR elementary body (EB) demonstrated a unique morphology and structure distinct from those of other chlamydial organisms. It was pleomorphic but typically pear shaped. The average size was 0.38 micron, with a long axis of 0.44 micron, a short axis of 0.31 micron, and a ratio of the long to the short axes of 1.42. The cytoplasmic mass was round, with an average diameter of 0.24 micron. There was a large periplasmic space. Small, round electron-dense bodies (0.05 micron in diameter), which were attached to the cytoplasm by a stringlike structure, were seen in the periplasmic space. These features are in contrast to those of other chlamydiae, which are typically round with a narrow or barely discernible periplasmic space. The TWAR reticulate body (RB) was morphologically and structurally similar to those of other Chlamydia species, having an average diameter of 0.51 micron and being circular in shape. The ultrastructural observations of the intracellular growth of TWAR in HeLa cells revealed that TWAR underwent the same developmental cycle as do other chlamydiae, i.e., transformation of EB to RB, multiplication by binary fission, and maturation by transformation of RB to EB via the intermediate-form stage. Images

Chi, E Y; Kuo, C C; Grayston, J T

1987-01-01

365

2,4-Dinitrotoluene dioxygenase from Burkholderia sp. strain DNT: similarity to naphthalene dioxygenase.  

PubMed Central

2,4-Dinitrotoluene (DNT) dioxygenase from Burkholderia sp. strain DNT catalyzes the initial oxidation of DNT to form 4-methyl-5-nitrocatechol (MNC) and nitrite. The displacement of the aromatic nitro group by dioxygenases has only recently been described, and nothing is known about the evolutionary origin of the enzyme systems that catalyze these reactions. We have shown previously that the gene encoding DNT dioxygenase is localized on a degradative plasmid within a 6.8-kb NsiI DNA fragment (W.-C. Suen and J. C. Spain, J. Bacteriol. 175:1831-1837, 1993). We describe here the sequence analysis and the substrate range of the enzyme system encoded by this fragment. Five open reading frames were identified, four of which have a high degree of similarity (59 to 78% identity) to the components of naphthalene dioxygenase (NDO) from Pseudomonas strains. The conserved amino acid residues within NDO that are involved in cofactor binding were also identified in the gene encoding DNT dioxygenase. An Escherichia coli clone that expressed DNT dioxygenase converted DNT to MNC and also converted naphthalene to (+)-cis-(1R,2S)-dihydroxy-1,2-dihydronaphthalene. In contrast, the E. coli clone that expressed NDO did not oxidize DNT. Furthermore, the enzyme systems exhibit similar broad substrate specificities and can oxidize such compounds as indole, indan, indene, phenetole, and acenaphthene. These results suggest that DNT dioxygenase and the NDO enzyme system share a common ancestor.

Suen, W C; Haigler, B E; Spain, J C

1996-01-01

366

Natural Electrotransformation of Lightning-Competent Pseudomonas sp. Strain N3 in Artificial Soil Microcosms  

PubMed Central

The lightning-competent Pseudomonas sp. strain N3, recently isolated from soil, has been used to study the extent of natural electrotransformation (NET) or lightning transformation as a horizontal gene transfer mechanism in soil. The variation of electrical fields applied to the soil with a laboratory-scale lightning system provides an estimate of the volume of soil affected by NET. Based on the range of the electric field that induces NET of Pseudomonas strain N3, the volume of soil, where NET could occur, ranges from 2 to 950 m3 per lightning strike. The influence of DNA parameters (amount, size, and purity) and DNA soil residence time were also investigated. NET frequencies (electrotransformants/recipient cells) ranged from 10?8 for cell lysate after 1 day of residence in soil to 4 × 10?7 with a purified plasmid added immediately before the lightning. The electrical field gradient (in kilovolts per cm) also played a role as NET frequencies ranging from 1 × 10?5 at 2.3 kV/cm to 1.7 × 10?4 at 6.5 kV/cm.

Ceremonie, Helene; Buret, Francois; Simonet, Pascal; Vogel, Timothy M.

2006-01-01

367

Algicidal metabolites produced by Bacillus sp. strain B1 against Phaeocystis globosa.  

PubMed

The bloom of Phaeocystis globosa has broken out frequently in the coastal areas of China in recent years, which has led to substantial economic losses. This study shows that Bacillus sp. strain B1, which was previously identified by our group, is effective in regulating P. globosa by excreting active metabolites. Heat stability, pH stability and molecular weight range of the algicidal compounds from strain B1 were measured and the results demonstrated that the algicidal activities of these compounds were not affected by pH or temperature variation. The algicidal compounds extracted with methanol were isolated and purified by ODS-A column chromatography and HPLC. The algicidal compounds corresponding to peaks 2-5 eluted from HPLC were further analysed by quadrupole time-of-flight mass spectrometry (Q-TOF-MS). PeakView™ Software determined the compounds corresponding to peaks 2-5 to be L-histidine, o-tyrosine, N-acetylhistamine and urocanic acid on the basis of the accurate mass information, the isotopic pattern and MS-MS spectra. Furthermore, these compounds were also able to eliminate Skeletonema costatum, Prorocentrum donghaiense and Heterosigma akashiwo. This is the first report of bacteria-derived algicidal compounds being identified only by Q-TOF-MS and PeakView™ Software, and these compounds may be used as the constituents of algicides in the future. PMID:24370882

Zhao, Ling; Chen, Lina; Yin, Pinghe

2014-03-01

368

Sulfur from benzothiophene and alkylbenzothiophenes supports growth of Rhodococcus sp. strain JVH1.  

PubMed

Rhodococcus sp. strain JVH1 was previously reported to use a number of compounds with aliphatic sulfide bridges as sulfur sources for growth. We have shown that although JVH1 does not use the three-ring thiophenic sulfur compound dibenzothiophene, this strain can use the two-ring compound benzothiophene as its sole sulfur source, resulting in growth of the culture and loss of benzothiophene. Addition of inorganic sulfate to the medium reduced the conversion of benzothiophene, indicating that benzothiophene metabolism is repressed by sulfate and that benzothiophene is therefore used specifically as a sulfur source. JVH1 also used all six isomers of methylbenzothiophene and two dimethylbenzothiophene isomers as sulfur sources for growth. Metabolites identified from benzothiophene and some methylbenzothiophenes were consistent with published pathways for benzothiophene biodesulfurization. Products retaining the sulfur atom were sulfones and sultines, the sultines being formed from phenolic sulfinates under acidic extraction conditions. With 2-methylbenzothiophene, the final desulfurized product was 2-methylbenzofuran, formed by dehydration of 3-(o-hydroxyphenyl) propanone under acidic extraction conditions and indicating an oxygenative desulfination reaction. With 3-methylbenzothiophene, the final desulfurized product was 2-isopropenylphenol, indicating a hydrolytic desulfination reaction. JVH1 is the first microorganism reported to use all six isomers of methylbenzothiophene, as well as some dimethylbenzothiophene isomers, as sole sulfur sources. JVH1 therefore possesses broader sulfur extraction abilities than previously reported, including not only sulfidic compounds but also some thiophenic species. PMID:17091342

Kirkwood, Kathlyn M; Andersson, Jan T; Fedorak, Phillip M; Foght, Julia M; Gray, Murray R

2007-10-01

369

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.

