bluuebunny/crossref_metadata_2025 huggingface dataset:
A multinuclear magnetic resonance study of crystalline tripotassium tetracyanocuprate
Authors: Kroeker Scott , Wasylishen Roderick E
Published: April 2011

Direct NMR observation of copper-63/65 nuclei in solid K3Cu(CN)4 provides the first experimental example of anisotropic copper chemical shielding. Axially symmetric by virtue of the space group symmetry, the shielding tensor spans 42 ppm, with the greatest shielding when the unique axis is perpendicular to the applied magnetic field. The nuclear quadrupole coupling constant is also appreciable, CQ(63Cu) = -1.125 MHz, reflecting a deviation of the Cu(CN)43- anion from pure tetrahedral symmetry. Spin-spin coupling to 13C nuclei in an isotopically enriched sample is quantified by line-shape simulations of both 13C and 63/65Cu magic-angle spinning (MAS) NMR spectra to be 300 Hz. It is shown that this information is also directly available by 63/65Cu triple-quantum (3Q) MAS NMR. The relative merits of these three approaches to characterizing spin-spin couplings involving half-integer quadrupolar nuclei are discussed. Chemical shielding tensors for nitrogen-15 and carbon-13 are obtained from NMR spectra of non-spinning samples, and are compared to those of tetrahedral group 12 tetracyanometallates. Finally, 2J(63/65Cu,15N) detected in 15N MAS experiments are found to be 19 and 20 Hz for the two crystallographically distinct cyanide ligands.Key words: NMR, quadrupolar nucleus, chemical shielding tensor, multiple-quantum magic-angle spinning, metal cyanide, spin-spin coupling.
Heterotrophic nitrification by a thermophilicBacillusspecies as influenced by different culture conditions
Authors: Mével Geneviève , Prieur Daniel
Published: April 2011

The nitrification activity of a thermophilic heterotrophic bacterium, Bacillus MS30 isolated from a deep-sea hydrothermal vent, was studied under various growth conditions. Nitrification was estimated from the nitrogen balance calculations in the culture media. The results showed that this isolate actively nitrified in culture conditions similar to those prevailing in hydrothermal sites. Therefore, its ecological significance was considered. In standard aerobic conditions, MS30 produced nitrite from ammonia and acetate (1.13 µmol NO2-·mg-1dry wt), but nitrate was never produced, and a low nitrite reduction was often observed. Higher nitrification activities were observed in defined optimal conditions (simple carbon substrate, 65°C, pH 7.5, and 15 g sea salts · L-1). In addition, discrepancies between the optima for growth and nitrification were observed, showing the ability of MS30 to adapt to changing environmental conditions typical of hydrothermal sites.Key words: thermophilic bacteria, heterotrophic nitrification, environmental parameters.
Evidence for the occurrence of nucleotide-activated oligosaccharides inSaccharomyces cerevisiae
Authors: Sprenger Silvia , König Helmut
Published: April 2011

Recently, nucleotide-activated oligosaccharides have been found to be involved in the biosynthesis of certain glycoconjugates in archaeal and bacterial procaryotes. This paper describes the isolation and partial chemical characterization of nucleotide-activated oligosaccharides from the eucaryotic microbe Saccharomyces cerevisiae. We purified four different nucleotide-activated oligosaccharides from cell extracts of Saccharomyces cerevisiae. Three of the oligosaccharides were UDP, and one was TDP-activated. D-Glucose was the only carbohydrate constituent, except for one oligosaccharide, which also contained glucosamine. The chain length varied between two and four sugar residues.Key words: nucleotides, oligosaccharides, Saccharomyces cerevisiae, yeast.
Effects ofPinus sylvestrisroot growth and mycorrhizosphere development on bacterial carbon source utilization and hydrocarbon oxidation in forest and petroleum-contaminated soils
Authors: Heinonsalo Jussi , Jørgensen Kirsten S , Haahtela Kielo , Sen Robin
Published: April 2011

The hypothesis that Pinus sylvestris L. root and mycorrhizosphere development positively influences bacterial community-linked carbon source utilization, and drives a concomitant reduction in mineral oil levels in a petroleum hydrocarbon- (PHC-) contaminated soil was confirmed in a forest ecosystem-based phytoremediation simulation. Seedlings were grown for 9 months in large petri dish microcosms containing either forest humus or humus amended with cores of PHC-contaminated soil. Except for increased root biomass in the humus/PHC treatment, there were no other significant treatment-related differences in plant growth and needle C and N status. Total cell and culturable bacterial (CFU) densities significantly increased in both rhizospheres and mycorrhizospheres that actively developed in the humus and PHC-contaminated soil. Mycorrhizospheres (mycorrhizas and extramatrical mycelium) supported the highest numbers of bacteria. Multivariate analyses of bacterial community carbon source utilization profiles (Biolog GN microplate) from different rhizosphere, mycorrhizosphere, and bulk soil compartments, involving principal component and correspondence analysis, highlighted three main niche-related groupings. The respective clusters identified contained bacterial communities from (i) unplanted bulk soils, (ii) planted bulk PHC and rhizospheres in PHC-contaminated soils, and (iii) planted bulk humus and rhizosphere/mycorrhizosphere-influenced humus, and mycorrhizosphere-influenced PHC contaminated soil. Correspondence analysis allowed further identification of amino acid preferences and increased carboxylic/organic acid preferences in rhizosphere and mycorrhizosphere compartments. Decreased levels of mineral oil (non-polar hydrocarbons) were detected in the PHC-contaminated soil colonized by pine roots and mycorrhizal fungi. These data further support our view that mycorrhizosphere development and function plays a central role in controlling associated bacterial communities and their degradative activities in lignin-rich forest humus and PHC-contaminated soils.Key words: Scots pine, mycorrhizosphere, bacterial community, Biolog, carbon source utilization, non-polar hydrocarbons, phytoremediation.
Bacterial dynamics in first year sea ice and underlying seawater of Saroma-ko Lagoon (Sea of Okhotsk, Japan) and Resolute Passage (High Canadian Arctic): Inhibitory effects of ice algae on bacterial dynamics
Authors: Monfort Patrick , Demers Serge , Levasseur Maurice
Published: April 2011

The seasonal development of bacterial abundance in first year bottom ice and underlying seawater were studied at Saroma-ko Lagoon in Hokkaido, Japan, and at Resolute Passage in the High Canadian Arctic during the algal bloom in spring 1992. The aim of this study was to evaluate whether the high algal concentrations reached during the bloom of ice algae have inhibitory effects on bacterial dynamics. Bacterial abundance (measured as total cell count and colony-forming units CFU) increased with the increase of the algal biomass up to 500 µg Chla·L-1in both locations. Culturable fraction (measured as the percentage of CFU counts versus the total cell counts) was between 7% and 22% at Saroma-ko, and approximately 0.08% at Resolute Passage. When algal biomass exceeded 500 µg of Chla·L-1, both bacterial abundance and culturable fraction decreased significantly. There was a maximum threshold of algal biomass (between 500 and 800 µg of Chla·L-1) after which bacterial dynamics become negatively coupled to the algal biomass. These results suggest that bactericidal and/or bacteriostatic compounds from these extremely high algal concentrations could explain the decrease in bacterial abundance and culturability in bottom ice observed after the ice algae bloom.Key words: bacteria, culturability, algae, inhibitory effects, sea ice, Arctic.
Molecular analysis of variability within the toxigenicAspergillus ochraceusspecies
Authors: Varga János , Kevei Éva , Tóth Beáta , Kozakiewicz Zofia , Hoekstra Rolf F
Published: April 2011

Genetic variability of Aspergillus ochraceus was examined at the DNA level. Based on the HaeIII-BglII generated mitochondrial DNA restriction profiles, most isolates could be classified into two distinct groups. These two groups could also be distinguished by the random amplified polymorphic DNA technique, and with telomeric PCR amplifications. Phylogenetic analysis of sequences of the intergenic transcribed spacer region of some of the strains resulted in a dendrogram with the same topology as that based on mitochondrial DNA and amplified DNA data. None of the isolates with type 2 mtDNA profiles produce ochratoxins. Some strains (e.g., A. ochraceus ICMP 939) displayed strain-specific mitochondrial DNA patterns, and their amplified DNA profiles were also different from all other A. ochraceus strains examined.Key words: Aspergillus ochraceus, phylogenetic analysis, mitochondrial DNA, ITS region.
Co-culture of Aeromonas salmonicida and host cells in intraperitoneal implants is associated with enhanced bacterial survival
Authors: Garduño Rafael A , Lizama Angela L , Moore Anne R , Garduño Elizabeth , Olivier Gilles , Kay William W
Published: April 2011

An experimental procedure that we named "in vivo co-culture technology" allowed us to study the interactions between Aeromonas salmonicida and host cells, inside semipermeable chambers implanted in the peritoneal cavity of Atlantic salmon. Intraperitoneal implants containing bacteria and host cells, or bacteria and lysed cells, consistently yielded higher numbers of viable bacteria than implants containing bacteria only. Electron microscopy confirmed that 30 min after chamber inoculation, numerous bacteria were already internalized by exudate cells, and that at 3 h, destruction of these cells was evident. Thus, the rapid invasion and (or) the A. salmonicida-mediated lysis of host cells may constitute a survival strategy in vivo. The co-culture of bacteria with exudate peritoneal cells may be applicable to the in vivo study of other pathogens.Key words: Aeromonas salmonicida, in vivo, intraperitoneal implants, exudate cells, furunculosis.
Phenotypic characterization of the Xenorhabdus bacterial symbiont of a Texas strain of the entomopathogenic nematode Steinernema riobrave, and characterization of the Xenorhabdus bovienii bacterial symbiont of a Newfoundland strain of Steinernema feltiae
Authors: He Hongjun , Gordon Roger , Gow John A
Published: April 2011

Two bacterial symbionts of entomopathogenic nematodes, one of which originated from Texas, U.S.A., and the other from Newfoundland, Canada, were characterized phenotypically. These strains belonged to the genus Xenorhabdus. The Newfoundland (NF) strain was shown to be X. bovienii but the Texas (TX) strain was not identified at the species level. Four additional cultures of Xenorhabdus were included in the study. These were a strain of X. bovienii (Umeå), which was from a nematode of European origin, and strains of X. nematophilus, X.beddingii, and X.poinarii. The tests used in this study indicated identical properties for the NF (North American) and Umeå (European) strains of X. bovienii. These could be differentiated from the other strains studied by their failure to grow at 34°C and resistance to low concentrations of a mixture of amoxilline and clavulanic acid. The Xenorhabdus TX strain could be differentiated from the other strains studied by its failure to grow at 10°C. Of the tests done, approximately 30 were useful in distinguishing between the strains and species studied.Key words: symbionts, nematode, Steinernema, Xenorhabdus, Xenorhabdus bovienii.
Physical degradation of wheat straw by the in-vessel and windrow methods of mushroom compost production
Authors: Lyons G A , McCall R D , Sharma H SS
Published: April 2011