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

2013-01-01

370

Enhancement of the potential to utilize octopine in the nonfluorescent Pseudomonas sp. strain 92  

SciTech Connect

The nonfluorescent Pseudomonas sp. strain 92 requires the presence of a supplementary carbon source for growth on octopine, whereas the spontaneous mutant RB100 has acquired the capacity to utilize this opine as the sole carbon and nitrogen source. Insertional mutagenesis of RB100 with transposon Tn5 generated mutants which were unable to grow on octopine and others which grew slowly on this substrate. Both types of mutants yielded revertants that had regained the ability to utilize octopine. Some of the revertants had lost the transposon, whereas in others the transposon was retained but with rearrangements of the insertion site. Genes of octopine catabolism from strain 92 were cloned on a cosmid vector to generate pK3. The clone pK3 conferred the ability to utilize octopine as the sole carbon and nitrogen source on the host Pseudomonas putida KT2440. Although they conferred an equivalent growth phenotype, the mutant genes carried by RB100 and the cloned genes on pK3 differed in their regulation. Utilization of ({sup 14}C)octopine was inducible by octopine in RB100 and was constitutive in KT2440(pK3).

Gill, S.S.; Boivin, R.; Dion, P. (Univ. Laval, Quebec City, Quebec (Canada))

1991-08-01

371

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.

Rapp, Peter; Timmis, Kenneth N.

1999-01-01

372

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

373

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

374

Biodegradation of RDX and MNX with Rhodococcus sp. Strain DN22: New Insights into the Degradation Pathway.  

National Technical Information Service (NTIS)

Previously we demonstrated that Rhodococcus sp. strain DN22 can degrade RDX (hexahydro-1,3,5- trinitro-1,3,5-triazine) aerobically via initial denitration. The present study describes the role of oxygen and water in the key denitration step leading to RDX...

A. Halasz D. Manno J. Hawari N. C. Bruce S. E. Strand

2010-01-01

375

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

376

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

PubMed Central

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 a closely related isomer) and 3-methylbenzoate. Kinetic studies conducted with permeabilized cells and whole-cell suspensions of m-xylene-grown Azoarcus sp. strain T demonstrated that the specific rate of in vitro (3-methylbenzyl)succinate formation accounts for at least 15% of the specific rate of in vivo m-xylene consumption. Based on these findings, we propose that Azoarcus sp. strain T anaerobically oxidizes m-xylene to 3-methylbenzoate (or its CoA thioester) via (3-methylbenzyl)succinate and E-(3-methylphenyl)itaconate (or its CoA thioester) in a series of reactions that are analogous to those recently proposed for anaerobic toluene oxidation to benzoyl-CoA. A deuterium kinetic isotope effect was observed in the (3-methylbenzyl)succinate synthase reaction (and the benzylsuccinate synthase reaction), suggesting that a rate-determining step in this novel fumarate addition reaction involves breaking a C-H bond.

Krieger, Cynthia J.; Beller, Harry R.; Reinhard, Martin; Spormann, Alfred M.

1999-01-01

377

Efficient gene transfer in Synechococcus sp. strains PCC 7942 and PCC 6301 by interspecies conjugation and chromosomal recombination.  

PubMed Central

We developed a versatile, efficient genetic transfer method for Synechococcus sp. strains PCC 7942 and PCC 6301 that exceeds natural transformation efficiencies by orders of magnitude. As a test case, we complemented a histidine auxotroph and identified a hisS homolog of PCC 7942 as the complementing gene.

Tsinoremas, N F; Kutach, A K; Strayer, C A; Golden, S S

1994-01-01

378

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.

Krzyzanowska, Dorota M.; Ossowicki, Adam

2014-01-01

379

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

PubMed

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

Adriaenssens, Evelien M; Guerrero, Leandro D; Makhalanyane, Thulani P; Aislabie, Jackie M; Cowan, Don A

2014-01-01

380

Draft Genome Sequence of Potassium-Dependent Alkaliphilic Bacillus sp. Strain TS-2, Isolated from a Jumping Spider.  

PubMed

The potassium-dependent alkaliphilic Bacillus sp. strain TS-2 was isolated from the mashed extract of a jumping spider, and its draft genome sequence was obtained. Comparative genomic analysis with a previously sequenced sodium-dependent alkaliphilic Bacillus species may reveal potassium-dependent alkaline adaptation mechanisms. PMID:24855304

Fujinami, Shun; Takeda, Kiyoko; Onodera, Takefumi; Satoh, Katsuya; Sano, Motohiko; Narumi, Issay; Ito, Masahiro

2014-01-01

381

Draft Genome Sequence of Nesterenkonia sp. Strain F, Isolated From Aran-Bidgol Salt Lake in Iran  

PubMed Central

The draft genome of the aerobic, Gram-positive, halophilic chemoorganotroph Nesterenkonia sp. strain F consists of a 2,812,133-bp chromosome. This study is the first to report the shotgun-sequenced draft genome of a member of the genus Nesterenkonia.

Sarikhan, Sajjad; Azarbaijani, Reza; Yeganeh, Laleh Parsa; Fazeli, Abolhassan Shahzadeh; Amoozegar, Mohammad Ali; Salekdeh, Ghasem Hosseini

2011-01-01

382

Draft Genome Sequence of Potassium-Dependent Alkaliphilic Bacillus sp. Strain TS-2, Isolated from a Jumping Spider  

PubMed Central

The potassium-dependent alkaliphilic Bacillus sp. strain TS-2 was isolated from the mashed extract of a jumping spider, and its draft genome sequence was obtained. Comparative genomic analysis with a previously sequenced sodium-dependent alkaliphilic Bacillus species may reveal potassium-dependent alkaline adaptation mechanisms.

Fujinami, Shun; Takeda, Kiyoko; Onodera, Takefumi; Satoh, Katsuya; Sano, Motohiko; Narumi, Issay

2014-01-01

383

Draft Genome Sequence of Pseudomonas sp. Strain Ant30-3, a Psychrotolerant Bacterium with Biodegradative Attribute Isolated from Antarctica.  

PubMed

Pseudomonas sp. strain Ant30-3, isolated from fuel-contaminated Antarctic soil, exhibited distinctive psychrotolerant attributes and the potential for degrading aromatic hydrocarbon compounds at cold temperatures. We report here the 6.14-Mb draft genome of Ant30-3, which will provide insights into the genomic basis for the psychrotolerant and biodegradative properties of this bacterium. PMID:24903870

Koo, Hyunmin; Basu, Malay K; Crowley, Michael; Aislabie, Jackie; Bej, Asim K

2014-01-01

384

Draft genome sequence of Nesterenkonia sp. strain F, isolated from Aran-Bidgol Salt Lake in Iran.  

PubMed

The draft genome of the aerobic, Gram-positive, halophilic chemoorganotroph Nesterenkonia sp. strain F consists of a 2,812,133-bp chromosome. This study is the first to report the shotgun-sequenced draft genome of a member of the genus Nesterenkonia. PMID:21914888

Sarikhan, Sajjad; Azarbaijani, Reza; Yeganeh, Laleh Parsa; Fazeli, Abolhassan Shahzadeh; Amoozegar, Mohammad Ali; Salekdeh, Ghasem Hosseini

2011-10-01

385

Degradation of chlorobenzenes at nanomolar concentrations by Burkholderia sp. strain PS14 in liquid cultures and in soil  

SciTech Connect

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 of 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 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.

Rapp, P.; Timmis, K.N. [GBF-National Research Centre for Biotechnology, Braunschweig (Germany). Div. of Microbiology

1999-06-01

386

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.

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

387

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.

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

2014-01-01

388

Draft Genome Sequence of Pseudomonas sp. Strain Ant30-3, a Psychrotolerant Bacterium with Biodegradative Attribute Isolated from Antarctica  

PubMed Central

Pseudomonas sp. strain Ant30-3, isolated from fuel-contaminated Antarctic soil, exhibited distinctive psychrotolerant attributes and the potential for degrading aromatic hydrocarbon compounds at cold temperatures. We report here the 6.14-Mb draft genome of Ant30-3, which will provide insights into the genomic basis for the psychrotolerant and biodegradative properties of this bacterium.

Basu, Malay K.; Crowley, Michael; Aislabie, Jackie; Bej, Asim K.

2014-01-01

389

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.

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

390

Identification of the Major Glycolipid from Mycoplasma SP., Strain J as 3,4,6-Triacyl-beta-D-Glucopyranose.  

National Technical Information Service (NTIS)

Mycoplasma sp., strain J, contains two glycolipids, cholesteryl beta-D-glucoside and 3,4,6-triacyl-beta-D-glucopyranose. The structure of the latter was proven by standard chemical procedures. Glycolipids comprise about 20% of the total lipids of the orga...

P. F. Smith W. R. Mayberry

1968-01-01

391

Draft Genome Sequence of Nitrosospira sp. Strain APG3, a Psychrotolerant Ammonia-Oxidizing Bacterium Isolated from Sandy Lake Sediment.  

PubMed

Bacteria in the genus Nitrosospira play vital roles in the nitrogen cycle. Nitrosospira sp. strain APG3 is a psychrotolerant betaproteobacterial ammonia-oxidizing bacterium isolated from freshwater lake sediment. The draft genome revealed that it represents a new species of cluster 0 Nitrosospira, which is presently not represented by described species. PMID:24201205

Garcia, Juan C; Urakawa, Hidetoshi; Le, Vang Q; Stein, Lisa Y; Klotz, Martin G; Nielsen, Jeppe L

2013-01-01

392

Variation in composition and yield of exopolysaccharides produced by Klebsiella sp. strain K32 and Acinetobacter calcoaceticus BD4.  

PubMed Central

The exopolysaccharides produced by Klebsiella sp. strain K32 and Acinetobacter calcoaceticus BD4 under different growth conditions have been analyzed for sugar composition. The first use of ion chromatography for the quantitative determination of microbial exopolysaccharide composition is reported. Klebsiella sp. strain K32 produced a polymer composed of rhamnose, galactose, and mannose early in its fermentation. The composition of the polymer varied markedly depending on the growth stage of the organism. Klebsiella sp. strain K32 grown in a fermentor produced a polymer which was rich in mannose during early exponential growth in a complex medium, but in the late stationary phase it did not contain detectable levels of mannose. The rhamnose present in the polymer increased from 12 to 55% over the course of growth, whereas galactose decreased from 63 to 45%. A. calcoaceticus BD4 produced a polymer containing rhamnose, glucose, mannose throughout its growth and stationary phase. Klebsiella sp. strain K32 and A. calcoaceticus BD4 were grown on various carbon sources in shake flasks. The polymer yield and composition from both organisms were found to vary with the carbon source. The exopolysaccharide with the highest mannose composition was obtained by using rhamnose as a carbon source for both organisms. These and other data suggest that regulatory changes caused by growth on different substrates result in either the production of a different distribution of polymers or a change in exopolysaccharide structure.

Bryan, B A; Linhardt, R J; Daniels, L

1986-01-01

393

Draft Genome Sequence of the Polyextremophilic Exiguobacterium sp. Strain S17, Isolated from Hyperarsenic Lakes in the Argentinian Puna  

PubMed Central

Exiguobacterium sp. strain S17 is a moderately halotolerant, arsenic-resistant bacterium that was isolated from Laguna Socompa stromatolites in the Argentinian Puna. The draft genome sequence suggests potent enzyme candidates that are essential for survival under multiple environmental extreme conditions, such as high levels of UV radiation, elevated salinity, and the presence of critical arsenic concentrations.

Ordonez, Omar F.; Lanzarotti, Esteban; Kurth, Daniel; Gorriti, Marta F.; Revale, Santiago; Cortez, Nestor; Vazquez, Martin P.; Farias, Maria E.

2013-01-01

394

Hydrolytic enzyme activity of Paenibacillus sp. strain B2 and effects of the antagonistic bacterium on cell integrity of two soil-borne pathogenic fungi  

Microsoft Academic Search

Paenibacillus sp. strain B2, isolated from the mycorrhizosphere of Sorghum bicolor and having an antagonistic activity towards soil-borne fungal pathogens, possessed extracellular cellulolytic, proteolytic, chitinolytic and pectinolytic enzyme activities. The eventual role of these lytic enzymes in cellular interactions between Paenibacillus sp. strain B2 and Phytophthora parasitica and Fusariumoxysporum was investigated by electron microscopy and molecular cytology. Electron microscopic observations

S. W Budi; D van Tuinen; C Arnould; E Dumas-Gaudot; V Gianinazzi-Pearson; S Gianinazzi

2000-01-01

395

Characterization and purification of bile salt hydrolase from Lactobacillus sp. strain 100-100  

SciTech Connect

The authors have characterized and purified the bile salt hydrolase from Lactobacillus sp. strain 100-100. Bile salt hydrolase from cells of the strain was purified with column and high-performance liquid chromatography. The activity was assayed in whole cells and cell-free extracts with either a radiochemical assay involving ({sup 14}C)taurocholic acid or a nonradioactive assay involving trinitrobenzene sulfonate. The activity was detectable only in stationary-phase cells. Within 20 min after conjugated bile acids were added to stationary-phase cultures of strain 100-100, the activity in whole cells increased to levels three- to fivefold higher than in cells from cultures grown in medium free of bile salts. In cell-free extracts, however, the activity was about equal whether or not the cells have been grown with bile salts present. When supernatant solutions from cultures grown in medium containing taurocholic acid were used to suspend cells grown in medium free of the bile salt, the bile salt hydrolase activity detected in whole cells increased two- to threefold. Two forms of the hydrolase were purified from the cells and designated hydrolases A and B. They eluted from anion-exchange high-performance liquid chromatography in two sets of fractions, A at 0.15 M NaCl and B at 0.18 M NaCl. Their apparent molecular weights in nondenaturing polyacrylamide gel electrophoresis were 115,000 and 105,000, respectively. However, discrepancies existed in the apparent molecular weights and number of peptides detected in sodium dodecyl sulfate-polyacrylamide gel electrophoresis of the two forms. Whether the enzyme exists in two forms in the cells remains to be determined.