Mushroom compost manufacturers in Ireland are moving away from the traditional outdoor phase I windrow method, favouring in-vessel production. Composters and growers have reported better quality compost with faster spawn run and higher yields produced by this process. In the present study, physical examination of samples highlighted differences when comparing the windrow and in-vessel methods of compost production. Observations using scanning electron microscopy suggest that the cuticle of wheat straw from in-vessel production is damaged during phase I, peeling away from the surface in fragments, and exposing the epidermis. Changes in silicon levels on the straw surface acted as a marker for cuticle damage when comparing both composting systems. Cuticle damage may be important during composting and afterwards, as substrate colonisation is faster, and consequently spawn run is shorter. The phase I compost microbial community is altered by the in-vessel technique, producing a predominantly thermophilic bacterial flora in contrast to the mesophilic and thermophilic bacteria and fungi found in windrow phase I compost. These differences may be significant in mushroom compost production.Key words: windrow, in-vessel, compost, cuticle, straw.
Improved growth and viability of lactobacilli in the presence ofBacillus subtilis(natto), catalase, or subtilisin
Authors: Hosoi Tomohiro , Ametani Akio , Kiuchi Kan , Kaminogawa Shuichi
Published: April 2011

In an effort to demonstrate the potential usefulness of Bacillus subtilis (natto) as a probiotic, we examined the effect of this organism on the growth of three strains of lactobacilli co-cultured aerobically in vitro. Addition of B. subtilis (natto) to the culture medium resulted in an increase in the number of viable cells of all lactobacilli tested. Since B. subtilis (natto) can produce catalase, which has been reported to exhibit a similar growth-promoting effect on lactobacilli, we also examined the effect of bovine catalase on the growth of Lactobacillus reuteri JCM 1112 and L. acidophilus JCM 1132. Both catalase and B. subtilis (natto) enhanced the growth of L. reuteri JCM 1112, whereas B. subtilis (natto) but not catalase enhanced the growth of L. acidophilus JCM 1132. In a medium containing 0.1 mM hydrogen peroxide, its toxic effect on L. reuteri JCM 1112 was abolished by catalase or B. subtilis (natto). In addition, a serine protease from B. licheniformis, subtilisin, improved the growth and viability of L. reuteri JCM 1112 and L. acidophilus JCM 1132 in the absence of hydrogen peroxide. These results indicate that B. subtilis (natto) enhances the growth and (or) viability of lactobacilli, possibly through production of catalase and subtilisin.Key words: Bacillus subtilis (natto), Lactobacillus, probiotic, catalase, subtilisin.
A review of antimicrobial resistance in Canada
Authors: Blondeau J M , Vaughan D
Published: April 2011

Antimicrobial resistance is a global concern. Over the past 10 years, considerable efforts and resources have been expended to detect, monitor, and understand at the basic level the many different facets of emerging and increasing resistance. This review summarizes our current understanding of bacterial antimicrobial resistance issues in Canada with particular emphasis given to the Enterobacteriaceae, Pseudomonas aeruginosa, Staphylococcus aureus, Enterococcus, Neisseria meningitidis, Haemophilus influenzae, Streptococcus pneumoniae, Moraxella catarrhalis, and Streptococcus pyogenes. In addition, future concerns and programs for ongoing surveillance are discussed.
A factorial design analysis of chitin production by Cunninghamella elegans
Authors: Andrade V S , Neto B B , Souza W , Campos-Takaki G M
Published: April 2011

Chitin production by Cunninghamella elegans (IFM 46109) was studied with a two-level full factorial design, varying time of cultivation and the concentration of D-glucose, L-asparagine, and thiamine in the culture medium. The material extracted was characterized by infrared and NMR spectroscopy. The highest chitin yield, 28.8%, was comparable with the highest in the literature and was obtained with a medium containing 60 g·L-1 of glucose, 3 g·L-1 of asparagine, and 0.008 mg·L-1 of thiamine. Increasing the time of cultivation from 24 h to 72 h did not affect chitin production. The three factors showed significant positive effects on chitin production, without interactions between them.Key words: chitin, chitosan, zygomycetes, Cunninghamella elegans.
Combined effects of Brassica napus seed meal and Trichoderma harzianum on two soilborne plant pathogens
Authors: Dandurand Louise-Marie , Mosher Rachel D , Knudsen Guy R
Published: April 2011

The effects of soil amendment with rapeseed meal from Brassica napus cv. 'Dwarf Essex' (high glucosinolate concentrations) and 'Stonewall' (low glucosinolate concentrations) on the biological control activity of Trichoderma harzianum towards Sclerotinia sclerotiorum and Aphanomyces euteiches were evaluated. Trichoderma harzianum added to soil reduced myceliogenic germination of S. sclerotiorum by 94%, but did not affect carpogenic germination. In contrast, 100% reduction in carpogenic germination was observed in soil amended with Dwarf Essex meal, along with a 33% reduction in myceliogenic germination. With Stonewall meal as soil amendment, carpogenic germination was reduced by 44% and myceliogenic germination was not affected. Both Dwarf Essex and Stonewall meals inhibited colonization of sclerotia in soil by T. harzianum, from 100% to 0% and 8%, respectively, so that biocontrol activity of T. harzianum was reduced in the presence of either meal. Aphanomyces euteiches root rot of pea was significantly reduced by T. harzianum alone (100%), by amendment with Dwarf Essex meal alone (77%), and by T. harzianum in combination with Dwarf Essex meal (100%). Amendment with Stonewall meal alone did not control root rot, and combination of Stonewall meal with T. harzianum reduced the biocontrol efficacy of T. harzianum.
A survey of 16S rRNA andamoAgenes related to autotrophic ammonia-oxidizing bacteria of the β-subdivision of the class proteobacteria in contaminated groundwater
Authors: Ivanova Iliana A , Stephen John R , Chang Yun-Juan , Brüggemann Julia , Long Philip E , McKinley James P , Kowalchuk George A , White David C , Macnaughton Sarah J
Published: April 2011