Lundeen, S.G.; Savage, D.C. (Univ. of Tennessee, Knoxville (USA))

1990-08-01

396

Alginate-Dependent Gene Expression Mechanism in Sphingomonas sp. Strain A1.  

PubMed

Sphingomonas sp. strain A1, a Gram-negative bacterium, directly incorporates alginate polysaccharide into the cytoplasm through a periplasmic alginate-binding protein-dependent ATP-binding cassette transporter. The polysaccharide is degraded to monosaccharides via the formation of oligosaccharides by endo- and exotype alginate lyases. The strain A1 proteins for alginate uptake and degradation are encoded in both strands of a genetic cluster in the bacterial genome and inducibly expressed in the presence of alginate. Here we show the function of the alginate-dependent transcription factor AlgO and its mode of action on the genetic cluster and alginate oligosaccharides. A putative gene within the genetic cluster seems to encode a transcription factor-like protein (AlgO). Mutant strain A1 (?AlgO mutant) cells with a disrupted algO gene constitutively produced alginate-related proteins. DNA microarray analysis indicated that wild-type cells inducibly transcribed the genetic cluster only in the presence of alginate, while ?AlgO mutant cells constitutively expressed the genetic cluster. A gel mobility shift assay showed that AlgO binds to the specific intergenic region between algO and algS (algO-algS). Binding of AlgO to the algO-algS intergenic region diminished with increasing alginate oligosaccharides. These results demonstrated a novel alginate-dependent gene expression mechanism. In the absence of alginate, AlgO binds to the algO-algS intergenic region and represses the expression of both strands of the genetic cluster, while in the presence of alginate, AlgO dissociates from the algO-algS intergenic region via binding to alginate oligosaccharides produced through the lyase reaction and subsequently initiates transcription of the genetic cluster. This is the first report on the mechanism by which alginate regulates the expression of the gene cluster. PMID:24816607

Hayashi, Chie; Takase, Ryuichi; Momma, Keiko; Maruyama, Yukie; Murata, Kousaku; Hashimoto, Wataru

2014-07-15

397

Three dehalogenases and physiological restraints in the biodegradation of haloalkanes by Arthrobacter sp. strain HA1.  

PubMed Central

Arthrobacter sp. strain HA1 utilizes 18 C2-to-C8 1-haloalkanes for growth and synthesizes an inducible 1-bromoalkane debrominase of unknown physiological function (R. Scholtz, T. Leisinger, F. Suter, and A.M. Cook, J. Bacteriol. 169:5016-5021, 1987) in addition to an inducible 1-chlorohexane halidohydrolase which dehalogenates some 50 substrates, including alpha, omega-dihaloalkanes. alpha, omega-Dihaloalkanes were utilized by cultures of strain HA1 under certain conditions only. C9 and C8 homologs prevented growth. At suitable concentrations, C7-to-C5 homologs could serve as sole sources of carbon and energy for growth. C4 and C3 homologs could be utilized only in the presence of a second substrate (e.g., butanol), and the C2 homolog was not degraded. Kinetics of growth and substrate utilization indicated that cells of strain HA1 growing in butanol-salts medium could be used to test whether compounds induced the 1-chlorohexane halidohydrolase. No gratuitous induction of synthesis of the enzyme was observed. Many enzyme substrates (e.g., bromobenzene) did not induce synthesis of the enzyme, though the enzyme sequence to degrade the product (phenol) was present. Some inducers (e.g., bromomethane) were enzyme substrates but not growth substrates. In an attempt to find a physiological role for the 1-bromoalkane debrominase, we observed that several long-chain haloaliphatic compounds (greater than C9; e.g., 1-bromohexadecane and 1-chlorohexadecane) were utilized for growth and that induced cells could dehalogenate several 1-haloalkanes (at least C4 to C16). The dehalogenation of the long-chain compounds could not be assayed in the cell extract, so we presume that a third haloalkane dehalogenase was present.(ABSTRACT TRUNCATED AT 250 WORDS)

Scholtz, R; Messi, F; Leisinger, T; Cook, A M

1988-01-01

398

"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

399

Cyclodextrin glycosyltransferase production by new Bacillus sp. strains isolated from brazilian soil  

PubMed Central

Three strains of Bacillus sp. (BACRP, BACNC-1 and BACAR) were isolated from soil adhered to cassava husk. CGTase specific activity for the three isolated strains was higher when cultivated at 40°C. Potato starch, cassava starch, maltodextrin and glucose were used as carbon source and growth temperatures varied from 25 to 55°C. The three isolates presented higher CGTase specific activity when cultivated with potato starch at 40°C. Isolated BACRP and BACAR presented specific activity of 4.0×10–3 and 2.2×10–3 U/mg prot at pH 7.0, respectively, when cultivated in mediums added with NaCl 2%; at pH 10,0 their activities were of 3.4×10–3 and 3.0×10–3 U/mg prot, respectively, in the same concentration of NaCl. On the other hand, the isolated BACNC-1 presented activity specific of 2.4×10–3 U/mg prot when cultivated at pH 7.0 added of NaCl 1%, and at pH 10.0 the specific activity was of 3.4×10–3 U/mg prot without NaCl addition. This work also showed the presence of cyclodextrins formed during fermentation process and that precipitation with acetone or lyophilization followed by dialysis was efficient at removing CDs (cyclodextrins), thus, eliminating interference in the activity assays. The enzyme produced by the BACAR strain was partially purified and ?-CD was liberated as a reaction product.

Menocci, Vivian; Goulart, Antonio Jose; Adalberto, Paulo Roberto; Tavano, Olga Luisa; Marques, Daniela Parreira; Contiero, Jonas; Monti, Rubens

2008-01-01

400

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

401

Regulation by hetC of Genes Required for Heterocyst Differentiation and Cell Division in Anabaena sp. Strain PCC 7120  

PubMed Central

Unlike those of the wild-type strain, proheterocysts of the Anabaena sp. strain PCC 7120 hetC strain keep dividing. ftsZ, the most critical cell division gene, is up-regulated in hetC proheterocysts. Heterocyst differentiation genes hglD, hglE, patB, nifB, and xisA are no longer expressed in the hetC mutant. hetC also regulates the expression of patA, a pattern formation gene.

Wang, Yu; Xu, Xudong

2005-01-01

402

Isolation and characterization of a Cr(VI)-reduction Ochrobactrum sp. strain CSCr-3 from chromium landfill.  