In this study, we investigated the size and structure of autotrophic ammonia oxidizer (AAO) communities in the groundwater of a contamination plume originating from a mill-tailings disposal site. The site has high levels of dissolved N from anthropogenic sources, and exhibited wide variations in the concentrations of NO3-and NH3+ NH4+. Community structures were examined by PCR-DGGE targeting 16S rDNA with band excision and sequence analysis, and by analysis of amoA fragment clone libraries. AAO population sizes were estimated by competitive PCR targeting the gene amoA, and correlated significantly with nitrate concentration. Most samples revealed novel diversity in AAO 16S rDNA and amoA gene sequences. Both 16S rDNA and amoA analyses suggested that all samples were dominated by Nitrosomonas sp., Nitrosospira sp. being detected in only 3 of 15 samples. This study indicated numerical dominance of Nitrosomonas over Nitrosospira in groundwater, and suggests that groundwater ammonia oxidizers are more similar to those dominating freshwater sediments than bulk soil.Key words: Nitrosomonas, Nitrosospira, nitrification, groundwater, amoA, 16S.
Functional integrity and structural stability of freeze-dried ectomycorrhizal fungi established through viability assays
Authors: Sundari S Krishna , Adholeya Alok
Published: April 2011

Lyophilized vegetative mycelium of ectomycorrhizal fungi was subjected to various viability tests to confirm functional integrity. Physical integrity of freeze-dried cultures was comparable to that of non-lyophilized cultures. Inter- and intraspecific variations in morphology, physiology, and metabolic rate were maintained after lyophilization. Maintenance of total protein content confirmed metabolic stability. According to the assays of viability, a plating assay and determination of total biomass confirmed stable mitotic activity of the freeze-dried cultures.Key words: lyophilization, physical integrity, structural stability, total protein, total biomass.
ICC/PCR detection of enteroviruses and hepatitis A virus in environmental samples
Authors: Reynolds Kelly A , Gerba Charles P , Abbaszadegan Morteza , Pepper Ian L
Published: April 2011

This study applied the integrated cell culture/polymerase chain reaction methodology (ICC/PCR) for rapid and specific detection of both cytopathogenic and noncytopathogenic viruses. Results of this study showed that the use of direct RT-PCR or conventional cell culture alone may yield erroneous results with the analysis of environmental samples. The purpose of this study was to compare cultural, molecular, and combined assays for the most effective method of virus detection in variable environmental samples. Using ICC/PCR, stock enterovirus inocula of [Formula: see text]10 PFU were PCR positive in at least 4/5 replicate flasks after only 5 h of incubation in cell culture, and in all flasks after [Formula: see text]10 h. An inoculum of one PFU was detected by PCR after 20 h of cell culture incubation while for concentrations of virus below one PFU, 25 h of incubation was sufficient. Similarly, hepatitis A virus (HAV) inocula of 100 MPN/flask, produced indeterminate CPE in cell culture, but were clearly detected by ICC/PCR following 48 h of incubation. Lower levels of HAV, 1 and 10 MPN, were detected by ICC/PCR after 96 to 72 h of incubation, respectively. Cell culture lysates from 11 environmental sample concentrates of sewage, marine water, and surface drinking water sources, were positive for enteroviruses by ICC/PCR compared to 3 positive by direct RT-PCR alone. Results from ICC/PCR eventually agreed with cell culture but required [Formula: see text]48 h of incubation, compared to as long as 3 weeks for CPE following incubation with BGM and FRhK cells.Key words: RT-PCR, cell culture, ICC/PCR, enterovirus, hepatitis A virus.
Early production of rhizopine in nodules induced bySinorhizobium melilotistrain L5-30
Authors: Heinrich K , Ryder M H , Murphy P J
Published: April 2011

The rhizopine L-3-O-methyl-scyllo-inosamine (3-O-MSI) is metabolized by approximately 10% of the strains of Rhizobium leguminosarum bv. viciae and Sinorhizobium meliloti. Rhizopine strains enjoy a substantial competitive advantage in nodulation, which is manifest before 14 days post-inoculation, implying that rhizopine is produced before this time. We were able to detect this compound in the roots of alfalfa (Medicago sativum L. cv. Hunter River) four days after germination (six days post-infection) with S. meliloti strain L5-30 by gas chromatography-mass spectrometry (GC-MS). At four days, nodules were not visible, and the concentration of rhizopine was extremely low, estimated at 67 pg/gfw (picograms/gram fresh weight). The amount increased gradually but remained low until 16 days, when there was a 50-fold increase from day four, by which time nodules were well established. This pattern of synthesis is consistent with previous studies indicating that rhizopine synthesis is regulated by nifA/ntrA regulatory genes, which are maximally expressed in bacteroids at the onset of nitrogen fixation. However, the low level of rhizopine synthesis must be responsible for the early effects on competition for nodulation. Production of rhizopine at this time most likely results from micro-aerobic induction of mos genes in free-living bacteria, either in the infection threads or in the rhizosphere.Key words: Medicago sativum, nodulation competitiveness, Rhizobium, rhizopine, Sinorhizobium meliloti.
Sensitivity ofSaccharomyces cerevisiaeto tannic acid is due to iron deprivation
Authors: Wauters T , Iserentant D , Verachtert H
Published: April 2011

Tannic acid inhibited the growth of the yeast Saccharomyces cerevisiae. Growth medium supplementation with more nitrogen or metal ions showed that only iron ions could restore the maximal growth rate of S. cerevisiae. Tannic acid resistant mutants were previously isolated by screening for tannic acid resistance and were all cytoplasmic petite mutants. While the wild type was very sensitive to iron deprivation conditions when grown in aerobic conditions, the mutants, whether grown aerobically or anaerobically, showed the same growth rate under iron-limited conditions as under iron-repleted conditions. Also, the wild type grown anaerobically was not affected by iron-limited conditions. Cytoplasmic petite mutants obtained by ethidium bromide mutagenesis behaved like the other mutants. During iron limitation, the wild type showed a reduced oxygen uptake rate. Maximal growth rate of the wild type in iron-limited conditions could be restored by the addition to the media of unsaturated fatty acids and sterol. Iron deprivation caused by tannic acid may thus affect the synthesis of a functional respiratory chain as well as the synthesis of unsaturated fatty acids and (or) sterol.Key words: Saccharomyces cerevisiae, tannic acid resistance, iron deprivation, cytoplasmic petite mutant.
Effect of growth conditions on the production of manganese peroxidase by three strains of Bjerkandera adusta
Authors: Wang Yuxin , Vazquez-Duhalt Rafael , Pickard Michael A
Published: April 2011

We were looking for a strain of Bjerkandera adusta that produces high titres of manganese peroxidase under optimal conditions for large-scale enzyme purification. We have chosen two strains from the University of Alberta Microfungus Collection and Herbarium, UAMH 7308 and 8258, and compared the effects of growth conditions and medium composition on enzyme production with the well-characterized strain BOS55 (ATCC 90940). Of four types of cereal bran examined, rice bran at 3% (w/v) in 60 mM phosphate buffer pH 6 supported the highest levels of enzyme production. Using 100 mL medium in 500-mL Erlenmeyer flasks, maximum enzyme levels in the culture supernatant occurred after about 10 days of growth; 5.5 U·mL1 for UAMH 7308, 4.4 U·mL1 for UAMH 8258, and 1.7 U·mL1 for BOS55, where units are expressed as micromoles of Mn-malonate formed per minute. Growth as submerged cultures in 10-L stirred tank reactors produced 3.5 U·mL1 of manganese peroxidase (MnP) by UAMH 8258 and 2.5 U·mL1 of MnP by 7308, while enzyme production by BOS55 was not successful in stirred tank reactors but could be scaled up in 2-L shake flasks containing 400 mL rice bran or glucose  malt  yeast extract (GMY)  Mn-glycolate medium to produce MnP levels of 1.7 U·mL1. These results show that the two strains of B. adusta, UAMH 7308 and 8258, can produce between two and three times the manganese peroxidase level of B. adusta BOS55, that they are good candidates for scale up of enzyme production, and that the rice bran medium supports higher levels of enzyme production than most previously described media.Key words: growth conditions, cereal bran, manganese peroxidase, Bjerkandera adusta, white rot fungi.
Séquences répétées des génomes de Rhizobium sp. NGR234 et Sinorhizobium meliloti : une analyse comparative par séquençage aléatoire
Authors: Perret Xavier , Parsons Jeremy , Viprey Virginie , Reichwald Kathrin , Broughton William J
Published: April 2011

Amongst prokaryotic genomes, those of nitrogen-fixing members of the Rhizobiaceae family are relatively large (69 Mb), often include mega-plasmids of 1.52 Mb, and contain numerous families of repeated DNA sequences. Although most essential nodulation and nitrogen fixation genes are well characterized, these represent only a small fraction of the DNA content. Little is known about the detailed structure of rhizobial genomes. With the development of sequencing techniques and new bio-informatic tools such studies become possible, however. Using the 2275 shot-gun sequences of ANU265 (a derivative of NGR234 cured of pNGR234a), we have identified numerous families of repeats. Amongst these, the 58-bp-long NGRREP-4 represents the third most abundant DNA sequence after the RIME1 and RIME2 repeats, all of which are also found in Sinorhizobium meliloti. Surprisingly, studies on the distribution of these elements showed that in proportion to its size, the chromosome of NGR234 carries many more RIME modules than pNGR234a or pNGR234b. Together with the presence in NGR234 and S. meliloti 1021 of an insertion sequence (IS) element more conserved than essential nodulation and nitrogen fixation genes, these results give new insights into the origin and evolution of rhizobial genomes.Key words: shot-gun, repeats, BIME.
Hopanoid lipids inFrankia: identification of squalene-hopene cyclase gene sequences
Authors: Dobritsa Svetlana V , Potter Dan , Gookin Timothy E , Berry Alison M
Published: April 2011

In Frankia, the microsymbiont in actinorhizal root nodules, nitrogen fixation takes place in specialized structures called vesicles. The lipidic vesicle envelope forms a barrier to oxygen diffusion, an essential part of the nitrogenase oxygen protection system. We have shown previously that the vesicle envelope is composed primarily of two species of hopanoid lipids, sterol-like molecules that are synthesized in a wide range of bacteria, including Frankia, several cyanobacteria, and rhizobia. The levels of hopanoid found in Frankia are among the highest of any organism known to date. Here we report that short (328-bp) DNA sequences from several strains of Frankia spp. have been identified that are homologous to a portion of the coding region of squalene-hopene cyclase (shc) genes. The fragments and corresponding polymerase chain reaction (PCR) primers can be used in phylogenetic comparisons of Frankia, both within Frankiaceae and among bacteria that synthesize hopanoids.Key words: Frankia, squalene-hopene cyclase, shc, hopanoid, phylogeny, actinorhizal.
Sorption and metabolism of selected herbicides in river biofilm communities
Authors: Lawrence J R , Kopf G , Headley J V , Neu T R
Published: April 2011