PubMed

A strain CSCr-3 with high Cr(VI)-reducing ability under alkaline conditions was isolated from a chromium landfill and identified as Ochrobactrum sp. on the basis of 16S rRNA gene sequence analysis. The cells were rod shaped, Gram-negative and motile. The physiological characteristics and Cr(VI)-reduction of the strain were also studied. The results showed that the Ochrobactrum sp. strain CSCr-3 was tolerant to very high concentration of Cr(VI) (800 mg/L) and capable of reducing different forms of Cr(VI) (chromate and dichromate), under a wide range of temperatures (25-40 degrees C) and pH (7-11) with optimum at 35 degrees C and initial pH 10. Higher rates of Cr(VI)-reduction were observed with higher initial cell and Cr(VI) concentrations. Strain CSCr-3 could reduce Cr(VI) very efficiently over a wide range of Cr(VI) concentrations (100-800 mg/L). The addition of glucose caused a dramatic increase in Cr(VI)-reduction by Ochrobactrum sp. CSCr-3, while the presence of sulfate or nitrate had no influence. The presence of other metals, such as Cu, Co, Mn, etc., significantly stimulated Cr(VI)-reduction ability by the strain CSCr-3. The results obtained in this study have significance for the bioremediation of chromate pollution. PMID:18722054

He, Zhiguo; Gao, Fengling; Sha, Tao; Hu, Yuehua; He, Chao

2009-04-30

403

Soluble methane monooxygenase gene clusters from trichloroethylene-degrading Methylomonas sp. strains and detection of methanotrophs during in situ bioremediation  

SciTech Connect

The soluble MMO (sMMO) gene clusters from group 1 methanotrophs were characterized. An 9.1-kb KpmI fragment from Methylomonas sp. strain KSWIII and a 7.5-kb SalI fragment from methylomonas sp. strain KSPIII which contained the sMMO gene clusters were cloned and sequenced. The sequences of these two fragments were almost identical. The sMMO gene clusters in the fragment consisted of six open reading frames which were 52 to 79% similar to the corresponding genes of previously described sMMO gene clusters of the group 2 and group 10 methanotrophs. The phylogenetic analysis of the predicted amino acid sequences of sMMO demonstrated that the sMMOs from these strains were closer to that from M. capsulatus Bath in the group X methanotrophs than to those from Methylosinus trichosporium OB3b and Methylocystis sp. strain M in the group 2 methanotrophs. Based on the sequence data of sMMO genes of the strains and other methanotrophs, the authors designed a new PCR primer to amplify sMMO gene fragments of all the known methanotrophs harboring the mmoX gene. The primer set was successfully used for detecting methanotrophs in the ground-water of trichloroethylene-contaminated sites during in situ-biostimulation treatments.

Shigematsu, Toru; Hanada, Satoshi; Eguchi, Masahiro; Kamagata, Yoichi; Kanagawa, Takahiro; Kurane; Ryuichiro

1999-12-01

404

Soluble Methane Monooxygenase Gene Clusters from Trichloroethylene-Degrading Methylomonas sp. Strains and Detection of Methanotrophs during In Situ Bioremediation  

PubMed Central

The soluble MMO (sMMO) gene clusters from group I methanotrophs were characterized. An 8.1-kb KpnI fragment from Methylomonas sp. strain KSWIII and a 7.5-kb SalI fragment from Methylomonas sp. strain KSPIII which contained the sMMO gene clusters were cloned and sequenced. The sequences of these two fragments were almost identical. The sMMO gene clusters in the fragment consisted of six open reading frames which were 52 to 79% similar to the corresponding genes of previously described sMMO gene clusters of the group II and group X methanotrophs. The phylogenetic analysis of the predicted amino acid sequences of sMMO demonstrated that the sMMOs from these strains were closer to that from M. capsulatus Bath in the group X methanotrophs than to those from Methylosinus trichosporium OB3b and Methylocystis sp. strain M in the group II methanotrophs. Based on the sequence data of sMMO genes of our strains and other methanotrophs, we designed a new PCR primer to amplify sMMO gene fragments of all the known methanotrophs harboring the mmoX gene. The primer set was successfully used for detecting methanotrophs in the groundwater of trichloroethylene-contaminated sites during in situ-biostimulation treatments.

Shigematsu, Toru; Hanada, Satoshi; Eguchi, Masahiro; Kamagata, Yoichi; Kanagawa, Takahiro; Kurane, Ryuichiro

1999-01-01

405

A novel competence gene, comP, is essential for natural transformation of Acinetobacter sp. strain BD413.  

PubMed Central

Acinetobacter sp. strain BD413 (= ATCC 33305), a nutritionally versatile bacterium, has an extremely efficient natural transformation system. Here we describe the generation of eight transformation-affected mutants of Acinetobacter sp. strain BD413 by insertional mutagenesis. These mutants were found by Southern blot analysis and complementation studies to result from single nptII marker insertions at different chromosomal loci. DNA binding and uptake studies with one mutant, T205, revealed that the transformation deficiency of this mutant results from a complete lack of DNA binding and, therefore, uptake activity. A novel competence gene essential for natural transformation, named comP, was cloned by complementation of mutant T205. The nucleotide sequence of comP was determined, and its deduced 15-kDa polypeptide displays significant similarities to type IV pilins. Analysis of the ultrastructure of a transformation-deficient comP mutant and the transformation-competent wild-type strain revealed that both are covered with bundle-forming thin fimbriae (3 to 4 nm in diameter) and individual thick fimbriae (6 nm in diameter). These results provide evidence that the pilinlike ComP is unrelated to the piluslike structures of strain BD413. Taking all data into account, we propose that ComP functions as a major subunit of an organelle acting as a channel or pore mediating DNA binding and/or uptake in Acinetobacter sp. strain BD413.

Porstendorfer, D; Drotschmann, U; Averhoff, B

1997-01-01

406

Biodegradation of phenol in batch culture by pure and mixed strains of Paenibacillus sp. and Bacillus cereus.  

PubMed

The bacterial strains, Paenibacillus sp. (AY952466) and Bacillus cereus (DQ002384), have proven capacity to degrade lignin and pentachlorophenol. In the present study, both strains were screened at different concentrations of phenol on mineral salt agar medium in the presence of glucose. At optimized condition (pH 7.5 +/- 0.2, 37 +/- 1 degrees C, 120 rpm, 1% glucose w/v), it was observed that both Paenibacillus sp., B. cereus and its mixed culture degraded phenol (500 mg/l) up to 53.86%, 91.63% and 67.76% within 168 h of incubation, respectively. Phenol degradation was routinely monitored spectrophotometrically and further confirmed by HPLC. Catechol and 2-hydroxy muconic semialdehyde were identified as intermediate products from degraded samples using GC-MS. It was also observed that, in the absence of glucose, bacterial strains were unable to utilize phenol indicating the phenomenon of co-metabolism. PMID:20380142

Singh, Shail; Singh, Beer Bahadur; Chandra, Ram

2009-01-01

407

First genomic analysis of the broad-host-range Rhizobium sp. LPU83 strain, a member of the low-genetic diversity Oregon-like Rhizobium sp. group.  

PubMed

Alfalfa (Medicago sativa) is the most cultivated forage legume for cattle and animal feeding, occupying about 32 million hectares over the world. Management of the N?-fixing symbiosis of this plant to maximize crop production is therefore an important objective. A fundamental constraint to this aim emerges when a moderately low soil pH hampers the establishment of an effective symbiosis with indigenous and/or inoculated rhizobia. Besides the association of alfalfa with Ensifer (Sinorhizobium) meliloti, this legume is able to establish a symbiosis with Ensifer (Sinorhizobium) medicae and with less characterized types of rhizobia, such as the Oregon-like strains, Rhizobium sp. Or191 initially isolated in the USA, and the Rhizobium sp. LPU83 strain, from Argentina. These strains are acid-tolerant, highly competitive for acidic-soil-alfalfa nodulation, but inefficient for biological nitrogen fixation with alfalfa. These features position the Oregon-like rhizobia as strains of potential risk in agricultural soils compared with the efficient symbiont E. meliloti. Moreover, the collected genetic information has revealed that the genomic structure of these rhizobial isolates is complex in terms of sequence similarities shared with other rhizobia. Such a "patched" genetic composition has obviously imposed severe restrictions to the classical taxonomy of these rhizobia. In this work we summarize the accumulated knowledge about the Oregon-like rhizobia and present a phylogenetic analysis based on genome sequence data of Rhizobium sp. LPU83 obtained by a high-throughput sequencing on the Genome Sequencer FLX Titanium platform. The accessibility of the complete genomic sequence will release up more experimental possibilities since this information will then enable biochemical studies as well as proteomics and transcriptomics approaches. PMID:21329739

Tejerizo, Gonzalo Torres; Del Papa, María Florencia; Draghi, Walter; Lozano, Mauricio; Giusti, María de Los Ángeles; Martini, Carla; Salas, María Eugenia; Salto, Ileana; Wibberg, Daniel; Szczepanowski, Rafael; Weidner, Stefan; Schlüter, Andreas; Lagares, Antonio; Pistorio, Mariano

2011-08-20

408

Growth substrate effects on acetate and methanol catabolism in Methanosarcina sp. strain TM-1.  

PubMed Central

When Methanosarcina sp. strain TM-1 is grown in medium in which both methanol and acetate are present, growth is biphasic, with methanol used as the primary catabolic substrate during the first phase. To better understand this phenomenon, we grew cells on methanol or on acetate or on both and examined the abilities of anaerobically washed cells to catabolize these substrates. Washed acetate-grown cells incubated with 10 mM acetate, 10 mM methanol, or both substrates together produced methane at initial rates of 325, 3, and 315 nmol min-1 mg of protein-1, respectively. Although the initial rate of methanogenesis from both substrates was nearly identical to the rate for acetate alone, after several hours of incubation the rate was greater for cells provided with both substrates. Studies with 14C-labeled methanol indicated that methanol was catabolized to methane at increasing rates by acetate-grown cells in a manner reminiscent of an induction curve, but only when cells were provided with acetate as a cosubstrate. Acetate was presumably providing energy and carbon for induction of methanol-catabolic enzymes. Methanol-grown cells showed a pattern of substrate utilization significantly different from that of acetate-grown cells, producing methane from 10 mM acetate, 10 mM methanol, or both substrates at initial rates of 10, 280, and 450 nmol min-1 mg of protein-1, respectively. There was significant oxidation of the methyl group of acetate during metabolism of both substrates. Cells grown on methanol-acetate and harvested before methanol depletion (methanol phase) showed catabolic patterns nearly identical to those of methanol-grown cells, including a low rate of methanogenesis from acetate. Cells harvested from methanol-acetate cultures in the acetate phase were capable of significant methanogenesis from either methanol or acetate alone, and the rate from both substrates together was nearly equal to the sum of the rates for the single substrates. When both 10 mM methanol and 10 mM acetate were presented to the acetate-phase cells, there was a preference for the methanol. These results are consistent with a model for regulation in Methanosarcina sp. strain TM-1 in which methanol represses acetate catabolism while methanol catabolism is inducible.

Zinder, S H; Elias, A F

1985-01-01

409

Draft Genome Sequence of Marine Cyanobacterium Synechococcus sp. Strain NKBG042902, Which Harbors a Homogeneous Plasmid Available for Metabolic Engineering  

PubMed Central

The marine cyanobacterium Synechococcus sp. strain NKBG042902 was isolated from coastal areas in Japan. Strain NKBG042902 has four plasmids: pSY8, pSY9, pSY10, and pSY11. Moreover, the hybrid plasmid pUSY02 containing pSY11 and Escherichia coli plasmid pUC18 was constructed for this strain. The genetic manipulation technique using pUSY02 was established for this strain and used in metabolic engineering. Here, we report the draft genome sequence of this strain, which has 77 contigs comprising a total length of 3,319,479 bp, with a G+C content of 49.4%.

Honda, Toru; Liang, Yue; Arai, Daichi; Ito, Yasuhito; Yoshino, Tomoko

2014-01-01

410

Cloning, Expression, and Characterization of the katG Gene, Encoding Catalase-Peroxidase, from the Polycyclic Aromatic Hydrocarbon-Degrading Bacterium Mycobacterium sp. Strain PYR-1  

Microsoft Academic Search

A 81-kDa protein from Mycobacterium sp. strain PYR-1 was expressed in response to exposure of the strain to the polycyclic aromatic hydrocarbon pyrene and recovered by two-dimensional gel electrophoresis. The N-terminal sequence of the protein indicated that it was similar to catalase-peroxidase. An oligonucleotide probe designed from this sequence was used to screen a genomic library of Mycobacterium sp. strain

RONG-FU WANG; DAVID WENNERSTROM; WEI-WEN CAO; ASHRAF A. KHAN; CARL E. CERNIGLIA

2000-01-01

411

Characterization of the 4-Hydroxybenzoyl-Coenzyme A Thioesterase from Arthrobacter sp. Strain SU  

PubMed Central

The Arthrobacter sp. strain SU 4-chlorobenzoate (4-CBA) dehalogenation pathway converts 4-CBA to 4-hydroxybenzoate (4-HBA). The pathway operon contains the genes fcbA, fcbB, and fcbC (A. Schmitz, K. H. Gartemann, J. Fiedler, E. Grund, and R. Eichenlaub, Appl. Environ. Microbiol. 58:4068-4071, 1992). Genes fcbA and fcbB encode 4-CBA-coenzyme A (CoA) ligase and 4-CBA-CoA dehalogenase, respectively, whereas the function of fcbC is not known. We subcloned fcbC and expressed it in Escherichia coli, and we purified and characterized the FcbC protein. A substrate activity screen identified benzoyl-CoA thioesters as the most active substrates. Catalysis of 4-HBA-CoA hydrolysis to 4-HBA and CoA occurred with a kcat of 6.7 s?1 and a Km of 1.2 ?M. The kcat pH rate profile for 4-HBA-CoA hydrolysis indicated optimal activity over a pH range of 6 to 10. The amino acid sequence of the FcbC protein was compared to other sequences contained in the protein sequence data banks. A large number of sequence homologues of unknown function were identified. On the other hand, the 4-HBA-CoA thioesterases isolated from 4-CBA-degrading Pseudomonas strains did not share significant sequence identity with the FcbC protein, indicating early divergence of the thioesterase-encoding genes.

Zhuang, Zhihao; Gartemann, Karl-Heinz; Eichenlaub, Rudolf; Dunaway-Mariano, Debra

2003-01-01

412

Starvation-specific formation of a peripheral exopolysaccharide by a marine Pseudomonas sp., strain S9.  