In the present study, biofilms were grown in rotating annular bioreactors with river water as inoculum and sole source of nutrients. The herbicides atrazine and diclofop methyl were applied to the bioreactors, while an identical reactor acted as a control. Biofilm structure was visualized using specific fluorescent probes in conjunction with confocal laser scanning microscopy. The concentration of both herbicides in the bulk water phase followed the pattern of application. Atrazine and metabolites were detected in biofilm samples using direct insertion probe tandem mass spectrometry (DIP-MS/MS) and only trace levels were detected after the addition phase. Monoclonal antibody (MAb) studies indicated that sorption of atrazine was associated with a unique microcolony type. In contrast, diclofop and metabolites reached a maximum level in the biofilm at the end of the addition phase and persisted in the biofilm. Experiments with14C-labeled atrazine and diclofop methyl indicated that mineralization of these compounds to CO2(<1%) occurred in the river biofilms. Thus, both herbicides were sorbed and metabolized by the river biofilm community and detected in biofilms when they were not detected in the bulk water phase. These results indicate that biofilms and specific community members may act as a sink for herbicides, and that this should be taken into account in terms of both sampling and studies of the environmental chemodynamics of contaminants.Key words: biofilm, confocal, image analyses, herbicide, sorption.
Effects of some salts and sodicity on the growth of a Rhizobium leguminosarum bv. viceae strain isolated from a salt-affected soil
Authors: Faituri M Y , El-Mahi Y E , El-Hassan G A
Published: April 2011

The effects of sodium (Na+), calcium (Ca2+), magnesium (Mg2+), and boron (B) concentrations and sodicity, as measured by the sodium adsorption ratio (SAR), on the growth of a Rhizobium leguminosarum bv. viceae strain isolated from a salt-affected soil were studied. The rate of growth was measured in a yeast extract - mannitol broth, amended with salts having electrical conductivity (EC) of 4, 8, and 16 dS·m-1. Each salinity level was prepared to achieve SAR values of 10, 20, and 30 with or without graded B concentrations of 0.5, 1, 3, and 5 mg·L-1. We found that salinity levels equal to or more than 8 dS·m-1 had negative effects on Rhizobium growth during the first days of incubation, but the effects became less pronounced after 1 week. Na+ concentrations of more than 1.1 g·L-1 retarded growth, especially at high SAR values (i.e., at low Ca2+ concentrations). The retardation of growth increased with increases in EC up to 16 dS·m-1, at all sodicity levels. Mg2+ added together with Na+ or with Ca2+ + Na+ affected growth more negatively than Ca2+ + Na+ alone. The effect of Mg2+ became more pronounced with increased salinities and sodicities. It was concluded that EC of more than 4 dS·m-1 retarded growth of Rhizobium, but only at high sodicity levels. The relative specific ion effect on growth was in the order Na+ < Ca2+ < Mg2+. The harmful effect of Mg2+ on this strain was accentuated by adding Ca2+ to the cultural medium. When SAR increased from 10 to 30, Na+ had no clear effect on growth, irrespective of the accompanied cations, i.e, Ca2+, Mg2+, or Ca2+ + Mg2+. Growth was reduced by B concentrations as low as 0.5 mg·L-1, and the B effect was enhanced by increased salinity.Key words: Rhizobium leguminosarum bv. viceae, salinity, sodicity, boron.
Sulfide oxidation in gram-negative bacteria by expression of the sulfidequinone reductase gene ofRhodobacter capsulatusand by electron transport to ubiquinone
Authors: Shibata Hiroomi , Kobayashi Shigeki
Published: April 2011

The oxidation of sulfide was studied in recombinant bacteria expressing the sulfidequinone reductase gene (sqr) from Rhodobacter capsulatus. Sulfide was oxidized by the Escherichia coli strain W3110 harboring the sqr construct (pKKSQ) under anaerobic conditions and nitrate was utilized as a terminal electron acceptor. Following the oxidation, elemental sulfur and nitrite were produced as the final reaction products. This activity was retained in the membrane preparation and was sensitive towards antimycin A, stigmatellin, and azide. As a consequence of the ubiquinone deficiency, this activity was markedly decreased. In additon, by recovery of ubiquinone, the oxidation was also restored to rates similar to those of the wild-type strain. These results indicate that sulfide oxidation in this strain occurs via the quinone pool in vivo, and that this sulfidequinone reductase (SQR) in particular utilizes ubiquinone as a more appropriate electron acceptor than menaquinone or demetylmenaquinone. To our knowledge, this is the first study to show a direct interaction between SQR and ubiquinone in cells. When expressed in Pseudomonas putida and Rhizobium meliloti, the SQR conferred on these organisms the ability to oxidize sulfide as well as E. coli in vivo.Key words: SQR, quinone, anaerobic sulfide oxidation, heterogeneous expression.
Binding activity of Natto (a fermented food) and Bacillus natto isolates to mutagenic-carcinogenic heterocyclic amines
Authors: Rajendran Rajam , Ohta Yoshiyuki
Published: April 2011

The fermented food, whole meal Natto, viscous polymeric material from Natto, Natto bean, cooked soya bean, and 28 bacterial isolates from Natto were studied for their binding capacity to foodborne mutagenic-carcinogenic heterocyclic amines. The mutagenic heterocyclic amines used were Trp-P-1 (3-amino-1,4-dimethyl-5H-pyrido(4,3-b)indole); Trp-P-2 (3-amino-1-methyl-5H-pyrido(4,3-b)indole); Glu-P-1 (2-amino-6-methyldipyrido(1,2-a:3'2'-d)imidazole); PhIP (2-amino-1-methyl-6-phenylimidazo(4,5-b)pyridine); IQ (2-amino-3-methylimidazo(4,5-f)quinoline); MeIQ (2-amino-3,4-dimethylimidazo(4,5-f)quinoxaline); MeIQx (2-amino-3,8-dimethylimidazo(4,5-f)quinoxaline); and MeAαC (2-amino-3-methyl-9H-pyrido(2,3)indole). The lyophilized Natto and other fractions of Natto exhibited high binding activity towards Trp-P-1, Trp-P-2, PhIP, and MeAαC, while Glu-P-1, IQ, and MeIQ were not effectively bound. The binding capacity of bacterial isolates (Bacillus natto) were isolate-mutagen dependent. Heat treated lyophilized cells, cell wall, and cytoplasmic contents of the bacterial isolate with the highest binding capacity were analyzed for their ability to bind different heterocyclic amines. The results indicate the importance of the cell wall in binding to heterocyclic amines, whereas the cytoplasmic contents were less effective. Heat-treated cells were not much different from that of viable cells in their binding. The impact of different factors, such as pH, incubation time, metal ions, different concentrations of sodium chloride and alcohol, various enzymes, and acetylation of mutagens on binding of Trp-P-1 and IQ, were discussed. The significance of the present results is also discussed from the viewpoint that Natto, a fermented food, is able to scavenge dietary mutagenic heterocyclic amines through binding.Key words: fermented food, mutagens, heterocyclic amines, Natto, binding.
The operon for cytokinin biosynthesis of Erwinia herbicola pv. gypsophilae contains two promoters and is plant induced
Authors: Guo Ming , Manulis Shulamit , Barash Isaac , Lichter Amnon
Published: April 2011

The operon for cytokinin biosynthesis in the gall-forming bacterium Erwinia herbicola pv. gypsophilae (Ehg) has been previously shown to reside on an indigenous plasmid (pPATHEhg) that is mandatory for pathogenicity. This operon consists of two genes: the first open reading frame (pre-etz) is of unknown function, whereas the second one (etz) encodes for isopentenyl transferase. Northern hybridization performed with the wild-type strain Ehg824-1 grown in Luria-Bertani broth demonstrated two transcripts of which an etz-specific transcript (1.0 kb) was predominant. Fusion of upstream DNA fragments of both pre-etz and etz to the ice nucleation reporter gene inaZ in pVSP61 showed high ice nucleation activity in both cultures, confirming the presence of two independent promoters. An increase of 11.5 orders in transcriptional activity of these promoters was observed following inoculation of gypsophila cuttings. Mutants of Ehg824-1 were generated by insertion of inaZ into pre-etz and etz using the transposon reporter Tn3-Spice. An increase of about two orders in transcriptional activity was recorded with both mutants following inoculation of gypsophila or bean cuttings. A similar induction was also observed when the bacteria were applied to the leaf surface of these plants. Unlike other virulence genes present on the pPATHEhg, neither pre-etz nor etz was regulated by the adjacent hrp gene cluster.Key words: pre-etz and etz operon, cytokinin, plant induction, ice nucleation activity.
Isolation of an esterase-producing Trichosporon brassicae and its catalytic performance in kinetic resolution of ketoprofen
Authors: Shen Duan , Xu Jian-He , Gong Peng-Fei , Wu Hui-Yuan , Liu You-Yan
Published: April 2011

A yeast strain CGMCC 0574, identified as Trichosporon brassicae, was selected from 92 strains for its high (S) selectivity in the hydrolysis of ketoprofen ethyl ester. The effective strains of the microorganisms were isolated from soil samples with the ester as the sole carbon source. The ethyl ester proved to be the best substrate for resolution of ketoprofen among several ketoprofen esters examined. The resting cells of CGMCC 0574 could catalyze the hydrolysis of ketoprofen ethyl ester with an enantiomeric ratio of 44.9, giving (S)-ketoprofen an enantiomeric excess of 91.5% at 42% conversion.Key words: ketoprofen, biocatalytic resolution, enantioselective hydrolysis, microbial esterase, Trichosporon brassicae.
Molecular assay to identifyAcetobacter diazotrophicusand detect its occurrence in plant tissues
Authors: Kirchhof Gudrun , Baldani J Ivo , Reis Veronica M , Hartmann Anton
Published: April 2011

The occurrence of Acetobacter diazotrophicus was directly demonstrated in plant tissues using a species-specific oligonucleotide probe and polymerase chain reaction (PCR) amplification of a 411-bp product. The oligonucleotide probe was derived from the sequence of a highly variable region of 23S rDNA and its specificity was tested with membrane-bound nucleic acids of 112 different microorganisms in hybridization experiments. It was found to be able to discriminate Acetobacter diazotrophicus from other Acetobacter spp. and other reference organisms. PCR amplification from pure cultured cells or colonies showed that the method was sensitive enough to detect as few as 200 cells in the reaction. The presence of Acetobacter diazotrophicus in tissues of micropropagated sugarcane plants inoculated with either this bacterium or a mixture of this bacterium and Herbaspirillum seropedicae was demonstrated by PCR amplification. Acetobacter diazotrophicus could also be detected by the PCR method in field-grown sugarcane plants, as well as in certain cultivars of Pennisetum purpureum Schumach but not in\i maize, sweet potato, and two samples of weed plants grown within or outside of a sugarcane field. The addition of 1% polyvinylpolypyrrolidone during preparation of the field samples, especially with root tissues, improved the amplificability of the target sequence. The minimum level of detection of this bacterium in sugarcane tissue using the universal 1440 and AD species-specific primers was about 105bacterial cells/g of fresh plant material. The sensitivity could be improved 10-fold by probing immobilized PCR products containing the target region with the32P-labeled oligonucleotide AD.Key words: Acetobacter diazotrophicus, diazotrophic endophytes, specific rRNA-targeting oligonucleotides, polymerase chain reaction (PCR).
Effects of alkaline earth metal ions on the growth ofCalothrixstrain RC3, a natural isolate from Rock Creek, British Columbia
Authors: Douglas Susanne
Published: April 2011