PubMed Central

The marine bacterium Pseudomonas sp. strain S9 produces exopolysaccharides (EPS) during both growth and total energy source and nutrient starvation. Transmission electron microscopy of immunogold-labeled cells demonstrated that the EPS is closely associated with the cell surface during growth (integral EPS), while both the integral form and a loosely associated extracellular (peripheral) form were observed during starvation. Formation and release of the latter rendered the starvation medium viscous. In addition, after 3 h of starvation in static conditions, less than 5% of the cells were motile, compared with 100% at the onset of starvation and approximately 80% subsequent to release of the peripheral EPS at 27 h of starvation. Inhibition of protein synthesis with chloramphenicol added before 3 h of starvation caused no increase in viscosity. However, addition of chloramphenicol at 3 h did not prevent the subsequent increase in viscosity displayed by S9 cells. The amount of integral EPS increased for both nontreated and chloramphenicol-treated S9 cells during the first hour of starvation, with a subsequent equal decrease. The chloramphenicol-treated cells, as well as cells of a transposon-generated mutant strain deficient in peripheral EPS formation, remained adhesive to a hydrophobic inanimate surface during the initial 5 h of starvation, whereas nontreated wild-type cells had progressively decreased adhesion capacity. During the initial 5 h of starvation, most of the nontreated cells but only a small fraction of the chloramphenicol-treated and mutant cells detached from the hydrophobic substratum.(ABSTRACT TRUNCATED AT 250 WORDS) Images

Wrangstadh, M; Szewzyk, U; Ostling, J; Kjelleberg, S

1990-01-01

413

Atrazine chlorohydrolase from Pseudomonas sp. strain ADP: gene sequence, enzyme purification, and protein characterization.  

PubMed Central

Pseudomonas sp. strain ADP metabolizes atrazine to carbon dioxide and ammonia via the intermediate hydroxyatrazine. The genetic potential to produce hydroxyatrazine was previously attributed to a 1.9-kb AvaI DNA fragment from strain ADP (M. L. de Souza, L. P. Wackett, K. L. Boundy-Mills, R. T. Mandelbaum, and M. J. Sadowsky, Appl. Environ. Microbiol. 61:3373-3378, 1995). In this study, sequence analysis of the 1.9-kb AvaI fragment indicated that a single open reading frame, atzA, encoded an activity transforming atrazine to hydroxyatrazine. The open reading frame for the chlorohydrolase was determined by sequencing to be 1,419 nucleotides and encodes a 473-amino-acid protein with a predicted subunit molecular weight of 52,421. The deduced amino acid sequence matched the first 10 amino acids determined by protein microsequencing. The protein AtzA was purified to homogeneity by ammonium sulfate precipitation and anion-exchange chromatography. The subunit and holoenzyme molecular weights were 60,000 and 245,000 as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and gel filtration chromatography, respectively. The purified enzyme in H2(18)O yielded [18O]hydroxyatrazine, indicating that AtzA is a chlorohydrolase and not an oxygenase. The most related protein sequence in GenBank was that of TrzA, 41% identity, from Rhodococcus corallinus NRRL B-15444R. TrzA catalyzes the deamination of melamine and the dechlorination of deethylatrazine and desisopropylatrazine but is not active with atrazine. AtzA catalyzes the dechlorination of atrazine, simazine, and desethylatrazine but is not active with melamine, terbutylazine, or desethyldesisopropylatrazine. Our results indicate that AtzA is a novel atrazine-dechlorinating enzyme with fairly restricted substrate specificity and contributes to the microbial hydrolysis of atrazine to hydroxyatrazine in soils and groundwater.

de Souza, M L; Sadowsky, M J; Wackett, L P

1996-01-01

414

Pathways for degrading TNT by Thu-Z: a Pantoea sp. strain.  

PubMed

2,4,6-Trinitrotoluene (TNT), an extensively used and versatile explosive, is harmful in soil and water. In the present study, four bacterial strains capable of degrading TNT have been isolated from contaminated sites and named as Thu-A, Thu-B, Thu-C, and Thu-Z. Thu-Z, which gave the highest degradation efficiency compared to the others, was assigned to the genus Pantoea according to its 16S rRNA gene. Similarities in both biochemical properties and morphology suggested that Thu-Z was a Pantoea sp. strain. Thu-Z was proved to be capable of using TNT as a sole nitrogen source by cleaving NO(2) from the nitroaromatic ring by direct aromatic ring reduction. Under nitrogen-limited conditions, 96.6 %?N of TNT was consumed by Thu-Z for growth, which was determined in terms of NaNO(2). Trace nitro reduction metabolites such as 2,4-diamino-6-nitrotoluene (24Dam) and 2,6-diamino-4-nitrotoluene (26Dam) were identified in the presence of (NH(4))(2)SO(4). On the other hand, 4,4',6,6'-tetranitro-2,2'-azoxytoluene (22Azo) and 2,2',6,6'-tetranitro-4,4'-azoxytoluene (44Azo) were detected in the absence of (NH(4))(2)SO(4). These indicated the existence of a dual pathway for Thu-Z, while the direct aromatic ring reduction was predominant. Addition of a nitrogen source ((NH(4))(2)SO(4)) after inoculation stimulated the growth of Thu-Z and accelerated TNT degradation. PMID:23076565

Zou, Liangdong; Lu, Diannan; Liu, Zheng

2012-12-01

415

Metabolomic Analysis of Cold Acclimation of Arctic Mesorhizobium sp. Strain N33  

PubMed Central

Arctic Mesorhizobium sp. N33 isolated from nodules of Oxytropis arctobia in Canada’s eastern Arctic has a growth temperature range from 0°C to 30°C and is a well-known cold-adapted rhizobia. The key molecular mechanisms underlying cold adaptation in Arctic rhizobia remains totally unknown. Since the concentration and contents of metabolites are closely related to stress adaptation, we applied GC-MS and NMR to identify and quantify fatty acids and water soluble compounds possibly related to low temperature acclimation in strain N33. Bacterial cells were grown at three different growing temperatures (4°C, 10°C and 21°C). Cells from 21°C were also cold-exposed to 4°C for different times (2, 4, 8, 60 and 240 minutes). We identified that poly-unsaturated linoleic acids 18?2 (9, 12) & 18?2 (6, 9) were more abundant in cells growing at 4 or 10°C, than in cells cultivated at 21°C. The mono-unsaturated phospho/neutral fatty acids myristoleic acid 14?1(11) were the most significantly overexpressed (45-fold) after 1hour of exposure to 4°C. As reported in the literature, these fatty acids play important roles in cold adaptability by supplying cell membrane fluidity, and by providing energy to cells. Analysis of water-soluble compounds revealed that isobutyrate, sarcosine, threonine and valine were more accumulated during exposure to 4°C. These metabolites might play a role in conferring cold acclimation to strain N33 at 4°C, probably by acting as cryoprotectants. Isobutyrate was highly upregulated (19.4-fold) during growth at 4°C, thus suggesting that this compound is a precursor for the cold-regulated fatty acids modification to low temperature adaptation.

Ghobakhlou, Abdollah; Laberge, Serge; Antoun, Hani; Wishart, David S.; Xia, Jianguo; Krishnamurthy, Ramanarayan; Mandal, Rupasri

2013-01-01

416

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

417

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

418

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

PubMed Central

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 (less than 0.01 atm [1 atm = 101.29 kPa]). Induced cells were capable of O2 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; Hoffmann, M R

1986-01-01

419

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

420

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.

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

2012-01-01

421

Thermodynamics and kinetics of heat inactivation of a novel keratinase from Chryseobacterium sp. strain kr6.  

PubMed

A novel keratinase from Chryseobacterium sp. strain kr6 was purified to homogeneity by (NH(4))(2)SO(4) precipitation, gel permeation on Sephadex G-100, and Q-Sepharose Fast Flow anion-exchange chromatography. The molecular weight of the purified enzyme was around 20 kDa. Kinetic and thermodynamic parameters for thermal inactivation were determined. The influence of Ca(2+) and Mg(2+) ions and purification degree on the enzyme stability was evaluated in the range of 50 to 60 degrees C. The results showed that first-order kinetics explained well the thermal denaturation of the keratinase in this temperature interval. The presence of Ca(2+) increases significantly the enzyme stability. Compared with the controls, the half-life of the purified enzyme after two purification steps in the presence of Ca(2+) increased 7.3, 20.2, and 9.8 fold at 50, 55, and 60 degrees C, respectively. Thermodynamics parameters for thermal inactivation were also determined. PMID:19936635

Silveira, Silvana Terra; Casarin, Franciani; Gemelli, Sabrine; Brandelli, Adriano

2010-09-01

422

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

423

Kinetics of molybdenum reduction to molybdenum blue by Bacillus sp. strain A.rzi.  

PubMed

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 p max, K(s), S(m), 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

424

Utilization of Ganglioside-Degrading Paenibacillus sp. Strain TS12 for Production of Glucosylceramide  

PubMed Central

Gangliosides, sialic acid-containing glycosphingolipids, are membrane constituents of vertebrates and are known to have important roles in cellular differentiation, adhesion, and recognition. We report here the isolation of a bacterium capable of degrading gangliotetraose-series gangliosides and a new method for the production of glucosylceramide with this bacterium. GM1a ganglioside was found to be sequentially degraded by Paenibacillus sp. strain TS12, which was isolated from soil, as follows: GM1a ? asialo GM1 ? asialo GM2 ? lactosylceramide ? glucosylceramide. TS12 was found to produce a series of ganglioside-degrading enzymes, such as sialidases, ?-galactosidases, and ?-hexosaminidases. TS12 also produced ?-glucosidases, but glucosylceramide was somewhat resistant to the bacterial enzyme under the conditions used. Taking advantage of the specificity, we developed a new method for the production of glucosylceramide using TS12 as a biocatalyst. The method involves the conversion of crude bovine brain gangliosides to glucosylceramide by coculture with TS12 and purification of the product by chromatography with Wakogel C-300 HG.

Sumida, Tomomi; Sueyoshi, Noriyuki; Ito, Makoto

2002-01-01

425

Mechanism of biosynthesis of unsaturated fatty acids in Pseudomonas sp. strain E-3, a psychrotrophic bacterium  

SciTech Connect

Biosynthesis of palmitic, palmitoleic, and cis-vaccenic acids in Pseudomonas sp. strain E-3 was investigated with in vitro and in vivo systems. (1-{sup 14}C)palmitic acid was aerobically converted to palmitoleate and cis-vaccenate, and the radioactivities on their carboxyl carbons were 100 and 43%, respectively, of the total radioactivity in the fatty acids. Palmitoyl coenzyme A desaturase activity was found in the membrane fraction. (1-{sup 14}C)stearic acid was converted to octadecenoate and C16 fatty acids. The octadecenoate contained oleate and cis-vaccenate, but only oleate was produced in the presence of cerulenin. (1-{sup 14}C)lauric acid was aerobically converted to palmitate, palmitoleate, and cis-vaccenate. Under anaerobic conditions, palmitate (62%), palmitoleate (4%), and cis-vaccenate (34%) were produced from (1-{sup 14}C)acetic acid, while they amounted to 48, 39, and 14%, respectively, under aerobic conditions. In these incorporation experiments, 3 to 19% of the added radioactivity was detected in released {sup 14}CO{sub 2}, indicating that part of the added fatty acids were oxidatively decomposed. Partially purified fatty acid synthetase produced saturated and unsaturated fatty acids with chain lengths of C10 to C18. These results indicated that both aerobic and anaerobic mechanisms for the synthesis of unsaturated fatty acid are operating in this bacterium.

Wada, M.; Fukunaga, N.; Sasaki, S. (Hokkaido Univ., Sapporo (Japan))

1989-08-01

426

Stimulation of Defense Reactions in Medicago truncatula by Antagonistic Lipopeptides from Paenibacillus sp. Strain B2? †  

PubMed Central

With the aim of obtaining new strategies to control plant diseases, we investigated the ability of antagonistic lipopolypeptides (paenimyxin) from Paenibacillus sp. strain B2 to elicit hydrogen peroxide (H2O2) production and several defense-related genes in the model legume Medicago truncatula. For this purpose, M. truncatula cell suspensions were used and a pathosystem between M. truncatula and Fusarium acuminatum was established. In M. truncatula cell cultures, the induction of H2O2 reached a maximum 20 min after elicitation with paenimyxin, whereas concentrations higher than 20 ?M inhibited H2O2 induction and this was correlated with a lethal effect. In plant roots incubated with different concentrations of paenimyxin for 24 h before inoculation with F. acuminatum, paenimyxin at a low concentration (ca. 1 ?M) had a protective effect and suppressed 95% of the necrotic symptoms, whereas a concentration higher than 10 ?M had an inhibitory effect on plant growth. Gene responses were quantified in M. truncatula by semiquantitative reverse transcription-PCR (RT-PCR). Genes involved in the biosynthesis of phytoalexins (phenylalanine ammonia-lyase, chalcone synthase, chalcone reductase), antifungal activity (pathogenesis-related proteins, chitinase), or cell wall (invertase) were highly upregulated in roots or cells after paenimyxin treatment. The mechanisms potentially involved in plant protection are discussed.

Selim, Sameh; Negrel, Jonathan; Wendehenne, David; Ochatt, Sergio; Gianinazzi, Silvio; van Tuinen, Diederik

2010-01-01

427

Kinetics of biotransformation of 1,1,1-trichloroethane by Clostridium sp. strain TCAIIB.  

PubMed Central

Batch experiments were conducted to examine the effects of high concentrations of 1,1,1-trichloroethane (TCA) on the biotransformation of TCA by Clostridium sp. strain TCAIIB. The biotic dehalogenation of TCA to 1,1-dichloroethane by nongrowing cells was measured at 35 degrees C, and the data were used to obtain the kinetic parameters of the Monod relationship half-velocity coefficient Ks (31 microM) and the coefficient of maximum rate of TCA biotransformation (kTCA; 0.28 mumol per mg per day). The yield of biomass decreased with an increase in the TCA concentration, although T