Calothrix is a filamentous cyanobacterium that has a single terminal heterocyst and a tapering morphology. It exists in two forms: mature filaments as described and motile hormogonia, which have a distinct morphology and serve as a dispersal mechanism for the organism. These cyanobacteria are common inhabitants of freshwater environments, where they are subjected to a variety of fluctuating conditions, including levels of dissolved metal ions. The present study represented an initial investigation of the effects of increasing metal ion concentrations on Calothrix as assessed ultrastructurally by transmission electron microscopy and through alterations observable by light microscopy and growth studies. Exposure of filaments to various levels of the alkaline earth cations Ca2+, Mg2+, Sr2+, and Ba2+led to various changes in structure, indicating effects on the organism's physiology. These included perturbation of cell envelope layers, such that the formation of outer membrane vesicles was enhanced, alteration to the patterns and abundance of sheath material formed, alteration of thylakoid (photosynthetic) membrane structure, and inhibition of hormogonium formation and release. It was interesting to note that even cations that are not typically thought of as toxic (Ca2+and Mg2+) could have profound effects on the cells to the extent of inhibiting growth at the maximum levels used in this study (5 mM), which are below these often found in natural environments. These results give an indication that the presence of metal ions in natural environments can have an important influence on the structural and growth characteristics of commonly found cyanobacteria to the extent of making them appear, on a macroscopic basis, as different organisms entirely. This puts a note of caution on future field observations and interpretations of the effects of pollutants on natural microbial communities.Key words: cyanobacteria, metals, ultrastructure.
Nutritional requirements for growth of fungal endophytes of grasses
Authors: Naffaa Walid , Ravel Catherine , Guillaumin Jean-Jacques
Published: April 2011

Fifteen isolates of fungal endophytes of grasses were studied for their ability to metabolize different sources of carbon and nitrogen. These endophytes had been isolated from 12 different species of Poaceae and included Clavicipitaceae with or without a teleomorph (genera Epichloë and Neotyphodium, respectively) and species belonging to the genus Acremonium sensu stricto (Acremonium chilense-like). Pectin and cellulose as carbon sources and tryptophan and methionine as nitrogen sources appeared to support poorly the growth of most isolates. Hexoses, disaccharides, complex nitrogen sources, asparagine, and glutamine supported growth of all isolates. The isolates of genus Neotyphodium were characterized by limited growth whatever the substrate, the inhibition of their growth by high concentrations of glucose and fructose, and their inability to assimilate pentoses (xylose, arabinose) and nitrates. The isolates of genus Epichloë showed better growth than those of the previous group and their growth was not inhibited by high concentrations of glucose, but they were also unable to use pentoses. The Acremonium chilense-like isolates showed rapid growth and were distinguished by their ability to use the pentoses and nitrates. In contrast, they showed relatively poor growth on methionine and alanine as nitrogen sources. They showed the most rapid growth on high concentrations of glucose or fructose.Key words: carbon sources, nitrogen sources, Neotyphodium, Epichloë, Acremonium, grass endophytes.
Emulsification of crude oil by an alkane-oxidizingRhodococcusspecies isolated from seawater
Authors: Bredholt Harald , Josefsen Kjell , Vatland Arild , Bruheim Per , Eimhjellen Kjell
Published: April 2011

A Rhodococcus species, the best of 99 oil-emulsifying bacteria isolated from globally distributed seawater samples, was characterized. The bacterium produced very stable oil-in-water emulsions from different crude oils with various contents of aliphatic and aromatic compounds by utilizing the C11to C33n-alkanes as carbon and energy sources. The presence of alkanes induced the formation of a hydrophobic cell surface that permitted oil-associated exponential growth and where an extensive emulsification of the residual oil and accumulation of acidic oxidation products occurred. The acidic products were consumed in a second step characterized by linear growth and an increasing number of cells growing in the water phase. Adhesion of cells resulted in some stabilization of oil droplets, but the most extensive emulsification occurred at the end of the exponential phase and coincided with an increasing number of cells in the water phase. No surfactant could be detected in the water phase during exponential growth, but a polymeric compound with emulsifying activity, tightly bound to the oil droplets, could be isolated. This suggests that the emulsification was caused by the release of the hydrophobic cell surface discarded by the cells during conditions of growth limitations.Key words: Rhodococcus,emulsification, adhesion, n-alkanes, hydrophobicity.
Purification and characterization of a thermostable glucoamylase fromAspergillus fumigatus
Authors: da Silva William Brandani , Peralta Rosane Marina
Published: April 2011

A thermostable glucoamylase from Aspergillus fumigatus was purified to homogeneity. It was a glycoprotein with 23% carbohydrate content and an apparent molecular mass of 42 kDa. The enzyme showed maximal activities at pH 4.5-5.5 and 65°C and preferentially attacked polysacharides, such as starch, glycogen, amylopectin, and amylose, rather than maltose and maltoriose. The Kmand Vmaxof soluble starch hydrolysis at 40°C and pH 5.0 were 0.1 mg ·mL-1and 161 µmol glucose equivalents liberated ·min-1·mg protein-1, respectively. The purified enzyme was remarkably insensitive to glucose. It was not affected by 500 mM D-glucose and retained about 80% of its original activity in the presence of 1000 mM of this sugar.Key words: amylase, Aspergillus fumigatus, enzyme purification, glucose insensitive, thermostableglucoamylase.